Les séminaires passés de l'ISYEB

2016 - 2015 - 2014 - 2013

2017

- 19 décembre 2017 : Hervé Le Guyader, UMR 7138.

Le rôle capital de Joseph Banks (1743-1820) dans l’émergence de la pensée darwinienne

En 1768, Banks embarque sur l’HMS Endeavour pour le premier voyage de James Cook, consacré à l’astronomie. Il en revient avec des collections naturalistes et ethnographiques, classées par Daniel Solander, et qui étonnent Londres. C’est un retour triomphal, et Linné lui-même est très élogieux. Pour la Grande-Bretagne, c’est le début de toute une série de voyages autour du monde, dont les finalités sont autant politiques que scientifiques. Banks n’embarquera pas pour le second voyage de Cook. FRS depuis 1766, à 23 ans, il devient un personnage influent de la Royal Society dont il devient le président en 1778, à 35 ans, et sans avoir écrit un seul article. Il est président, certes, mais président à vie, car il va le rester 41 ans, jusqu’à sa mort. Confident du roi George III, il va jouer un rôle déterminant dans l’évolution de la Royal Society et dans l’implication des sciences naturelles dans l’économie anglaise. Il encourage l’horticulture, l’acclimatation, la sélection dans l’élevage... Du côté scientifique, il est à la manoeuvre pour de nouvelles explorations lointaines, pour l’étude géologique de la Grande Bretagne. Il développe les jardins de Kew... D’un point de vue politique, il est à l’origine de la colonisation de l’Australie. Sous son impulsion, les naturalistes des générations ultérieures, dont l’histoire a retenu les noms, vont participer à des voyages de découverte, tout en s’intéressant aux sciences appliquées. Ce sont ces derniers qui ont construit le climat scientifique dans lequel Charles Darwin s’est épanoui - il avait 11 ans à la mort de Banks.

 

 12 décembre 2017 : Christophe Lavelle, CNRS UMR 7196 & Food 2.0 Lab

La biodiversité dans l’assiette

Notre alimentation dépend fortement de notre environnement, lui-même influencé par l’intense activité humaine qui résulte de la production, de la transformation et du transport des aliments. Des pratiques agricoles aux comportements alimentaires, de la cuisine domestique à la restauration commerciale, nous discuterons des enjeux écologiques, économiques et politiques auxquels nous sommes confrontés pour préserver la quantité, la qualité et la variété de ce que nous mettons ou trouvons dans nos assiettes.
 

 5 décembre 2017 : Odile Maliet et Amaury Lambert, Collège de France, SMILE.

Ranked tree shapes, non-random extinctions and the loss of phylogenetic diversity

Phylogenetic diversity (PD) is a measure of the evolutionary legacy of a group of species, which can be used to define conservation priorities. It is defined as the sum of branch lengths of the phylogenetic tree of these species. It has been shown that an important loss of species diversity can sometimes lead to a much less important loss of PD, depending on the topology (balance) of the species tree and on the temporal distribution of its branch lengths. However, the loss of PD also strongly depends on the relative depths of the nodes in the tree, and on the order in which species are lost. Here, we propose a unifying framework to study these different effects. We introduce a new, sampling-consistent, three-parameter model generating random trees with covarying : topology, clade relative ages and clade relative extinction risks. This approach leads to a more accurate characterization of phylogenetic trees and allows us to better understand the conditions in which species extinctions lead to higher loss of PD. We propose a procedure to infer the three parameters from empirical ranked phylogenies and apply it to phylogenies of bird families. The parameters inferred predict higher future loss of PD than from random extinctions.
 

 28 novembre 2017 : Guillame Achaz, ABI, ISYEB

Lire la co-évolution intra-organisme dans le marc de la phylogénie : modèles, tests et données

Comment définir, détecter et enfin quantifier la co-évolution au sein d’un même organisme. Nous proposons un cadre théorique ancré dans l’approche phylogénétique permettant de caractériser la co-évolution à plusieurs niveaux d’organisation du vivant, aussi bien moléculaire que morphologique. Ce cadre permet d’une part de tester formellement l’indépendance entre des processus évolutifs mais également, le cas échéant, de quantifier la nature et la force des interactions entre ces processus. Nous illustrerons son large champ d’application à l’aide de quelques exemples moléculaires et morphologiques.
 

 21 novembre 2017 : Ben Warren, ISYEB.

Biogeography and the generation and loss of diversity in insular settings

As a result of their discrete and isolated nature, oceanic islands provide special opportunities to understand the processes involved in the formation and loss of biological diversity. An example is the observation that speciation has a spatial scale that varies among taxa (Kisel & Barraclough 2010). Using this starting point, the first half of this presentation contrasts results of phylogeographic studies in a common island setting (the western Indian Ocean) from good dispersers (e.g. birds) and poor dispersers (e.g. land snails). Contrasting elements are highlighted that may contribute to differences in intrinsic potential for radiation with dispersal ability. In the second half, I give examples of how genetic data from threatened and recently extinct insular species in museum bird collections can inform us about biodiversity loss. This includes both direct links to conservation action, as well as understanding how evolutionary processes operating over many branches of lineage history may contribute to patterns of biodiversity loss.

 

 14 novembre 2017 : Guillaume Lecointre, ISYEB

La Biologie à la lumière du désordre

La biologie s’est amplement déployée au vingtième siècle en prenant les régularités du vivant (en gros, l’ordre apparent du vivant) comme principe causal. Elle s’est mise à produire des invariants (un certain usage de l’espèce, de l’information génétique, le plan d’organisation (body plan), le "programme génétique") qui n’auraient dû rester que des accommodements de langage, mais qui sont loin de n’avoir été que cela. Les abus métaphoriques continuent d’émailler les articles d’aujourd’hui dans les plus grandes revues, où les espèces sont réelles (dans Nature), les gènes "contrôlent" des "plans d’organisation" (PNAS, Science). Nous verrons que cette posture idéaliste est incompatible avec la théorie de l’évolution. En effet, l’ordre n’est pas du registre de la cause des phénomènes biologiques, mais il est la conséquence d’un désordre fondamental à micro-échelle dont il résulte une moyenne reproductible à macro-échelle, ou bien qui se trouve avoir été sélectionné. On peut montrer que la même inversion logique entre les causes et les effets habite l’usage du grade (où la dynamique du changement est affecté à la catégorie au lieu de l’être à son contenu), ou caractérise la convergence évolutive entendue comme processus particulier produisant du semblable, et non comme conséquence d’un processus général de sélection naturelle.
En d’autres termes la sélection naturelle est d’abord une source de régularités avant que d’être une source de changement, comme l’énonce clairement le sous-titre de l’Origine des Espèces. Mais au vingtième siècle, la théorie synthétique l’a enseignée à l’envers : la sélection naturelle avait pour rôle d’expliquer comment les espèces changent. La régularité, elle, était assurée par le "programme". Depuis la démonstration faite en 2002 du caractère stochastique de l’expression des gènes, toutes ces cartes sont en train d’être redistribuées.
Pour qu’il y ait sélection naturelle, il faut trois propriétés fondamentales des entités analysées : variation, transmission, contraintes. Sous cet angle, nous verrons que le module "transmission" a énormément changé au cours des vingt dernières années (comme en témoignent de nombreux articles de synthèse dans Nature, dans Science ou même La Recherche), et que la variation va se nicher jusqu’à des niveau insoupçonnés. La sélection naturelle entre aujourd’hui dans le corps, et se trouve sur le point de révolutionner les thérapies anti-cancéreuses. De tout cela il résulte un nouveau statut pour le gène, qui n’est plus un notaire ou un maître, mais un partenaire, dont les réalisations contributives dépendent de l’environnement. La métaphore du "programme" devient superflue. Les conséquences pour la biologie de demain sont considérables : il n’y a plus de distinction à faire entre génotype et phénotype, ni entre ontogenèse et phylogénèse, ni même entre ce qui relève du "naturel" et ce qui relève du "culturel". L’Evo-Devo a raté en partie son ambitieux programme, parce que ce n’est pas elle qui a initié le mouvement. Au contraire, la plupart des articles d’Evo-Devo continuent à véhiculer des concepts idéalistes, au lieu d’adopter une pensée véritablement phylogénétique.
L’ordre n’est pas un principe causal, il est une régularité, conséquence d’un tri, sur laquelle nous posons un mot parce que nous avons besoin de parler de ce qui se ressemble (sans jamais postuler l’identique). Deux entités biologiques n’étant jamais identiques, l’ordre est à gérer en termes d’homologie, au sens étymologique du terme. Nous verrons par exemple que l’ "information génétique" peut être comprise comme une homologie des processus qui mènent à des structures semblables, un opérateur du repérage des régularités dans les processus biologiques, tout comme l’homologie en anatomie comparée est un opérateur du repérage des régularités dans les structures. En d’autres termes, un mouvement s’opère aujourd’hui pour faire de la biologie moderne une biologie nominaliste, la seule compatible avec le changement physico-chimique permanent, et la seule compatible avec la théorie de l’évolution.

Référence : LECOINTRE, G. 2017. Les contenants et les contenus. Que faire des invariants en Biologie ? Actes du Colloque de Cerisy « Sciences du Vivant, sciences de l’information » (septembre 2016). ISTE Éditions. pp. 129-143

 

 17 octobre  2017 : Marc-André Selosse, ISYEB
The pantropically introduced Polygonaceae Coccoloba uvifera was followed by specific, pseudovertically transmitted Scleroderma spp.

Coccoloba uvifera (Polygonaceae) is an ectomycorrhizal tree endemic to Caribbean beaches. It has been introduced pantropically for ornament, fruits production and stabilization of sandy soils. Investigating three Caribbean regions of origin (ROs) of C. uvifera (Guadeloupe, Martinique and Porto Rico) and six regions of introduction (RIs) of the tree (Brazil, Senegal, Guyana, La Réunion (Pacific Ocean), Okinawa and Malaysia), ITS barcoding revealed that C. uvifera associates with diverse fungi mostly in ROs but with single species of semi-hypogeous Scleroderma in RIs. These species, also present in ROs, are an unknown Scleroderma in Brazil, Japan and Malaysia, and Scleroderma bermudense in Guyana, Senegal and La Réunion. To further assess whether S. bermudense was introduced or native in RIs, we analyzed populations using six microsatellite markers. No founder effect was observed in RIs, but the pattern of isolation by distance was congruent with independent introductions to Senegal and La Réunion. These two populations were less divergent from each other than expected, and very close to some ROs’ populations. Moreover, in Senegal, C. uvifera cannot associate with local ectomycorrhizal fungi, but forms spontaneously ectomycorrhizas with S. bermudense, even in sterile soil. Scanning electron microscopy revealed that some dried fruit aggregates sand and spores, likely during the drying process on soil, likely transmitting the fungus with limited founder effect. Specific ectomycorrhizal Scleroderma species from the RIs were thus introduced with C. uvifera seeds, in an accidental microbial co-introduction with plants, thanks to a hitherto undescribed pseudovertical transmission of mycorrhizal symbionts.
 

 10 octobre 2017 : Eric Bapteste, UMR 7138, UPMC

Le vivant a sa matière noire

Le monde microbien demeure largement méconnu. Dévoiler la diversité et la complexité des gènes, des virus, des organismes microscopiques et celles de leurs relations figurent donc parmi les objectifs les plus enthousiasmant des microbiologistes et des évolutionnistes qui espèrent (avec raison) découvrir de nouvelles formes de vie et d’organisations. Cette recherche de l’inconnu conduit à nous interroger sur l’état de notre savoir : ce que nous connaissons aujourd’hui du monde vivant est-il représentatif de sa richesse et de son histoire ? Pouvons-nous découvrir des acteurs et des processus cachés dans les systèmes biologiques ? Durant cet exposé, je présenterai quelques nouveaux venus dans le monde microbien et mettrait en avant quelques aspects des méthodes utilisées dans ces études.
 

 3 octobre 2017 : Maël Montévil, ISYEB

Enjeux de l’historicité du vivant pour la modélisation mathématique en
biologie

En physique, les objets sont définis théoriquement par les relations qu’il
entretiennent les uns avec les autres. Ce sont ces relations qui sont
instanciées dans les modèles mathématiques et qui expliquent le lien profond
entre physique et mathématiques.
Les modèles mathématique en biologie héritent de cet épistémologie. Nous
montrerons pourtant que l’historicité des objets biologiques a des
conséquences profondes sur la manière dont on peut envisager ces modèles. Ces
conséquences portent d’abord sur l’étude d’organismes actuels qui ne peuvent
être envisagée sans leurs histoires évolutives. Elles interviennent ensuite
dans la modélisation de la variation phénotypique elle même, laquelle semble
bien nécessiter des changements d’espace des possibles et une théorie des
contraintes biologiques.
 

 26 septembre 2017 : André Nel, ISYEB

Les insectes fossiles, témoins privilégiés de l’histoire de la biodiversité terrestre

Before the years 2000, palaeoentomology has been neglected in the morpho-anatomic and phylogenetic studies on insects. A increase of interest happened uring the 17 last years, due to the discoveries of extraordinary konservat-lagerstattes filling important gaps in the fossil record, and the development of dating techniques in phylogenies. Well dated and documented fossils are necessary to calibrate them.
New techniques of observation (3D tomography reconstructions of many structures that were not available before) allow in many cases to study fossil insects as if they were recent.
A new overview of the recent advances in palaeoentomology is now possible to do, showing that several old ideas are questionable, viz. the keystone characters of holometaboly for the diversification of the most diverse insect clade ; the impacts of the major crises of terrestrial diversity on the insects ; what were the crucial periods of diversifications of the insects, and ’why’.
 

 19 septembre 2017 : Hannah ter Hofstede, Dartmouth College, Hanover, NH, USA

Acoustic and vibratory communication signals in crickets and katydids

Thanks to pioneering neuroethological studies and continued research over many decades, we have a detailed understanding of the sensory basis for many forms of communication in crickets and katydids (Orthoptera, Ensifera), making them excellent study animals for testing both proximate and ultimate questions about animal communication. In particular, many ensiferans use both acoustic and vibratory signals for communicating with mates, raising questions about the role each modality plays in communication and the potential for tradeoffs or interactions between these two modalities. In this talk, I will review some aspects of ensiferan acoustic and vibrational communication, describe research by my colleagues and me into mechanisms and functions of these forms of communication, and outline our future research directions.
 

 12 septembre 2017 : Maram Caesar, Pos-doctorante ISYEB

Micro-endémisme en Nouvelle-Calédonie : une réalité biologique ou un effet d’échantillonnage ?

La littérature sur la faune et la flore de la Nouvelle-Calédonie est pleine d’exemples d’espèces qui ont des aires de répartition très restreintes et ces informations éparpillées laissent penser que le micro-endémisme est un trait commun de la biodiversité calédonienne. Néanmoins, à ce jour il n’a pas d’étude de synthèse qui permet de distinguer entre réalité biologique et efforts d’échantillonnage trop réduits.
On a analyse un ensemble de 1149 espèces de la faune néocalédonienne étudiés dans le Zoologia Neocaledonica, dont 982 endémiques et 167 non endémiques de la Nouvelle-Calédonie. Nos résultats montrent que seulement 51% et 57%, respectivement, ont été suffisamment échantillonnées pour statuer sur leur aire de répartition. De ce sous-ensemble, 12% des espèces sont avérés micro-endémiques, et 22% des espèces non-endémiques de la Nouvelle Calédonie ont aussi des très petites aires de répartition dans l’archipel. L’autre résultat majeur de cette étude est que le micro-endémisme est commun à une grande diversité de groupes taxonomiques de cette faune.
Dans cet exposé je montrerais les détails de cette étude ainsi que les méthodes utilisées pour la caractérisation de l’adéquation de l ‘effort d’échantillonnage.

Caesar M, Grandcolas P, & Pellens R (2017) Outstanding micro-endemism in New Caledonia : more than one out of ten animal species have a very restricted distribution range Plos One sous presse.

 

 5 septembre 2017 : P. J. Taylor, Université de Venda (RSA)

The New Age of mammal species discovery : “taxonomic anarchy” or an inconvenient truth for conservation ?

Species discovery rates of mammals have intensified in the past two decades, contrasting with a preceding period of taxonomic stability throughout most of the twentieth century. I provide examples from different orders of African mammals. The period of status preceding this recent renaissance can be attributed largely to the paradigm of the polytypic species under the Biological Species Concept that has largely been superseded by the Evolutionary Species Concept in some disciplines but not others. Although based on scientific evidence and critical discourse among systematists for more than a century, this “New Age of Discovery” may represent an inconvenient truth for some conservationists. Recent articles, mostly written by conservationists in journals such as Nature, Systematic Biology, Mammalian Biology and Hystrix have labelled this process of species discovery as “taxonomic inflation” or “taxonomic anarchy”, alleging that it harms conservation. They further argue for an independent committee to regulate the process of species recognition. The debate has been largely sparked by recent publications that propose large increases in the number of species in large mammals such as primates and ungulates, with little attention given to similar trends proposed for small mammals such as rodents, shrews and bats. In my presentation, I provide several examples among African small mammals where an integrative taxonomic approach (the “Consilient Solution” of Cotterill) under the ESC has multiplied the number of recognised species. The implications of this process in terms of macroecology, conservation and climate change are discussed.

 

 20 juin 2017 : Ray Tangney, Principal Curator Botany (Cryptogams), National Museum Wales, Cardiff

Systematics of the moss family Lembophyllaceae.

The Lembophyllaceae has undergone considerable revision during the last century, reflecting diverse views of the generic and familial relationships of this pleurocarpous moss family. During this time up to 15 genera have been included in the family, and as few as one, with the very existence of the family questioned. Similarly, the systematic position of the family has varied with changing generic composition. Based around the Australasian genus Lembophyllum, the family has been associated with a range of families including Brachytheciaceae, Meteoriaceae, Thamnobryaceae and Echinodiaceae. Recent analyses based on molecular data have supported a family of 14 genera, similar to classifications of the family in the early 20th century, and in contrast to those of the late 20th century, with strong relations to the Neckeraceae.This talk will introduce the morphology of the family and outline the impact of molecular analyses on the family concept and its biogeography, as well as ongoing research.

 

 13 juin 2017 : Vyacheslav Yurchenko, Associate Professor and Lab Head,
Laboratory of Molecular Protozoology, University of Ostrava, Czech Republic - SYNTHESIS UMR 7245

Trypanosomatids in NGS era

In this talk I will focus on two recently described trypanosomatid species which allow us to dissect molecular mechanisms governing some fundamental biological processes.

Part 1 will be devoted to Blastocrithidia spp., a clade of trypanosomatids with a unique nuclear genetic code. A limited number of non-canonical genetic codes have been described in eukaryotic nuclear genomes. Most involve reassignment of one or two termination codons as sense ones, but no code variant is known that would have reassigned all three termination codons. Here, we describe such a variant that we discovered in a clade of trypanosomatids comprising nominal Blastocrithidia spp. In these protists, UGA has been reassigned to encode tryptophan, while UAG and UAA (UAR) have become glutamate encoding. Strikingly, UAA and, less frequently, UAG also serve as bona fide termination codons. The release factor eRF1 in Blastocrithidia contains a substitution of a conserved serine residue predicted to decrease its affinity to UGA, which explains why this triplet can be read as a sense codon. However, the molecular basis for the dual interpretation of UAR codons remains elusive. Our findings expand the limits of comprehension of one of the fundamental processes in molecular biology.

Part 2 will deal with a recently established trypanosomatid-endosymbiont association. Recently, we described a novel symbiotic association between a kinetoplastid protist, Novymonas esmeraldas gen. nov., sp. nov., and an intracytoplasmic bacterium, “Candidatus Pandoraea novymonadis” sp. nov., discovered as a result of a broad-scale survey of insect trypanosomatid biodiversity in Ecuador. We characterize this association by describing the morphology of both organisms, as well as their interactions, and by establishing their phylogenetic affinities. Importantly, neither partner is closelyrelated to other known organisms previously implicated in eukaryote-bacterial symbiosis. This symbiotic association seems to be relatively recent, as the host does not exert a stringent control over the number of bacteria harbored in its cytoplasm. We argue that this unique relationship may represent a suitable model for studying the initial stages of establishment of endosymbiosis between a single-cellular eukaryote and a prokaryote. Based on phylogenetic analyses, Novymonas could be considered a proxy for the insect-only ancestor of the dixenous genus Leishmania and shed light on the origin of the two-host life cycle within the subfamily Leishmaniinae.
 

 6 juin 2017 : Julien Clavel, Institut de Biologie de l’École Normale Supérieure (IBENS).

Modelling phenotypic evolution on phylogenetic trees

Methods for modeling the evolution of species traits on phylogenetic trees, also known as phylogenetic comparative methods, have exploded since Felsenstein’s seminal paper in 1985. Developed at the beginning as a statistical fix for comparative analysis, these approaches are now routinely used to address macroevolutionary and macroecological questions with extant and fossil data. However, most of these approaches are still limited to very simplistic models assuming that traits or species are evolving independently of each other’s and from their environment. We recently developed various models that deal with biotic interactions, abiotic effects and coevolution of traits that we implemented in the R packages mvMORPH and RPANDA. By using our phylogenetic comparative framework for examining the effects of past climate changes on morphological evolution ; we show that global temperatures fluctuations through the Cenozoic impacted body size evolution in most endotherms. The evolution of body size was faster during periods of global cooling in most of the groups, challenging the hypothesis that evolution is faster under warm climates. We also show that models that account for competition and geography perform better than others models to morphological data from a classical adaptive radiation, the Greater Antillean Anolis lizards. Finally, this talk will also briefly present some of our recent and ongoing developments on phenotypic evolution modeling with some emphasis on high-dimensional multivariate datasets.

 

 30 mai 2017 : Hervé Sauquet, Université Paris-Sud, Lab. Écologie, Systématique, Évolution (ESE)

The ancestral flower of angiosperms and its early diversification : results from the eFLOWER project

Flowers are central to the biology and evolution of angiosperms (flowering plants). Here, we focus on the history of floral diversification through deep evolutionary time. A comprehensive understanding of global patterns of floral evolution has been prevented so far by the lack of an adequate morphological data set spanning all major angiosperm lineages. Using a new flexible and innovative approach, centered on a multi-user database (PROTEUS), we have built such a data set. Unlike most earlier studies of character evolution at the scale of angiosperms, we have recorded exemplar species instead of higher taxa such as genera or families. This approach allows for explicit reconstructions without assumptions about ancestral states or monophyly of supraspecific taxa, although we acknowledge that it also entails the risk of undersampling morphological variation. Importantly, the exemplar approach allows a direct match with the species sampled in molecular phylogenetic trees, providing the possibility to take branch lengths into account and to explore character evolution with probabilistic models. We report our first results from a data set of floral traits for 792 species representing all orders and 367 families (87%) of angiosperms, sampled from a recently published timetree calibrated with 136 fossil age constraints. Using this data set and tree, we reconstruct ancestral states for 27 key floral traits using parsimony, maximum likelihood, and Bayesian approaches and infer ancestral flowers for 15 key nodes (incl. Angiospermae, Mesangiospermae, Magnoliidae, Monocotyledoneae, Eudicotyledoneae, Pentapetalae, Rosidae, and Asteridae) as well as all extant orders of flowering plants. Further, we explore the sensitivity of our results to phylogenetic, dating, and model uncertainty. Importantly, all of our analyses converge on the same results in most cases, except near the root of the angiosperm tree, where parsimony continues to provide equivocal answers for some important floral traits, consistent with previous work. Lastly, the use of an explicit temporal framework for reconstructing ancestral states allows, for the first time, a direct comparison of inferred ancestral flowers with the known fossil record of each geological time interval. These results shed new light on long-standing questions on floral evolution across angiosperms, with important implications for a wide range of disciplines including Evo-Devo, pollination biology, and paleobotany.
 

 23 mai 2017 : Pierre Brezellec, MC à l’université de Versailles Saint-Quentin, Membre de l’ABI - ISYEB.

Initiation de la réplication chez les bactéries : encore une fois, "rien n’a de sens (en biologie) si ce n’est a la lumiere de l’evolution"

Chez les bactéries, le début de l’initiation de la réplication est marquée par le recrutement et la charge de l’hélicase réplicative à l’origine de réplication. Nous verrons, dans un premier temps, que dnaC et dnaI - les chargeurs d’hélicase réplicative de coli et de subtilis - sont absents de la majorité des phyla bactériens. Nous montrerons ensuite que dnaC et dnaI sont très vraisemblablement des "éléments" d’origine phagique qui ont été domestiqués au dépend d’un gène - probablement présent chez l’ancêtre commun de toutes les bactéries - que nous avons identifié et appelé dciA (dnaC/I Antecedent). Durant cette première partie, nous soulignerons que i/ le concept d’organismes modèles (ici coli et subtilis comme modèle de la réplication) a longtemps masqué la découverte de dciA, i.e., dnaC/I ont longtemps été présentés comme "universel" alors qu’ils ne représentaient que des "exceptions" à une règle plus générale, ii/ un échantillonnage plus exhaustif de la "diversité" couplé à "une phylogénie" sont des leviers puissants de la découverte en biologie. Dans un second temps, nous montrerons que quelques ordres bactériens sont peuplés d’organismes ne possédant ni dnaC/I ni dciA. Nous verrons que chez les Cellvibrionales et une partie des Oceanospirillales, la perte de dciA est - encore une fois - probablement le résultat d’un transfert horizontal suivi de la domestication des deux gènes d’origine phagique. Nous finirons notre exposé en suggérant des pistes expliquant les raisons pour lesquelles dciA est "régulièrement "perdu" au profit "d’éléments de type phagique".

 

 16 mai 2017 : Flora Vincent, IBENS.

Diatom interactions in the open ocean : from the global patterns to the single cell

Diatoms are unicellular photosynthetic microeukaryotes that play a critical role in the functioning of marine ecosystems. They are responsible for 20% of global photosynthesis on Earth and lie at the base of marine food webs, ever more threatened by climate change. Diatoms establish microbial interactions with numerous organisms across the whole tree of life, through complex mechanisms including symbiosis, parasitism and competition. The goal of my thesis was to understand how those biotic interactions structure the planktonic community at large spatial scales, by using new approaches based on the unprecedented Tara Oceans dataset, a unique and worldwide circumnavigation that collected over 40.000 samples across 210 sites to explore the diversity and functions of marine microbes. Through the analysis of microbial association networks, I show that diatoms act as repulsive segregators in the ocean, in particular towards potentially harmful organisms such as predators as well as parasites, and that species co-occurrence is driven by environmental factors in a minority of cases. By leveraging the singularity of the Tara Oceans data, I provide a comprehensive characterization of a prevalent biotic interaction between a diatom and heterotrophic ciliates at large spatial scale, illustrating the success of data-driven research. Overall, my thesis contributes to our understanding and discovery of diatom biotic interactions, from the global patterns to the single cell.

 9 mai 2017 : Jean-Lou Justine, ISYEB.
Publications, Impact Factor, H-index, Altmetrics, Réseaux Sociaux : la vie du chercheur au début du XXI° siècle

Ceci ne sera pas une conférence par un expert, mais une présentation pour discussion par un utilisateur.
Idéalement, en 3-4 parties de 10 minutes de présentation et 5 minutes de discussion et d’échange à chaque fois.
Je compte bien apprendre au cours de ces discussion autant que vous !

Introduction
La préhistoire – Tout sur papier !

Facteur d’Impact, DOI, ISSN, Altmetrics, H-index
Identité numérique des articles : le DOI
Facteur d’impact, méthodes de calcul pour les journaux
Journaux modernes et journaux ringards (Altmetrics, compteurs)
Facteurs d’impact alternatifs (Altmetrics)
Évaluation des chercheurs, méthodes métriques (H-index et autres)

Réseaux
Utilisation des Réseaux Sociaux dédiés aux chercheurs (ResearchGate, Academia et autres)
Poser une question sur ResearchGate – y réfléchir avant !
Rôle d’Orcid pour les chercheurs – qui n’a pas d’Orcid dans la salle ?
Valoriser son travail de reviewer (Publons)
Voir l’impact (Altmetrics) de ses articles en un coup d’œil (ImpactStory, ScienceOpen)
Utilisation des Réseaux Sociaux généraux (Twitter, FaceBook, Linkedin)

Identité numérique des chercheurs
Vote identité numérique existe déjà
Mais vous pouvez l’améliorer / la contrôler
ResearchGate, ZooBank, VIAF, SUDOC, GoogleScholar, Orcid, ResearcherId
Identité numérique des chercheurs vs vie privée

Gratuité et légalité
Ce qui est payant : Web of Sciences (mais payé par CNRS)
Ce qui est gratuit ou faussement gratuit (« si c’est gratuit, vous êtes le produit ! »)
Tout se vend – Mendeley et Linkedin
Ce qui est légal et ce qui ne l’est pas

Conclusion
Être geek en 1993 c’était avoir un email…

 5 mai 2017 : Kenny Travouillon, Western Australia Museum.

Integrating modern and fossil museum collections to resolve taxonomic problems : the journey of a Churchill Fellow

Museum collections often house some hidden treasures. New species are sometimes found amongst specimens of another, unnoticed for decades. Though specimens can often be scattered across several museums, in different stated or countries, making it difficult and expensive to access and study them properly.
The Churchill Fellowship, supported by the Churchill Trust, gives a unique opportunity to travel to multiple museums in multiple countries, to undertake such study. This journey will aim to study closely all museum specimens in the order Peramelemorphia (bandicoots and bilbies), to review type specimens, historical specimens (collected in the 1800s), and even fossil specimens (as old as later Oligocene in age), to uncover new species, revise current species, and uncover the evolutionary history of this group. The preliminary results of this journey, undertaken in April and May 2017, will be presented, providing a unique insight and highlight future research that can help continue broadening our understanding of this order of mammals, and help with the conservation of this highly endangered group of marsupials.

 18 avril 2017 : Charles Davis, Professor of Organismic and Evolutionary Biology, Curator of Vascular Plant Collection, Director, Harvard University Herbaria

The big, the bad, and the beautiful : parasitism and the origin of the world’s largest flowers

Parasitic plants are bizarre and have remained one of the last great challenges to resolve the flowering plant tree of life. The most charismatic of these species are Rafflesiaceae, which hold the distinction of producing the world’s largest flowers. I will discuss our efforts to clarify their evolutionary relationships. I will then draw on these findings to address their genetic and developmental origins from humbler beginnings. And finally, I will address how broad genomic studies in the group have elucidated the magnitude and directionality of host-to-parasite gene transfer in flowering plants.
 

 28 mars 2017 : Susana Coelho, UMR8227 - Station Biologique CNRS UPMC

Origin and evolution of the sexes : new insights from the brown algae

Although the core mechanisms of sexual reproduction (meiosis and syngamy) are highly conserved across eukaryotes, the mechanisms that determine whether an individual is male or female are remarkably labile. In genetically controlled sexual systems, gender is determined by sex chromosomes, which have emerged independently and repeatedly during evolution. We are using the brown algae, a group that diverged from plants and animals more than a billion years ago, to gain insights into the evolution of haploid (UV) sex chromosomes. We investigated the conservation of sex-linked gene content among six brown algal species, belonging to two lineages, the kelps and the Ectocarpales, focusing on gene movement in/out of the U and V-specific regions. We analysed the consequences of sex linkage for the evolution of genes that have been residing in the sex-specific region in the different lineages at different evolutionary times. Our results highlight the dynamic nature of the U and V gene content across the different species compared with autosomes. We discuss how U and V gene content evolution may be related with the specific life history traits of each lineage, focusing on the level of sexual dimorphism, life cycle and sexual system.

 21 mars 2017 : Eric Dugat-Bony, Chargé de Recherche INRA, UMR782 GMPA

Highlighting the microbial diversity of 12 French cheese varieties

Surface-ripened cheeses host complex microbial communities responsible for the transformation of milk into cheese as well as the development of important properties in terms of texture, color and sensory perception. In this study, we used high-throughput amplicon sequencing to decipher the bacterial and fungal diversity of 60 cheeses belonging to 12 popular French cheese varieties. Using this approach, 76 bacterial and 44 fungal phylotypes were identified. Major differences were observed between rind and core samples and also according to cheese varieties and manufacturing processes. Occurrence analysis revealed the presence of widespread taxa as well as operational taxonomic units (OTUs) specific to one or several cheese varieties. Finally, we observed patterns specific to the cheese production facility, supporting the importance of indigenous microorganisms for the microbial assemblage of cheese microbiota.
 

 14 mars 2017 : Aurelie Khimoun, ISYEB, equipe BIPEM.

Landscape structure influences within-island gene flow in a forest specialist bird species

Within the framework of landscape genetics, resistance surface modelling is particularly relevant to explicitly test competing hypotheses about landscape effects on gene flow. To investigate how fragmentation of tropical forest affects population connectivity in a forest-specialist bird species, we optimized resistance surfaces without a priori specification, using least-cost (LCP) or resistance (IBR) distances. We implemented a two-step procedure in order i) to objectively define the landscape thematic resolution (level of detail in classification scheme to describe landscape variables) and spatial extent (area within the landscape boundaries) and then ii) to test the relative role of several landscape features (elevation, roads, land cover) in genetic differentiation in the Plumbeous Warbler (Dendroica plumbea). We detected a small-scale reduction of gene flow mainly driven by land cover, with a negative impact of the non-forest matrix on landscape functional connectivity. However, matrix components did not equally constrained gene flow, as their conductivity increased with increasing structural similarity with forest habitat : urban areas and meadows had the highest resistance values whereas agricultural areas had intermediate resistance values. The higher performance of IBR compared to LCP in explaining gene flow reflected non-optimal movements across this human-modified landscape, challenging the common use of LCP to design habitat corridors and advocating for a broader use of circuit theory modelling. Finally, our results pleaded for an objective definition of landscape scales (landscape extent and thematic resolution) and underlined potential pitfalls associated with parameterization of resistance surfaces.
 

 7 mars 2017 :  François Michel, chercheur à l’Institut de Biologie Intégrative de la Cellule (I2BC, CNRS), Gif-sur-Yvette

Hérédité d’une incompatibilité physiologique récurrente dans des croisements interspécifiques de lépidoptères / A recurrent pattern of physiological incompatibility in interspecific butterfly crosses

Traditional views of species formation, which hold that physiological incompatibilities linked to ecological divergence are the primary cause of speciation, predict recurrent themes of hybrid inviability for any particular lineage. Lepidoptera provide an opportunity to test these ideas, since provoked mating (‘hand-pairing’) makes it possible to investigate in a systematic manner the developmental problems that affect the progeny of interspecific crosses. One common source of interspecific incompatibility in these insects is the inability of F1 hybrids either to enter diapause or to resume development when in a diapausing state. By taking examples from experiments I carried out on members of two butterfly families, I will show that analysis of diapause-connected phenotypes in hybrid offspring allows one to order indvidual species along a quantitative scale, from which it is possible to ‘predict’ their propensity to skip diapause in natural settings. As hybrids between these closely related species tend to be fertile, at least in backcrosses, and were found to pass on their imbalances to part of their offspring, it should be straightforward nowadays to identify the genes involved in the breakdown of diapause regulation. Tracking the alleles of those genes at locations at which introgression has been shown to occur could then be used to probe their role in speciation.
 

 28 février 2017 :  Laure Schneider-Maunoury, ISYEB

Ecology and reproduction biology of the black truffle Tuber melanosporum

The black truffle Tuber melanosporum – the “black diamond” of French gastronomy – is an ascomycete fungus living in mycorrhizal symbiosis with tree roots. Few things are known about the ecology and biology of this iconic mushroom. The black truffle is potentially hermaphroditic but reproduction and formation of the edible organ, the ascocarp, require mating between individuals from opposite mating type : a maternal parent that forms the ascocarp flesh and a paternal one whose genes are only left in the meiotic spores within the ascocarp. Maternal genotypes are also found on the surrounding mycorrhizae, suggesting that maternal partners are established as symbiont on the host trees. In contrast, paternal genotypes are never found in mycorrhizae, and are more numerous and transient than maternal genotypes. Several questions arise therefore : what are the paternal partners (mycelium, spores...) and where do they come from ? We conducted population genetics studies using microstallites which revealed a high level of inbreeding, raising the question of the existence of gametic gene flow. Another mysterious aspect of T. melanosporum ecology is the presence of an area at the base of the host trees characterized by few herbaceous species, called a brûlé. Not a lot is known about causes or consequences of the brûlé, but it has been shown recently that, unexpectedly, T. melanosporum may be detected molecularly and genotyped within the roots of the herbaceous plants. We now want to elucidate what kind of interaction is involved in this particular niche and whether paternal partners could be there.
 

 21 février  2017 : Jean-Yves Dubuisson, PR UPMC, ISYEB.

Comment et pourquoi les espèces se distribuent-elles altitudinalement ? le cas d’une lignée de fougères hygrophiles.

La majorité des études sur la distribution altitudinale des espèces proposent d’explorer le patron de distribution altitudinale des communautés d’organismes dans une ou des localités données et de tester si cette dernière s’éloigne ou pas d’un patron « hump-shaped » (maximum de diversité aux altitudes moyennes) qui serait le modèle le plus fréquemment observé (Sander & Rahbeck 2012, Ecography 35 : 1-3). Les processus expliquant les distributions font majoritairement appel soit aux variations des conditions environnementales et des optima écologiques, soit à un effet stochastique type « mid-domain effect » (MDE) (McCain & Grytnes 2010, Encyclopedia of Life Sci.), mais rarement au facteur historique (les relations évolutives entre les espèces). Pourtant il ne faut pas négliger la prise en compte de la phylogénie pour vérifier l’agrégation (qui indiquerait du conservatisme de niche) ou la sur-dispersion phylogénétique (qui pourrait suggérer une radiation adaptative, qu’il conviendra également de valider) des lignées étudiées en fonction de l’altitude. C’est cette multiple approche que nous développons au sein de l’équipe INEVEF dans un cadre intégratif et comparatif sur plusieurs groupes végétaux dans la localité modèle de l’île tropicale océanique de La Réunion (projet ATM ALTIBIODIV). Avec près de 117 points altitudinaux de 17 à 2400 m, nous avons pu affiner la répartition altitudinale du modèle de fougères hygrophiles Hymenophyllaceae. Les dernières données sur cette famille montrent ainsi une distribution bimodale (voire trimodale) inattendue qui suggère la superposition d’au moins deux distributions « hump-shaped ». Pour ce séminaire nous proposons d’exposer quelques études entreprises sur la lignée (et qui ont permis de préciser le cadre taxonomique et historique de la famille) et d’explorer la ou les origines des taxons réunionnais. Ainsi une étude de la distribution altitudinale des trichomanoides (une des deux lignées sœurs des Hymenophyllaceae) à diverses échelles géographiques couplée à une approche phylogénétique suggère que la distribution (même locale) est fortement liée à l’histoire de la famille avec des diversifications ayant débuté au Mésozoïque.
 

 31 janvier 2017 :  Philippe Le Gall, Chercheur IRD UMR Evolution, Génomes, Comportement & Ecologie, CNRS, IRD, Univ.Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette

Edible insects : from a traditional food resource to a solution for the future. The example of White grubs in Central Africa.

Forest insects are the most diverse group of living organism on earth, representing more than 60% of global biodiversity. They also play an important role in rural livelihood in tropical areas, where they constitute an important source of food to forest dependent people. A great attention has been paid these last years to the potential role of insects as a food resource for human or for feed available for animal nutrition.
The larvae (grubs) of the African palm weevil (Rhynchophorus phoenicis Fabricius, 1801) are consumed by the majority of the inhabitants of the Congo Basin. The exploitation and trade of weevil grubs is an important source of income for most forest dependent communities. As raffia ecosystems are under threat and weevil grubs can provide an alternative food and income source through community-based forest management in Cameroon, a project was jointly implemented by the Living Forest Trust (LIFT), the Centre for International Forestry Research (CIFOR) and Institut de Recherche pour le Développement (IRD) to study the sustainability of indigenous harvesting methods and trade in grubs, and to find ways to farm these insect resources.
 

 24 janvier 2017 :  Ingrid Lafontaine, membre associé de l’Atelier de Bioinformatique, ISYEB, UPMC/MNHN

Dynamic of gene creations in yeasts

We recently reconstructed the genome history of the entire Lachancea yeast genus covering a continuous evolutionary range from closely related to more diverged species, unifying the evolution of the genome architecture and gene repertoire [1]. A significant fraction of the genes (ca. 2%) has been gained since divergence from the Lachancea common ancestor, with several dozens of horizontally transferred genes and hundreds of potential gene creations from previously non-coding sequences [1]. We subsequently performed modelisation and functional genomic analysis to better estimate the impact of de novo gene emergence in Lachancea and Saccharomyces sensu stricto yeasts.

1. Vakirlis N, Sarilar V, Drillon G, Agier N, Meyniel JP, Blanpain L, Carbone A, Devillers H, Dubois K, Fleiss A, Gillet Markowska A, Graziani S, Nguyen HV, Poirel M, Reisser C, Schott J, Schacherer J, Lafontaine I, Llorente B, Neuvéglise C, Fischer G, Reconstruction of ancestral chromosome architecture and gene repertoire in a model yeast genus reveals principles of genome evolution. Genome Research, 26(7):918-32
 

 17 janvier 2017 :  François-Joseph Lapointe, Université de Montréal (Chercheur invité ISYEB)

LES RECHERCHES SUR LE MICROBIOME :
AUX FRONTIERES DE LA SCIENCE, DE L’ART ET DE LA PHILOSOPHIE

Depuis l’avènement des technologies de séquençage nouvelle génération, les recherches sur le microbiome humain représentent un domaine en pleine expansion. Cette véritable révolution scientifique a des impacts dans plusieurs champs de la connaissance. Afin d’illustrer la diversité des recherches actuelles sur le microbiome, je présenterai divers exemples des projets réalisés au sein de mon laboratoire ayant comme thématique commune le microbiome. Notamment, dans le cadre de mes travaux en biologie, je m’intéresse à l’étude du microbiome chez des populations animales et humaines menacées. Dans le cadre de mes travaux artistiques, j’utilise le microbiome comme substrat de création. Dans le cadre de mes travaux philosophiques, je cherche à formuler de nouvelles définitions du concept d’identité à la lueur des découvertes du projet du microbiome humain. Ce séminaire présentera un survol de mes projets actuels et futurs à l’interface de l’art et de la science.
 

 10 janvier  2017 : Sandra Goutte, Universidade Estadual de Campinas (UNICAMP), Brésil.

Communication breakdown : vestigial calls in earless frogs

The emergence and maintenance of animal communication systems involve co-evolution of signal and receiver. In most anurans, acoustic communication is pivotal for reproduction and their ears are typically tuned to the frequency of their vocalisations. This tuning allows discrimination of specific calls from background noise and heterospecific calls. A number of anuran species are called “earless” because they partially or totally lack tympanic middle ears. These species however retained the inner ear sensory organs and most of them are known to vocalise and perceive their own calls. We found evidence that two earless frog species (Brachycephalus ephippium and B. pitanga) are deaf to their own vocalisations, which are most likely vestigial. Using auditory brainstem response tests (ABR) and laser Doppler vibrometry, we showed that these frogs are insensitive to airborne sounds in the frequency range of their own vocalisations. We confirmed that their ears are partially non-functional by examining their inner ear structures. Acoustic signals are energetically costly and expose the sender to predators and parasites. If the production of vocalisations does not increase individual fitness, for example by increasing mating success, it should be strongly selected against. Brachycephalus ephippium and B. pitanga contradict this paradigm by producing acoustic signals that neither sex can perceive. High toxicity and the presence of visual communication in these frogs might explain their deficient acoustic perception and why calling has not yet disappeared.
 

2016

 13 décembre 2016 : Stuart Newson, British Trust for Ornithology (UK).

Bats, Bush-crickets and the Science of Monitoring

Stuart Newson is a Senior Research Ecologist at the British Trust for Ornithology (BTO), where he is mainly involved in survey design and analyses of data from large national ‘Citizen Science’ surveys. Whilst the core of his work has been on birds, he has a personal interest in bats and acoustic monitoring, and in particular how technology can deliver new opportunities for conservation, and provide new ways to engage with larger audiences. Stuart set up the Norfolk Bat Survey www.batsurvey.org in 2013, a novel citizen science approach for enabling unprecedented large-scale bat recording using static acoustic detectors, an approach which was extended this year to a larger area of southern Scotland through the Southern Scotland Bat Survey, with plans now to develop this idea more widely across the UK. Being awarded a Research Fellowship at the BTO, Stuart is currently working on a variety of topics under the heading “Bats, Bush-crickets and the Science of Monitoring”. This talk will give an overview of this work, collaborations and plans for the future.

 

 6 décembre 2016 :  Yasukazu Okada, Ph.D., Univ. of Tokyo, Japan.

Social dominance alters nutrition-related gene expression immediately : transcriptomic evidence from a monomorphic queenless ant Diacamma

Queen-worker differentiation and reproductive division of labor in eusocial organisms may have originated from decoupling of maternal care and reproductive behaviors. The mechanisms of conditional (i.e. environmentally-induced) expressions of behavior and physiology are one of the central issues in sociobiology.
At the dawn of eusociality, it seems likely that morphologically undifferentiated, monomorphic females underwent physiological differentiation that yielded egg-laying and caretaking castes. The molecular basis of such physiological differentiation may provide evolutionary insight into the emergent state of eusociality.
Here, we identify genes associated with monomorphic caste differentiation, specifically focusing on the onset of queen-worker differentiation, using a monomorphic queenless ant, Diacamma sp., that secondarily lost morphological castes. We identified 1,546 caste-biased transcripts in brain and 10 in gaster. Because in Diacamma, caste differentiation occurs soon after eclosion via highly ritualized behavioral dominance, identified transcripts are interpreted as molecular agents responding immediately to dominance rank formation. Our comparative transcriptome revealed that genes involved in nutrition processing and storage, such as insulin-signaling genes and hexamerins, show caste-specific transcriptions soon after the dominance rank formation. We conclude that the rapid modification of nutrition-related genes in response to social rank may be the fundamental mechanism underlying caste differentiation in Diacamma. I will discuss how behavioral variations are generated by fine-tunings of physiology, primarily in this species, and generally in other social systems.
 

 29 novembre  2016 : Yoan Coudert, CR CNRS ISYEB.

Hormonal control and evolution of branching forms in mosses

Branching patterns are a primary determinant of plant architecture and strongly impact on productivity by regulating light harvesting potential and resource allocation. Plants colonized land over 450 million years ago, and underwent architectural diversification in the haploid (gametophyte) and diploid (sporophyte) genetic stages of the life cycle independently.
Although similar branching mechanisms evolved in both genetic stages, our functional understanding of branching is limited to diploid flowering plant models such as Arabidopsis. To test whether the same molecular cues regulate branching mechanisms which have evolved convergently, we undertook a computational and genetic analysis of branching patterns in the haploid leafy shoot of a moss.
We show that a simple model co-ordinating the activity of shoot tips across the plant can account for the branch distribution, and that three known hormonal regulators of branching in flowering plants generate the pattern. Importantly, these cues have been independently recruited in evolution to regulate branching patterns in both haploid and diploid life cycle stages, and may be integrated via a novel mechanism in moss.
These results provide a framework to explore the hormonal control of branching form evolution in the moss lineage.
 

 22 novembre 2016 :  Amir Yassin, CR CNRS ISYEB.

A genomic perspective on drosophilid evolution

Unraveling the genomic basis of adaptive traits is a major challenge in evolutionary biology, but few clades present large phenotypic diversity and advanced genetic toolkits that are appropriate for this task. Drosophila melanogaster is undoubtedly a genetics star, but our understanding of the morphological and ecological diversity of non-melanogaster drosophilids is still quite nebulous. I attempt to present a comprehensive phylogenetic classification of the Drosophilidae ( 4,000 species) based on molecular and morphological data. I then combine population and functional genomics approaches to reveal the basis of two traits : first, an apparent case of sexual color mimicry that has independently evolved in more than 20 species, and second, a recurrent specialization on a toxic fruit in an island population of a generalist species. In both cases, natural selection seems to have favored few target genes to converge phenotypes across genetically isolated lineages. These results provide an improved understanding of the genomic mechanisms underlying phylogenetic diversification.
 

 15 novembre 2016 :  Leandro Quadrana , Institut de Biologie de l’ENS.

Causes and consequences of mobilome activity in Arabidopsis thaliana

Transposable elements are powerful motors of genome evolution yet a comprehensive assessment of the “mobilome” and its impact at the species level is lacking. Using genome sequencing data for hundreds of Arabidopsis thaliana accessions taken from across the globe, we show that contrary to the prevailing view, the majority of the >300 TE families present in the Arabidopsis genome have been subject to recent transpositional activity in this plant species. Furthermore, mobilome activity varies extensively between accessions and by applying genome-wide association studies (GWASs) we identified genetic and environmental factors underlying this variation. Transposition often occurs near or within genes, with consequences on their expression and DNA methylation status. Remarkably, loci controlling adaptive responses to the environment such as pathogen resistance and flowering time are the most frequent transposition targets observed. Our findings reveal the pervasive, species-wide impact that a rich mobilome can have and demonstrate the importance of transposition as a recurrent source of rare alleles with large effects.
 

 8 novembre 2016 :  Gopalasamy Reuben Clements, Université de Terrenganu, Malaisie. Prof. invité MNHN Labex BCDIV (ECOTROP/ISYEB/CESCO)

Where and How Are Roads Endangering Mammals in Southeast Asia’s Forests ?

Habitat destruction and overhunting are two major drivers of mammal population declines and extinctions in tropical forests. The construction of roads can be a catalyst for these two threats. In Southeast Asia, the impacts of roads on mammals have not been well-documented at a regional scale. Before evidence-based conservation strategies can be developed to minimize the threat of roads to endangered mammals within this region, we first need to locate where and how roads are contributing to the conversion of their habitats and illegal hunting in each country. We interviewed 36 experts involved in mammal research from seven Southeast Asian countries to identify roads that are contributing the most, in their opinion, to habitat conversion and illegal hunting. Our experts highlighted 16 existing and eight planned roads - these potentially threaten 21% of the 117 endangered terrestrial mammals in those countries. Apart from gathering qualitative evidence from the literature to assess their claims, we demonstrate how species distribution models, satellite imagery and animal-sign surveys can be used to provide quantitative evidence of roads causing impacts by (1) cutting through habitats where endangered mammals are likely to occur, (2) intensifying forest conversion, and (3) contributing to illegal hunting and wildlife trade. To our knowledge, ours is the first study to identify specific roads threatening endangered mammals in Southeast Asia. Further through highlighting the impacts of roads, we propose several measures to limit road impacts in the region.
 

 18 octobre 2016 :  Larisse Faroni Perez, Universidade Federal de Santa Catarina (UFSC)

On the distribution of Sabellariidae : inference from functional morphology

Sabellariidae is a highly specialized group of marine annelids and occurs from deep to intertidal seas. They live in characteristic tubes of cemented mineral particles, and sometimes attached to one another forming large reefs that can extend over several kilometers. Although sabellariids have been considered by several studies, some morphological traits and behaviours are poorly understood. For instance, recent advances have demonstrated sensorial organs and their relationship with settlement sociability (i.e. gregarious or solitary) and bathymetric ranges. Moreover, the shape of the operculum has a phylogenetic signal. However, no study has evaluated how the traits of operculum relate to adaptive radiations across bathymetric habitats. Here, the aims were 1) to understand if different opercular forms and paleae would promote differences in their effectiveness for tube sealing, and if such morphological variability can be useful for understanding evolutionary radiation into intertidal habitats ; and 2) to report new morphological traits and behaviour in Sabellaria alveolata. Analysis of specimens from collection hosted in MNHN-Paris and literature review of sabellariids was used to create a dataframe of their distribution and opercular traits. Afterward, the opercular traits and tube sealing behaviour of two intertidal species with different opercular shapes (Phragmatopoma caudata and S. alveolata) were investigated. These traits were assessed using light microscopy, SEM, and observations of live organisms. Results indicated that number of rows of paleae, their shape and orientation are the foremost divergence among sabellariids from intertidal and deep seas, and it could function as a key morphological feature for living between tides. P. caudata have entire opercular crown, double layer of paleae that close tube opening, likely to minimize desiccation process during low tide. S. alveolata close their tube openings with sediment at low tide, and this behaviour can minimize the environmental stress which intertidal organisms face. Finally, this species has an ability to perceive movements, and potential photoreceptors features are described.
 

 11 octobre 2016 :  Jean De Matha Ndengué, Université de Douala, Cameroun

The arthropod fauna associated to human habitat in South Cameroon in an endemic area of the Buruli’s Ulcer

Buruli ulcer (BU) is a skin infection, caused by Mycobacterium ulcerans (MU), whose transmission mode remains unknown. Several studies have shown that Arthropods were involved in the circulation, and possibly transmission, of MU. In Africa, Heteroptera and other aquatic organisms were found positive for MU using PCR. Epidemiological studies identified the use of a bednet as a protective factor against BU. These elements warrant the search for possible Arthropods carriers of MU in the domestic environment. A survey of the literature shown that there was nearly no data on the Arthropod from the human habitat in Africa. The aim of this study was to search for, and identify arthropods within and around the houses in the BU-endemic region of Akonolinga, Cameroon. Monthly entomological collections were performed from January 2013 to January 2014, in the town of Akonolinga, in 4 rural hamlets close to the Nyong River and in a hamlet near Mbalmayo. Nightly collection was performed using light traps and residual fauna was collected in the morning after indoors spraying with insecticide. After taxonomic identification, Arthropod samples were sorted and pooled according to family, place and month of collection. MU molecular signature was detected using MU-specific PCR (IS2404 and KR). Over 13 months, 306052 Arthropods were collected in 252 houses. These belonged to 214 families within 28 orders from the Myriapoda, Crustaceans, Arachnida and Hexapoda. Partial results after PCR analysis of 108036 arthropods showed 168 positive pools out of 2302 tested (7.3%). Twenty taxa were found positive for MU. The house entomofauna of South Cameroon shows a great diversity of species out of pests and disease vectors as it has been shown by the study of Bertone et al. (2016) in South Carolina. MU is found in terrestrial fauna at the same level as in the aquatic fauna (Garchitorena et al., 2014).
 

 4 octobre 2016 : Gopalasamy Reuben Clements, Université de Terrenganu, Malaisie. Prof. invité MNHN Labex BCDIV (ECOTROP/ISYEB/CESCO)

A picture is sometimes worth a thousand names

In biodiversity hotspots such as Southeast Asia, it is not difficult for taxonomists to discover species new to science, especially if they work on poorly studied invertebrates in neglected ecosystems. In Peninsular Malaysia, the discovery of new land snail species and genera in rainforests is now not difficult, mainly because roads have provided access to places that British and French malacologists could not easily reach in the 20th century. Unfortunately, roads have also provided greater access for natural resource extraction in countries such as Malaysia where economies are still developing. All of a sudden, we are faced with the prospect of never being able to make further discoveries because the habitats we want to work in will disappear. Based on my experiences as a taxonomist and conservation scientist, I provide real-world examples to illustrate why we have to be smarter when it comes to naming species we discover, and in one scenario, how pictures have proven to be more effective in lobbying for better protection of the habitats that still hold plenty of promise in terms of novel scientific discoveries.
 

 27 septembre 2016 :  Benjamin Yguel, postdoc ECOTROP.

Use of Community phylogenies

Phylogenetic information has been increasingly used in community ecology since the year 2000. In fact local communities harbor ultimately evolutionary history, reflecting maintenance of different mixture of lineage and this information may be used i.e. to question
(i) how local coexistence may control macroevolution of the habitat lineage-pool, and (ii) how macroevolution within the habitat lineage-pool may control local coexistence/ecological function of differently related species). In the first part, I will present two studies of my phd thesis performed in Rennes 1 university about how phylogenetic structure of plants community may change plants interaction, and interactions of associated species and the possible implication for evolutionary diversification. In a second part, I will present one theoretical study realized in the synthesis center iDiv Leipzig on the design of a new phylogenetic measurement and tested to predict productivity of experimental plant communities.
 

-----

 

 20 septembre 2016 :  Ariadna Burgos, postdoc Labex BcDiv.

Savoirs écologiques et choix comportementaux dans la collecte de mollusques en Indonésie et Papouasie Nouvelle-Guinée

Les dépôts et amas coquilliers parsemés dans de multiples sites archéologiques témoignent de la profondeur temporelle et du rayonnement spatial des pratiques de collecte de coquillages. De nos jours, la collecte de coquillages est une activité de subsistance d’une importance socio-économique capitale. Elle implique une profonde connaissance écologique des mollusques (diversité, associations, modes de vie) en premier lieu, mais également des dynamiques de transformation socio-écologiques du littoral. Cette recherche ethno-malacologique s’intéresse aux savoirs naturalistes et aux pratiques comportementales de collecte de mollusques de deux sociétés côtières en Asie et Océanie. Il s’agit d’examiner plus précisément le corpus de savoirs naturalistes mobilisés dans la quête de bivalves et de gastéropodes et de comprendre les stratégies de collecte : choix de l’espèce, du lieu de collecte et des techniques engagées. La cohérence et l’acuité des savoirs malacologiques incitent finalement à ouvrir la réflexion, en insistant sur la pertinence d’une meilleure intégration des savoirs locaux associés aux mollusques dans le suivi des changements côtiers.

Mots-clés : ethno-malacologie, savoirs locaux, coquillages alimentaires, techniques de collecte, interdisciplinarité, changements environnementaux.

-----

 

 13 septembre 2016 :  Valentin Thouzeau, musée de l’Homme.

Reconstructing demographic and cultural histories of Central Asian populations from genetic and linguistic polymorphism data

The main aim of our research is to develop methods for analyzing language and genetic polymorphism data in a unified framework, in order to infer the past history of separation, exchanges and admixture among human populations. For this purpose, we have developed a new computer program that simulates simultaneously the evolution of gene and vocabulary diversities in a set of populations for which both types of data are available. These simulations are then compared to real genetic and linguistic polymorphism data, using Approximate Bayesian Computations (ABC) methods to identify the most realistic historical scenarios underlying each type of data, and to infer the corresponding model parameters. So far, we applied this approach to Central Asia, an area where Turkic-Mongol and Indo-Iranian speaking populations historically met, and where our laboratory has already gathered both genetic (sequences, microsatellites, genome-wide genotypes) and language (vocabulary lists, cognates) data.

-----

 

- 6 Septembre 2016 :  Camila Gonzales, Universidad de Los Andes, Colombia.

Spatial distribution and eco-epidemiology of insects with medical importance in Colombia

The Research Center on Tropical Microbiology and Parasitology (CIMPAT) at Universidad de los Andes, addresses several research projects aiming to analyze the relationships between vectors’ spatial distribution, disease incidence, and changes in the structure of transmission cycles due to climate change and land use transformations.
Ecological niche modeling has been used as a tool to explore the potential distribution of Leishmaniosis and Chagas Disease insect vectors in Colombia, and to assess their relation to transmission areas based on collection records. We highlight the importance of spatial analysis as a tool for the development of strategies for prevention and control of diseases.
In addition, our group is collaborating with the MNHN to address the diversity and spatial distribution of Lepidoptera in genus Lonomia, whose venomous caterpillars are responsible of fatal accidents in South America. Preliminary results will be presented, highlighting the importance of correctly delimiting species through an integrative approach (DNA barcoding and morphology).

-----

 

 5 juillet 2016 :  Mailyn Gonzalez, Investigador Programa de Ciencias de la Biodiversidad, Instituto Alexander von Humboldt, Bogotá, Colombia.

Overview of biodiversity research in a megadiverse country for conservation planning

The Institute Alexander von Humboldt is a research institute that belongs to the National Environmental System in Colombia and acts as a bridge between the academy and environmental authorities. We currently lead research on integrating different components of diversity (taxonomic, functional, phylogenetic) at different geographic scales and in different taxonomic groups in order to identify conservation priorities. The Institute holds one of the largest biological collections of the country and the largest tissue biorepository of Latin America. We coordinate the national network for DNA barcoding and we have been generating DNA barcodes in birds, plants and insects. I would like to present a general overview of our research systems and provide more details on studies carried out on bird’s diversity.
 

-----

 

 24 mai 2016 :  Monica Arias, ISYEB
A computer game to explore the evolution of adaptive variations in mimetic colour patterns

The persistence of several warning signals in sympatry is a puzzling evolutionary question, given the positive selection favouring convergence exerted by predators. The evolutionary convergence of complex colour patterns shared by toxic species is shaped by predators’ reaction to similar but not identical stimulus, i.e. generalisation behaviour. However, the study of generalisation behaviour in complex natural community of predators is challenging, and is thus generally limited to simple variations of prey colour patterns. Here, we considered visitors of the Grand Galerie de l’Evolution in Paris, as surrogate predators. We investigated human generalisation behaviours on diverse signals variations displayed in natural populations by the polymorphic butterfly species Heliconius numata. The attack behaviour of natural predators’ community on the same colour pattern variations was previously tested in a field experiment, allowing comparisons between humans and natural predators’ generalisation behaviour. Humans’ generalisation capacities were estimated using a computer game simulating a community of toxic and palatable butterflies exhibiting different colour patterns displayed by H. numata. In each trial, the same 10 distinct colour patterns were used, and two randomly chosen patterns were associated with a penalty when attacked. Attack rates on the different toxic and palatable colour patterns were recorded, as well as survival time. We found that profitable prey gain protection from increased resemblance to unprofitable prey, as previously described for natural predators. Additionally, phenotypic similarity between the two colour patterns associated with toxicity decreased their predation rate, in accordance with Müllerian mimicry expectations whereby shared signals benefit from increased protection. The consistence between our results on humans with the reaction of predators’ community on the same variations of colour pattern suggests that our game played by humans is a good proxy of predators’ behaviour. This experimental set-up can thus be compared to natural systems, enabling further investigations of generalisation on mimicry evolution.
 

-----

 

- 10 mail 2016 :  Thibaud Decaens, CEFE de Montpellier.

Highlighting earthworm biodiversity hotspots in French Guiana

Despite being recognized as important actors of soil functioning, earthworms have been poorly considered from a taxonomic perspective. As a consequence, the nearly 6000 species currently recognized worldwide probably represent at best half the actual biodiversity of the group. This taxonomic deficit is particularly critical in the tropics, resulting in difficult species identifications and a lack of ecological studies on earthworm communities.
Earthworm communities were sampled in eight study sites of French Guiana (grants from CNRS-Nouagues and Labex CEBA). In each site, a rapid screening of communities was achieved in a selection of habitats using a standardized protocol based on the systematic harvesting of specimens in all types of microhabitats available in a 1 ha area. DNA barcodes (COI gene) obtained for a selection of specimens were used to delimit molecular operational taxonomic units (MOTUs), the number and composition of which was further used to describe community diversity and structure at different spatial scales.
DNA barcodes produced for 2826 specimens clustered into 166 MOTUs, resulting in a great improvement of our knowledge of regional diversity, as compared to the 22 species that were reported for French Guiana in a recent checklist. Beta-diversity among sites was high, with up to 70% of the MOTUs only found in a single study site. As a consequence, the number of species accumulates steadily with the number of study sites sampled, and a rough estimates suggests that at least 400 species could be found in French Guiana. This region of Amazonian forests could therefore represent one of the richest hotspots for earthworm diversity, and additional research is critically needed to progress toward documenting the actual number of species in this region.
At a local scale, assemblages seem to be dominated by specialist species, with only a small fraction of generalists able to colonize a broad range of habitats or microhabitats. The number of species co-existing in a given habitat never exceeded 15 MOTUs, suggesting that interspecific competition may drive niche saturation during the process of community assembly. The ongoing development of a functional trait database will allow combining functional, phylogenetic and taxonomic diversity approaches in order to disentangle the relative contribution of habitat filters, biotic interactions and neutral processes in the structuring of earthworm communities in the rainforest of French Guiana.
 

-----

 3 mai 2016 : Claire Spotiswoode, Université de Cambridge.

Coevolution in the tropics : cuckoos versus hosts

This talk will be about the coevolutionary arms races that arise between brood parasites and their hosts they exploit to raise their young, focussing on various African bird species that I study in the field Zambia. In particular, I’ll ask how antagonistic coevolution drives phenotypic diversification within species, and how this might be genetically maintained. I’ll finish with some new work on the double life of one my brood-parasitic study species, the greater honeyguide, which is also a mutualistic cooperator with human honey-hunters.

-----

 

 12 avril 2016 : Martine Boccara, Professeur UPMC, ISYEB.

A new optical method to count viruses and other nanoparticles : Environmental and medical Applications

Seawater contains an extraordinary abundance of nanoparticles. Among biotic nanoparticles are the viruses which are known to affect carbon cycling and composition of microbial communities. A growing body of evidence has recently shown that membrane vesicles could be as abundant as viruses in the oceans. Discrimination between these different particles is therefore crucial.
We developed a new interferometric detection method coupled with the analysis of Brownian motion to detect, quantify, and differentiate a number of marine biotic nanoparticles. We have applied this method to Tara-oceans samples and characterize the content in viruses and vesicles from different ocean regions.
Recently we used the same method to analyse nanoparticles from the intestinal tract. Indeed there are some evidence that they are associated with dysbiosis.

-----

 5 avril 2016 :  Eric Duchaud, DR INRA, ISYEB.

Marine flavobacteria : from pathology to blue technology

Bacteria belonging the family Flavobacteriaceae, are abundant components of marine bacterial ecosystems. This Tenacibaculum genus currently encompasses 23 species with validly published names, all isolated from marine environments. While some Tenacibaculum species (e.g. T maritimum and T. discolor) are devastating fish pathogens of great significance to the marine fish farming industry, others, presumably harmless, have been isolated from diverse marine animals, macro-algae, tidal flats and the open sea. The latter likely play significant roles in organic mater recycling. Despite the ecomomic significance and prevalence in different marine environments of Tenacibaculum species, little is known about the molecular traits defining their life styles. In order to identify relevant features in relation to their ecological niches, including virulence determinants for the pathogenic species, we carried out complete genome sequencing of the type strains of all Tenacibaculum species and performed extensive comparative genomic studies. Our results yielded significant insights into the evolution of this bacterial genus. These unique genomic data encompassing a whole genus could serve as references to facilitate further studies, to devise new genotyping tools for epidemiological survey and to help identifying new relevant enzymes involved in the degradation of algal polysaccharides.
 

-----

 

 29 mars 2016 : Dan Faith, Professeur Invité par Roseli Pellens (ISYEB) et Sandrine Pavoine (CESCO) dans le cadre de un projet Labex/MNHN.

Phylogenetic Diversity and Decision Making

The phylogenetic diversity (PD) measure (Faith 1992) is a widely-used measure of biodiversity, reflecting evolutionary heritage. The PD of a subset of species is calculated as the minimum total length of all the phylogenetic branches required to connect all those species on the tree. PD measures the representation of evolutionary history. PD’s evolutionary process model, where shared ancestry accounts for shared features, means that PD can be interpreted as counting-up the features represented by a given set of species. Thus, PD values indicate option values at the level of features of species. There has been much debate about how to use PD in decision-making, including identifying high conservation priority for both species and areas. I show that a consistent framework is found by application of “expected-PD” methods – merging PD and estimated probabilities of extinction. An endangered species can have high priority for conservation because, if protected, the gain in expected PD is large compared to other species. Three factors can contribute to this large gain : the initial high probability of extinction, the length of the branches ancestral to the species, and the degree to which any near-relatives also are threatened. This logic nicely extends to priority areas for conservation. Further, we can look at “good news” species and areas. For example, we can consider hypothetical loss of a secure species, and ask whether the reduction in expected PD would be relatively large. For areas, the same logic can identify special places with high amounts of secure PD heritage value.
 

-----

 22 mars 2016 : hanh-Lan Gluckman, Collège de France.
The mechanisms underlying convergent evolution in the plumage patterns of birds.

Abstract : Convergent evolution is a central theme in biology. Birds are an ideal system to examine the mechanisms underlying convergent evolution. Although bird patterning is diverse, within-feather patterns have repeatedly converged on the same four types : mottled patterns, scales, bars and spots. Other avian patterns occur, e.g. stripes, but are rare. Some of the major mechanisms underlying convergent evolution in bird plumage patterns are natural selection for signaling and camouflage and evolutionary development. My research highlights that the mechanisms of convergent evolution are diverse, and that natural selection and development have contributed to pattern evolution.

 15 mars 2016 :  Josef Bryja, Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic and Masaryk University, Faculty of Science, Department of Botany and Zoology, Brno, Czech Republic.

Genetic studies of rodents in Eastern African biodiversity hot-spot - from biodiversity surveys to general evolutionary models

Zambezian, Somali-Masai and Ethiopian biogeographical regions are spreading in a wide belt around the Congo Basin from Angola to Ethiopia. They are dominated by savannahs and woodlands, but there are also the highest African mountains. Phylogeographic structure of animals living in these areas is relatively poorly known and often limited to large-sized species of mammals, thus reducing the power of phylogeographical interpretations. Thanks to intensive collection of fresh samples from small mammals in the last decade, it is now possible to use the comparative phylogeographic approach to assess the role of past climate and geomorphology on evolution of biodiversity of rodents inhabiting various habitat types. Most of the phylogeographic studies in Eastern Africa have been focused on taxa living in mountain forests, while savannah species were largely overlooked. By analyzing genetic data of widespread rodents living in open habitats, we provide evidence for Pleistocene refugia of savannah-woodland habitats during otherwise unsuitable climatic conditions. Subsequent population expansions were often stopped by large water bodies (e.g. Zambezi, Kafue or Lake Malawi) and forested mountains (e.g. Eastern Arc Mountains), which is confirmed by largely concordant spatial genetic structure among different rodent taxa. We also detected several secondary contact zones that can serve as models for speciation studies and represent important hot-spots also for organisms associated with rodents, e.g. viruses or host-specific parasites.

-----

 8 mars 2016 :  Sandra Lai.

Social and spatial organization of a population of arctic foxes in the Canadian High Arctic

Various ecological or individual factors may promote spatial tolerance and group living in socially flexible species, but the importance of each one remains unclear. We tested two hypothesis relating to the socio-spatial organization of a small canid, the arctic fox (Vulpes lagopus), during the breeding season. The ressources/predation trade‒off hypothesis predicts the social organization depending on the levels of ressource abundance and predation pressure in the environment, while the kin selection hypothesis predicts that relatedness mediate tolerance towards neighbors and subordinates. We worked on Bylot Island (Nunavut, Canada), an ecosystem with highly fluctuating food resources but where larger predators are almost absent. We genotyped 157 individuals using nine microsatellites to assess the kin structure of the population. We also used visual observations at dens and satellite telemetry data to determine group composition and estimate the territoriality of neighbors in relation to the availability of the two main food resources (lemmings and goose eggs) and the relatedness of individuals. The basic social unit was composed of a mated pair, with only a few cases of groups, all within the goose colony. Spatial tolerance was overall higher within the goose nesting colony, as shown by the shorter nearest neighbor distance between occupied dens and higher home range overlaps, but was not influenced by lemming density. We found no strong genetic structure within the population. Range overlaps were not correlated with relatedness, except inside the goose colony for male-female dyads, but the relationship was weak. These results suggest that the food abundance in the goose colony promotes spatial tolerance and may favor group living in arctic foxes, but without a selective tolerance among kin. Understanding the determinants of spacing patterns and group formation gives insight into the evolution of sociality in canids and other animal societies.
 

-----

 1er mars 2016 : Jean-Pierre Hugot.

D’où viennent les parasites de l’Homme ? Géographie, écologie et origine des parasites humains, une analyse du livre publié en 2003 par R W Ashford & W Crewe

Dans ce livre, les auteurs ont donné une liste de 437 espèces de parasites,
que l’on peut rencontrer sur ou dans le corps humain. Les différentes espèces
de parasites sont classées selon leurs groupes taxonomiques respectifs. Pour
chacune d’entre elles les principales informations concernant la taxonomie, la
répartition géographique, le cycle biologique et la pathogénicité du parasite
sont présentés dans une liste, incluant les rubriques suivantes :
Statut : évaluation du nombre de cas humains signalés et de leur dispersion.
Distribution : nombre de cas enregistrés selon les parasites et selon les aires
biogéographiques.
Habitat : localisation du parasite chez l’hôte humain.
Hôtes : liste des hôtes non humains qui ont un rôle dans la persistance du
cycle parasitaire.
Transmission : mécanismes permettant la contamination des patients
humains.
Spécificité : adaptation plus ou moins étroite à l’hôte.
Nous avons utilisé ces informations afin :
 d’identifier les animaux avec lesquels les humains partagent le plus de
parasites, en prenant en compte l’influence des processus de
domestication et celle des migrations humaines.
 d’évaluer la diversité des parasites susceptibles d’infester les
représentant de l’espèce humaine selon les provinces biogéographiques.
 d’évaluer quels sont les groupes parasitaires que l’on rencontre le plus
fréquemment chez l’Homme.
Les résultats ne sont pas toujours ceux que l’on pouvait imaginer
intuitivement. Ainsi : ce ne sont pas les Primates, nos plus proches parents
dans l’évolution, avec lesquels nous partageons le plus grand nombre de
parasites ; les régions tropicales ne sont pas obligatoirement celles où
l’Homme est confronté à la plus grande diversité parasitaire potentielle.
Les résultats de ces analyses sont discutés en référence aux principaux
événements historiques ayant influencé l’évolution de l’homme et ses
migrations.

Référence :
Ashford R. W. and Crewe W. "The parasites of Homo sapiens : an
annotated checklist of the protozoa, helminthes and arthropods for which we
are home." Liverpool School of Tropical Medicine, 2003, 142 p.
 

-----

 23 février 2016 :  Mark Phuong, ISYEB.

Diet and venom evolution in cone snails

Although diet is believed to be a major factor underlying the evolution of venom, few comparative studies examine both venom composition and diet across a radiation of venomous species. Cone snails within the family, Conidae, comprise more than 700 species of carnivorous marine snails that capture their prey by using a cocktail of venomous neurotoxins (conotoxins or conopeptides). Using venom duct transcriptome sequencing and comparative phylogenetic methods, we test the hypotheses that venom composition should be shaped by (a) prey taxonomic class (i.e., worms, molluscs, or fish) and (b) dietary breadth. In contrast with the dominant paradigm for interpreting Conidae venom evolution, we found that prey taxonomic class did not predict venom composition patterns among species. Our results suggest that cone snails have either evolved species-specific expression patterns likely as a consequence of the rapid evolution of conotoxin genes, or that traditional means of categorizing prey type and conotoxins (i.e., by gene superfamily) do not accurately encapsulate evolutionary dynamics between diet and venom composition. We also found a significant positive relationship between dietary breadth and measures of conotoxin complexity. These results confirm patterns predicted by Van Valen’s niche variation hypothesis (1965) and suggest that species with wider dietary breadth utilize a greater number of venom genes for prey capture. Whether this increased gene diversity confers an increased capacity for evolutionary change remains to be tested. Overall, our results corroborate the key role of diet in influencing patterns of venom evolution in cone snails and other venomous radiations.
 

-----

 16 février 2016 : Julie Marin.

Time best explains global variation in species richness of amphibians, birds, and mammals.

The general pattern of higher species richness in tropical areas has been long recognized but the underlying cause is still debated. Two major hypotheses have emerged in recent years. The Rate Hypothesis attributes this pattern to a high rate of diversification whereas the Time Hypothesis attributes it to greater lineage age.
We revisited these two hypotheses with global data sets of amphibians, birds, and mammals.
To test these hypotheses we evaluated the relationship between crown age and species richness, and between diversification rate and species richness within biogeographic regions.
We also compared diversification rates of tropical and temperate clades, and assessed the usefulness of two phylometrics, evolutionary distinctiveness (ED) and evolutionary rate (ER), as proxies of age and diversification rate. Finally, we used those phylometrics in a grid cell approach to explore the spatial distribution of clade age and diversification rate.
We found species richness of these tetrapods is best described by time (age of lineages) and that diversification rates are not significantly different between tropical and temperate areas.
In addition to time, we found that historical biogeography, in some cases, has an influence on species richness patterns.
This suggests that the latitudinal diversity gradient is a result of the gradient in climatic stability, with younger assemblages (hence, fewer species) occupying higher latitudes.
 

-----

 9 février 2016 :  Magalie Castelin, ISYEB.

A new integrative framework for large-scale assessments of biodiversity and community dynamics, using littoral gastropods and crabs of British Columbia, Canada

Improving our understanding of species responses to environmental changes is an important contribution ecologists can make to facilitate effective management decisions. Novel synthetic approaches to assessing biodiversity and ecosystem integrity are needed, ideally including all species living in a community and the dynamics defining their ecological relationships. Here we present and apply an integrative approach that links high-throughput, multi-character taxonomy with community ecology. The overall purpose is to enable the coupling of biodiversity assessments with investigations into the nature of ecological interactions in a community-level data set. We collected 1,195 gastropods and crabs in British Columbia. First, the General mixed Yule-coalescent (GMYC) and the Poisson Tree Processes (PTP) methods for proposing primary species-hypotheses based on cox1 sequences were evaluated against an integrative taxonomic framework. We then used data on the geographic distribution of delineated species to test species co-occurrence patterns for non-randomness using community-wide and pairwise approaches. Results showed that PTP generally outperformed GMYC and thus constitutes a more effective option for producing species-hypotheses in community-level datasets. Non-random species co-occurrence patterns indicative of ecological relationships or habitat preferences were observed for grazer gastropods, whereas assemblages of opportunistic omnivorous gastropods and crabs appeared influenced by random processes. Species-pair associations were consistent with current ecological knowledge, thus suggesting that applying community assembly within a large taxonomical framework constitutes a valuable tool for assessing ecological interactions. Combining phylogenetic, morphological and co-occurrence data enabled an integrated view of communities, providing both a conceptual and pragmatic framework for biodiversity assessments and investigations into community dynamics.

-----

 2 février 2016 :  Marie Fisler.

Un arbre des idées

En biologie, le cladogramme est utilisé pour classer les espèces en fonction ce qu’elles partagent d’original. Pris dans un cadre évolutionniste, ces points communs sont la trace de leurs liens de parenté.
Cependant, l’arbre classificatoire n’a pas besoin d’un présupposé généalogique pour être utilisé. Réalisé suivant le principe de parcimonie, il formalise les partages. Il permet de voir, parmi un ensemble d’auteurs, d’idées ou d’organismes, qui partage quoi avec qui. Ces regroupements permettent de déterminer des ensembles, des « écoles » de pensée parmi ces auteurs, des ensembles d’idées.
En philosophie politique, on distingue souvent des groupes de penseurs : gauche, droite, centre, monarchistes, démocrates, républicains, etc. Cependant, ces groupes ne sont pas rigoureusement formalisés : l’on ne sait pas précisément sur quels ensembles de points communs des idées sont regroupées, ni si les groupes qu’elles forment peuvent s’inclure les uns dans les autres : la pensée citoyenne est-elle une pensée républicaine ? Qu’est-ce qu’une pensée républicaine ? Pourquoi ?
Dans le passé, en Histoire Naturelle, il en était de même : on distinguait d’une part ce qui est vivant, de l’autre ce qui ne l’est pas. Parmi les êtres vivants, certains étaient capables de se mouvoir. Ils ont été appelés « animaux ». D’autres ne le pouvaient pas : ils ont été nommés « végétaux ». Et l’arrangement de certaines espèces était problématique : où classer par exemple les coraux, les éponges ou les unicellulaires ? Des points de contact entre certaines catégories ont alors parfois été créés : les zoophytes, par exemple, espèce mi-animales, mi-végétales.
La méthode cladistique permet ainsi, en créant des ensembles formalisés rigoureux, de savoir précisément qui partage quoi d’original avec qui. Certains groupes, préalablement reconnus par les spécialistes du domaine d’étude, sont reconnus sur l’arbre des idées ainsi réalisé. Mais d’autres de ces groupes peuvent ne pas être retrouvés, et disparaître. D’autres enfin peuvent apparaître, qui n’avaient encore jamais été reconnus en histoire des idées. L’arbre classificatoire et la méthode permettant son élaboration sont ainsi des modes d’étude novateurs des pensées politiques.
Mais cette méthode permet également, a posteriori, d’examiner les circulations et échanges d’idées entre les auteurs. Il permet ainsi de reconstruire l’histoire, les enjeux et les déplacements d’un concept.
Après un récapitulatif du mode de lecture et de réalisation d’un cladogramme, nous vous présenterons deux études d’Histoire des Idées en cours de réalisation. La première consiste en une classification des pensées politiques en langue française, entre 1793 et 1871. La seconde consiste en une catégorisation des correspondants de Pierre Bayle, auteur s’inscrivant dans la République des Lettres.

-----

 26 janvier 2016 :  Alexis Matamoro-Vidal, Institut Jacques Monod.

A cell-based computational model for the study of wing morphogenesis and evolution in Drosophila

One of the aims of evolutionary developmental biology is to discover the developmental origins of morphological variation. The discipline has mainly focused on qualitative morphological differences (e.g., presence or absence of a structure) between species. Studies addressing subtle, quantitative variation are less common. The Drosophila wing is a model for the study of development and evolution, making it suitable to investigate the developmental mechanisms underlying the subtle quantitative morphological variation observed in nature. Using a cell-based computational model that explicitly simulates wing morphogenesis, we investigate what variation in development is capable of generating variation in wing shape. In this talk I will focus on how forces arising from epithelial tension patterns drive the cell processes in order to establish tissue shape.
 

-----

 19 janvier 2016 :  Thibaud Monnin, UPMC.

Reproductive allocation in an ant reproducing by colony fission

Social insects produce new colonies following two alternative strategies. Independent Colony Foundation (ICF) consists in the mother colony producing many queens that fly far away, start new colonies on their own and suffer high mortality (coloniser strategy). In contrast, colony fission consists in one (or a few) queen departing the mother colony on foot with many workers and thus suffering low mortality (competitor strategy). We studied resource allocation during colony fission in the ant Cataglyphis cursor. Field observations showed that colonies that reproduced differed markedly in size. Larger colonies produced larger new colonies but did not produce more new colonies, and resource allocation among new colonies was highly biased. We tested whether C. cursor may adjust the number and size of new colonies to the intensity of competition by transplanting colonies in enclosure varying in colony density. These colonies produced fewer and larger new colonies than in the field, suggesting that they may indeed adjust resource allocation. Lastly, we used agent-based modelling to compare the success of colony fission with that of ICF. Our simulations show that the two strategies coexist under a wide range of parameter values because of a competition-colonization trade-off, and that environmental heterogeneity enhances coexistence conditions.
 

-----

 12 janvier 2016 : Juliette Delavenne, ISYEB.

New Caledonia deep sea biodiversity. Insights from the Tropical Deep Sea Benthos program.

The exploration program “Tropical Deep Sea Benthos” (TDSB) has launched deep-sea surveys in the South West Pacific for over 30 years. In particular, 37 surveys (3800 stations) were organized to sample the New Caledonian exclusive economic zone (EEZ) and its numerous seamounts. The TDSB program, which relies on a worldwide network of taxonomists, led to numerous new species descriptions and taxonomy revisions.
These taxonomic and geographic data were gathered to be available from museum databases (INVMAR and BASEXP) and analyzed to describe species associations in New Caledonian deep sea waters. Only datasets for which a taxonomist had studied all the existing samples held in the Paris museum collections were used. After a presentation of the global project, I will present results about species diversity for different taxa such as the Scleractinia (Cnidaria : Anthozoa) and the Stylasteridae (Cnidaria : Hydrozoa : Anthoathecata) which represent structuring habitats taxa.

 

2015

- 15 décembre 2015 : Charlotte Prieu-Darondeau, ISYEB.

Évolution et développement des grains de pollen chez les angiospermes

Chez les organismes pluricellulaires, la diversité morphologique observée à tous les niveaux est frappante, que ce soit au niveau de la taille, des couleurs, ou de la forme des individus, et des différentes parties qui les composent. La sélection naturelle, ainsi que les contraintes développementales, influencent l’évolution de ces différents attributs, sur le court terme comme sur le long terme. Le modèle choisi ici pour étudier l’évolution des formes est le grain de pollen des plantes à fleurs, qui présente une très grande diversité morphologique. Nous nous sommes focalisés sur un caractère morphologique, les apertures, qui sont des structures de la paroi du grain de pollen impliquées dans la survie et la reproduction. Nous avons étudié l’évolution des apertures à grande échelle taxonomique chez les angiospermes, et nous montrons que s’il existe de nombreuses variations, deux types principaux dominent : un pollen à une aperture chez les Monocotylédones et les angiospermes divergeant à la base, et un pollen à trois apertures chez les Eudicotylédones. En étudiant la dominance du pollen à trois apertures, nous avons pu montrer que la stase chez les Eudicotylédones était vraisemblablement due à une sélection stabilisante plutôt qu’à des contraintes développementales.
Nous avons également montré, grâce à l’utilisation de mutants de la plante modèle Arabidopsis thaliana, qu’un nombre d’apertures élevé est défavorable face à un stress osmotique, ce qui pourrait suggérer que les pollens triaperturés représentent un bon compromis entre survie et germination.
Enfin, nous nous sommes intéressés à un type particulier de pollen possédant de nombreuses apertures, dont nous avons étudié la distribution chez les angiospermes. L’apparition de ce type de pollen est récurrente, mais il n’est que rarement fixé à grande échelle taxonomique, suggérant l’existence d’un mécanisme de sélection interphylétique éliminant ce type de pollen sur le long terme.

-----

- 8 décembre 2015 : Diego Llusia, ISYEB.
Evolution of animal acoustic communication in changing environments
Conveying and receiving information to and from the environment is a key adaptive trait in animals. A wide variety of organisms relies on acoustic signals for sexual selection, territory defence and risk detection, among other functions. Yet the profound environmental changes caused by human activities, the so-called global change phenomenon, pose new challenges to animal communication systems. In this talk, I will review our current knowledge of how amphibians and birds deal with problems derived from climate change, noise pollution or introduced species in communicating by sounds, and what this tells us about the evolutionary mechanisms shaping acoustic diversity. Novel technologies, in combination with long-established methods, enable us now to better understand the capacity of animals to communicate in changing environments, shedding light on how the vast diversity of acoustic signals has evolved to perform their basic biological functions. However, we are still far from a fully comprehension of this complex phenomenon.
 

-----
 

 1er décembre 2015 : Roselli Pellens, ISYEB.
The contribution of phylogenetic systematics to biodiversity conservation
Phylogenetic diversity is now a core part of conservation biology, reflecting its link to option values and to evolutionary potential. Due to recent advances in molecular biology, which is enormously increasing facilities and reducing costs of obtaining large amounts of sequences and or part or entire genomes, phylogenetic diversity will be one of the first (and sometimes the only) information we get for a species. This, associated with the sheer magnitude of biological and environmental data now available in the public domain, is leading to a new paradigm in biodiversity assessments for conservation. It is also an important instrument for linking local-to regional-to global conservation demands, a goal strongly emphasized in global agendas and so hard to achieve. In this talk I will present an overview of the evolution and present state of the art of this disciplinary field, and present some questions urging for more clarification. My aim is to show some points for which we can contribute and indicate some directions of research.

-----

 24 novembre 2015 : Nicola Nadeau, University of Sheffield.
Iridescence in the Heliconius butterflies : mimicry and genetics
Some of the brightest and most striking colours found in nature are produced not by pigments but through coherent scattering of light by nano-scale structures. Despite the importance of this type of colour for animal and plant signalling and communication, and its application in man-made products, very little is known about its synthesis in natural systems. The Heliconius butterflies have been an important system in advancing our understanding of how changes in the genome can bring about adaptive differences between populations. They are also an ideal system to study the evolution and genetics of iridescent structural colours because they exhibit within and between species variation in iridescent blue structural colour, giving us a system where we can begin to unravel both the phenotypic and genetic changes underlying this variation.
 

-----

- 17 novembre 2015 : Christopher M. Austin Professor, University Malaysia
Diving into the deep end of the gene pool : Genomics approaches to phylogenetic and systematic studies of fish and decapod crustaceans.

The recent development of next-generation DNA sequencing technologies provides opportunities to characterize the genomic composition of individuals, populations and species in unprecedented detail. It is now possible to obtain genetic information from throughout the genome and to address a variety of questions relating to evolutionary and comparative genomic research that can contribute to may disciplines of the biological sciences. Nevertheless there are many fields of study that are only slowly taking advantage of this sequencing revolution and there are many animal groups for which there is only limited genomic information. In this presentation I am going to describe some recent genomic studies on fish and crustaceans conducted at Monash University Malaysia that attempt to fill important knowledge gaps and contribute to our understanding of the evolution and diversity of these groups. These case studies consist of (1) genome sequencing projects for the Malaysian arowana (dragon fish), the Australian Murray cod and the red claw crayfish and (2) mitogenome evolution in decapod crustaceans.
 

-----

 

 10 novembre 2015 : Tony Robillard, ISYEB.
Recent endemism and rapid acoustic diversification in the New Caledonian Agnotecous crickets
Islands are bounded areas where high endemism is explained either by allopatric speciation through the fragmentation of the limited amount of space available, or by sympatric speciation and accumulation of daughter species. In previous studies, we analyzed the mode, tempo and geography of speciation in Agnotecous, a cricket genus endemic to New Caledonia showing a generalized pattern of sympatry. The results suggested that the diversification occurred mostly through recent allopatric speciation and that current sympatry was due to secondary range expansion.
However, crickets are also acknowledged for their diverse calling songs playing a major role in preventing hybridization in closely related species. In the context of allopatric speciation, there is a possible interplay between speciation and acoustic diversification. We therefore analyzed the diversification of the mechanism of sound production in Agnotecous, since the species of this genus are very similar in terms of morphology, but produce songs with a wide range of frequencies (10-20 kHz). The study consisted in fine scale analyses of the morphological and behavioral variables of the system using comparative methods in reference to phylogeny. Unexpectedly, we have found that the studied species developed two different strategies to produce high-frequencies : (1) some species increased the speed of the stridulatory movement until reaching directly high dominant frequencies, (2) while others exploited the vibration capacities of their forewings to amplify harmonic frequencies coming from slow stridulatory movements. These results support the hypothesis that high-frequency songs and the mechanism of sound production evolved quickly, accompanying each event of speciation.

 

 3 novembre 2015 :  Jawad Abdelkrim, ISYEB.
Transcriptome-based exon capture phylogenomics : a practical approach with the example of the Conoidea (neogastropoda)

The Conoidea (a superfamily of predatory marine snails) represent a hyper-diversified clade, with an estimation of up to 15000 species. These species are characterized by an important diversity of morphological and anatomical structures linked to the use of a huge catalogue of toxins to capture their preys. The evolution of this predatory arsenal is thought as one of the main causes of the diversification of the group. In order to test such evolutionary hypotheses, one has to rely on a solid and stable phylogeny. Such phylogeny doesn’t exist yet for this group since classical approaches based on a limited number of PCR-targeted genes prove to be of limited use when it comes to the resolution of deeper, inter-familial relationships (up to 100 My for the Conoidea). In order to overcome these technical limits, we present an approach of transcriptome-based exon capture conducted on 50 species from the 14 families of Conoidea. I will introduce the main steps of such an approach and detail some practical aspects of an exon capture protocol. Finally, the results of a preliminary phylogenetic analysis based on an alignment of 103000 bp will be shown.
 

-----

 27 octobre 2015 : Simon Boitard, INRA Toulouse, MNHN-EPHE.
Inferring population size history from large samples of genome wide molecular data - an approximate Bayesian computation approach.
Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context.
However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey), our approach revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles.
 

-----

 20 octobre 2015 :  Florian Jabbour, ISYEB.
Development, anatomy, and genetic control of some teratological phenotypes of Ranunculaceae flowers

Teratological organisms originate from developmental anomalies, and exhibit structures and a body organization that deviate from the species standard. In plants, teratological forms are often of horticultural interest. However, besides their aesthetic value, these monsters give essential clues about the formation and evolutionary significance of the wild-type groundplan. We focus on flower terata, which can be affected in their sterile and/or fertile organs, with special emphasis on the Ranunculaceae. The diversity of perianth shapes and organizations in flowers of this family is huge, and is even increased when anomalies occur during organo- and/or morphogenesis.
To begin with, we synthesize the observations and research conducted on the Ranunculacean floral terata, following a phylogenetic framework.
Then, we report results regarding the morphology of developing meristems, the anatomy of buds, and the genetic control of selected teratological phenotypes of Ranunculaceae flowers. We focus on species and horticultural varieties belonging to the genera Aquilegia, Delphinium, and Nigella. Wild-type flowers of these species are actinomorphic (Aquilegia, Nigella) or zygomorphic (Delphinium), spurred (Aquilegia, Delphinium) or with pocket-like petals (Nigella).
Last, we discuss the evolutionary potential of such teratological phenotypes when they occur in the wild.
 

-----

 13 octobre 2015 : Sylvain Gerber, ISYEB.
Visualizing constraints and the anisotropy of phenotype space
Morphospaces are quantitative representations of phenotype space that have proved particularly useful in the broad field of evolutionary morphology. Yet, do current conceptualizations of morphospaces appropriately echo the evolutionary dynamics of organisms depicted in such spaces ? Many studies implicitly consider the phenotype space as an isotropic state-space, but several lines of evidence suggest that such a view is inadequate. In particular, advances in evolutionary developmental biology have shed light on the statistical properties of the genotype-phenotype map and their consequences for the structure of variation. Here, I use a trilobite case study to illustrate the effect of constraints on the accessibility structure of phenotype space. The morphospace obtained is strongly anisotropic and reveals discordances between the apparent range of possible phenotypes and their actual accessibility. It is advised that geometric measures of distance in morphospace should be taken with caution and complemented with developmentally meaningful measures of evolutionary accessibility.

 

-----

 6 octobre 2015 : Dr Benjamin Zuckerberg, University of Wisconsin-Madison, USA.
Climatic variability drives the broad-scale population dynamics of cold-adapted birds in North America

Many birds of northerly ecosystems exhibit oscillations in their population dynamics ranging from discrete population cycling to irruptive movements. These dynamics can range in periodicity from biennial to decadal cycles, and while their exact reasons are not entirely clear, it is thought that these patterns are related to climatic variability. I will present on recent research from two case studies : irruption dynamics of Pine Siskins (Spinus pinus) and population cycling of Ruffed Grouse (Bonasa umbellus). Pine Siskins exemplify normally boreal seed-eating birds that can be sparse or absent across entire regions of North America in one year and then appear in large numbers the next. These dramatic avian “irruptions” are thought to stem from intermittent but broadly synchronous seed production (masting) in one year and meager seed crops in the next. A prevalent hypothesis is that widespread masting in the boreal forest at high latitudes is driven primarily by favorable climate during the two to three consecutive years required to initiate and mature seed crops in most conifers. We analyzed more than 2 million Pine Siskin observations from Project FeederWatch, a citizen science program, and revealed two principal irruption modes (North-South and West-East), both of which were correlated with climate variability, and continental-scale pairs of oppositely signed precipitation and temperature anomalies (i.e., dipoles). The climate dipoles juxtapose favorable and unfavorable conditions for seed production and wintering habitat, motivating a push-pull paradigm to explain irruptions of Pine Siskins and possibly other boreal bird populations in North America. For our second case study, we used spatially explicit demographic modeling to model the 8-11 year population cycle of Ruffed Grouse throughout the Midwest and Great Lakes region of the United States. We found that aspects of cyclic dynamics are related to inter-annual variation in temperature and precipitation anomalies, particularly as they influence winter survival. Furthermore, the use climate models forecasted a dampening of these cycles in southerly regions by the end of the 21st century.
 

-----

 29 septembre 2015 : James Mallet, Harvard University.
Gene flow between Heliconius species : how butterflies mess with our concepts of species and phylogeny

James Mallet, Distinguished Lecturer Harvard University (Department of Organismic & Evolutionary Biology) & Emeritus Professor of Biological Diversity, UCL (Department of Genetics, Evolution & Environment).

It is a seductive idea that species are independent evolutionary units. In Heliconius butterflies we have new data to disprove it. There is unprecedented genomic admixture among some species. Our concepts of "species" and "phylogeny" may need to change.
 

-----

 22 septembre 2015 :  PierPaolo Maisano Delser, ISYEB.
Population genomics of C. melanopterus using target gene capture data : demographic inferences and conservation perspectives

Population genomics of non-model organisms can be challenging when a closely related reference genome is not available. Here we applied a recently developed target gene capture approach that circumvents the need for a reference genome to obtain deep sequence information for 1000 independent autosomal regions for the blacktip reef shark (Carcharhinus melanopterus). We used the data collected to explore and contrast estimates of demographic history and population structure in a single deme (SID) from Northern Australia with a scatter sample (SCD) collected from various locations throughout the Indian Ocean. We developed an ABC with recombination algorithm, using the site frequency spectrum computed on unphased data as summary statistic, to explore the genealogical signature of population dynamics detected from both sampling schemes. We then contrasted these results with those obtained by fitting the data to a non-equilibrium finite island model. Both approaches supported a Nm value 40, consistent with philopatry in this species and the moderately to high Fst found using microsatellite markers in previous work. Finally, we tested for signatures of recent bottleneck due to overfishing and human disturbance. We demonstrate through simulation that metapopulations exhibit greater resilience to recent changes in effective size compared to unstructured populations which can obscure detection of recent population bottlenecks. We propose an empirical approach to detect recent bottlenecks which may help to explain why several overfished species do not show a decrease in effective population size. When applied to C. melanopterus it suggested that the conservation status of the sampled deme is healthy.
 

-----

 15 septembre 2015 : Flora Jay, Musée de l’homme.
Infering demographic history from whole genome data using Approximate Bayesian Computation.

Approximate Bayesian Computation (ABC) has proven to be useful for inferring demography from microsatellite or SNP data. Whole-genome data are expected to be extremely rich in information about past demography but, because simulations were, until recently, computationally too costly, ABC methods have not been thoroughly tested on such very long sequences. Dense polymorphism data contain extra information that is not available from unlinked site polymorphisms, and should improve the reconstruction of demographic history. We investigate how summary statistics computed from sequences, such as the lengths of haplotypes shared between individuals, or the decay of linkage disequilibrium with distance, can be combined with classical statistics (eg heterozygosity, Tajima D) and efficiently integrated to an ABC framework. We then quantify their influence on the inference of demographic parameters, particularly in the presence of expansions or bottlenecks in a single population. Furthermore, we describe how errors that are usually more frequent in sequence than SNP data impact the inference, and show that modeling the error process in the ABC framework increases accuracy. Finally, we apply our method to publicly available European and African complete genomes.
 

-----

 8 septembre 2015 :  Emmanuel Toussaint, Université du Kansas, Etats-Unis.
From molecular taxonomy to macroevolutionary pattern inference : A case study with the charismatic Nawab butterflies (Nymphalidae, Charaxinae, Polyura)

The genus Polyura comprises butterflies dwelling in the geologically highly complex Indomalayan-Australasian archipelago. Passion for this group among amateurs and scientists for more than two centuries has made of this group a taxonomic conundrum preventing the study of its systematics and evolution. I present the results of a large project aiming at deciphering the taxonomy of this group, inferring its systematics, and reconstructing its historical biogeography and diversification dynamics through geological times. Multiple specimens of all described species were gathered and sequenced from Museum collections and field expeditions to assemble a comprehensive taxon sampling. The latest methods of molecular species delimitation were used on the generated multimarker matrix to investigate species boundaries and genetic differentiation in the genus. Based on the clarifications of species contours, the phylogenetic relationships of the genus were inferred using a species tree approach. The biogeographic history of Polyura butterflies and their diversification dynamics were reconstructed using an array of maximum-likelihood based methods. The genus likely originated during the Miocene in India from where it initially colonized Greater Sunda Islands and East Palearctic. The biogeographic pattern inferred is highly dynamic with reverse colonization events and late Plio-Pleistocene dispersal. This is in agreement with the reconstructed pattern of constant diversification since the Miocene associated with the emergence of new islands in particular East of Wallace’s line.
 

-----

 21 juillet 2015 : Luis-Alberto Garcia.
Coancestry via identity coefficients and their use on genomic estimates of kinship

Following Gillois’s work, relatedness or kinship can be decomposed into 15 coefficients of identity. Traditionally, a subset of 9 coefficients have been used for many purposes. In this talk, I will show a new method to estimate these 15 coefficients of identity, which can then be used to infer the expected variance of genomic estimates of inbreeding. I will present examples of this method on calculations of allelic diversity from more than two individuals, at least from a theoreticall point of view. Lastly, by using the coefficients of identity, I will show how the coefficients of dominance cannot be calculated from biallelic data like SNPs.
 

-----

 7 juillet 2015 : Mario de Pinna.
Roots and rooting in phylogenetic networks
The talk is a general overview of the theory and metodology of directionality in phylogenetic trees. The conceptual and methodological significance of unrooted trees is analyzed. Directionality in phylogenetic diagrams is explained as to its logical core, with different expressions as asymmetric probabilities of character-state changes and extrinsic information on directionality. Methods for rooting are discussed separately and organized according to their fundamental assumptions. The need for a clear representation of partially-directed trees is emphasized. Finally, the advantages and pitfalls of understanding phylogeny in unrooted and rooted dimensions are explored.
 

-----

 30 juin 2015 : Marine Robuchon.
Studying biodiversity by an integrative approach of population genetics and community ecology : a way to better predict the fate of our marine forests in a changing ocean ?

Species diversity and genetic diversity have traditionally remained the exclusive domains of community ecology and population genetics, respectively, despite repeated recognition of close parallels between these levels of biodiversity the literature. Species diversity within communities and genetic diversity within populations are hypothesised to co-vary because of locality characteristics that influence the two levels of diversity via parallel processes (drift, selection and migration) or because of direct effects of one level of diversity on the other. Corroborating these hypotheses, several studies on different taxa from various geographic zones have revealed correlated patterns of species and genetic diversity (mostly positive correlations), suggesting that the SGDC (species genetic diversity correlation) might be a general pattern. In this work, we tested for spatial SGDC patterns in kelp forests along the Brittany coastline (France) by conducting a multi-level biodiversity sampling in 20 localities : in each one, we sampled specimens belonging to the two dominant kelp species Laminaria digitata (Hudson) J.V. Lamouroux and Laminaria hyperborea (Gunnerus) Foslie as well as macroalgal communities living underneath the canopy formed by these two species. Genetic diversity for these two kelp species was investigated using microsatellites while the species identity of macroalgal communities’ specimens was determined based on both morphological and molecular criteria. We tested SGDC for different diversity metrics and at several spatial scales. Our results revealed a majority of positive SGDC, suggesting that genetic diversity within kelp populations and species diversity within macroalgal communities are probably influenced by parallel processes. However, the significance and strength of the correlation varied among the target species, the metrics and the spatial scale considered. These findings allow highlighting in which cases i) anthropogenic pressures and/or conservation measures have similar effects on species and genetic diversity and ii) one level of diversity can be used as a surrogate for predicting the other.
 

-----

 23 juin 2015 : Ralph Britz
The fascinating world of miniature fishes

In the last decade a number of miniature fishes have been described. They can be assigned to two very different types : proportioned dwarves and developmentally truncated miniatures. While proportioned dwarves are only shrunk versions of their larger relatives with few, if any, reductions, developmentally truncated miniatures exhibit the anatomical condition of a larval stage of their larger relatives. It is these developmentally truncated miniatures that show a collection of highly unusual, often unique characters. It appears that the evolutionary mechanism of truncation has taken the organism back to its developmental foundations and enabled it to vary more dramatically from its bauplan than any of the proportioned dwarfs. This talk will illustrate some of the discoveries of miniature teleosts the speaker has been involved in and introduce the world of developmentally truncated fishes.
 

-----

 16 juin 2015 : Emmanuelle Baudry, Laboratoire Ecologie Systematique et Evolution, Universite Paris Sud

Évolution de la personnalité : la timidité est-elle avantageuse chez les écureuils ?

Depuis une dizaine d’année, il a été observé que dans beaucoup d’espèces animales, les individus présentent des différences de comportements stables dans le temps, c’est à dire des personnalités différentes. Il existe souvent une relation forte entre la personnalité et la fitness d’un individu, ce qui pose la question du maintien des variations de personnalité dans les populations en présence de sélection.
Après une introduction sur le concept de personnalité chez les animaux et sur les relations entre personnalité et fitness chez l’homme, je vous présenterai les résultats d’une étude réalisée avec Jean-Louis Chapuis et son équipe sur le type de sélection qui existe sur un trait de personnalité dans une population d’écureuil de Corée.
 

-----

 11 juin 2015 : SEMINAIRE EXCEPTIONNEL : Dan Faith

Planetary boundaries as a safe operating space for humanity : can phylogenetic diversity (PD) provide the basis for a biodiversity boundary ?

“Planetary boundaries” (see Rockstrom et al 2009 ; Steffen et al 2015) refer to the idea of a “safe operating space” for humanity. The planetary boundaries framework considers processes relating to climate change, biodiversity loss, land-system change, biogeochemical flows, stratospheric ozone depletion, ocean acidification, freshwater use, atmospheric aerosol loading, and chemical pollution. Beyond the identified boundaries, thresholds and undesirable changes threaten human well-being. Is there a meaningful boundary related to biodiversity ? The current rate of extinctions and the corresponding biodiversity crisis suggest a possible focus on global extinction rates. However, recent work has focused more on phylogenetic and functional diversity ; these may have a good regional-to-global scope, and appealing links to current and future well-being. I have been investigating these two key aspects for a biodiversity boundary as part of bioGENESIS, one of the core projects in a global change international program called “Future Earth”. We focus on a measure of phylogenetic diversity called “PD”. Our proposal for phylogenetic diversity “tipping points” and boundaries highlights the importance of evolutionary or evo-system services. Such services include option values (unanticipated future benefits for humans) and evolutionary potential. Such option values of biodiversity typically reflect global-scale benefits for future generations, and so they are a natural consideration for planetary boundaries. Early warnings with respect to a PD planetary boundary may focus on the changing status of Phylogenetic Key Biodiversity Areas – those places on the planet that are outstanding in their current contribution to retaining global phylogenetic diversity. PD is useful, but does not tell us all we need to know about functional traits. bioGENESIS is exploring ways to make general inferences about functional traits diversity. At the global scale, this could provide, for multiple taxonomic groups, a running report card on risk of loss of functional trait diversity. This would nicely complement the emerging use of a PD report card to assess risks associated with resilience-loss, tipping points and planetary boundaries.
 

-----

 9 juin 2015 : Dimitri Neaux, Laboratoire IPHEP, Université de Poitiers

Intérêt de l’étude de l’intégration des structures crâniofaciales chez les hominidés

Plusieurs grandes tendances évolutives sont observées au sein des structures crâniennes des membres du rameau humain : la mise en place d’une face courte, l’augmentation de la taille du cerveau et la flexion de la base du crâne. Les modalités d’apparition de ces traits restent, à l’heure actuelle, toujours débattues. Le crâne est une structure globalement intégrée, composée d’éléments osseux liés par des relations de natures diverses : génétique, développementale, fonctionnelle et/ou évolutive. Afin de mieux appréhender les mécanismes ayant permis l’apparition des structures crâniofaciales des hominidés, il est nécessaire de définir et de quantifier l’intégration morphologique existant entre ces traits crâniofaciaux. Les techniques d’imagerie 3D, les méthodes de morphométrie géométrique et les outils d’analyse statistique multivariée permettent l’identification du type et l’intensité de l’intégration entre ces structures. Ce type d’étude appliqué aux hominidés modernes (humain moderne, chimpanzé, gorille et
orang-outan) permet d’apporter des informations cruciales concernant les questions relatives (1) aux schémas structuraux qui différencient les humains des autres grands singes actuels et (2) aux mécanismes évolutifs et développementaux ayant permis l’émergence des humains modernes. Ces travaux mettent en évidence plusieurs interactions crâniofaciales propres aux hominines. Ils permettent également la caractérisation des mécanismes ayant abouti à la mise en place de la face courte des humains modernes. Ce type d’analyse est donc essentiel à une meilleure définition du rôle de l’intégration morphologique dans l’évolution du rameau humain et ouvre la voie à de nouveaux travaux portant sur d’autres taxons actuels et fossiles.
 

-----

 2 juin 2015 : Jean-Pierre Hugot

Diversité génétique de Talpa europaea et de l’hantavirus NOVA (NVAV) en France

Les Hantavirus (Bunyaviridae) sont principalement hébergés par des rongeurs, Muridae (rats, souris, mulots, etc.). Toutefois, les recherches effectuées depuis une dizaine d’années ont révélé que les musaraignes (Soricidae), les taupes (Talpidae) et certains chiroptères peuvent également les héberger. Certains Hantavirus sont susceptibles de contaminer les Humains. Outre son intérêt pour l’étude des mécanismes de l’évolution, ce groupe, présent chez des micromammifères dans le Monde entier, a par conséquent un intérêt épidémiologique.
Dans le cadre d’une étude menée d’octobre 2012 à novembre 2014 nous avons capturé en France, en divers sites, plusieurs centaines de taupes (Talpa europaea). La recherche de la présence d’Hantavirus s’est révélée positive chez 94 des spécimens capturés soit 47-50% des taupes examinées. Pour une partie de cet échantillonnage l’ARN des virus a pu être extrait et séquencé. L’étude des séquences des gènes L ou S montre que ces virus peuvent être identifiés à l’espèce NOVA (NVAV) découverte en 2007 chez un spécimen unique de Talpa europaea en provenance de Hongrie.
Ces résultats confirment la présence d’une espèce virale spécifique : NOVA, chez Talpa europaea hors du pays de sa découverte initiale et, peut-être, dans l’ensemble de l’ère de répartition de l’espèce hôte. Ils révèlent également que la prévalence de ce virus est forte ce qui suggère que les mécanismes de transmission entre individus fonctionnent efficacement. L’analyse phylogénétique des séquences obtenues montre : - que l’espèce NOVA est génétiquement très divergente des autres Hantavirus connus ; - que les virus que nous avons isolés s’agrègent dans l’arbre selon leurs origines géographiques. Il existe par conséquent chez ce virus une variabilité populationnelle, probablement corrélée avec celle des hôtes.
Lorsque nous avons entamé l’étude populationnelle des taupes capturées, afin de la comparer à celle des virus, nous avons obtenus des résultats inattendus. Une partie des échantillons collectés en France se sont révélés génétiquement très divergents de Talpa europaea, suggérant qu’ils puissent appartenir à une espèce différente.

S Hun Gu, J Dormion, J-P Hugot, R Yanagihara. 2013 High prevalence of Hantavirus infection in the European common mole (Talpa europaea) in France. Epidemiology and Infection, FirstView Article pp 1-5 (IP 2.867).

J-P Hugot, S Hun Gu, C Feliu, J Ventura, A Ribas, J Dormion, R Yanagihara, V Nicolas. 2014 Genetic variability of Talpa europaea and Nova hantavirus (NVAV) in France. Bull. Acad. Vét. France 167(3) : 177-184.
 

-----

 26 mai 2015 : Lounes Chikhi
Social structure matters : on some genetic consequences of social and population structure

Most species are spatially and socially organised. However, population geneticists tend to ignore both facts and typically use demographic models that assume random mating over wide geographical areas (i.e. they ignore population structure) or over more limited/local areas (i.e. they ignore social structure). This is sometimes surprising given that structured models, such as the n-island (Wright, 1931) or the stepping-stone (Kimura, 1953) models were actually devised more than sixty years ago. I will present some recent results obtained in the group on the impact of (i) social structure and mating systems on genetic and genotypic diversity of "populations" and (ii) population structure on demographic inference.
 

-----

 19 mai 2015 :  Guillaume Billet CR2P
Morphological variation of a highly functional structure : the bony labyrinth of the inner ear in Xenarthra (Mammalia)

Understanding the factors that influence the phenotypic variation of a highly functional and complex structure is a major goal of modern evolutionary biology. The bony labyrinth of the inner ear houses organs that serve for balance and audition. As such it offers a good opportunity to scrutinize morphological variation in relation to several functional and non-functional parameters. We analyzed the labyrinthine shape among extant and fossil members of the mammalian superorder Xenarthra (armadillos, anteaters and sloths), which present a variety of sizes and locomotor behaviours. In this presentation, I will discuss our main results on variation at different hierarchical levels within Xenarthra : i) the weak allometric influence on labyrinthine shape variation but the strong influence of a probable serial homology of the semicircular canals, ii) the existence of fluctuating levels of intraspecific variation, which suggests for some species a relaxation of constraints, possibly in relation to locomotor behaviour, and iii) the strong phylogenetic imprint found on the shape of the bony labyrinth in Xenarthra in general as well as the existence of repeated striking convergences in some taxa with similar locomotor behaviours. Together with recent studies from other teams, these results significantly enhance our understanding of the morphological variation of the inner ear and allow suggesting new lines of future research.
 

-----

 12 mai 2015 Johan Pansu Laboratoire LECA, Université de Grenoble

Caractériser l’impact des activités anthropiques sur la biodiversité à travers différentes échelles spatiales et temporelles par analyse de l’ADN environnemental

Caractériser l’impact des activités anthropiques sur la biodiversité à travers différentes échelles spatiales et temporelles par analyse de l’ADN environnemental
Résumé : La plupart des écosystèmes sont aujourd’hui soumis à une pression anthropique croissante. Les études portant sur l’effet des activités humaines sur la biodiversité se multiplient mais elles se focalisent, principalement pour des raisons méthodologiques, sur un nombre restreint de groupes taxonomiques. L’analyse de l’ADN environnemental (e.g., issu d’échantillons de sols, sédiments, eau…) permet aujourd’hui d’accéder rapidement à l’ensemble de la diversité biologique. Je propose ici de présenter, à travers plusieurs exemples, l’application d’une approche dite de metabarcoding environnemental afin d’étudier l’impact des activités anthropiques sur les communautés biologiques, et la résilience de ces dernières, à travers différentes échelles spatiales et temporelles. La première partie sera ainsi consacrée à la caractérisation des communautés édaphiques sous l’influence de diverses perturbations anthropiques récentes, dans des milieux contrastés, grâce à l’ADN contenu dans les sols. La seconde partie se propose d’examiner l’impact à long terme des activités anthropiques au travers d’un exemple particulier en milieu de montagne par analyse de l’ADN contenu dans les archives sédimentaires lacustres. Cette approche a notamment permis de retracer l’histoire des activités pastorales au cours de l’Holocène mais également les changements environnementaux que ceux-ci ont engendrés dans le bassin versant.
 

-----

 5 Mai 2015 Raphaël Boulay, Université de Tours, France.
Innovation sociale et speciation récente chez des fourmis thermophiles du genre Cataglyphis

Les fourmis du genre Cataglyphis sont distribuées dans les régions arides et semi arides paléarctiques. Elles possèdent des adaptations comportementales, physiologiques et morphologiques exceptionnelles leur permettant de résister à des températures extrêmes. Les milieux dans lesquels elles évoluent ont subi d’importants bouleversements au cours des derniers millions d’années. Ces bouleversements, associés à de faibles capacités de dispersion sont probablement à l’origine de nombreux phénomènes de spéciation et, peut être, d’innovations de leurs structures sociales
 

-----

 28 avril 2015 Anne-Claire Fabre, Duke University, USA.
How can the interplay between form and function enlighten our understanding of the evolution of organisms in their ecological context ?

Form and function are linked at a fundamental level. Bones, for example, are clearly functionally important. They allow movement and, whilst supporting loads, also need to respond and resist to muscular forces. Indeed, bones are shaped by force and motion and thus, presumably intimately related to the movements executed, and thus also the lifestyle of a species. This is the background of this presentation where the origin and nature of phenotypic variation is studied in relation to phylogenetic constraints and mechanistic form‐function relationships in the context of adaptations of species to specific ecological demands. To study this form-function relation I investigate the influence of different factors on the shape of the postcranial bones of mammals using geometric morphometric methods and comparative approaches that take into account phylogeny. Here, I will present the some results of my PhD and current postdoc that show how many factors influence the morphology of the postcranial skeleton ranging from the body mass, over locomotor strategies, to more specialized behaviours such as grasping ability in addition to shared ancestry. Finally, these results shown that there is a relation between form and function, but that our understanding thereof often remains hampered by a lack of quantitative data on the locomotor behaviour in the taxa under study.
 

-----

 21 avril 2015 Adrien Perrard American Museum of Natural History, Etats-Unis.
Combining landmark data and phylogenetic analyses : Can we tell the story of social wasps from the lines of their wings ?

The wing venation provides useful characters to classify extant and fossil insects. Quantification of its shape using landmarks has pushed even further the potential of the wing venation to distinguish taxa. During my PhD, I found that wing shapes of hornets (Hymenoptera, Vespidae) presented a strong phylogenetic signal. As a postdoc at the American Museum of Natural History, I am now exploring whether and how we could use this kind of data to improve our phylogenetic inferences.

I tested a recent method called “landmark optimisation” to include wing shape data in the phylogenetic analysis of hornets and yellow jackets based on 68 morphological characters and nine genes. I also tested the influence of landmark optimisation parameters using simulated data with a known phylogeny.

The results confirmed that even if it is based on landmark coordinates, landmark optimisation is invariant to the original orientation of configurations. However, it is influenced by other parameters. Single landmark configurations never accurately reflected the true topology but results were close when compared to random topologies. Wing landmarks were thus not reliable phylogenetic characters when treated independently, but could provide useful insights when combined with other data. Our phylogeny confirmed the monophyly of most groups described on the basis of morphology and showed the fossil Palaeovespa as sister to the extant genera.
 

-----

 14 avril 2015 Sébastien Dutertre Institut des Biomolécules Max Mousseron, Montpellier.

Evolution of separate predation- and defence-evoked venoms in carnivorous cone snails

Venomous animals are thought to inject the same combination of toxins for both predation and defence, presumably exploiting conserved target pharmacology across prey and predators. Remarkably, cone snails can rapidly switch between distinct venoms in response to predatory or defensive stimuli. Here, we show that the defence-evoked venom of Conus geographus contains high levels of paralytic toxins that potently block neuromuscular receptors, consistent with its lethal effects on humans. In contrast, C. geographus predation-evoked venom contains prey-specific toxins mostly inactive at human targets. Predation- and defence-evoked venoms originate from the distal and proximal regions of the venom duct, respectively, explaining how different stimuli can generate two distinct venoms. A specialized defensive envenomation strategy is widely evolved across worm, mollusk and fish-hunting cone snails. We propose that defensive toxins, originally evolved in ancestral worm-hunting cone snails to protect against cephalopod and fish predation, have been repurposed in predatory venoms to facilitate diversification to fish and mollusk diets.
 

-----

 7 avril 2015 Guillermo Orti George Washington University, USA
how to build the tree of life of all fishes

 

-----

 31 mars 2015 :  Doris Gomez
L’iridescence et la communication, une approche interdisciplinaire

L’iridescence - changement de coloration avec l’angle d’observation/d’illumination - est une stratégie de coloration d’une étonnante universalité, tant écologique que taxonomique. Pourtant, par comparaison avec les couleurs pigmentaires, elle reste peu étudiée, et on connaît encore mal les fonctions qu’elle remplit. En effet, seule la physique possède le savoir théorique et les outils indispensables pour caractériser l’iridescence et répondre aux questions de biologie. A l’interface entre les deux disciplines, on peut caractériser la forme des signaux iridescents, identifier leur contenu informatif ainsi que les partenaires de la communication, et déterminer les pressions de sélection qui agissent sur la forme des signaux à l’échelle micro et macroévolutive. Ces différentes questions seront abordées au travers d’exemples d’études sur des insectes et des oiseaux iridescents.
 

-----

 24 mars 2015 : Regine Vigne, Professeur, ISYEB.
A proposal to manage taxonomic descriptions : Xper2 – Xper3

Morphological descriptions are crucial information in taxonomy, complementing sequences, images, sounds etc… This information is mandatory to identify, to inventory, to compare, to analyse and to teach biodiversity. However these descriptions are heterogenous and scattered.

Different models and formats have been proposed to encode taxonomic descriptions for computer processing and online publishing. Xper2 and Xper3 are the two versions, local and online, of a knowledge management software we are developing to store and to analyse structured descriptions, and to assist identification of specimens.

We will present different applications developed in the MNHN with Xper2 and Xper3. We will discuss the limits of the knowledge representation and methods, and propose some perspectives. Xper2 was used on various recent and fossil taxonomic groups including plants, marine species, and parasites. Xper3 is a web platform allowing collaborative work through a web platform. The flexibility of its architecture makes it possible to adapt the identification key interface depending on the content and the audience.
 

-----

 17 mars 2015 : Purificacion Lopez-Garcia, Université Paris-sud.
Questions ouvertes sur l’origine des eucaryotes
Lors de son exposé, Puri nous présentera l’état des connaissances actuelles et les différents grands types de modèles sur l’origine des eucaryotes de manière critique avant de pointer les questions qui restent vraiment ouvertes.
 

-----

 10 mars 2015 : Stefano Mona, ISYEB.
On the role played by the carrying capacity and the ancestral population size during a range expansion
Range expansions (RE) occurred several times in many species. Despite their abundance, many details of their genetic consequences need yet to be fully investigated. We focused on two aspects of RE : i) the influence of N (effective population size) and m (migration rate) for fixed Nm ; ii) the role of the effective population size of the ancestral deme (Nanc). Our simulations suggest that larger N increases the length of the scattering phase, determining a higher within deme variability (lowering the degree of population differentiation), an excess of rare variants and an increase in number of lineages reaching the ancestral deme. These lineages accumulate mutations according to Nanc : for larger N this increases the between-population component of molecular variance, contrasting the decrease in population differentiation due to the heterozigosity excess. These findings open a new window to estimate separately N and m and make inferences on the ancestral population structure of a species.

 

-----

 3 mars 2015  Julian Kerbis, Chicago Field Museum.
The Man-eating Lions of Tsavo" with insights into the circumstances of Man-eating by lions.

This talk reviews a notorious man-eating incident by lions in Tsavo Kenya in 1898. Two lions stopped the construction of the railway being built by the British from the Indian Ocean to the source of the Nile River in Uganda. This event has been popularized in 3 Hollywood Movies including, most recently, ’The Ghost and the Darkness’ with Val Kilmer and Michael Douglass. I will focus on the causes of man-eating behavior among lions along with a reconstruction of the circumstances in Kenya in 1898 that contributed to this episode.
 

-----

 24 Février 2015  Erwan Delrieu-Trottin, ISYEB, MNHN
 

Living at the margin : Evolutionary history of endemic coral reef fishes from two peripheral areas of the Indo-Pacific, French Polynesia archipelago and Mascarene Islands.

Endemic species have been a popular focus of evolutionary science for those wishing to understand the causes and consequences of the geographical distribution of life on the Earth. If some regions are known to concentrate a high number of endemic coral reef species, the evolutionnary history of these endemic faunas remains understudied. I will present how genetic tools help us to shed some light on the origin, ages and population histories of endemic coral reef fishes from 2 hotspots of endemism, French Poynesia and Mascarenes Islands.
 

-----

 17 Février 2015 : Thierry Wirth, ISYEB, MNHN
 

Mycobacterium tuberculosis Beijing lineage : origin, spread and selection signatures.

During the last decade increasing numbers of multidrug resistant (MDR) and extensively drug resistant (XDR) Mycobacterium tuberculosis complex (MTBC) strains have been reported worldwide. Intriguingly, high rates of MDR tuberculosis (TB) have been found to be associated with particular phylogenetic MTBC lineages, e.g. the Beijing lineage in Eurasia. The reasons for this “success” have not yet been investigated at a global population scale, nor the fitness of the strains evaluated in relation to MDR/XDR resistance. Indeed, little is known about the evolutionary mechanisms that allow MDR strains to compensate for the fitness costs of resistance mutations and to transmit efficiently in the community.
Here, we reconstructed the biogeographic structure and evolution of this lineage by genetic analysis of 5,000 isolates from 99 countries using 24 loci MIRU-VNTR (mycobacterial interspersed repetitive units – variable number of tandem repeats) typing. Moreover, whole genome sequencing of 110 representative strains allowed us to reconstruct the phylogeny and past demography of this lineage in a Bayesian framework.
We show that this lineage initially originated in the Far East, from which it radiated worldwide in several migratory waves. Successive increases in the pathogen’s population size were detected over the last 200 years, practically coinciding with the industrial revolution, World War I, and HIV epidemics. More recently, two MDR clones of this lineage started to spread throughout Central Asia and Russia concomitantly with the collapse of the Public Health system in the former Soviet Union. Last but not least, we detected a set of novel potential targets of drug resistance or fitness compensation mechanisms, including mmpL11, folC and Rv2670c, in addition to expected genes like rpoC, embA, inhA and eis that might have favoured the expansion of the most successful Beijing sublineages.
 

-----

 10 Février 2015 :  Morgane Barbet-Massin, CESCO, MNHN
 

Conservation biology under climate change : input from species distribution modeling.

Biodiversity is facing severe anthropogenic threats, including potentially dramatic climate change-induced contractions and shifts of species geographic ranges. The potential impact of climate change on species distribution has thus become a critical focus for conservation science : how will climate change further affect threatened species ? Will the reserve network be efficient under climate change ? What could be the potential effect of climate change on biodiversity (species richness, functional and phylogenetic diversity) ? Improved approaches to modeling species distributions and climate have led to significant advances in our understanding of potential species distribution changes. In my talk I will present results from my recent work that aimed at answering the above conservation questions, for bird species.
 

-----

 3 Février 2015 : Guillaume Chomicki, Université Ludwig Maximilian de Munich (Allemagne)
Evolution and functional specialization in ant/plant symbioses
Guillaume Chomicki

Symbioses between ants and plants, where plants provide housing to ants in exchange for defense or trophic payback, involve a mix of obligate and facultative mutualisms. The temporal build-up and steps through which ant/plant symbioses evolved and in some instances specialized are poorly understood. In this talk, I will first present a molecular clock-dated study of the domatium-bearing lineages across vascular plants, pointing out a recent origin that I discuss in light of the dynastic-succession hypothesis of ant evolution. I will then present a study of a small clade of epiphytic ant-plants, Squamellaria as an example of specialization. Squamellaria forms a subclade of the Hydnophytinae, the largest clade of ant plants with some 98 species in Australasia. Field ecology and phylogeny reveal a transition from facultative to obligate symbiosis following a dispersal event within the Fijian archipelago, ca. 2.3 Ma. The transition involves a switch from morphologically unspecialized domatia hosting facultatively many ant species and other animals to highly specialized domatia with a single ant mutualist. The specialization also involved the evolution of entrance holes matching the symbiont ; a unique type of food bodies involving post-anthesis nectar production and obligate seed dispersal by the mutualist. Moreover, the evolution of obligate seed dispersal has resulted in a tight control of ant colony structure and a sun exposed location in the canopy that is associated with the evolution of CAM metabolism. This unique system is an outstanding example of non-gradual specialization of a symbiosis.
 

-----

 27 Janvier 2015 : Romain Nattier ISYEB
Role of climate and soil in speciation and microendemism in New-Caledonia

New Caledonia, located in the south-west Pacific, is considered one of the major hotspots of biodiversity. One major feature of New Caledonian biodiversity is its strong endemism. Regional endemism, including relicts, is extremely high, since many species or even whole groups are only found on Grande Terre. Local microendemism is even more striking, with thousands of species of vertebrates, plants, molluscs and insects that have very narrow distributions limited to just one mountain or one river. Such repeated speciation events giving rise to microendemism have often been assumed to be favoured by two environmental factors : i) the diversity of soils, especially the presence of metalliferous soils that might have led to adaptive speciation ; and ii) climatic variation coupled with orography, which may have determined mountaintop endemics or more commonly allopatric speciation with niche conservatism on neighbouring mountains. The grasshopper genus Caledonula, endemic to New Caledonia, was studied to understand the evolution of species distributions in relation to climate and soil types. Based on a comprehensive sampling of 80 locations throughout the island, the genus was represented by five species. All the species have limited distributions in New Caledonia. Bioclimatic niche modelling shows that all the species were found in association with a wet climate and reduced seasonality, explaining their restriction to the southern half of the island. The results suggest that the genus was ancestrally constrained by seasonality. A molecular phylogeny was reconstructed using two mitochondrial and two nuclear markers. The partially resolved tree showed monophyly of the species found on metalliferous soils, and molecular dating indicated a rather recent origin for the genus. Adaptation to metalliferous soils is suggested by both morphological changes and radiation on these soils. The genus Caledonula is therefore a good model to understand the origin of microendemism in the context of recent and mixed influences of climate and soil type.
 

-----

 20 Janvier 2015 : Willy Rodriguez Institut de Mathématiques de Toulouse, Institut National des Sciences Appliquées.
Demographic inference using genetic data from a single individual : separating population size variation from population structure

In the last years, the rise of NGS data has opened new unexplored ways in population genetics studies. As a result, new methods make possible not only processing a huge ammount of information but also obtaining more precise estimations for the parameters of the model that we apply. However, estimations that could look fine from an statistical point of view may be meaningless if the model we apply is too far from actual conditions. This fact must be taken into account when trying to infer population size histories from genomic data. For example, it is known that structured populations generate signals of population size change. In this presentation, I will show some cases where the violation of the hypothesis of random mating can lead to wrong conclusions about the population history. Hence, it is very important to test the accuracy of our model before applying it to data. As a first approach to this problem, I will describe two simple scenarios : (1) a model considering one panmitic population that underwent a size change at some point in the past and (2) a structured population with constant size. For both cases I will :

(i) derive the distribution of coalescence times for a sample of size two,
(ii) use a maximum likelihood approach to estimate the parameters,
(iii) present a model choice procedure by using a Kolmogorov-Smirnov test.

I will show simulation results that suggest that this strategy is useful in order to decide which scenario is the most accurate one according to the data. Moreover, I will discuss how the relationship between independent coalescence times and the number of mutations at independent locus makes this approach useful when we analyse real data. At the same time, I would like to stress the fact that the estimation strategy for the structured case is very powerful since it allows to have good estimations for the number of islands as well as the migration rate from the gnome of one single individual.
 

-----

 13 Janvier 2015 : Rodolphe Rougerie, nouveau recruté à l’ISYEB

Patrons de diversité chez les invertébrés terrestres – impact et perspectives de l’essor des outils moléculaires de caractérisation des espèces.

Diversity patterns in terrestrial invertebrates – impact and perspectives of the development of DNA-based species characterization.

Documenting and describing the diversity of invertebrates are very challenging tasks for biologists. Invertebrates are generally small, cryptic, with complex life cycles and biology. Species, whose morphological identification is generally reserved to a few (if any) specialists, number in the millions, of which only a small portion – possibly as little as 20% – has been formally described so far.

DNA-based identification methods, such as DNA barcoding, offer an alternative to traditional morphological approaches. Species identifications can be carried out through the use of a reference library linking DNA sequences to taxon names, or through automated species delineation algorithms that can be used to discriminate operational units.

Using examples from studies in different taxa, at a scale ranging from local to global, and at temperate and inter-tropical latitudes, I will present how DNA barcoding and metabarcoding (its high-throughput application using NGS technologies) can quickly and effectively produce basic diversity data and metrics for biodiversity assessments in invertebrates. Some pitfalls, limitations and difficulties will be illustrated and discussed, emphasizing the importance of using reference libraries and standard DNA markers.
 

-----

 6 Janvier 2015 : Elisa Thebault, Institut d’écologie et des sciences de l’environnement de Paris (UPMC)

Structure and stability of networks with mutualistic and antagonistic interactions.

Understanding which structures and processes contribute to biodiversity persistence and ecosystem functioning is a major issue for both ecological theory and ecosystem conservation. In natural communities, the organization of interactions between species often presents non-random patterns at the origin of complex network structures. There is growing evidence that these particular structures can affect long-term species coexistence and stability. Several recent studies have highlighted structural differences between networks depending on the type of ecological interaction involved, i.e. mutualistic or antagonistic. Moreover, whereas historically network analyses have considered mutualistic and antagonistic interactions separately, a few recent studies have also begun to describe networks with both mutualistic and antagonistic interactions.
These findings raise the following questions : (i) To what extent does the structure of ecological networks differ depending on the type of interaction considered ? (ii) How do these different structures affect ecosystem persistence and stability depending on the type of ecological interaction involved ? (iii) To what extent do structural characteristics known to promote stability in networks made of a single interaction type still matter for the stability of networks with interaction type diversity ? (iv) How can we analyse the structure of networks with both mutualistic and antagonistic interactions ?
We investigate these questions by using both theoretical approaches with dynamical models of interaction networks, and comparative approaches on empirical datasets describing mutualistic and antagonistic networks.
 

-----

2014

 16 Décembre 2014 : Vincent S.F.T. Merckx , Naturalis Biodiversity Center, Leiden, the Netherlands
 

Evolution of cheating in the arbuscular mycorrhizal symbiosis.

Cooperation between different species is intrinsically unstable. Yet, the arbuscular mycorrhizal (AM) mutualism between the majority of land plants and Glomeromycota fungi is arguably the most prevalent mutualism on earth. Plants and their AM fungal symbionts interact in complex underground networks involving multiple partners. Evolutionary stability is maintained by bidirectional control, and because partners offering the best rate of exchange are rewarded. Nevertheless, the existence of several cheater plant lineages – fully mycoheterotrophic plants that exploit AM fungi for carbon – demonstrates that the AM ‘fair-trade’ mutualism is vulnerable to subversion. In this talk I present an overview of the evolution of mycoheterotrophic lineages in angiosperms in relation to their biogeographic history and their interactions with AM fungi. Based on these data I will discuss common evolutionary and ecological patterns related to the breakdown of the arbuscular mycorrhizal mutualism.
 

-----

 4 Décembre 2014 : Séminaire exceptionnel : Jeffrey D. Karron University of Wisconsin, Milwaukee
10h30 à l’Amphithéâtre de Paléontologie
 

Influence of pollinator visitation patterns on multiple paternity in flowering plants

Mating patterns often vary markedly within flowering plant populations. This among-plant variation in mate diversity and outcrossing rate may have profound consequences for fitness, yet the mechanisms accounting for this variation remain largely unexplored. My research combines detailed observation of pollinator behavior with unambiguous assignment of paternity to tease apart genetic and ecological factors influencing mating. I show that a heritable floral trait regulates the frequency of multiple mating, and explore how this trait influences male and female fitness. I conclude my talk by addressing how these mating patterns would respond to changes in bumble bee species abundance and diversity.
 

-----

 9 Décembre 2014 :  Niklas Wahlberg , Université de Turku (Finlande) Grand Amphi d’entomologie (45, rue Buffon)
 

The 215 million years of Lepidoptera diversification : lessons from an ever changing world

Understanding how the diversity of life responds to radical climate change has become an urgent task. Using the megadiverse order Lepidoptera as my model group, I will discuss how biotic and abiotic phenomena have interacted to influence the diversification rates of a group of organisms over millions of years. We have estimated a timeframe for the evolution of Lepidoptera and find that the crown group originated about 215 million years ago in the late Triassic. There appear to be three points in time where diversification rates have changed, first in the late Cretaceous coincidentally with the diversification of angiosperm plants, second after the great Cretaceous-Paleogene extinction event, and third in the Oligocene when the Earth cooled down and dried up. I will discuss the implications of these results to ongoing elevated extinction rates and climate change scenarios.
 

-----

 2 Décembre 2014 : Antoine Branca Université Paris Sud
Adaptation génomique des champignons Penicillium à l’environnement fromager

Le fromage est un environnement biochimique complexe et riche en nutriments où les bactéries et les champignons luttent pour l’accès aux ressources. La compétition entre ces microorganismes a aidé les hommes à développer une grande variété de saveurs. La fabrication du fromage prend son origine dans la domestication du microcosme associé au fromage. De façon similaire à ce qui est observée chez les macroorganismes, la domestication des microorganismes est suivie de changement phénotypiques et physiologiques drastiques. La découverte de la fabrication du fromage a été suivie d’étapes successives de sélection des meilleures souches de bactéries et de champignons qui ont grandement remodelées le génome de ces microbes. Nous cherchons à caractériser les changements génomiques qui ont lieu durant la domestication des champignons Penicillium pour la fabrication du fromage. Tout d’abord, nous avons comparer des génomes d’espèces de Penicillium adaptées ou non au milieu fromager. Nous avons pu mettre à jour des singularité génomiques chez les espèces adaptées au fromage tels des transferts de gènes horizontaux ainsi que l’expansion d’éléments transposables. Désormais, nous étudions la diversité génomique de Penicillium roqueforti, utilisé pour la fabrication de fromage bleu. Dans une approche de génomique des populations, nous comparons les champignons utilisés pour la production de fromages à ceux récoltés dans des environnements variés.
 

-----

 25 Novembre 2014 : Sina Adl, Université de Saskatchewan (Canada)

Pourquoi y a-t-il tant de protistes ?

Depuis la stabilisation de la classification des protistes, au moins pour le moment, nous nous sommes penchés sur la question de la diversité des protistes. Combien d’espèces il y at-il, et pourquoi tant d’espèces ? A travers manipulations et études des réseaux trophiques, puis en s’appuyant sur de nouvelles techniques en imagerie, nous abordons le sujet pour y proposer quelques règles.
 

-----

 18 Novembre 2014 : Tim O’Hara, Museum Victoria (Melbourne, Australia)

Industrialising phylogenomics : A 400+ gene exon-capture strategy for a class of marine invertebrates.

 

-----

 4 Novembre 2014 :  Pierpaolo Maisano Delser ISYEB , Grand amphi d’entomologie (45 rue Buffon)

X-chromosomal markers and the histories of European populations

Human population history has been described by analysing different genetic markers. Much attention has focused on haploid markers (such as mtDNA and Y chromosome), but this study addresses the X chromosome (haploid in males, and with a female bias in its history) in order to describe genetic diversity and to infer human population history in Western Europe.

HapMap Phase I/II data reveal haplotype blocks on the X chromosome, called PHAXs (Phylogeographically informative Haplotypes on Autosomes and X chromosome), in which recombination is historically absent and mutations are likely to be the only source of genetic variation. Three such regions were chosen to meet several criteria such that mutations in these loci are putatively neutral. These loci have been deep sequenced in 240 samples from Europe, the Middle East and Africa using the Ion Torrent PGM next-generation sequencing (NGS) platform.

Short-tandem repeats (STRs) were also typed in order to provide : i) greater discrimination, and ii) a test of different software tools able to call STRs from NGS data. This dataset was validated against a standard STR typing procedure using capillary electrophoresis.

PHAXs were confirmed to be largely non‐recombining across European samples. All three loci show a remarkably homogeneous pattern across Europe and high Fst values with the African sample. Overall, 30% of singleton variants are European-specific, and this excess of rare alleles is consistent with signals of expansion in Europe, with the Middle East and Africa showing a weaker pattern. Additional samples from the Complete Genomics dataset confirmed these patterns showing
European- and Middle Eastern-specific haplotypes. Bayesian skyline plots suggest a European-specific expansion around 20 KYA with a more recent peak around 10 KYA. This study demonstrates the value of the use of haplotype blocks, and the accurate ascertainment of rare variants to infer human demographic history.
 

-----

 28 Octobre 2014 :  Christophe Douady, Université de Lyon 1

Réconciliation phylo-écologique de la relation patron / processus.

Les approches scientifiques fondées sur la description et l’interprétation des patrons de biodiversité souffrent toutes de la même difficulté rencontrée lorsqu’il s’agit de déterminer le ou les mécanismes à l’origine de ces patrons. En effet, différents mécanismes peuvent in fine produire le même patron. Pour faire face à cette difficulté, nous avons développé un nouveau cadre phylogénétique et écologique dont les propriétés nous permettent aujourd’hui d’approcher les mécanismes responsables. Trois exemples sélectionnés parmi trois niveaux d’organisation biologique sont présentés, à savoir : quels sont les mécanismes responsables de la diversification biologique ? quels sont les mécanismes façonnant les aires de répartition géographique ? quels sont les mécanismes responsables de l’architecture génomique ?
 

-----

 21 Octobre 2014 :  Paul Verdu , Musée de l’Homme
 

Parallel trajectories of genetic and linguistic admixture in a genetically admixed creole population.

Joint analyses of genes and languages provide a powerful approach for analyzing human evolutionary history. Whereas such analyses have capitalized on extensive data on genetic variation among individuals, their use of linguistic data has not considered idiolectal differences—differences in the particular variants of a language used by different people. To examine the cotransmission of genetic and linguistic variation within populations, we performed a joint analysis of genes and idiolects in an admixed creole group with extensive variation across individuals in components of genetic ancestry and language attributable to different sources. For 44 individuals from Cape Verde, we collected both genome-wide genetic marker data and recordings of spontaneous speech in the Cape Verdean Kriolu language. In accord with the expectation for a Portuguese-derived creole population close to Senegal on the African mainland, genetic variation in Cape Verde is intermediate between Africa and Europe, varying in admixture on an axis separating Iberian and Mandenka populations. In parallel to vertical genetic transmission, we observed vertical transmission of idiolect from parents to offspring in that idiolect is predicted by parental birthplace, even after controlling for shared parent/child birthplaces. Genetic and idiolectal distances between pairs of individuals were correlated, and African genetic admixture proportions were correlated with an index tabulating African words in an idiolect. The results suggest that Cape Verdean genetic and linguistic admixture have followed parallel evolutionary trajectories, with cotransmission of genetic and linguistic variation. They provide insight into the way in which admixture and creolization jointly generate human genetic and linguistic diversity.
 

-----

 14 Octobre 2014 : Serge Muller
L’intérêt des herbiers pour la connaissance des modifications macro-écologiques et environnementales des territoires.

Les premiers herbiers ont été réalisés en Italie dès le XVIème siècle. Ces collections de plantes séchées ont ensuite connu un développement important au cours des siècles suivants. D’après l’Index Herbariorum, ce sont environ 3400 herbiers publics qui ont été inventoriés, comportant plus de 350 millions de spécimens d’herbier.
Leur intérêt avait été remis en question à la fin du XXème siècle avec le développement des outils modernes d’étude de la flore (biologie moléculaire, génétique, …). Toutefois de nombreuses études menées au cours des deux dernières décennies ont réhabilité l’intérêt des herbiers, principalement pour la taxonomie, systématique et phylogénie, ainsi que la conservation de matériel végétal permettant des analyses génétiques. Mais les herbiers présentent également d’autres intérêts « secondaires », au niveau ethnobotanique, historique et environnemental. La présentation proposée s’attachera à montrer tout l’intérêt des herbiers pour la connaissance des modifications macroécologiques et environnementales des territoires.
Des exemples relatifs à différents domaines seront présentés, comme l’évaluation des connaissances floristiques des territoires et l’identification des « points chauds » de biodiversité végétale, la caractérisation des régressions floristiques de certaines espèces, l’historique des introductions et de l’expansion d’espèces exotiques envahissantes, l’utilisation des herbiers pour retracer l’histoire d’organismes pathogènes (virus, bactéries, champignons, insectes…) conservés avec les échantillons d’herbier, la caractérisation des modifications passées ou actuelles de la qualité de l’air (liées à des pollutions locales ou des changements plus globaux) grâce à des analyses chimiques réalisées sur des fragments d’échantillons d’herbier, les impacts du changement climatique sur la phénologie (grâce aux informations des dates de collectes des échantillons) et éventuellement la morphologie des espèces.
Une condition du maintien de l’intérêt des herbiers au cours du XXIème siècle reste cependant qu’ils continuent à être vivants, c’est-à-dire alimentés par des récoltes végétales régulières.
 

-----

 7 Octobre 2014 :  Suzanne Saenko ISYEB , Grand amphi d’entomologie (45 rue Buffon)
 

Mechanisms of colour variation and colour change in lizards.

Reptile skin coloration provides a promising model system for exploring the mechanisms generating phenotypic variation in an ecological and phylogenetic framework. In particular, lizards exhibit a broad range of pigmentary and structural colours generated by different types of chromatophores, and some of them have the remarkable ability to change colour rapidly during social interactions such as male contests or courtship. Despite the crucial role of coloration in thermoregulation, photoprotection, camouflage, and visual communication, little is known about the physical mechanism that generate variation in colour traits in this lineage. We address this problem via an integrated approach that combines histology and microscopy with spectroscopy, videography, and optical modelling. In this presentation, I will show the results of comparative analysis of skin ultrastructure in relation to pigmentary and structural coloration and colour change in lizards.
 

-----

 30 Septembre 2014 : Yoan Coudert, Université de Cambridge

Three ancient hormonal cues co-ordinate shoot branching in a moss.

Branching patterns are a primary determinant of plant architecture and strongly impact on productivity by regulating light harvesting potential and resource allocation. Plants colonized land over 450 million years ago and underwent architectural diversification in the haploid and diploid stages of the life cycle independently. Although similar branching mechanisms evolved in both life cycle stages, our functional understanding of branching is limited to diploid flowering plant models such as Arabidopsis. To test whether the same molecular cues regulate branching mechanisms that have evolved convergently, we undertook a computational and genetic analysis of branching patterns in the haploid leafy shoot of a moss, Physcomitrella patens. We show that a simple model co-ordinating the activity of shoot tips across the plant can account for the branch distribution, and that three known hormonal regulators of branching in flowering plants generate the pattern. Importantly, these cues have been independently recruited during evolution to regulate branching patterns in both haploid and diploid life cycle stages, and may be integrated via a novel mechanism in moss.

 

-----

 23 Septembre 2014 :  Marion Chatelain (UPMC Paris 6)

Comment les métaux traces pourraient engendrer des pressions de sélection sur la coloration mélanique du plumage chez le pigeon biset (Columba livia)

La mélanine est le pigment le plus répandu dans le monde animal. Certains de ses groupements chimiques se fixent aux métaux traces. L’incorporation des métaux dans les parties inertes via la mélanine (cellules pigmentaires des phanères par exemple) permettrait de les séquestrer et de diminuer leur concentration dans la circulation générale et les organes vitaux. Cette propriété particulière pourrait constituer un avantage adaptatif dans les milieux à fortes concentrations en métaux (comme la ville). Nous avons testé cette hypothèse en simulant une exposition chronique à des concentrations naturelles en plomb et/ou en zinc chez 96 pigeons bisets (Columba livia) montrant différents degrés de mélanisme, et estimé leur valeur sélective à travers des mesures de leur système immunitaire et de leur succès reproducteur. Cette étude nous a permis de mettre en évidence des effets antagonistes du plomb et du zinc, suggérant que ces métaux sont susceptibles d’engendrer des pressions de sélection. Contrairement à notre hypothèse, les individus au plumage le plus mélanique montraient des concentrations sanguines en plomb plus élevées que les individus les plus clairs, ceci bien que nous ayons mis en évidence une relation positive entre la coloration mélanique du plumage et la concentration en zinc. Enfin, si les réponses aux expositions aux métaux traces ne différaient pas entre individus plus ou moins mélaniques, nous avons mis en évidence des différences physiologiques entre individus eumélaniques (coloration noire) et phéomélaniques (coloration rousse).
 

-----

  16 Septembre 2014 :  Thomas Tully ,ENS Institut d’Ecologie et des sciences de l’environnement de Paris - UMR 7618, Université Pierre et Marie Curie

Disposable springtails : highly plastic ageing patterns are explained by resource allocation trade-offs in Folsomia candida.

Thomas Tully & François Mallard

Although often neglected, the evidences of senescence occurring in the wild are accumulating (1) and there is a growing interest towards a clarification of how the mortality trajectories have been shaped by the ecological conditions (2). The question now lies in understanding the evolutionary origin of the diversity of shapes observed in the way survival decline with age (3).
We developed an experimental system in the laboratory to assess these questions on the small and long-living Collembola Folsomia candida (4, 5). We performed long term microcosms experiments to question how mortality trajectories have been shaped on the short- and long-term by trade-offs between traits. We found that within species genetic differences in ageing patterns can be explained with differences in growth and reproductive strategies : comparison of different lineages showed that initial mortality rate and age at onset of senescence are negatively correlated - a result coherent with recent predictions based on the ’disposable soma’ theory of ageing (6). We also demonstrate that plastic adjustments of major life history traits triggered by changes in resource availability even late in life lead cohorts to shift from constant mortality trajectories (negligible senescence) to accelerated senescence. Our results emphasises the need for a more integrated ecological comprehension of the effects of environment and its fluctuations to understand how natural selection shapes ageing patterns.
1. D. H. Nussey et al., Ageing Research Reviews 12, 214-25 (2013).
2. A. Baudisch, J. W. Vaupel, Science 338, 618-9 (2012).
3. M. Bronikowski et al., Science 331, 1325-8 (2011).
4. T. Tully, R. Ferrière, PLoS One 3, e3207 (2008).
5. T. Tully, A. Lambert, Evolution 65, 3013-20 (2011).
6. M. J. Wensink et al. Biogerontology 13, 197-201 (2012).

 

-----

- 9 Septembre 2014 : Johanna Mappes,Université de Jyväskylä (Finlande)

Evolution and maintenance of variation in antipredator defences

Conspicuous warning signals of unprofitable prey are a defense against visually hunting predators. They work because predators learn to associate unprofitability with bright coloration and because strong signals are detectable and memorable. As selection should favor traits that positively affect fitness, the genes underlying the strong signal should reach fixation, thereby preventing the evolution of polymorphisms. However, many species that can be considered defended are not very conspicuous and unexpectedly many aposematic species carry variable signal and even polymorphism is not rare. I will go through some candidate mechanisms, by using wood tiger moths as a model species, and discuss about scenarios where signal diversity can be maintained. I show that variation in signaling of aposematic species can evolve if predators vary in their tendency to attack defended prey facilitating the coexistence of diverse antipredator strategies.

 

----

 

- 1 juillet 2014 :  Peggy Motsch,Centre International de Recherche Médicales de Franceville (Gabon) - Contact : Lauriane Cacheux
 

Projet KIKI : Projet de conservation et de réintroduction des cercopithèques du Gabon.

Depuis deux ans, nous avons développé un partenariat qui nous lie désormais au Ministère gabonais des Eaux et Forêts pour la protection et la réhabilitation des orphelins de chasse cercopithèques. Bien souvent malheureusement, des chasseurs abattent une mère, et son enfant, non sevré et accroché à son ventre, est récupéré comme animal de compagnie. Cet orphelin sera non seulement élevé maladroitement et sans congénères, mais aussi risquera de mordre et de transmettre des agents pathogènes sauvages aux enfants qui vivent en contact avec.

Dans ce contexte, notre mission a consisté à mettre en place un réseau de communication avec nos partenaires, puis d’accueillir au centre de primatologie du CIRMF (Centre International de recherches Médicales de Franceville) des orphelins cercopithèques saisis par les autorités locales. Après une période de quarantaine qui constitue a suivi sanitaire de 3 contrôles durant 6 semaines, les animaux sont alors mis en période de réhabilitation, avant leur future réintroduction en condition de semi-liberté. La réhabilitation consiste en premier lieu à rassurer l’animal et veiller à son bien-être puis à le sociabiliser avec d’autres primates. L’empreinte de l’homme est en parallèle réduite au maximum, et les contacts deviennent, au fur et à mesure de la réhabilitation, de plus en plus rares.

Ce projet vise en premier lieu à sauver des orphelins sachant que le taux de survie des jeunes orphelins dans les villages, en particulier les bébés non sevrés encore entièrement dépendants de leur mère, est extrêmement bas. Mais c’est également l’occasion de permettre aux Eaux et Forêts de faire appliquer le Code des Forêts Gabonais puis, une fois les animaux saisis par leur autorité, leur offrir une structure d’accueil où les replacer. En outre, le projet a pour but de sensibiliser les populations aux risques liés à la détention d’animaux issus du milieu sauvage (transmission de maladies, blessures) ainsi qu’à la conservation des espèces emblématiques de la biodiversité du Gabon (mise en place de plaquette de sensibilisation). Nous citons en exemple un ancien détenteur de singe, saisi en 2011 par les agents des Eaux et Forêts, qui plusieurs mois plus tard, a pris la décision de lui-même de prévenir le CIRMF de la présence d’un nouvel orphelin dans son village. Par la suite, il a confié ce jeune singe, aux agents des Eaux et Forêts qui l’ont placé au CIRMF. Ceci démontre que, bien qu’à petite échelle, les mentalités peuvent évoluer.

Nous avons enfin, fin 2013, réintroduit ces singes en enclos forestier de semi-liberté dans la réserve privée de la Lékédi (Bakoumba), composé de la végétation naturelle luxuriante des forêts gabonaises, et ainsi leur offrir une seconde chance de vivre dans un environnement adapté. Dans cette réserve, ils sont protégés du braconnage ; ils peuvent consommer des aliments naturels, fleurs, feuilles ou fruits, mais aussi des insectes, et surtout ils peuvent se reproduire et former une population viable. Cette population sert désormais à l’éducation des enfants et à la formation d’animaliers et d’étudiants en conservation gabonais et elle témoigne de la réussite de notre partenariat.
 

-----

- 24 juin 2014 :  Alex Pyron, George Washington University, Washington DC. Contact ISYEB : Frédéric Legendre

The Evolutionary and Ecological Roots of Diversity of Species and Traits

Various ecological and evolutionary processes are hypothesized to result in the spectacular diversity of species and traits observed in ecosystems. Various models have been proposed to account for these processes in different systems, and many appear to have strong predictive ability. However, few studies have attempted to unify the short-term ecological processes that affect variability within populations with the long-term evolutionary processes responsible for broad-scale biodiversity patterns. I will discuss three examples of this synthesis that allow us to observe biodiversity processes across timescales in reptiles and amphibians, uniting community assembly, regional species richness, and global diversity.

----

 

- 17 juin Joël Meunier, Université de Mayence, Allemagne. Contact : Claudie Doums.

Sibling cooperation in earwig families : insights into the early evolution of social life

La coopération dans les familles de forficules et l’évolution de la socialité.
The evolutionary transition from solitary to social life is driven by direct and indirect fitness benefits of social interactions. Understanding the conditions promoting the early evolution of social life therefore requires identification of these benefits in non-derived social systems, such as animal families where offspring are mobile, able to disperse and survive independently. Family life is well known to provide benefits to offspring through parental care, but research on sibling interactions generally focused on fitness costs to offspring due to competitive behaviors. Using the European earwig, Forficula auricularia, as model species, I will demonstrate that sibling interactions not only result in competition, but also reflect cooperative behaviors in the form of food sharing in a species with non-derived families. I will discuss how these novel results emphasize that sibling cooperation could promote the emergence and persistence of family life and more generally, that sibling cooperation possibly represents a key driver in the early evolution of social life.
 

-----

- mardi 10 Juin 2014 :  Julien Massoni, Université de Paris-Sud, Orsay
Phylogeny, molecular dating, and floral evolution of Magnoliidae (Angiospermae)

Deep phylogenetic relationships in the angiosperms had long been uncertain. However, by the end of the 1990s, large-scale studies contributed to the current well resolved picture of the tree of flowering plants, in which eudicots, monocots, and magnoliids are the three largest clades. Whereas monocots and eudicots have been recognized since the very first phylogenetic analyses, the monophyly of magnoliids (Canellales, Laurales, Magnoliales, and Piperales) is a more recent result. Magnoliidae, as now circumscribed, consist of 20 families and ca. 10,000 species mostly distributed in the tropics (with a few exceptions extending into the temperate zone). Before the present work, several parts of the magnoliid tree had been well studied, but little was known about the evolutionary history of Magnoliidae as a whole. We conducted a phylogenetic study to clarify the phylogenetic relationships among families and orders of Magnoliidae. To do so, we sampled 199 species of Magnoliidae and 12 molecular markers from the three genomes. The results confirm, with a greater level of support, two clades in Magnoliidae : Canellale + Piperales, and Laurales + Magnoliales. In addition, the relationships among the 20 families are generally well supported. In a second time, the ages and phylogenetic positions of 10 fossils attributed to Magnoliidae were reviewed in detail. The goal of this study was to provide new reliable calibration points in order to conduct molecular dating analyses. These fossils were selected from the rich fossil record of the group because of their previous inclusion in phylogenetic analyses with extant taxa. The resulting calibration scheme provides six solid, internal minimum age constraints. Taking advantage of these two first studies, we conducted molecular dating analyses. This study tends to push back in time the ages of the crown nodes of Magnoliidae (127.1-198.9 Ma), and of the four orders, Canellales (126.3-141.0 Ma), Piperales (88.2-157.7 Ma), Laurales (111.8-165.6 Ma), and Magnoliales (115.0-164.2 Ma). We investigated the mode of diversification in the group. The strongly imbalanced distribution of species appears to be best explained by models of diversification with 6 to 14 diversification rate shifts. Finally, we traced the evolution of 26 floral characters to reconstruct the ancestral flowers in key nodes of Magnoliidae. Our results show that the most recent common ancestor of all Magnoliidae was a tree bearing actinomorphic, bisexual flowers with a differentiated perianth of two alternate, trimerous whorls of free perianth parts (outer and inner tepals) and probably three free stamens. This work provides key results on the evolution of Magnoliidae and raises several new questions such as the impact of geological crises on diversification of the group or the influence of pollinators and the environment on the evolution of floral morphology.
 

-----

- 10 juin 2014 :  Julien Massoni, Université de Paris-Sud, Orsay

Phylogeny, molecular dating, and floral evolution of Magnoliidae (Angiospermae)

Deep phylogenetic relationships in the angiosperms had long been uncertain. However, by the end of the 1990s, large-scale studies contributed to the current well resolved picture of the tree of flowering plants, in which eudicots, monocots, and magnoliids are the three largest clades. Whereas monocots and eudicots have been recognized since the very first phylogenetic analyses, the monophyly of magnoliids (Canellales, Laurales, Magnoliales, and Piperales) is a more recent result. Magnoliidae, as now circumscribed, consist of 20 families and ca. 10,000 species mostly distributed in the tropics (with a few exceptions extending into the temperate zone). Before the present work, several parts of the magnoliid tree had been well studied, but little was known about the evolutionary history of Magnoliidae as a whole. We conducted a phylogenetic study to clarify the phylogenetic relationships among families and orders of Magnoliidae. To do so, we sampled 199 species of Magnoliidae and 12 molecular markers from the three genomes. The results confirm, with a greater level of support, two clades in Magnoliidae : Canellale + Piperales, and Laurales + Magnoliales. In addition, the relationships among the 20 families are generally well supported. In a second time, the ages and phylogenetic positions of 10 fossils attributed to Magnoliidae were reviewed in detail. The goal of this study was to provide new reliable calibration points in order to conduct molecular dating analyses. These fossils were selected from the rich fossil record of the group because of their previous inclusion in phylogenetic analyses with extant taxa. The resulting calibration scheme provides six solid, internal minimum age constraints. Taking advantage of these two first studies, we conducted molecular dating analyses. This study tends to push back in time the ages of the crown nodes of Magnoliidae (127.1-198.9 Ma), and of the four orders, Canellales (126.3-141.0 Ma), Piperales (88.2-157.7 Ma), Laurales (111.8-165.6 Ma), and Magnoliales (115.0-164.2 Ma). We investigated the mode of diversification in the group. The strongly imbalanced distribution of species appears to be best explained by models of diversification with 6 to 14 diversification rate shifts. Finally, we traced the evolution of 26 floral characters to reconstruct the ancestral flowers in key nodes of Magnoliidae. Our results show that the most recent common ancestor of all Magnoliidae was a tree bearing actinomorphic, bisexual flowers with a differentiated perianth of two alternate, trimerous whorls of free perianth parts (outer and inner tepals) and probably three free stamens. This work provides key results on the evolution of Magnoliidae and raises several new questions such as the impact of geological crises on diversification of the group or the influence of pollinators and the environment on the evolution of floral morphology.
 

-----

- 3 juin 2014 : Juan Carlos Villarreal, Ludwig-Maximilians-Universitãt, Munich, Allemagne. Contact : Florian Jabbour

Evolutionary biology of the most enigmatic group of bryophytes : the hornworts

Following a general overview of the systematics of hornworts, the least familiar bryophyte lineage and a phylogenetically critical group that appears to be sister to vascular plants, I will focus on two main questions. The first is the evolution of pyrenoids, proteinaceous bodies consisting of up to 90% RuBisCO, while the second pertains to a unique case of horizontal gene transfer (HGT) from hornworts to ferns.
RuBisCO has a crucial role in carbon fixation but a slow catalytic rate, a problem overcome in some plant lineages by physiological and anatomical traits that elevate carbon concentrations around the enzyme. Such carbon-concentrating mechanisms (CCMs) are hypothesized to have evolved during periods of low atmospheric CO2. Hornworts have a CCM that relies on pyrenoids, structures easily seen in living cells at 20x magnification but not visible in dried herbarium material. A molecular clock-dated phylogeny for 36% of hornwort species (Villarreal and Renner, PNAS, 2012) implies at least 5-6 origins and an equal number of subsequent losses of pyrenoids in hornworts, with the oldest pyrenoid origin ca. 100 mya, and others <35 mya. The non-synchronous appearance of pyrenoid-containing clades, the successful diversification of pyrenoid-lacking clades during periods of low atmospheric CO2 and the maintenance of pyrenoids during episodes of high CO2 all argue against the previously proposed relationship between pyrenoid origin and low CO2.
Most ferns are well known to favour shady habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor — neochrome — that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome was a mystery. We have found neochrome genes in hornworts and demonstrate that fern neochrome was acquired from hornworts via HGT (Li, Villarreal et al, PNAS, 2014). Sequences of fern neochromes nest within sequences of hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 mya, long after the split between the two plant lineages (at least 400 mya). Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns.
 

-----

- 27 mai 2014 :  Frédéric Austerlitz, MNHN, Éco-anthropologie et Ethnobiologie (UMR 7206)

Inférence de l’histoire des populations à partir des données génétiques

L’accès à des données de polymorphisme génétique pour de nombreuses populations permet de reconstituer l’histoire de celles-ci grâce à des méthodes statistiques (ABC, MCMC). J’illustrerai ces méthodes au travers de leur application sur des populations humaines, pour lesquelles nous avons pu reconstituer l’histoire sur des échelles de temps relativement anciennes. Je montrerai aussi l’exemple d’une population de marsouin commun, pour laquelle nous avons montré l’impact de changements écologiques sur son évolution démographique.
 

-----

- 20 mai 2014 :  Thomas Heams, AgroParisTech, invité par Guillaume Lecointre
L’expression aléatoire des gènes : conséquences fonctionnelles et évolutives
Des procaryotes aux eucaryotes, l’expression des gènes a une forte composante stochastique. Cette dimension du fonctionnement des génomes, documentée par des travaux expérimentaux sur cellules isolées, est parfois considérée comme du bruit de fond, mais des indices croissants montrent qu’elle peut au contraire être héritable, contrôlée, et fonctionnelle. Ce phénomène peut bousculer nos représentations classiques et souvent déterministes de l’expression génétique. L’objectif de cette intervention et d’analyser les causes de cette dynamique probabiliste au coeur de nos cellules et de souligner les défis épistémiques qu’elle pose à notre compréhension du fonctionnement et de l’évolution des organismes.
 

-----

- Mercredi 21 mai 2014 :  Anthony Long University of California, Irvine
Séminaire exceptionnel à 11h, Amphi Rouelle
The Genetic Architecture of Complex Traits : Learning to Love the Allelic Heterogeneity Hypothesis
I will review the current state of the art with respect to the Drosophila Synthetic Population Resource (DSPR). The DSPR is a collection of 1500 Recombinant Inbred Lines ultimately derived from 15 highly inbred founders that can be used to dissect complex traits. An interesting observation is that most QTLs mapped to date appear to have more than two alleles segregating in the DSPR. This observation of within gene genetic heterogeneity has many implications for the dissection of complex traits in flies and beyond.

Anthony Long is a world expert on quantitative genetics and experimental evolution. He has worked with drosophila, butterfly, yeast and E. coli to unravel the genetic base of quantitative traits

 

- 13 mai 2014 :  Violaine Llaurens, MNHN ISyEB

La perception visuelle des variations de couleurs des ailes chez des papillons mimétiques et son influence sur leur évolution
Cryptic color differences among Müllerian mimics : how can the visual capacities of predators and prey shape the evolution of wing colors ?

Antagonistic interactions between predators and prey often lead to co-evolution among interacting traits. In the case of toxic prey, aposematic colors are likely to act as warning signals for predators and thus play a protective role. Evolutionary convergence in color patterns among toxic prey is then enhanced by positive density-dependent selection, through the shared cost of educating predators. Co-mimetic species thus exhibit highly similar color patterns, which can lead to confusion in species recognition, especially in polymorphic species. Using spectrophotometry measures, we investigated variation in wing coloration among co-mimics from highly divergent genera. We focused on seven morphs of the polymorphic species Heliconius numata and on seven corresponding co-mimetic species from the genus Melinaea. Significant differences in the yellow, orange and black patches of the wing were detected between genera. Perceptions of these cryptic differences by bird and butterfly observers were then estimated using models of animal vision based on physiological data. Our results showed that the most strikingly perceived differences were obtained for the contrast of yellow against a black background. The capacity to discriminate between co-mimetic genera based on this color contrast was also shown to be higher for butterflies than for birds, suggesting that the cryptic variation in color between genera were generally undetectable by birds but might be used by butterflies for distinguishing mating partners. The evolution of wing color in mimetic butterflies thus seems shaped by the opposite selective pressures exerted by predation and species recognition.
 

-----

- 6 mai 2014 :  Thomas Lecocq, Université de Mons, Belgique, invité par Vincent Bels

La trace d’une rupture : histoire récente des populations et divergence des traits reproducteurs chez les bourdons. Approche phylogéographique et communication chimique

Pleistocene climatic oscillations are considered as a major driving force of intraspecific divergence and speciation. During Ice Ages, populations isolated in allopatric glacial refugia can experience differentiation in reproductive traits through divergence in selection regimes. This phenomenon may lead to reproductive isolation and dramatically accentuates the consequences of the climatic oscillations on species. Alternatively, when reproductive isolation is incomplete and populations are expanding again, further mating between the formerly isolated populations can result in the formation of a hybrid zone, genetic introgression or reinforcement speciation through reproductive trait displacements. Therefore changes in reproductive traits driven by population movements during climatic oscillations can act as an important force in promoting pre-zygotic isolation. Notwithstanding, divergence of reproductive traits has not been approached in the context of climatic oscillations. Here we investigate the impact of population movements driven by climatic oscillations on a reproductive trait of five bumblebee species. We characterize the pattern of variation and differentiation across the species distribution (i) with five genes (nuclear and mitochondrial), and (ii) in the chemical composition of male marking secretions, a key trait for mate attraction in bumblebees.
 

-----

- 29 avril 2014 :  Mathieu Molet, UPMC, invité par Vincent Debat

La plasticité phénotypique, moteur de l’évolution chez les fourmis

Traditionnellement, la plasticité phénotypique est étudiée en tant qu’adaptation à l’environnement, et donc conséquence de la sélection naturelle. Nous nous intéressons au contraire à la façon dont la plasticité phénotypique peut générer de la nouveauté, c’est à dire de la diversité sur laquelle peut ensuite agir la sélection naturelle. Pour ce faire, nous utilisons pour modèle les fourmis, taxon hautement polyphénique. Nous étudions la morphologie adulte, le développement larvaire, le comportement, et les traits d’histoire de vie au niveau de la colonie. Nos résultats montrent que les nouvelles castes de fourmis telles que soldats et reines sans ailes peuvent évoluer à partir d’anomalies développementales recombinant les modules des castes classiques reines ailées et ouvrières. La plasticité phénotypique pourrait donc faciliter et accélérer l’évolution.
 

-----

- 30 avril 2014 : Adrien Perrard American Museum of Natural History, New York
(Attention séminaire supplémentaire à 14h, Grand Amphi d’Entomologie)

La couleur ne fait pas l’espèce : analyse de la diversité génétique et de coloration des populations asiatiques du frelon Vespa velutina (Hymenoptera : Vespidae)

Le frelon asiatique prédateur d’abeilles, Vespa velutina , a été introduit en Aquitaine il y a 10 ans ; il s’est répandu depuis à travers une grande partie de la France et a atteint plusieurs pays voisins. Dans son aire d’origine, qui va du Pakistan à la Chine orientale et au Sulawesi, sa coloration présente de fortes variations qui ont conduit à la description d’une autre espèce (depuis mise en synonymie) et d’une douzaine de variétés. La coloration des frelons est dite aposématique : elle permet de signaler aux prédateurs la venimosité de l’insecte. Or, les principales variations de couleur de V. velutina correspondent à du mélanisme, une augmentation de la pigmentation noire souvent associée à des adaptations à l’environnement ou au climat. Ses couleurs sont donc potentiellement soumises à différentes contraintes liées à l’aposématisme ou au mélanisme. Pour mieux comprendre l’origine de ce polymorphisme, les motifs mélaniques d’individus récoltés à travers l’aire d’origine de V. velutina ont été caractérisés par codage, et leur variation quantifiée et comparée aux variations génétique, géographique et climatique. Les résultats suggèrent l’existence de multiples convergences évolutives. L’analyse du gène CO1 et de 11 marqueurs microsatellites montre que des populations génétiquement très éloignées présentent des colorations similaires alors que des populations apparentées ont des motifs très différents. En revanche, les variations de couleur ne suivent pas un gradient géographique et n’ont pu être liées à des variables climatiques. Cette mosaïque de coloration à travers l’aire de répartition de l’espèce semble plus probablement induite par des pressions localisées liées à l’aposématisme, sous l’influence d’un mimétisme Müllerien au sein de communautés de guêpes, d’abeilles et de bourdons.
 

-----

- 15 avril 2014 :  Pierre Taberlet, Université Joseph Fourier (Grenoble),

DNA metabarcoding and biodiversity assessment

Ecosystems across the globe are threatened by climate change and human activities. Assembling large and standard datasets is the major difficulty for understanding how biological diversity is distributed over time and space, and for predicting its response to environmental factors in the 21st century. DNA sequencing technologies are currently evolving at a fast pace and offer unique opportunities to make a significant progress for biodiversity surveys in the near future. After a brief review of the technologies and of the power of next generation sequencers, I will first introduce the classical barcoding approach. Then, I will present the metabarcoding approach that takes full advantage of next generation sequencers for high-throughput and simultaneous taxa identification based on a very short (usually less than 100 base pairs) but informative DNA fragment. DNA fragments of less than 100 bp allow the use of degraded DNA from environmental samples. Environmental DNA extracted from soil allows to assess the diversity of plants and animals in different environments, from Arctic to tropical ecosystems. We applied this approach to tropical ecosystems. We collected 361 samples of surface soil (0-10 cm depth), on a 1 hectare plot with a 5 x 5 m grid system, in the Nouragues Field Station (French Guiana). Extracellular DNA was extracted in the field station within a few hours after collection. DNA amplifications were carried out using several metabarcodes targetting all eukaryotes, plants, fungi, and termites. The results obtained with the eukaryote metabarcode show that plant, fungi, metazoa, and unicellular organisms represent 6%, 41%, 47%, and 6% of the sequence reads, respectively. Several hundreds of maps showing the distribution of different taxa over the plot were produced. The same metabarcoding approach can also be implemented for reconstructing past plant communities, using either permafrost samples from the Arctic or lake sediments from French Alps. Finally, it also offers opportunities to assess herbivore diet. Such results demonstrate that high-throughput biodiversity data collection is possible via a standardized DNA metabarcoding approach. This is true for plants, but also for other organisms using the same DNA extract.
 

-----

- 8 avril 2014 : Doyle McKey, CEFE Montpellier

Naturel, culturel, hybride ? Ecologie, archéologie et ethobiologie dans les "champs de buttes" des savanes inondables de l’Amérique du Sud et l’Afrique

Les savanes saisonnièrement inondées de l’Amérique du Sud et de l’Afrique recèlent une diversité de paysages « à buttes » montrant une hétérogénéité topographique d’une régularité frappante. Ces paysages sont tous très peu étudiés. Certains sont des constructions humaines—des champs surélevés sur lesquels les gens ont pu planter des cultures ne tolérant pas l’inondation. En Amérique du Sud, où l’agriculture sur champs surélevés a largement disparu après la conquête européenne, les vestiges de ces anciens paysages agricoles sont étudiés par les archéologues. En Afrique, l’agriculture sur champs surélevés persiste aujourd’hui, mais elle n’a pas attiré l’attention d’anthropologues. Sur les deux continents il existe aussi des paysages « à buttes » d’origine apparemment naturelle. Malgré les questions fascinantes soulevées par la régularité spectaculaire de ces paysages, ils n’ont guère piqué l’intérêt des écologues et leurs origines restent mystérieuses. Nos études en cours sur les paysages « à buttes » d’origine humaine et naturelle suggèrent des liens entre ingénieurs du sol humains et non-humains, et soulèvent des questions venant des domaines allant de l’écologie de l’auto-organisation spatiale à l’ethnoagronomie, en passant par le biomimétisme à l’échelle de l’écosystème. Ces paysages demandent pour leur compréhension des apports à la fois de l’écologie théorique, de l’archéologie et de l’anthropologie. En plus d’apporter de la lumière sur des questions fondamentales en écologie et en archéologie, leur étude peut éclairer des voies vers l’intensification durable de l’agriculture dans un type de milieu qui subira dans les années à venir d’énormes pressions démographiques.
 

-----

- 1 avril 2014 : Jean-François Flot, Max Planck Institute, Göttingen (Allemagne)

L’hétérozygotie, une clé méconnue pour la délimitation moléculaire des espèces et l’étude de leurs génomes

L’hétérozygotie, ou co-occurrence de deux demi-génomes semblables mais différents, est une caractéristique générale des organismes diploïdes qui pose de gros problèmes techniques lors de leur séquençage : double pics, impossibilité d’assembler les données,... En dépit de ces difficultés apparentes, les séquences d’organismes hétérozygotes apportent une mine d’informations très utiles à la délimitation des espèces et à l’analyse de leurs génomes. Après avoir montré comment reconstruire les allèles d’individus hétérozygotes par séquençage direct, sans cloner, j’introduirai une approche graphique pour la délimitation moléculaire des espèces basée sur l’analyse des séquences alléliques. Dans la deuxième partie de mon exposé, je montrerai comment l’analyse récente du génome d’un rotifère hétérozygote a permis de prouver son asexualité et de comprendre son évolution.
Références principales :
Flot 2007 Mol.Ecol.Notes http://dx.doi.org/10.1111/j.1471-8286.2007.01857.x
Flot et al 2010 BMC Evol.Biol http://dx.doi.org/10.1186/1471-2148-10-372
Flot et al 2013 Nature http://dx.doi.org/10.1038/nature12326
 

-----

- 25 mars 2014 :  Marion Chartier , Université de Vienne (Autriche)
L’espace morphologique des fleurs - une approche comparative moderne pour étudier l’évolution des angiospermes.
Les espaces morphologiques sont des outils mathématiques dédiés à l’étude de l’évolution de la diversité morphologique et à l’évaluation de la proportion des formes réalisées dans la nature parmi les possibles. Les espaces morphologiques ont beaucoup été utilisés en zoologie, mais peu en botanique. Cette lacune est encore plus importante lorsqu’il s’agit de l’étude de l’évolution des fleurs.
Nous décrirons ici les bases théoriques et pratiques de l’utilisation des espaces morphologiques, et reverrons de quelle manière ils ont été utilisés jusqu’à présent en écologie florale. Enfin, nous illustrerons les méthodes présentées en traitant de manière plus moderne les données ayant servi à construire le premier (et l’unique) espace morphologique des fleurs à l’échelle des angiospermes, publié par G. Ledyard Stebbins en 1951.
The floral morphospace - a modern comparative approach to study angiosperm evolution.
Morphospaces are mathematical tools for studying the evolution of morphological diversity and for the evaluation of evolved shapes among theoretically possible ones. Although widely used in zoology, they – with few exceptions – have been disregarded in plant science and in particular in the study of broad-scale patterns of floral structure and evolution. Here, we provide basic, theoretical information on the morphospace approach ; we review earlier morphospace applications in plant science ; and as a practical example, we construct and analyze a floral morphospace.
Prochain séminaire : 1 avril, Jean-François Flot, Max Planck Institute, Göttingen (Allemagne) - L’hétérozygotie, une clé méconnue pour la délimitation moléculaire des espèces et l’étude de leurs génomes
 

-----

- 11 mars 2014 :  Claudie Doums, MNHN, Institut Systématique Evolution Biodiversité (UMR 7205)

Sexe et socialité : évolution de la parthénogenèse thélytoque chez la fourmi Cataglyphis cursor

The evolutionary paradox of sex remains one of the major debates in evolutionary biology. The study of species capable of both sexual and asexual reproduction can elucidate factors important in the evolution of sex. One such species is the ant Cataglyphis cursor, where the queen maximises the transmission of her genes by producing new queens (gynes) asexually while simultaneously maintaining a genetically diverse workforce via the sexual production of workers. We show that the queen can also produce gynes sexually, and may do so to offset the costs of asexual reproduction. While workers in this species can also use thelytoky, we found no evidence of worker production of gynes. Gynes are thus mainly, and potentially exclusively, produced by the queen. Simulations of gynes inbreeding level following one to ten generations of automictic thelytoky suggest that the queen switches between or combines thelytoky and sex, which may reduce the costs of inbreeding. This is supported by the relatively small size of inbred gynes in one colony and by the potential cost of producing diploid males. Such facultative use of sex and thelytoky by individual queens contrasts with other known forms of parthenogenesis in ants, which are typically characterised by distinct lineages specialising in one strategy or the other.
 

-----

- 4 mars 2014 :  Frédéric Mery, CNRS Gif-sur-Yvette (UPR 9034 LEGS)

How interactions between genetic and socio-environmental factors affect behavioral decision.

Animals are constantly confronted to various behavioral decisions. Some decisions may have low impact on fitness whereas others can dramatically impact long term fitness. How individuals base these decisions may depend on a large array of interaction among genetic, developmental and environmental factors. Using drosophila as a biological model we investigate how individuals balance the different source of information and how these balance affect individual fitness.
 

-----

- 25 février 2014 :  Tom van Dooren, team VPA Phenotypic Variability and Adaptation, iEES Paris.

South-American annual killifish : a vertebrate model for the comparative analysis of life history variation and speciation processes.

Annual killifish inhabit ponds that dry up completely during the summer. An egg (embryo) bank in the soil allows populations
to persist in this environment, which is extreme for fish. Embryos have been hatched at an age of over three years, such that it is
likely that the time spent in the egg bank can span several dry seasons. Often several killifish species coexist in a single pond, with congeneric small and large species in a predator-prey system. Many species can be kept in the lab in nearly identical conditions, which makes them extremely suited as a model system for comparative life history analysis and eco-evo-devo.
The emergence of a large and small species pair where the large cannibalizes the small has been named “giant-dwarf” diversification and we investigated whether this is a plausible scenario in the diversification of Austrolebias South-American species. The analysis suggests that species evolve towards one of three size optima. Species evolving towards the largest optimal size appeared at least three times from small in the Austrolebias genus. The first large ancestral species per event appeared in a trait change with relatively high speed in all three cases, consistent with expectations of cannibalism evolution. A comparative analysis of lower jaw length, a proxy for the level of specialization in piscivory suggests that in one clade of large species trait values indicate a very weak or no specialization towards piscivory, and that in the two other clades species are selected towards two optima with relatively large jaw lengths. By means of a reconstruction of ancestral species ranges we show that speciation events leading to a large and smaller species pair were sympatric with a large likelihood. For the clade of large species with little specialization, the probability that speciation was non-sympatric is largest among the three events. Conditional on the data we analysed, one can therefore conclude that giant-dwarf speciation by cannibalism most probably occurred twice in Austrolebias and that a third appearance of large species in the genus likely occurred by other selective or non-selective processes.
I will briefly discuss genome size and egg size variation in Austrolebias in relation to body size changes.
 

-----

- 18 février 2014 :  Graeme Oatley, Université d’Olomouc (Tchéquie), invité par Jérôme Fuchs

Southern African Zosterops – from systematics to phylogeography and hybridization

White-eyes (Family Zosteropidae) are small passerine birds, with many taxa showing many variations of underpart plumage colouration making them a notoriously difficult group to classify. The situation in southern Africa is no different, with past and present classifications varying in the number of white-eye taxa recognized. Taxa have been split according to underpart colouration or lumped together due to interbreeding between taxa. I use phenotypic, vocal and molecular data sets to establish the systematic relationship of white-eyes found in southern Africa. With the use of multiple lines of evidence, three species of southern African Zosterops are recognized. They are : Orange River White-eye Zosterops pallidus, African Yellow White-eye Zosterops senegalensis, Cape White-eye Zosterops virens, of which two subspecies are recognized : Zosterops virens capensis and Zosterops virens virens.
Performing phylogeographic analyses, which incorporated microsatellites with the molecular markers mentioned above, I also investigated whether there is any population structure within Z. virens and Z. pallidus, and whether any significant gene flow occurs between these taxa. Additionally, ecological modelling analyses were performed to look at whether there is any effect of climate and/or habitat of Zosterops connectivity within South Africa.
Finally, through the observation of individuals of intermediate plumage colourations, hybridization among some Zosterops taxa has been known to occur – these hybridization events have yet to be fully investigated. Here I will present results from cline analysis of molecular and phenotypic characters from a zone of contact between Z. pallidus and Z. v. capensis located in central South Africa.
 

-----

- 11 février 2014 :  Marianne Elias, MNHN (UMR CNRS 7205 ISyEB)

Le paradoxe de la diversité chez les papillons mimétiques
The paradox of diversity in mimetic butterflies

Le mimétisme Müllérien est l’une des illustrations les plus spectaculaires de la sélection naturelle : des proies possédant des défenses chimiques partagent des motifs colorés qui sont reconnus et évités par les prédateurs. Alors que la valeur adaptative du mimétisme a maintes fois été démontrée, un paradoxe intrigue les biologistes : si la sélection pour partager le même motif est si forte, pourquoi toutes les espèces ne convergent-elles pas vers un unique motif ? En effet, on trouve une forte diversité mimétique non seulement entre différentes régions, mais aussi au sein même des communautés, qui peuvent abriter jusqu’à 10 complexes mimétiques. Dans cet exposé je présenterai brièvement un modèle stochastique qui montre que la diversité mimétique peut être maintenue de façon stable localement à condition que les complexes mimétiques et les prédateurs soient distribués de façon hétérogène entre différents microhabitats. Le modèle prédit en outre une convergence écologique (microhabitat) entre espèces partageant le même motif. Les données sur le terrain confirment les prédictions du modèle. Dans une communauté de papillons mimétiques en Amazonie, nous avons montré que les complexes mimétiques et les oiseaux insectivores étaient ségrégés de la même façon entre différents microhabitats, et que des papillons dans le ‘mauvais’ microhabitat (là où leur motif est rare) étaient plus souvent attaqués. De plus, nous avons montré une convergence évolutive pour le microhabitat entre espèces qui partagent un même motif (espèces co-mimétiques), ce qui leur permet d’augmenter leur chance de rencontrer des prédateurs ‘éduqués’. La sélection pour partager le microhabitat est si forte qu’elle efface toute signature de compétition entre espèces co-mimétiques. A une plus large échelle, le long des Andes, nous avons également détecté une ségrégation des complexes mimétiques ainsi que de la convergence adaptative pour la niche altitudinale entre espèces co-mimétiques, malgré de fortes contraintes phylogénétiques sur l’adaptation à l’altitude. Les interactions mimétiques de type müllérien sont des interactions positives entre espèces qui peuvent par ailleurs entrer en compétition pour les ressources. Ces interactions sont suffisamment fortes pour influencer durablement la structure des assemblages d’espèces à diverses échelles spatiales et écologiques. Nos travaux plaident pour incorporer les interactions positives entre membres d’une même guilde dans les études en écologie des communautés et en conservation. Enfin, le mimétisme a certainement joué un rôle important dans la diversification des papillons mimétiques.

English - One of the most spectacular examples of adaptation is Müllerian mimicry, whereby chemically-defended prey species are selected to converge on a conspicuous colour pattern that advertises their toxicity to predators. While the adaptive value of mimicry has been clearly demonstrated in field and laboratory studies, an outstanding puzzle remains : if selection is so strong, why do all species not converge on a single colour pattern ? In fact, mimetic lineages often display a large diversity of wing patterns, throughout their ranges but also within single communities, which may harbour up to 10 mimicry complexes. Here I briefly present a stochastic individual-based model that shows that mimicry diversity can be achieved if both predator and butterfly suites are segregated ecologically (e.g., among different microhabitat or habitats). The model also predicts adaptive ecological convergence of species that share the same wing patterns. Model predictions were confirmed by field data. We surveyed a highly diverse community of mimetic butterflies in the upper Amazon. We found that insectivorous birds and mimicry complexes are segregated by microhabitats, and that butterflies in the ‘wrong’ microhabitat (ie, where their patterns is rare) are more likely to be predated. In addition, we found phylogenetic evidence for evolutionary convergence in microhabitat among co-mimetic species, thereby maximizing encounters with ‘educated’ predators. Selection on microhabitat is so powerful that it erases the signature of competition among co-mimetic species. At a regional scale, along the slopes of the Andes, we also found segregation of mimicry complexes and evidence for adaptive convergence in altitudinal niche among co-mimetic species, despite strong environmental filtering. Müllerian mimetic interactions are ultimately positive interactions among species that may otherwise compete for resources. Such positive interactions are strong enough to influence community structure at several spatial and ecological scales. I argue that positive interactions among guild members should be considered in community ecology and conservation studies. Finally, I discuss the implications of mimicry for the diversification of mimetic lineages.
 

-----

- 4 février 20104 : Emmanuelle Jacquin-Joly, INRA Versailles / (UMR INRA/UPMC 1272)

Mécanismes moléculaires de l’olfaction chez les papillons : approches transcriptomiques et contexte adaptatif

L’olfaction est un sens chimique déterminant pour les insectes, qu’ils utilisent pour détecter leurs hôtes, leurs partenaires sexuels ou leurs prédateurs. Toute modification des capacités olfactives peut entrainer des modifications dans la perception du milieu, et donc contribuer à des préférences. Inversement, l’adaptation à un nouveau milieu peut avoir des conséquences sur ce système chimiosensoriel. Ce système est en effet plastique et modulable, et ceci au cours de la vie d’un individu mais aussi à plus long terme au cours de l’évolution. Au laboratoire, nos objectifs sont de comprendre les mécanismes olfactifs, par l’identification et la caractérisation fonctionnelle des gènes olfactifs et en particulier les récepteurs olfactifs, mais également d’appréhender leur contribution à l’adaptation. Nous utilisons des modèles ravageurs des cultures pour l’essentiel, et nous développons des approches transcriptomiques et génomiques associées à l’expression hétérologue fonctionnelle de récepteurs.
 

-----

- 28 janvier 2014 :  Anthony Herrel, MNHN (UMR CNRS 7179 MABiodiv)

Rapid adaptive changes in morphology and function in natural population

Although rapid adaptive changes in morphology on ecological time scales are now well documented in natural populations, the effects of such changes on whole-organism performance capacity are often unclear. We present data on a study system where lizards have rapidly evolved differences in head morphology, bite strength, and digestive tract structure after experimental introduction into a novel environment resulting in a change in diet. Despite the short time scale ( 36 years) since this introduction, the changes in morphology and performance parallel those typically documented among species and even families of lizards in both the type and extent of their specialization. We present novel data on the seasonality of the observed changes in morphology, performance, and diet suggesting an important role for plasticity in driving some of the observed changes. Finally we document differences in intestinal tract structure and function (digestive assimilation capacity of different food resources) that underwrite the importance of the microbial gut community in allowing lizards to switch to an herbivorous diet. These data provide a compelling example of how the invasion of a novel habitat can drive variation on morphology through selection on function.
 

-----

- 21 janvier  2014 : Nicolas Puillandre, MNHN (UMR CNRS 7205 ISyEB)

Les Conoidea : délimitation d’espèces, phylogénie, évolution.

Avec un nombre total d’espèces estimé à plusieurs dizaines de milliers, les Conoidea (Gastropoda) constituent une manne pour les toxicologistes qui voient dans les toxines produites par ces prédateurs un réservoir virtuellement inépuisable de composés bioactifs. Mais l’hyperdiversification des Conoidea fait également de ce groupe un modèle biologique de premier choix pour les systématiciens : la classification et les délimitations d’espèces traditionnelles, essentiellement basées sur des caractères morphologiques hypervariables, ont, ces dernières années, volé en éclat à coup d’analyses moléculaires. Ainsi, d’une classification à trois familles, dont l’une largement polyphylétique, nous sommes passés à seize familles, dont l’histoire évolutive inférée à partir des phylogénies moléculaires contredit souvent les hypothèses établies sur la coquille. Au niveau spécifique, les approches de taxonomie intégrative, basées au moins dans un premier temps sur des marqueurs moléculaires, ont logiquement révélé un grand nombre d’espèces cryptiques, et modifient également nos connaissances sur la distribution et l’écologie de ces complexes d’espèces, et par conséquent nos hypothèses sur les processus de spéciation qui en sont à l’origine. Le dernier exemple en date concerne un groupe de trois espèces de cônes, pour lesquelles une analyse transcriptomique de la glande à venin a permis à la fois de confirmer les hypothèses d’espèces établies à l’aide de séquences génomiques et de proposer des hypothèses sur leur spéciation. Au niveau phylogénétique et alpha-taxonomique, le challenge sera dans le futur d’identifier les facteurs à l’origine de l’apparente accélération des taux de diversification dans certaines lignées et de confirmer l’hypothèse qu’un changement de proies, corrélé à l’apparition de nouvelles toxines, est bien un moteur de la spéciation.
 

-----

- 14 janvier 2014 :  Marie Manceau, Collège de France

Formation and Evolution of Skin Patterns

The distribution of color across the body (i.e., color pattern) is a crucial morphological trait involved in survival and reproductive success which varies tremendously both within and between species. Despite their ecological importance, the genetic and developmental mechanisms responsible for the formation and variation of naturally-occurring color patterns have remained a black box. We showed that in deer mice (genus Peromyscus), the formation of a simple bicolor pattern typical of most Vertebrates relies on the establishment of an embryonic “pre-pattern” (i.e., the spatial restriction of pigmentation genes) causing regional differences in pigment cell behavior. Moreover, we showed that large adaptive changes in the adult color pattern seen in a derived Peromyscus population are provoked by small accumulating changes in the pre-pattern. These findings laid the groundwork for studying (1) the embryonic origin of pre-patterns in the skin, (2) the molecular control of their formation and (3) the genetic basis of their evolution in other vertebrates groups. To this end, we propose to use analyses of gene expression and function in the Zebra Finch (genus Taeniopygia) which has the technical advantages of both an avian model (i.e., in ovo manipulation) and a genetic model (i.e., sequenced genome, molecular tools, transgenic strategies), as well as comparative studies in various species of birds displaying a vast array of skin patterns.
 

-----

- 7 janvier 2014 : Jean-Pierre Hugot, MNHN (UMR CNRS 7205 ISyEB)

Les dinosaures avaient-ils des oxyures ?

Les oxyures sont des nématodes parasites du tube digestif. L’Homme lui-même est parasité par une espèce qui lui est spécifique. Dans l’espèce humaine ce parasitisme affecte surtout les jeunes enfants. Les symptômes de cette parasitose sont bien connus : durant la nuit les parasites occasionnent un violent prurit anal lorsque les femelles oxyures viennent pondre leurs oeufs aux marges de l’anus du patient. Parmi les différents ordres de nématodes adaptés au parasitisme, les Oxyurida ont une particularité : ce sont les seuls parasites que l’on rencontre à la fois chez des hôtes invertébrés (Insecta, Diplopoda) et vertébrés (poissons, amphibiens, lézards, tortues, oiseaux, mammifères). Quels que soient les hôtes, on rencontre chez les oxyures les mêmes caractères biologiques singuliers et originaux : en particulier un système reproductif de type haplodiploïde. L’existence de ces singularités ainsi que les résultats des premières analyses phylogénétiques à partir de données moléculaires, soutiennent très fortement l’hypothèse de la monophylie des Oxyurida. Plusieurs études, basées sur les caractères morphologiques et/ou moléculaires, soutiennent également que leur distribution actuelle, notamment chez les Rongeurs et les Primates, puisse résulter d’un phénomène de cophylogénie : au cours de l’évolution ces parasites auraient été transmis de génération en génération par les parents à leurs descendants et leur arbre évolutif refléterait par conséquent fidèlement celui de leurs hôtes. Récemment, un oeuf d’oxyure a pu être identifié dans un coprolite (excrément fossilisé) vieux de 240 millions d’années (Figure 1). L’état de conservation exceptionnel de cet oeuf a permis de le classer dans une espèce nouvelle et de le ranger, parmi les Oxyurida, dans une famille particulière dont les hôtes actuels connus sont, soit des Rongeurs, soient des Oiseaux. Le coprolite a été découvert au Brésil parmi de très nombreux autres restes excrémentiels de même type, eux-mêmes associés à une faune fossile de Cynodontia. Les cynodontes sont des vertébrés fossiles parfois désignés comme des « reptiles mammaliens », appartenant à l’ordre des Thérapsides, qui vécurent du Permien supérieur au Jurassique inférieur (environ 260 à 180 millions d’années). Leurs restes fossiles ont été découverts en Afrique du Sud, en Chine, en Amérique du Sud, en Europe et en Amérique du Nord. Il est probable que les Mammifères, qui sont apparus au Trias moyen (il y a 245 à 228 millions d’années), dérivent de petits Chiniquodontidae ou Trithelodontidae carnivores, deux des cinq familles identifiées parmi les Cynodontia. Cette découverte permet de faire l’hypothèse que les oxyures étaient présents chez les Vertébrés dès l’époque où les principales lignées se sont différenciées (Figure 2). La présence d’Oxyurida étroitement apparentés chez des Mammifères, seul groupe survivant parmi les Cynodontia, et des Oiseaux, seuls survivants des Dinosauria, permet de discuter leur origine commune. Enfin, les particularités biologiques des Oxyurida, qui ne parasitent que des hôtes ayant une alimentation à forte composante herbivore, permettent de discerner quelles espèces parmi les cinq Cynodontia identifiés sur le site fossilifère, sont plus probablement les émetteurs du coprolite et donc les hôtes du nouveau parasite.
Auteurs associés : Jean-Pierre Hugot [1], Scott L. Gardner [2], Victor Borba [3], Priscilla Araujo [3], Daniela Leles [4], Átila Da-Rosa [5], Juliana Dutra [2], Luiz Fernando Ferreira [3], Adauto Araújo [3].
[1] MNHN, Paris. [2] University of Nebraska, USA. [3] Fundação Oswaldo Cruz, Rio de Janeiro, Brésil. [4] Universidade Federal Fluminense, Niterói, Brésil. [5] Universidade Federal de Santa Maria, Santa Maria, Brésil.
 

-----

2013

- 10 décembre 2013 :  Emmanuelle Porcher, MNHN (UMR CNRS 7204 CESCO)

Rôle de l’écologie de la pollinisation dans l’évolution des systèmes de reproduction des plantes à fleur

Les plantes à fleur présentent une grande diversité de systèmes de reproduction (répartition des fonctions mâle et femelle entre fleurs et entre individus, possibilité d’autofécondation, choix du partenaire par des système d’auto-incompatibilité...). Les nombreux travaux qui ont essayé de comprendre les forces évolutives à l’origine de ces systèmes de reproduction se sont intéressés prioritairement aux mécanismes génétiques (dépression de consanguinité par exemple). De façon assez contre-intuitive, l’écologie des espèces, et notamment les interactions avec les pollinisateurs, ont reçu beaucoup moins d’attention. Je présenterai quelques approches théoriques qui permettent d’intégrer génétique et écologie pour mieux comprendre comment l’écologie de la pollinisation influence l’évolution des systèmes de reproduction. Ces modèles montrent par exemple que les pollinisateurs peuvent représenter une contrainte pour l’évolution des plantes.
 

-----

- 26 novembre 2013 :  Dan Moen, Ecole Polytechnique (UMR CNRS 7641)

Why does diversification slow down ?

Molecular phylogenetic studies of diversification often show evidence for slowdowns in diversification rates over the history of clades. Recent studies seeking biological explanations for this pattern have emphasized the role of niche differentiation, as in hypotheses of adaptive radiation and ecological limits on clade diversity. Yet many other biological explanations might underlie diversification slowdowns. In this talk I focus on the geographic context of diversification, environment-driven bursts of speciation, failure of clades to keep pace with a changing environment, and protracted speciation. I argue that these alternatives, while currently underemphasized, represent biologically plausible explanations that in some cases may be more likely than niche differentiation. Furthermore, testing the importance of these alternative hypotheses might yield fundamentally different explanations for what influences species richness within clades through time.
 

-----

- 19 novembre 2013 :  Jérôme Fuchs, MNHN UMR 7205 (OSEB)

Diversification dynamics of falcons and allies (Falconidae)

Understanding how and why lineages diversify is central to understanding the origins of biological diversity. The avian family Falconidae (caracaras, forest-falcons, falcons) has an uneven distribution of species among multiple well-supported clades, and provides a useful system for testing hypotheses about diversification rate and correlation with environmental change.
Our analyses supported monophyly and similar diversification ages in the Early to Middle Miocene for the three traditional subfamilies, Herpetotherinae, Polyborinae and Falconinae. We estimated that divergences within subfamily Falconinae began about 16 mya and divergences within the most species-rich genus, Falco, including about 60% of all Falconidae species, began about 7.5 mya. We found evidence for a significant increase in diversification rate at the basal phylogenetic node for genus Falco, and the timing for this rate shift correlates generally with expansion of C4 grasslands beginning around the Miocene/Pliocene transition. Concomitantly, Falco lineages that are distributed primarily in grassland or savannah habitats, as opposed to woodlands, and exhibit migratory, as opposed to sedentary, behavior experienced a higher diversification rate.
 

-----

- 12 novembre 2013 :  Bernard Dutrillaux, MNHN UMR 7205 (OSEB)

Etude cytogénétique de coléoptères Scarabaeoidea

La plupart des travaux sur la cytogénétique des coléoptères sont anciens, et une approche plus moderne apporte bien des surprises qui ne demandent qu’à être exploitées. L’analyse chromosomique d’une centaine d’espèces de différentes familles et sous familles de scarabaeoides permet d’avoir une idée précise du caryotype ancestral de la super-famille, et de disposer ainsi d’une base solide pour toute reconstitution phylogénique. Partant de là, nous nous focaliserons principalement sur la sous famille des Dynastinae en donnant trois exemples amenant à réviser la systématique et/ou à préciser la phylogénie.
(1) Dans le genre Cyclocephala, mise en évidence de deux espèces cryptiques aux Petites Antilles et d’une évolution, encore en marche, dans le sens sud-nord (Martinique-Dominique-Guadeloupe).
(2) Dans le genre Dynastes, acquisition d’un remaniement entre autosomes et chromosomes sexuels chez les espèces des Etats-Unis et d’Amérique centrale, mais pas chez les deux espèces strictement sud-américaines, dont le caryotype représente une étape intermédiaire entre celui des premières et de l’ancêtre commun. Ceci montre l’origine sud-américaine du genre Dynastes.
(3) La répartition en Amérique et en Asie, avec une seule espèce africaine (Augosoma centaurus) de la tribu des Dynastini, évoque une origine gondwanienne. Toutefois, le caryotype de A. centaurus est très éloigné de celui des autres Dynastini, et très proche de celui des Oryctes dont O. nasicornis (Oryctini), notre scarabée rhinoceros. Nous confirmons cette proximité par la comparaison de la séquence du gène mitochondrial CO1. Ceci amène à revoir l’organisation de ces deux tribus de Dynastinae, soit en rattachant A. centaurus aux Oryctini, soit en regroupant les deux tribus. Les dangers d’utiliser les caractères phénotypiques exagérés des mâles pour la systématique seront évoqués.
Enfin, nous verrons que la distorsion du sex-ratio chez les Cyclocephala aux Antilles peut s’accompagner d’un caryotype femelle triploïde et démontrer le développement d’une parthénogénèse au sein d’une population sexuée. Ce mode de reproduction était jusqu’ici inconnu chez les Scarabaeidae, et amène à reconsidérer la relation insularité-parthénogenèse
 

-----

- 29 octobre 2013 :  Marc-André Selosse, MNHN UMR 7205 (OSEB)

La mycohétérotrophie sous les tropiques

The evolution of land plants provided repeated emergences of mycoheterotrophy, where achlorophyllous plants exploit carbon from their mycorrhizal fungi. This condition, suggested to be an adaptation to forest environments where little light is available, recently made strong achievements due to two tools : fungal molecular barcoding allowed identification of the (often uncultivable) mycorrhizal fungi ; natural isotopic abundances supported which fungal guild was giving carbon to the mycoheterotrophic plants.
Temperate and Mediterranean species, mainly orchids and Montropoideae (Ericaceae), proved to have specific basidiomycetous fungal partners, forming themselves ectomycorrhizae with surrounding trees. By contrast, subtropical and tropical species often connect to arbuscular-mycorrhizal (AM) fungi or even to saprotrophic, wood-or litter-decaying basidiomycetes. Their specificity is often lower, even if they remain selective in mycorrhizal associations (i.e. have preferenda within the targeted fungal guild). We demonstrate that the isotopic properties of the continuum between green tropical plant (providing carbon) - AM fungi - mycoheterotrophic plant shows differences as compared to the analogous continuum for mycoheterotrophs associated with saprotrophic or ectomycorrhizal basidiomycetes. Moreover, C/N values, that are low in mycoheterotrophs associated to basidiomycetes, are unexpectedly higher in AM associated mycoheterotrophs from the Gentianaceae and Burmaniaceae.
To account for this, we suggest that AM-associated mycoheterotrophy may have evolved solely to support carbon need of the mycoheterotrophs, in the framework of shaded, but not N-limited tropical forests. At the opposite, the evolution of basidiomycetes-associated mycoheterotrophs may be linked to N acquisition in N-limited, but not always dark, temperate forests. Beyond superficial similarities, the parallel evolution of mycoheterotrophy in land plants may result from different evolutionary pathways, linked to the ecology of the respective lineages involved.
 

-----

- 22 octobre 2013 : Claudine Ah-Peng, Université de La Réunion

Les îles, sentinelles du changement climatique

Les îles de par leur territoire délimité et leur flore indigène riche en espèces endémiques comptent parmi les systèmes les plus vulnérables face au changement climatique. Les effets de cette menace sur la perte de biodiversité dans les systèmes insulaires sont encore peu connus. Dans le cadre d’un projet de recherche ANR Net Biome (Moveclim), nous proposons d’utiliser deux groupes de plantes, les bryophytes et les fougères, comme modèles pour comprendre les conséquences de ces changements climatiques. Ce projet de macroécologie met en place pour la première fois des analyses comparatives de la diversité et distribution de ces plantes à spores le long de gradients d’altitude dans plusieurs îles et dans plusieurs océans : La Réunion (Mascareignes), la Guadeloupe (Antilles), Pico (Açores), La Palma (Canaries) et Tahiti (Polynésie Française). Dans le cadre de ce séminaire, je présenterai les résultats préliminaires de ces recherches sur les bryophytes, notamment (1) les patrons de diversité et distribution le long de ces gradients d’altitude du gène à la communauté, (2) la diversité fonctionnelle et le rôle des bryophytes dans les services écosystémiques. Dans ce projet, la systématique des bryophytes et la description de cette biodiversité prennent une place importante ; en effet les bryophytes ont fait l’objet de peu d’études et les spécialistes demeurent peu nombreux. Dans le futur ces mesures de la diversité, la distribution, l ‘écologie, et les fonctions de ces plantes pourront alimenter des modèles prédictifs plus réalistes sur les changements de la biodiversité en milieu insulaire.
 

-----

- 8 octobre 2013 : Mathilde Dufaÿ, Université de Lille 1

Pollinisation, autofécondation et unisexualité chez les plantes à fleurs.

Le système de reproduction des plantes à fleurs peut être globalement défini en fonction de trois caractéristiques : (i) le mode de pollinisation (anémophile ou entomophile), (ii) le taux d’allogamie qui varie de façon quasi continue entre espèces, et (iii) la distribution du type de gamètes produits au sein des fleurs et des individus (i.e. seulement des gamètes mâles, seulement des gamètes femelles, ou les deux). Les patrons de distribution de ces trois traits sur la phylogénie des Angiospermes suggèrent une histoire évolutive complexe : à partir d’un état ancestral considéré généralement comme hermaphrodite, entomophile et plutôt allogame, ces trois traits auraient évolué et subi des réversions plusieurs fois de façon indépendante. De nombreux travaux théoriques et empiriques tentent de ce fait de reconstruire leur dynamique évolutive, en cherchant notamment à comprendre comment la sélection naturelle peut façonner ces trois traits, mais en les considérant généralement comme totalement indépendants les uns des autres. Au cours de ce séminaire je présenterai en quoi ces trois traits du système de reproduction peuvent fortement interagir en me focalisant sur deux exemples : l’effet du taux d’autofécondation sur la dynamique plante-pollinisateur et l’effet du taux d’autofécondation sur la dynamique de l’unisexualité chez les plantes à fleurs.
 

-----

- 1 octobre 2013 : Nat Wheelwright, Bowdoin College (USA)

Incest avoidance, song learning and the genetic basis of complex traits in a natural island bird population

Do birds in the wild have the ability to avoid mating with close relatives ? Might song be a mechanism for kin recognition ? What is the genetic basis of different phenotypic traits in natural populations ? To try to answer these and other questions, in 1986 I began a long-term study of Savannah Sparrows nesting on Kent Island, New Brunswick, Canada, site of the Bowdoin Scientific Station. The population is unusual because young birds return from their long-distance migration to breed near where they were born, which allows us to measure fitness in terms of lifetime production of recruits and to investigate how the frequency of behaviors such divorce and polygyny vary between years and generations.
 

-----

- 24 septembre 2013 :  José Ricardo Inacio Ribeiro, São Gabriel, Rio Grande do Sul (Brésil) et MNHN UMR 7205 (OSEB)

The intensification of paternal care in Belostomatidae (Insecta : Heteroptera) and its effect on the evolution of the genitalia

Water bugs (Belostomatidae) are well-known insects from aquatic habitats throughout the world’s subtropical and tropical areas. Belostomatidae comprises eleven genera and approximately 150 species, most of which are reported from the New World. The unique phylogenetic analysis of the relationships of the Belostomatidae subfamilies proposed by Mahner in 1993 has led to the recognition of a single split between two brooding techniques, one called “emergent-brooding” behaviour, in which lethocerine males typically brood their eggs laid out of water onto emergent vegetation by females, and another one called “back-brooding” behaviour, in which the belostomatine females lay eggs on the back of their mates, where eggs are brooded until hatch. In Smith’s hypothetical evolutionary scenario, basal belostomatids (i.e., lethocerines) would be emergent-brooders and back-brooding behaviour would be a derived condition. Based on some belostomatine fossils, it was pointed out that there should be a maximum adult body size threshold of 30.0 mm for back-brooders, because if length surpasses the above mentioned size the oxygen supply becomes deficient for the submerged developing eggs. Given that a correlation between female body size and egg size (a corollary of Dyar’s Law), lethocerine water bugs were constrained to lay eggs outside the water because it was impossible to maintain large eggs alive inside the water. Since natural selection probably acted increasing body size in lethocerines, the larger the eggs, the smaller the surface-to-volume ratio, and this is important for gas exchange and embryo development. A sexual size dimorphism (SSD) whose degree varies with body size has been found among belostomatids. Such trend, an allometric pattern that has been formalized into Rensch’s rule, consists in (1) as body size increases in clades with male-biased SSD, SSD increases, and (2) as body size increases in clades with female-biased SSD, SSD decreases. Besides, the phenomenon of egg-nursery was found to be variable within the subfamily Belostomatinae, so different brooding-behaviours performances have been considered as a necessity for lineages of small species to adjust their mating to augment their fitness (“the performance-enhancing belostomatine males”). An enhancement in this behavioral strategy therefore might compensate the lack of big available male dorsum areas even more, maintaining different groups based on the balance between available space for deposition of eggs and a more refined care of their offspring. Although belostomatine males are supposed to become wider in order to offer available space on dorsum for oviposition even more, the sexual dimorphism found in size across Belostomatidae follows Rensch’s rule and this seems not to be compatible with such widespread idea. In fact, representatives of derived groups (Abedus, Belostoma and Diplonychus) tend to exhibit female-biased size dimorphisms. If polyandry increases in females of these derived groups, differences in terms of genitalic morphology should be really connected to those of males whose morphology becomes increasingly specialized in stimulating conspecific females during copulation. The beginning of a conflict among sexes could have been responsible for establishing narrower male bodies in contrast to more refined egg-nursery behaviour, while in basal belostomatine males, their backs could be wider becoming more attractive to conspecific females in contrast to less refined behaviours. Given that there is just a 20 years old morphology-based cladogram at my disposal, and such cladogram presents the relationships of just eight genera, the Smith’s evolutionary scenario of such described paternal care is revisited by including a new phylogeny of the Belostomatidae genera based on modifications or clarifications of both somatic and genitalic characters of males and females. Since making statistical comparisons among species is problematic when the phylogenetic effect has not to be taken into account, I re-investigate the evolution of body size of Belostomatidae using phylogenetic contrasts as a means to correct for the phylogenetic effect and test the hypothesis that shifts to emergent- and back-brooding behaviors were associated with changes in body size and in SSD, which apparently decreases with the increase of body size. An intersexual coevolution implying reciprocal gains of novelties between genitalic parts of males and females is also investigated using Geometric Morphometrics, for a sexual selection over mating rates probably has driven male and female genitalic morphology in Belostomatidae.
 

-----

- 17 septembre 2013 : Jean-Baptiste André, École Normale Supérieure (UMR CNRS 7625 Ecologie & Evolution)

On the evolutionary origin of reciprocal cooperation

An important mechanism by which two individuals can mutually benefit from helping each other is reciprocity (in a broad sense). However, reciprocity is the object of an evolutionary paradox : a gap between theoretical predictions and empirical observations. On one hand, evolutionary modelers have shown that it can evolve relatively easily in a wide array of circumstances. On the other hand, empirically, very few clear instances of reciprocity are found outside the human species.

In this talk, I will propose a simple explanation to resolve this paradox. Based on a multi-locus model, I will suggest that reciprocity has rarely evolved because it raises an evolutionary problem of « bootstrapping » of the same kind as communication : it entails the joint evolution of several functions in the same time. Therefore, even though reciprocity may be adaptive once it has already evolved (i.e. it can be an ESS) it cannot be shaped gradually by natural selection.

Although it raises a bootstrapping problem, however, reciprocal cooperation has been able to evolve in a few cases in non-humans, and is widespread in the human species. At the end of the talk, I will thus suggest some evolutionary pathways by which it may have emerged in spite of the boostrapping problem. I will show that understanding these pathways can be key in explaining both the distribution of reciprocity in extent species, and the evolutionary history of human cooperation.
 

-----

- 23 juillet 2013 : Mirna Moussa, MNHN UMR7205, Pasteur Guadeloupe, UAG, mirnamoussa@hotmail.fr

Les amibes libres pathogènes des eaux chaudes de la Guadeloupe

La Guadeloupe, située au coeur des Petites Antilles, est un archipel formé de deux îles principales dont la Basse-Terre, dominée par un volcan encore en activité. L’activité sismique importante de la région a ouvert de nombreuses failles dans lesquelles s’infiltrent l’eau de pluie et l’eau de mer qui ressortent à différents niveaux du massif montagneux sous forme de résurgences géothermales. Ces sources chaudes sont réputées depuis fort longtemps pour leurs propriétés curatives et très fréquentées par le public. En avril 2008, un jeune garçon âgé de neuf ans est décédé d’une méningite foudroyante quelques jours après une baignade dans le bain chaud de Dolé, c’était le premier cas de méningoencéphalite amibienne primitive (MEAP) déclaré sur le territoire Français. La présence de l’amibe pathogène, Nægleria fowleri, responsable de cette pathologie du système nerveux central ayant été mise en évidence dans ce bain à la suite de cet accident, l’Institut Pasteur de Guadeloupe a engagé un programme de recherche sur les différents bains chauds de la Guadeloupe, dans le but de mettre en évidence l’origine de la contamination, d’étudier l’écologie de ces amibes et leur modes de dissémination, d’analyser la biodiversité de ces microorganismes dans les eaux chaudes de la région, par séquençage de la région ITS1 du gène des ARNr, d’étudier l’interaction ente ces amibes et les bactéries potentiellement pathogènes qu’elles hébergent (métagénomique) et enfin de comprendre les mécanismes d’aiguillage moléculaire qui induisent la pathogénicité de l’espèce N.fowleri, par changement de forme et acquisition du phénotype virulent, remodelage du cytosquelette, modification des propriétés d’adhérence et de cytotoxicité. Les premiers résultats présentés ici montrent le niveau de contamination faible mais régulier de l’amibe pathogène dans la quasi totalité des bains chauds de Guadeloupe depuis 2011, la validation de la méthode de comptage, l’influence du temps et de la température de transport des échantillons et l’origine de la contamination. (Travaux de Mirna Moussa, Johan F. De Jonckheere, Marc Romana, Antoine Talarmin, et Jérôme Guerlotté)
 

-----

- 9 juillet 2013 : Nathalie Becker, MNHN UMR7205, mission de relais du MNHN à La Réunion, becker@mnhn.fr

Insectes invasifs en milieu insulaire (La Réunion) : mouches des légumes (Tephritidae) et aleurodes Bemisia tabaci : recherche et gestion agroécologique

La Réunion est sujette à de nombreux insectes invasifs ravageurs des cultures, dont les Tephritidae (mouches des légumes). Dans le but de limiter les usages de pesticides tout en contrôlant ces insectes nuisibles, un projet de gestion agroécologique a été mis en place ; de son succès émane un module d’enseignement « Insectes invasifs et gestion agroécologique : cas des Mouches des Légumes à La Réunion (IGAR) », issu d’une collaboration MNHN - CIRAD - Université de la Réunion, financé par l’Université Virtuelle Environnement et Développement Durable, qui vous sera brièvement présenté.
Une autre espèce invasive d’importance à La Réunion est l’aleurode Bemisia tabaci, provoquant de nombreux dégâts sur les cultures dans le monde entier, de par la transmission de phytovirus. Défini comme un complexe d’espèces, B. tabaci comprend 12 « espèces » dont l’une des plus invasives est Middle East-Asia Minor 1 (MEAM1), décrite à La Réunion dès 1997. L’île de La Réunion abrite également une espèce résidente, IO (Indian Ocean). Les travaux de recherche qui vous seront présentés, au sein d’une collaboration entre l’UMR OSEB et l’UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (CIRAD-Université de La Réunion), portent sur : i) la caractérisation, par PCR quantitative normalisée, du mode de transmission du virus transmis majoritairement par l’espèce MEAM1 à La Réunion ; ii) l’étude de différents facteurs susceptibles d’agir en synergie sur les interactions entre l’espèce invasive MEAM1 et l’espèce résidente IO (endosymbiotes hébergés, répartition différentielle sur plantes hôtes ...).
 

-----

- 25 juin 2013 :  Fabien Condamine, Polytechnique
(fabien.condamine@gmail.com).

Perspectives macroévolutives des changements environnementaux / Macroevolutionary perspectives to environmental change

Prédire comment la biodiversité sera affectée et répondra aux modifications anthropiques sur l’environnement est l’un des défis les plus importants auxquels font face les écologistes aujourd’hui. Ici, nous mettons actuellement changements environnementaux et leurs effets sur la biodiversité dans une perspective macroévolutive. Nous nous appuyons sur la recherche en paléontologie et les développements récents des approches phylogénétiques pour se demander si un cadre macroévolutif peut nous aider à comprendre comment les changements environnementaux ont affecté la biodiversité dans le passé, et comment ils pourraient affecter la biodiversité à l’avenir. De plus en plus de données paléontologiques et phylogénétiques sont accumulées, et nous estimons qu’une grande partie du potentiel de ces données reste à explorer pour comprendre les changements environnementaux.
Predicting how biodiversity will be affected and will respond to human-induced environmental changes is one of the most critical challenges facing ecologists today. Here, we put current environmental changes and their effects on biodiversity in a macroevolutionary perspective. We build on research in palaeontology and recent developments in phylogenetic approaches to ask how macroevolution can help us understand how environmental changes have affected biodiversity in the past, and how they will affect biodiversity in the future. More and more paleontological and phylogenetic data are accumulated, and we argue that much of the potential these data have for understanding environmental changes remains to be explored.
 

-----

- 18 juin 2013 : Lise Frézal, Ecole Normale Supérieure (frezal@biologie.ens.fr).

Microévolution dans un ménage à trois entre un nématode et deux virus à ARN

We recently found three viruses which naturally infect Caenorhabditis nematodes. These ss(+)RNA viruses cause intestinal cell symptoms and are horizontally transmitted. Whereas C. elegans can so far only be infected by one virus, European C. briggsae genotypes are susceptible to the other two viruses, both in the same locations. This vulnerability of C. briggsae to two viruses enables studies of in vivo viral competition and of the mechanisms driving their short-term evolution, as well as the impact of their competition on host fitness.
RNA viruses may evolve rapidly through both high mutation rates and recombination events. The impact of recombination widely varies from one viral species to another but in all cases, for recombination to occur, different virus types have to infect the same host cell. The first step is thus to assess whether different virus species can co-infect the same worm population, the same animal and the same cell.
By using quantitative RT-PCR, we demonstrate that the Le Blanc and Santeuil viruses can coexist in a worm population, even when originally introduced at widely different concentrations. The two viruses are jointly maintained over 10 worm generations. We presently investigate the co-infection at the whole organism and single cell levels by tracking the viral RNAs in co-infected worms using Fluorescent In Situ Hybridization (FISH).
 

-----

- 21 mai 2013 : Stefano Mona, MNHN (mona@mnhn.fr).

Investigating sex-specific dynamics using uniparental markers : West New Guinea as a case study

Mitochondrial DNA (mtDNA) and Y chromosome (NRY) genetic markers have been often contrasted to investigate sex-specific dynamics. Traditionally, isolation by distance, intra-population genetic diversity and population differentiation are estimated from both markers and compared. Two possible sources of bias are often neglected. First, kilometric distances are frequently used as predictor of the connectivity between groups, hiding the role played by environmental features at a micro-geographic scale. Second, the comparison of intra-population diversity and population differentiation between mtDNA and NRY is hampered by their different mutational mechanisms and rates. Here we show how to account for these biases by analyzing from a different perspective a published dataset of 8 West New Guinea (WNG) populations for which mtDNA control region sequences and 7 linked NRY microsatellites had been typed. First, we modeled the connectivity among sampled populations by computing the number of days required to travel between groups. Then, we investigated the differences between the two sexes accounting for the molecular characteristics of the markers examined to obtain estimates on the product of the effective population size and the migration rate among demes (Nm). We achieved this goal by studying the shape of the gene genealogy at several sampling levels and using spatial explicit simulations. Both the direction and the rate of migration differ between male and females, with an Nm estimated to be >6 times higher in the latter under many evolutionary scenarios. We finally highlight the importance of applying meta-population models when analyzing the genetic diversity of a species.
 

-----

- 14 mai 2013 : Florian Jabbour, MNHN (fjabbour@mnhn.fr).

Les renonculacées : systématique, biogéographie et morphologie des méristèmes

Les renonculacées sont des plantes à fleurs pour la plupart herbacées, distribuées majoritairement dans l’hémisphère nord. Cette famille comprend 62 genres et 2525 espèces, dont font partie la clématite, l’ancolie, le bouton d’or ou encore l’hellébore.

Ce séminaire sera l’occasion de vous présenter succinctement les travaux que j’ai effectués sur cette famille depuis la thèse, et surtout de vous exposer deux projets initiés au MNHN depuis mon entrée en fonctions en janvier de cette année.
a. Systématique et biogéographie d’un petit groupe d’espèces de pieds-d’alouettes (Delphinium L.) dont l’aire de répartition (Afrique tropicale de l’est et de l’ouest, côte ouest de l’Inde) et la diversité de la dimension de leurs éperons nectarifères demandent à être expliquées.
b. Description de la morphologie des méristèmes floraux dans deux morphes sauvage et mutant de nigelle de Damas (Nigella damascena L.) qui diffèrent par la structure de leur périanthe. L’objectif est de définir des stades de développements comparables entre morphes. Cette étude est un préalable indispensable à une étude de transcriptomique comparative.
 

-----

- 7 mai 2013 : Mathieu Chouteau, MNHN (mathieuchouteau@hotmail.com).

Sélection et polymorphisme chez des grenouilles mimétiques péruviennes / Selection and polymorphism in Peruvian mimetic frogs

The diversification of aposematic signals in Müllerian mimicry systems is a puzzling phenomenon. Although mimicry is expected to promote uniformity in warning signals, impressive variation may be observed among populations at relatively small spatial scales. It has been suggested that relaxation of selective pressures could enable the appearance of novel aposematic phenotypes while strong localized selective pressures maintain their geographic organisation. However, evidence of such variation of selective pressures in aposematic species is scarce. The aim of this study was to test the hypothesis of a relationship between predation and phenotypic variation in a Müllerian mimicry complex. Using clay models and population genetic tools, we investigated this relationship along a transient zone between two distinct fixed Müllerian warning signals in poison arrow frogs (Ranitomeya spp.) from Northern Peru. These distinct phenotypes are known to have appeared independently in separate valley refuges and the transient zone emerges from the asymmetric dispersal of species from these refuges. First, we confirmed the strong purifying selection of predators in valley refuges as novel aposematic and cryptic phenotypes are more attacked by visual predators than the local aposematic phenotype. In the transient zone, predation pressures are generally relaxed and phenotypic variability is extremely high. Interestingly, at the periphery of one of the valley refuges, a new Müllerian mimicry system is emerging where both species from different refuges (with different signals) overlap and predation is intermediary. As expected in such system, the warning signal of the more variable species seems to converge toward the one of the less variable species. These results highlight how dynamic Müllerian mimicry systems can be. Interplay between temporary relaxation and strong selective pressures enable the predominance of novel aposematic phenotypes at a local scale and the apparition of a geographic mosaic of warning signals and Müllerian relationships.
 

-----

- 30 avril 2013 : Amandine Cornille, Université Paris XI (amandine.cornille@gmail.com).

Diversification dans le genre Malus : histoires de domestication, de spéciation et phylogéographie chez les pommiers sauvages Eurasiatiques et le pommier cultivé.

Despite its economic, cultural and historical importance, few studies have investigated the evolutionary history of the domesticated apple (Malus domestica) as well as those of its wild relatives. Using new population genetic approaches (approximate Bayesian computation) with microsatellites and nuclear sequences, we aimed at unravelling, at different evolutionary scales (phylogeography, speciation, domestication), the natural and artificial diversification processes at play in the Malus genus. WE focused on the four wild apple species distributed across Eurasia (Malus orientalis (Caucasus), Malus sieversii (Central Asia), Malus sylvestris (Europe), and Malus baccata (Siberia)) and on the single domesticated apple species in the genus, Malus domestica. This work was divided into four parts : (i) domestication history of the cultivated apple, from its origin in Central Asia to Europe, (ii) post-glacial recolonization history of the European crabapple (M. sylvestris), (iii) the history of speciation among the five Malus species, (iv) crop-to-wild gene flow and dispersal capacities of the closest wild relative species (M. sylvestris, M. sieversii and M. orientalis). By investigating artificial diversification, we evidenced unique processes of domestication in this fruit tree, with no bottleneck and with extensive post-domestication introgressions by another wild species (M. sylvestris) than the ancestral progenitor (M. sieversii). Natural diversification patterns (phylogeography, speciation and population structure) revealed large effective population sizes, high dispersal capacities and weak spatial genetic structures. This work also revealed high levels of interspecific hybridizations, particularly high level of crop-to-wild gene flow in Europe and Central Asia. This study extended our knowledge about population structures for wild species that contributed to the cultivated apple genome, as well as the extent of hybridization rates. This work is essential for the conservation of wild apple populations, the integrity maintenance of wild species facing fragmentation and future breeding programs concerning the domesticated apple.
 

-----

- 23 avril 2013 :  Colin Fontaine, MNHN (cfontaine@mnhn.fr).

Structure, stabilité et contraintes phylogénétiques dans les réseaux d’interactions mutualistes et antagonistes

L’architecture des réseaux d’interactions écologiques est reconnue comme fortement liée à la dynamique et à la stabilité des communautés, ainsi qu’à l’histoire évolutive des espèces les constituant. Cependant, la majeure partie des travaux à ce jour s’est focalisée sur les interactions proie-prédateur alors que les espèces interagissent de façons variées, comme par exemple au travers d’interactions mutualistes ou parasitiques. Ce n’est que récemment que ces autres types d’interactions ont été étudiés sous l’optique des réseaux d’interactions.

L’accumulation de jeux de données décrivant des réseaux d’interactions basés sur différents types d’interactions permet de poser les questions suivantes : (i) L’architecture des réseaux d’interactions dépend-elle du type d’interaction étudié ? (ii) Comment les différentes architectures et types d’interactions affectent-ils la persistance et la stabilité des communautés ? (iii) les contraintes phylogénétiques sur les interactions diffèrent-elles selon les différents type d’interactions ?

Je présenterai diverses approches, basées sur des données empirique ou de la modélisation dynamique, visant à apporter des éléments de réponse à ces questions et mettre en lumière les similarités et singularités entre réseaux d’interactions mutualistes et antagonistes.
 

-----

- 17 avril 2013 :  (mercredi !), David Schindel, CBOL, invité Line Legall (contact MNHN linelegall@gmail.com)

Study of endangered species with support from Google’s Global Impact Awards
 

-----

- 16 avril 2013 :  Andre Langaney, MNHN (dd@mnhn.fr)

Spéciation, hybridation : que disent les génomes

Depuis plus de vingt ans les études de caryotypes ont montré que la différentiation des espèces et d’autres taxons pouvait être très complexe et remettre en cause, dans des cas plus nombreux que prévu, les conclusions parfois hâtives et excessives d’études de phylogénies, moléculaires en particulier. Ces résultats ne semblent pas avoir eu grand écho parmi les systématiciens, certains spécialistes ou théoriciens allant jusqu’à en nier l’intérêt, avec des arguments de circonstances discutables. En prenant quelques exemples, essentiellement chez les primates, on montrera comment ces résultats, confirmés par de récents séquençages de génomes complets, remettent en question la généralité de paradigmes communs concernant les espèces et la spéciation et rendent très problématiques les tentatives en cours de dénombrement des espèces inconnues.
 

-----

- 26 mars 2013 :  Elsa Petit, MNHN (epetit@mnhn.fr)

Consequences evolutives des co-infections par des champignons pathogenes apparentés

In nature, an individual host frequently harbors a community of pathogens but only recently has the field of disease ecology begun to focus on the consequences of such co-occurence within individuals, populations or species.
The occurrence of multiple pathogen species on a shared host is unexpected when they exploit the same micro-niche within the host. One explanation for such observations is the evolution of pathogen-specific resistances that segregate the host population into sites that are differentially occupiable by the competing pathogens.
If specific resistance does not provide micro-niche for the co-occurrence of related pathogens and they do not exclude one another via competition, genetic exchange via hybridization can lead to the movement of genetic material, and ultimately aid in the emergence of new pathogen genotypes and greatly impact the evolution of emerging diseases.
Using the fungal anther smut as a model system, I will present a study that test whether specific resistances may contribute to the maintenance of two related pathogens on the same host species and quantify the amount of hybridization in natural populations. This research aims to address fundamental questions about the consequences of multiple infections for both the evolution of resistance and the integrity of pathogen species boundaries as well as the hybridization as a vehicle for pathogen host range expansion. These questions are important for all types of systems, including public health and agriculture.
 

-----

- 12 mars 2013 : Karthik Vasudevan, invité Annemarie Ohler (contact MNHN : ohler@mnhn.fr)

Herpétofaune tropicales de montagnes et les îles de l’Inde / Tropical herpetofauna of mountains and islands in India

Le sous-continent indien compte environ 380 espèces d’amphibiens et 480 espèces de reptiles. La diversité de ces groupes est la plus élevée dans les montagnes du sud-ouest de la péninsule appelées les "Ghâts occidentaux", dans l’est de la chaîne de l’Himalaya et dans les îles Andaman et Nicobar. Ces régions forment quatre hotspots de méga-biodiversité mondialement reconnues. Les efforts en cours dans ces régions ont mis en évidence des espèces endémiques localisées et des espèces ayant des histoires évolutives distinctes. Au niveau local, des conditions environnementales bien identifiées ont causé une importante spécialisation des espèces, restreignant leur distribution. Il en résulte un remplacement important d’espèces d’une localité à l’autre. Au niveau régional, la juxtaposition de différentes zones biogéographiques à différentes périodes a ouvert des "fenêtres temporelles" pour l’échange d’éléments faunistiques. Cela a encore accentué la diversité phylogénétique de l’herpétofaune dans une région donnée. Les facteurs historiques et les conditions locales ont donc joué un rôle important dans la détermination des profils de la diversité de l’herpétofaune dans le sous-continent indien. Cet assemblage unique d’herpétofaunes est menacé par la perte d’habitats entraînée par l’expansion de la population humaine dans la région.
The Indian sub-continent has about 380 species of amphibians and 480 species of reptiles. The diversity of these groups is highest in the mountains in southwest of the peninsula called the "Western Ghats", in eastern Himalaya mountain range and in the Andaman and Nicobar Islands. These regions also fall in four globally recognised mega-biodiversity hotspots. The ongoing efforts in these areas have documented narrow endemics and species that have distinct evolutionary histories. At the local level, predictable environmental conditions have caused extensive specialization among species, thereby, restricting distribution of species. Consequently, there is also a large turnover of species from one locality to the other. At a regional level, the juxtaposition of different biogeographic zones at different time periods opened ’time windows’, for exchange of faunal elements. This has further accentuated the phylogenetic diversity of herpetofauna in any particular region. Therefore, historical factors and local conditions have played an important role in determining patterns in herpetofaunal diversity in the Indian sub-continent. This unique assemblage of herpetofauna is threatened by extensive habitat loss driven by expanding human population in the region.
 

-----

- 19 février 2013 : Jean-Pierre Hugot, MNHN (hugot@mnhn.fr)

L’étude de la biologie de Laonastes aenigmamus suggère un modèle de diversification des faunes associées au massif karstique du Khammouane Kebang (Laos et Vietnam)

Petit rongeur de la taille d’un rat, le "kanyou" a été collecté par hasard en 2005 sur un marché laotien, dans la Province du Khammouan. Ses découvreurs l’ont classé dans un genre et une espèce nouveaux. Des études ultérieures ont permis de le reconnaître comme le seul survivant d’une famille autrefois représentée dans toute l’Asie, mais que l’on croyait disparue depuis le Miocène. De sa phylogénie à son éthologie, tout était à étudier de ce Mammifère curieux, dont les meurs nocturnes, la répartition géographique limitée et l’habitat escarpé, expliquent la découverte tardive ; et probablement la survie, alors que toutes les espèces proches ont progressivement disparu. Afin de permettre l’étude de la nouvelle espèce, 250 individus ont été capturés entre 2006 et 2011 dans la province, de façon à représenter les blocs karstiques présents dans la totalité de l’aire de distribution. Cet échantillonnage exceptionnel ne pourra probablement pas être renouvelé car le gouvernement laotien a maintenant promulgué un décret de protection du kanyou. L’espèce est, d’autre part, inscrite sur la liste rouge de l’IUCN.
À partir de 137 individus provenant de 38 localités, nous avons étudié la phylogéographie de cette espèce en utilisant des données mitochondriales et nucléaires. Nos résultats montrent une forte structuration phylogéographique, selon 8 clades, eux-mêmes fréquemment subdivisés en sousclades, et la plupart d’entre eux correspondant à des blocs karstiques distincts (1). Une distance de 5 km entre deux blocs karstiques semble suffisante pour isoler génétiquement les populations. Ce qui constitue un exemple de micro-endémisme exceptionnel chez les mammifères : 8 à 16 unités évolutives pouvant être identifiées au sein d’une aire géographique mesurant environ 250 x 50 km.
Nos données suggèrent fortement que la distribution actuelle de Laonastes puisse résulter de la fragmentation progressive d’une population autrefois panmictique. L’isolement progressif des populations serait lié aux évènements de morcellement des karsts du fait de l’érosion. L’individualisation des phylogroupes, et leurs divergences, reflétant la chronologie des événements géologiques et paléoclimatiques. Ces résultats posent également la question du statut taxonomique des ensembles ainsi identifiés : simples populations, espèces ou sous-espèces ?
L’ensemble karstique qui s’étend du Khammouan à la région de Kébang au Vietnam est le plus vaste affleurement calcaire d’Asie du sud-est continental, et un des plus anciens. Cette formation est isolée par de vastes plaines et terrains non calcaires des autres formations de même nature, beaucoup plus réduite, du Cambodge, de Thaïlande et du nord Vietnam. A l’ouest, la région est bordée par le fleuve Mékong et, à l’Est, par les montagnes de Truong Son, qui forment la frontière entre le Laos et le Vietnam. Si la découverte la plus remarquable, faite dans cette région au cours des dernières années, est sans conteste celle de Laonastes aenigmamus, plusieurs autres espèces de vertébrés endémiques y ont été découvertes ; un gymnure, Hylomys megalotis (Jenkins et Robinson, 2002), une chauve-souris, Hipposideros scutinares (Robinson et al., 2003), un rongeur Muridae, Saxatilomys paulinae (Musser et al. 2005) et un oiseau, Pycnonotus hualon (Woxvold et al., 2009).
C’est également dans cette région qu’avait été découvert le Saola, Pseudoryx nghetinhensis, en 1992. En outre, d’immenses réseaux souterrains s’y sont développés, qui furent explorés et topographiés pour l’essentiel dans les années 90 par des expéditions françaises au Laos et des expéditions anglo-saxonnes au Vietnam. Plusieurs cavités dépassent 10 km de long, avec des passages atteignant fréquemment plus de 20 m de diamètre, et de nombreuses rivières souterraines telles que la Nam Hin Boun, utilisée comme voie de communication sur plusieurs kilomètres par les habitants de villages situés dans des dépressions fermées du karst. Si les karsts du Sud-est asiatique abritent une biodiversité élevée, ils sont pourtant parmi les écosystèmes les moins étudiés de la région. La partie vietnamienne de cet ensemble géologique unique est déjà classée par l’Unesco. La partie laotienne est protégée, mais les autorités, conscientes de sa valeur, souhaiteraient que des études multidisciplinaires et coordonnées de la faune et de la flore viennent étayer leurs démarches pour obtenir qu’elle soit à son tour classée. Les résultats déjà obtenus par des équipes du Muséum dans cette région, et les bonnes relations établies à cette occasion avec les chercheurs et les autorités locales, placeraient notre établissement en très bonne position, s’il souhaitait initier un tel programme.