Éditeur(s) : HAL CCSD
Résumé : Designing biodiversity conservation plans requires knowledge on the biogeographic distribution of taxabut also accurate estimates of species richness and diversification processes. However, measuring the phyleticrichness can be biased by the use of inappropriate taxonomical characters, leading to erroneous speciesdelimitation and diversity estimates.This work explores the phyletic richness at several taxonomic levels (generic, specific and intraspecific) ofthe hydrozoan family Aglaopheniidae (Marktanner-Turneretscher, 1890), with a particular focus on the South-Western Indian Ocean. Firstly, using several newly constructed phylogenies based on mitochondrial andnuclear markers, this study reveals that the phyletic diversity of this family is at underestimated by at least 50%:all studied genera are polyphyletic or with doubtful monophyletic status. Then, using several speciesdelimitation methods based on molecular markers, it sheds light on the richness of cryptic diversity of thisfamily, enlightening the potential of using an integrative taxonomic approach on these morphologically simpleorganisms. Finally, the population genetics of an Aglaopheniidae brooding species shows a high populationsstructuring with pervasive pattern of isolation by distance at several geographic scales (several to thousands ofkilometres), implying a potentially high cryptic diversity existing in this family.The results of this work provide new insights on Aglaopheniidae diversity, underlining the potentialinfluence of reproductive mode on the phyletic diversity and diversification processes of brooding hydrozoanbrooders. This thesis further highlights the relevance of using several complementary
La conservation et la gestion sur le long terme de la biodiversité nécessitent une connaissance de larépartition des taxons, mais également une estimation précise de leur diversité spécifique ainsi que desprocessus de spéciation ayant permis leur formation. Cependant, la mesure de la richesse phylétique peut êtrebiaisée par l’utilisation de caractères taxinomiques ne permettant pas de délimiter les espèces de manièreappropriée.Ce travail de thèse propose d’explorer la diversité phylétique à plusieurs niveaux taxinomiques(générique, spécifique et intra-spécifique) des Aglaopheniidae, une famille d’hydrozoaires, notamment présentedans le Sud-Ouest de l’océan Indien. Dans un premier temps, en utilisant des phylogénies basées sur plusieursmarqueurs (mitochondriaux et nucléaires), ce travail démontre que la diversité phylétique de cette famille est,au minimum, sous-estimée de moitié: tous les genres de la famille sont polyphyléthiques ou présentent un statutmonophylétique restant à confirmer. Dans un deuxième temps, l’utilisation de méthodes de délimitationd’espèces basées sur des données moléculaires met en évidence la diversité cryptique très élevée des morphoespècesétudiées, révélant l’intérêt potentiel des protocoles de taxinomie intégrative chez les organismesmorphologiquement simples. Enfin, l’étude de génétique des populations d’une espèce incubatriced’Aglaopheniidae révèle l’importance de la structuration des populations et de l’isolement par la distance chezcette espèce à plusieurs échelles géographiques (de quelques kilomètres à plusieurs milliers), impliquant unepotentielle diversité cryptique extrêmement élevée chez cette famille.L’ensemble des connaissances acquises lors de ce travail de thèse fournit un nouveau regard sur ladiversité de la famille des Aglaopheniidae, soulignant le potentiel impact du cycle de reproduction sur ladiversité phylétique et les processus de spéciation des hydrozoaires incubateurs. Cette thèse met en évidence lapertinence de l’utilisation de plusieurs procédures complémentaires de délimitation d’espèces pour étudier ladiversité des organismes morphologiquement simples.
https://hal.archives-ouvertes.fr/tel-01359424

tel-01359424
https://hal.archives-ouvertes.fr/tel-01359424
https://hal.archives-ouvertes.fr/tel-01359424/document
https://hal.archives-ouvertes.fr/tel-01359424/file/These%20manuscrit%20final.pdf

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
The genus Nasutitermes is among the most abundant wood-feeding Termitidae and an extremely diverse and heterogeneous group in terms of its biogeography and morphology. Despite the major role of several Nasutitermes species as structural pests, the phylogenetic status of this genus is still unclear, along with a confused taxonomy and species identification remaining difficult. The first aim of this review was thus to gather and discuss studies concerning the taxonomic status of the genus Nasutitermes in order to clarify this crucial point. Then, our goal was to gain new insights into the management of N. corniger, considered to be the most economically detrimental pest of this genus in South America and a Nasutitermes model species, while filtering available information concerning its biology through the prism of termite control, as well as critically examine the existing methods. We indeed strongly believe that increasing our knowledge of this species’ biological strategies is the key to progress in the challenging question of their sustainable management.
ISSN: 1612-4758

hal-01467356
http://hal.upmc.fr/hal-01467356
http://hal.upmc.fr/hal-01467356/document
http://hal.upmc.fr/hal-01467356/file/Boulogne_2017_Ecologysur termites.pdf
DOI : 10.1007/s10340-016-0796-x

Éditeur(s) : HAL CCSD Wiley Open Access
Résumé : Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species' threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project - and avert - future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups - including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems - ). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.
ISSN: 2045-7758

hal-01204216
https://hal.archives-ouvertes.fr/hal-01204216
DOI : 10.1002/ece3.1303
PRODINRA : 280886

Éditeur(s) : HAL CCSD Frontiers Media
Résumé : International audience
To date 142 species have been described in the Vibrionaceae family of bacteria, classified into seven genera; Aliivibrio, Echinimonas, Enterovibrio, Grimontia, Photobacterium, Salinivibrio and Vibrio. As vibrios are widespread in marine environments and show versatile metabolisms and ecologies, these bacteria are recognized as one of the most diverse and important marine heterotrophic bacterial groups for elucidating the correlation between genome evolution and ecological adaptation. However, on the basis of 16S rRNA gene phylogeny, we could not find any robust monophyletic lineages in any of the known genera. We needed further attempts to reconstruct their evolutionary history based on multilocus sequence analysis (MLSA) and/or genome wide taxonomy of all the recognized species groups. In our previous report in 2007, we conducted the first broad multilocus sequence analysis (MLSA) to infer the evolutionary history of vibrios using nine housekeeping genes (the 16S rRNA gene, gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA), and we proposed 14 distinct clades in 58 species of Vibrionaceae. Due to the difficulty of designing universal primers that can amplify the genes for MLSA in every Vibrionaceae species, some clades had yet to be defined. In this study, we present a better picture of an updated molecular phylogeny for 86 described vibrio species and 10 genome sequenced Vibrionaceae strains, using 8 housekeeping gene sequences. This new study places special emphasis on (1) eight newly identified clades (Damselae, Mediterranei, Pectenicida, Phosphoreum, Profundum, Porteresiae, Rosenbergii, and Rumoiensis); (2) clades amended since the 2007 proposal with recently described new species; (3) orphan clades of genomospecies F6 and F10; (4) phylogenetic positions defined in 3 genome-sequenced strains (N418, EX25, and EJY3); and (5) description of V. tritonius sp. nov., which is a member of the “Porteresiae” clade.
ISSN: 1664-302X

hal-01546980
http://hal.upmc.fr/hal-01546980
DOI : 10.3389/fmicb.2013.00414

Éditeur(s) : HAL CCSD
Résumé : The main objective of this thesis was to study the influence of Guianan terra firme rainforests types on medium- and large-sized vertebrates community organization. First, we choose a model species which permitted to develop an appropriate abundance estimation method which take into account the imperfect detection and temporary immigration of mobile species, and to test environmental conditions effects at different spatial scales of analysis. Second, given that bias due to animal detection can be important in the abundance estimation, we determinated the relative role of environmental conditions and species biological traits on detection probability. From this methodological framework, we studied then processes of community organization, by identifying the main determinants involved in community organization, using composition and alpha and beta diversities, and, in a complementary manner, three metrics (taxonomic, functional, and phylogenetic). We sought from these general framework to determinate the relative role of environmental conditions and historical contingency, responsible for the current community organization, and to test the forest refugia hypothesis. Finally, we downscaled the analysis to determinate, and tried to disentangle the effects of environmental conditions and interspecific interactions on species co-occurrence. We used then functional traits to test the relationship between species co-occurrence and similarities.This thesis highlights the important role of historical contingency and facilitation in the structure of regional diversity and the local assembly processes of medium- and large-sized vertebrates, respectively, in French Guiana.
Cette thèse a pour but d’étudier l'influence de l'hétérogénéité des forêts de terre ferme en Guyane sur l'organisation des communautés de moyens et grands vertébrés. Nous avons, d'abord, choisi une espèce modèle afin de déterminer une méthode adéquate d'estimation d'abondance prenant en compte la détection imparfaite et l'immigration temporaire des espèces, et de tester l'effet des conditions environnementales à différentes échelles d'analyse. Puis, partant du constat que les biais dus à la détection dans l'estimation d'abondance pouvaient être importants, nous avons déterminé l'importance relative des conditions environnementales et des traits biologiques des espèces sur la probabilité de détection. A partir de ce cadre d'étude, nous avons étudié la composition et les diversités alpha et beta en utilisant de façon complémentaire les métriques taxonomique, fonctionnelle, et phylogénétique pour déterminer le rôle relatif de l'environnement et de la contingence historique dans l'organisation des communautés, et de tester l’hypothèse des refuges forestiers. Enfin, en descendant dans l'échelle d'analyse, nous avons tenté de démêler l'effet de l'environnement et des interactions interspécifiques sur la cooccurrence des espèces, et utilisé les traits fonctionnels des espèces pour tester le lien entre cooccurrence et similitude fonctionnelle. Cette thèse met en avant les rôles prépondérants de la contingence historique et de la facilitation dans, respectivement, la structuration de la diversité régionale et les processus d’assemblages locaux des communautés de moyens et grands vertébrés en Guyane.
https://tel.archives-ouvertes.fr/tel-01537779

NNT : 2017YANE0004
tel-01537779
https://tel.archives-ouvertes.fr/tel-01537779
https://tel.archives-ouvertes.fr/tel-01537779/document
https://tel.archives-ouvertes.fr/tel-01537779/file/these_thomas_denis.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Ecological signs of Earth's biosphere forewarn an alarming trajectory towards a global mass-extinction. Assessing species performance and susceptibilities to decline is essential to comprehend and reverse this trend. Yet it is challenging, given difficulties associated with quantifying individual and population processes that are variable across time, space, and life-stages. We describe a new approach to estimating and comparing species performances that combines empirical data, a novel theoretical consideration of population dynamics, and modern statistics. Our approach allows for a more realistic continuous representation of individual performances along development stages while taking into account non-linearity, and natural variability as captured by spatio-temporally replicated observations. We illustrate its application in a coral meta-assemblage composed of populations of the three major reef-building taxa Acropora, Pocillopora, Porites. Using a unique set of highly replicated observations of individual coral dynamics under various environmental conditions, we show how taxa differ in their investment in recruitment and size-specific aptitude for growth and survival, notably through different use of clonal shrinkage, fragmentation, fission, and fusion processes. Our results reveal contrasting life-history trade-offs among taxa which, along with differing patterns of density-dependent recruitment, modulate species responses to decline. These differences in coral life history traits reflect opposing life-strategies, imply regulation at differing life-stages, and explain divergence in species trajectories. Our findings indicate a high potential for resilience in Pocillopora and Porites populations, thanks respectively to a sustained recruitment that promotes demographic elasticity through replacement of individuals, and a steady resistance to mortality which confers persistence through lingering of individuals. Resilience in Acropora appears more arbitrary, given high susceptibility to perturbations and dependency of recruitment on presence of established local populations. We identify management actions that can complement Acropora's life history and benefit recovery of its populations following mortality events. Our regression-modelling approach to quantifying and comparing species performances in different population processes is applicable to all taxa, as illustrated even those with complex clonal life histories, and can be implemented at wide spatio-temporal and taxonomic coverage. It can promote more accurate representation of species dynamics in both descriptive and predictive modelling approaches. The semi-parametric contrast curve method we develop facilitates comparing response variables along continuous explicative metrics while accounting for multiple sources of complexity in empirical data. It should widely benefit investigations in ecology and quantitative science.
ISSN: 1476-945X

hal-01212337
https://hal-univ-perp.archives-ouvertes.fr/hal-01212337
DOI : 10.1016/j.ecocom.2015.07.003

Éditeur(s) : HAL CCSD Wiley
Résumé : [b]Aim[/b][br/] Many tropical tree species have poorly delimited taxonomic boundaries and contain undescribed or cryptic species. We examined the genetic structure of a species complex in the tree genus Carapa in the Neotropics in order to evaluate age, geographic patterns of diversity and evolutionary relationships, and to quantify levels of introgression among currently recognized species.[br/] [br/] [b]Location[/b][br/] Lowland moist forests in the Guiana Shield, the Central and Western Amazon Basin, Chocó and Central America.[br/] [br/] [b]Methods[/b][br/] Genetic structure was analysed using seven nuclear simple sequence repeats (nuSSR), five chloroplast SSRs (cpSSR), and two chloroplast DNA (cpDNA) intergenic sequences (trnH-psbA and trnC-ycf6). Bayesian clustering analysis of the SSR data was used to infer population genetic structure and to assign 324 samples to their most likely genetic cluster. Bayesian coalescence analyses were performed on the two cpDNA markers to estimate evolutionary relationships and divergence times.[br/] [br/] [b]Results[/b][br/] Two genetic clusters (nu_guianensis and nu_surinamensis) were detected, which correspond to the Neotropical species C. guianensis (sensu latu) and C. surinamensis. Fourteen cpDNA haplotypes clustered into six haplogroups distributed between the two nuclear genetic clusters. Divergence between the haplogroups was initiated in the Miocene, with some haplotype structure evolving as recently as the Pleistocene. The absence of complete lineage sorting between the nuclear and chloroplast genomes and the presence of hybrid individuals suggest that interspecific reproductive barriers are incomplete. NuSSR diversity was highest in C. guianensis and, within C. guianensis, cpDNA diversity was highest in the Central and Western Amazon Basin. Regional genetic differentiation was strong but did not conform to an isolation-by-distance process or exhibit a phylogeographical signal.[br/] [br/] [b]Main conclusions[/b][br/] The biogeographical history of Neotropical Carapa appears to have been influenced by events that took place during the Neogene. Our results point to an Amazonian centre of origin and diversification of Neotropical Carapa, with subsequent migration to the Pacific coast of South America and Central America. Gene flow apparently occurs among species, and introgression events are supported by inconsistencies between chloroplast and nuclear lineage sorting. The absence of phylogeographical structure may be a result of the ineffectiveness of geographical barriers among populations and of reproductive isolation mechanisms among incipient and cryptic species in this species complex.
ISSN: 0305-0270

hal-01032395
https://hal.archives-ouvertes.fr/hal-01032395
DOI : 10.1111/j.1365-2699.2011.02678.x

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : Tree mortality in tropical forests is a complex ecological process for which modelling approaches need to be improved to better understand, and then predict, the evolution of tree mortality in response to global change. The mortality model introduced here computes an individual probability of dying for each tree in a community. The mortality model uses the ontogenetic stage of the tree because youngest and oldest trees are more likely to die. Functional traits are integrated as proxies of the ecological strategies of the trees to permit generalization among all species in the community. Data used to parametrize the model were collected at Paracou study site, a tropical rain forest in French Guiana, where 20,408 trees have been censused for 18 years. A Bayesian framework was used to select useful covariates and to estimate the model parameters. This framework was developed to deal with sources of uncertainty, including the complexity of the mortality process itself and the field data, especially historical data for which taxonomic determinations were uncertain. Uncertainty about the functional traits was also considered, to maximize the information they contain. Four functional traits were strong predictors of tree mortality: wood density, maximum height, laminar toughness and stem and branch orientation, which together distinguished the light-demanding, fast-growing trees from slow-growing trees with lower mortality rates. Our modelling approach formalizes a complex ecological problem and offers a relevant mathematical framework for tropical ecologists to process similar uncertain data at the community level.
ISSN: 1932-6203

hal-01190561
https://hal.archives-ouvertes.fr/hal-01190561
PRODINRA : 208582
PUBMED : 23675500
DOI : 10.1371/journal.pone.0063678

Éditeur(s) : HAL CCSD Sociedade Entomológica do Brasil
Résumé : Variations in diel activity among hyperdiverse tropical communities of moths, despite representing a key component of niche partitioning between species, have barely been studied so far. Using light trapping from dawn to sunset over a 1-year period in French Guiana, we investigated these variations within and between two families of moths (Sphingidae and Saturniidae). Our results revealed contrasting patterns in flight activity at night between Sphingidae and Saturniidae. Sphingidae reached their peak in species richness and abundance between 7:00 and 8:00 p.m., followed by a decrease around 11:00 p.m. to midnight, whereas Saturniidae were continuously present throughout the night, with a peak around midnight. In addition, we found changes in diel activity among some of the most common genera in each family, highlighting distinct behavioral, physiological, and functional traits among taxa. Given differences in flight activity at different taxonomic levels, it is strongly recommended to monitor by light trapping throughout the night to effectively sample saturniid and sphingid assemblages, even though the activity of Sphingidae sharply declines after midnight. These results improve the general natural history information of tropical moths and reinforce the need of further research on the ecological and taxonomic consequences of differences in diel activity.
ISSN: 1519-566X

hal-01536447
https://hal.archives-ouvertes.fr/hal-01536447
DOI : 10.1007/s13744-014-0264-3
PRODINRA : 320714

Éditeur(s) : HAL CCSD Wiley
Résumé : [b]Aim[/b][br/] [br/] The phylogeographical history of Neotropical species can be difficult to reconstruct because of superimposed Neogene and Quaternary histories, and because of taxonomic uncertainty. We analysed range-wide genetic diversity in a widespread pioneer tree species, Jacaranda copaia (Aubl.) D. Don, to characterize phylogeographical structure, date the evolutionary relationships among lineages, and evaluate the role of dispersal and vicariance in establishing the present geographical range.[br/] [br/] [br/] [b]Location[/b][br/] [br/] Guiana Shield; central, southern and western Amazon Basin; Chocó region; Central America.[br/] [br/] [br/] [b]Methods[/b][br/] [br/] We analysed nine nuclear simple sequence repeat loci (nuSSR), eight chloroplast SSRs (cpSSR), and two cpDNA intergenic sequences in 341 adult trees. Genetic differentiation at nuSSRs was inferred using Bayesian clustering. Dating of chloroplast lineage divergence was obtained using a range of published mutation rates and Bayesian coalescence analyses. Population divergence dating was performed using an isolation-with-migration model for eight loci (one cp sequence and seven nuSSRs).[br/] [br/] [br/] [b]Results[/b][br/] [br/] Nuclear SSR variation identified three geographically overlapping clusters (nu-1, nu-2, nu-3). Twelve cpDNA haplotypes were clustered into two haplogroups (cp-1, cp-2) with the central Amazon harbouring the highest diversity. Molecular dating analysis suggests that cpDNA haplotype diversification started around the end of the Pliocene (2.61 Ma on average), whereas population divergence was more recent and occurred during the mid-Quaternary (point estimates between 357 and 436 ka).[br/] [br/] [br/] [b]Main conclusions[/b][br/] [br/] The genetic variation of J. copaia in the Neotropics was shaped mainly by Pleistocene events. Chloroplast diversity did not display the expected cis/trans Andean disjunction, indicating recent dispersal. Nuclear variation revealed that separate regions share a recent history, with a centre of diversity in the central Amazon Basin. The geographical pattern of diversity is congruent with the distribution of the two subspecies, J. copaia copaia and J. copaia spectabilis, and evidence of nuSSR admixture between the two taxa supports their classification as subspecies.
ISSN: 0305-0270

hal-01032410
https://hal.archives-ouvertes.fr/hal-01032410
DOI : 10.1111/j.1365-2699.2012.02797.x

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
The Southwest Indian Ocean (SWIO) is a striking marine biodiversity hotspot. Coral reefs in this region host a high proportion of endemics compared to total species richness and they are particularly threatened by human activities. The island archipelagos with their diverse marine habitats constitute a natural laboratory for studying diversification processes. Rocky shores in the SWIO region have remained understudied. This habitat presents a high diversity of molluscs, in particular gastropods. To explore the role of climatic and geological factors in lineage diversification within the genus Nerita, we constructed a new phylogeny with an associated chronogram from two mitochondrial genes [cytochrome oxidase sub-unit 1 and 16S rRNA], combining previously published and new data from eight species sampled throughout the region. All species from the SWIO originated less than 20 Ma ago, their closest extant relatives living in the Indo-Australian Archipelago (IAA). Furthermore, the SWIO clades within species with Indo-Pacific distribution ranges are quite recent, less than 5 Ma. These results suggest that the regional diversification of Nerita is closely linked to tectonic events in the SWIO region. The Reunion mantle plume head reached Earth's surface 67 Ma and has been stable and active since then, generating island archipelagos, some of which are partly below sea level today. Since the Miocene, sea-level fluctuations have intermittently created new rocky shore habitats. These represent ephemeral stepping-stones, which have likely facilitated repeated colonization by intertidal gastropods, like Nerita populations from the IAA, leading to allopatric speciation. This highlights the importance of taking into account past climatic and geological factors when studying diversification of highly dispersive tropical marine species. It also underlines the unique history of the marine biodiversity of the SWIO region.
ISSN: 1932-6203

hal-01185713
https://hal.archives-ouvertes.fr/hal-01185713
https://hal.archives-ouvertes.fr/hal-01185713/document
https://hal.archives-ouvertes.fr/hal-01185713/file/PLoS%20ONE%202014%20Postaire.pdf
DOI : 10.1371/journal.pone.0095040