Éditeur(s) : HAL CCSD
Résumé : International audience
Recent studies have shown that accounting for intraspecific trait variation (ITV) may better address major questions in community ecology. However, a general picture of the relative extent of ITV compared to interspecific trait variation in plant communities is still missing. Here, weconducted a meta-analysis of the relative extent of ITV within and among plant communities worldwide, using a data set encompassing 629 communities (plots) and 36 functional traits. Overall, ITV accounted for 25% of the total trait variation within communities and 32% of the totaltrait variation among communities on average. The relative extent of ITV tended to be greater for whole-plant (e.g. plant height) vs. organ-level traits and for leaf chemical (e.g. leaf N and P concentration) vs. leaf morphological (e.g. leaf area and thickness) traits. The relative amount of ITV decreased with increasing species richness and spatial extent, but did not vary with plant growth form or climate. These results highlight global patterns in the relative importance of ITV in plant communities, providing practical guidelines for when researchers should include ITV in trait-based community and ecosystem studies.
Ecology Letters

hal-01237101
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01237101
DOI : 10.1111/ele.12508
PUBMED : 26415616

Éditeur(s) : HAL CCSD Wiley Open Access
Résumé : International audience
Plant responses to natural enemies include formation of secondary metabolites acting as direct or indirect defenses. Volatile terpenes represent one of the most diverse groups of secondary metabolites. We aimed to explore evolutionary patterns of volatile terpene emission. We measured the composition of damage-induced volatile terpenes from 202 Amazonian tree species, spanning the angiosperm phylogeny. Volatile terpenes were extracted with solid-phase micro extraction and desorbed in a gas chromatography–mass spectrometry for compound identification. The chemical diversity of the terpene blend showed a strong phylogenetic signal as closely related species emitted a similar number of compounds. Closely related species also tended to have compositionally similar blends, although this relationship was weak. Meanwhile, the ability to emit a given compound showed no significant phylogenetic signal for 200 of 286 compounds, indicating a high rate of diversification in terpene synthesis and/or great variability in their expression. Three lineages (Magnoliales, Laurales, and Sapindales) showed exceptionally high rates of terpene diversification. Of the 70 compounds found in >10% of their species, 69 displayed significant correlated evolution with at least one other compound. These results provide insights into the complex evolutionary history of volatile terpenes in angiosperms, while highlighting the need for further research into this important class of compounds.
ISSN: 2045-7758

Droits : http://creativecommons.org/licenses/by/
hal-01296640
http://hal.upmc.fr/hal-01296640
http://hal.upmc.fr/hal-01296640/document
http://hal.upmc.fr/hal-01296640/file/ece31810.pdf
DOI : 10.1002/ece3.1810

Éditeur(s) : HAL CCSD Royal Society, The
Résumé : International audience
Endemic species are frequently assumed to have lower genetic diversity than species with large distributions, even if closely related. This assumption is based on research from the terrestrial environment and theoretical evolutionary modelling. We test this assumption in the marine environment by analysing the mitochondrial genetic diversity of 33 coral reef fish species from five families sampled from Pacific Ocean archipelagos. Surprisingly, haplotype and nucleotide diversity did not differ significantly between endemic and widespread species. The probable explanation is that the effective population size of some widespread fishes locally is similar to that of many of the endemics. Connectivity across parts of the distribution of the widespread species is probably low, so widespread species can operate like endemics at the extreme or isolated parts of their range. Mitochondrial genetic diversity of many endemic reef fish species may not either limit range size or be a source of vulnerability.
ISSN: 0962-8452

hal-01333327
https://hal-univ-perp.archives-ouvertes.fr/hal-01333327
DOI : 10.1098/rspb.2014.1068

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
The Black Rat (Rattus rattus) spread out of Asia to become one of the world's worst agricultural and urban pests, and a reservoir or vector of numerous zoonotic diseases, including the devastating plague. Despite the global scale and inestimable cost of their impacts on both human livelihoods and natural ecosystems, little is known of the global genetic diversity of Black Rats, the timing and directions of their historical dispersals, and the risks associated with contemporary movements. We surveyed mitochondrial DNA of Black Rats collected across their global range as a first step towards obtaining an historical genetic perspective on this socioeconomically important group of rodents. We found a strong phylogeographic pattern with well-differentiated lineages of Black Rats native to South Asia, the Himalayan region, southern Indochina, and northern Indochina to East Asia, and a diversification that probably commenced in the early Middle Pleistocene. We also identified two other currently recognised species of Rattus as potential derivatives of a paraphyletic R.rattus. Three of the four phylogenetic lineage units within R. rattus show clear genetic signatures of major population expansion in prehistoric times, and the distribution of particular haplogroups mirrors archaeologically and historically documented patterns of human dispersal and trade. Commensalism clearly arose multiple times in R. Rattus and in widely separated geographic regions, and this may account for apparent regionalism in their associated pathogens. Our findings represent an important step towards deeper understanding the complex and influential relationship that has developed between Black Rats and humans, and invite a thorough re-examination of host-pathogen associations among Black Rats.
PLoS ONE

ird-00714383
http://hal.ird.fr/ird-00714383
http://hal.ird.fr/ird-00714383/document
DOI : 10.1371/journal.pone.0026357
IRD : fdi:010055548

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Projections of climate change impacts on coral reefs produced at the coarse resolution (~1°) of Global Climate Models (GCMs) have informed debate but have not helped target local management actions. Here, projections of the onset of annual coral bleaching conditions in the Caribbean under Representative Concentration Pathway (RCP) 8.5 are produced using an ensemble of 33 Coupled Model Intercomparison Project phase-5 models and via dynamical and statistical downscaling. A high-resolution (~11 km) regional ocean model (MOM4.1) is used for the dynamical downscaling. For statistical downscaling, sea surface temperature (SST) means and annual cycles in all the GCMs are replaced with observed data from the ~4-km NOAA Pathfinder SST dataset. Spatial patterns in all three projections are broadly similar ; the average year for the onset of annual severe bleaching is 2040–2043 for all projections. However, downscaled projections show many locations where the onset of annual severe bleaching (ASB) varies 10 or more years within a single GCM grid cell. Managers in locations where this applies (e.g., Florida, Turks and Caicos, Puerto Rico, and the Domini-can Republic, among others) can identify locations that represent relative albeit temporary refugia. Both downscaled projections are different for the Bahamas compared to the GCM projections. The dynamically downscaled projections suggest an earlier onset of ASB linked to projected changes in regional currents, a feature not resolved in GCMs. This result demonstrates the value of dynamical downscaling for this application and means statistically downscaled projections have to be interpreted with caution. However, aside from west of Andros Island, the projections for the two types of downscaling are mostly aligned; projected onset of ASB is within AE10 years for 72% of the reef locations.
ISSN: 1354-1013

Droits : http://creativecommons.org/licenses/by-nc/
hal-01223492
https://hal-univ-perp.archives-ouvertes.fr/hal-01223492
https://hal-univ-perp.archives-ouvertes.fr/hal-01223492/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01223492/file/Hooidonk_et_al-2015-Global_Change_Biology.pdf
DOI : 10.1111/gcb.12901

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
The Western Indian Ocean harbors one of theworld’s most diverse marine biota yet is threatened byexploitation with few conservation measures in place.Primary candidates for conservation in the region are theScattered Islands (Iles Eparses), a group of relativelypristine and uninhabited islands in the MozambiqueChannel. However, while optimal conservation strategiesdepend on the degree of population connectivity amongspatially isolated habitats, very few studies have beenconducted in the area. Here, we use highly variablemicrosatellite markers from two damselfishes (Amphiprionakallopisos and Dascyllus trimaculatus) with differing lifehistory traits [pelagic larval duration (PLD), adult habitat]to compare genetic structure and connectivity among theseislands using classic population structure indices as well asBayesian clustering methods. All classical fixation indexesFST, RST, G0ST, and Jost’s D show stronger genetic differentiationamong islands for A. akallopisos compared to D.trimaculatus, consistent with the former species’ shorterPLD and stronger adult site attachment, which may restrictlarval dispersal potential. In agreement with these results,the Bayesian analysis revealed clear genetic differentiationamong the islands in A. akallopisos, separating the southerngroup (Bassas da India and Europa) from the center(Juan de Nova) and northern (Iles Glorieuses) islands, butnot for D. trimaculatus. Local oceanographic patterns suchas eddies that occur along the Mozambique Channel appearto parallel the results reported for A. akallopisos, but suchfeatures seem to have little effect on the genetic differentiationof D. trimaculatus. The contrasting patterns ofgenetic differentiation between species within the samefamily highlight the importance of accounting for diverselife history traits when assessing community-wide connectivity,an increasingly common consideration in conservationplanning.
ISSN: 0722-4028

hal-01561992
https://hal-univ-perp.archives-ouvertes.fr/hal-01561992
DOI : 10.1007/s00338-016-1495-z

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high-copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the mitochondrial genome (mtDNA) with approximately 1000x, 450x and 120x sequencing depth respectively. The phylogenetic tree obtained with ptDNA resolved five of the seven internal nodes. In contrast, the tree obtained with mtDNA and nrDNA data were largely unresolved. This study demonstrates that genome skimming is a cost-effective approach and shows potential in plant molecular systematics within Chrysobalanaceae and other under-studied groups.
ISSN: 1755-098X

hal-01204217
https://hal.archives-ouvertes.fr/hal-01204217
DOI : 10.1111/1755-0998.12246
PRODINRA : 283530

Éditeur(s) : HAL CCSD Inter-Research
Résumé : International audience
Many large groupers form spawning aggregations, returning to the same spawning sites in consecutive spawning seasons. Connectivity between spawning aggregations is thus assured by larval dispersal. This study looks into the genetic structure and gene flow among spawning aggregations of a large grouper, the gulf coney Hyporthodus acanthistius, in the northern Gulf of California. First, using the mitochondrial control region and 11 microsatellites, we calculated FST metrics and conducted a Bayesian clustering analysis to determine structure among 5 spawning aggregations. Shallow genetic structure was found, separating the southernmost spawning aggregate from the remainder. Second, we used the results from the structure analysis and local water circulation patterns to delineate 3 distinct models of gene flow. The best-supported model, in which the southernmost spawning aggregate formed one group and all other spawning aggregates were nested into a second group, was the one that was consistent with water circulation during the species’ spawning season. Larval retention within a seasonal anticyclonic gyre that formed during the gulf coney’s spawning season may be responsible for the patterns found. This study highlights the importance of local oceanographic conditions in dictating the structure among spawning aggregations even at small geographic scales and contributes to informed management plans for this overexploited grouper.
Marine Ecology Progress Series

hal-01301199
https://hal-univ-perp.archives-ouvertes.fr/hal-01301199
DOI : 10.3354/meps10637

Éditeur(s) : HAL CCSD Wiley
Résumé : The extent of gene dispersal is a fundamental factor of the population and evolutionary dynamics of tropical tree species, but directly monitoring seed and pollen movement is a difficult task. However, indirect estimates of historical gene dispersal can be obtained from the fine-scale spatial genetic structure of populations at drift-dispersal equilibrium. Using an approach that is based on the slope of the regression of pairwise kinship coefficients on spatial distance and estimates of the effective population density, we compare indirect gene dispersal estimates of sympatric populations of 10 tropical tree species. We re-analysed 26 data sets consisting of mapped allozyme, SSR (simple sequence repeat), RAPD (random amplified polymorphic DNA) or AFLP (amplified fragment length polymorphism) genotypes from two rainforest sites in French Guiana. Gene dispersal estimates were obtained for at least one marker in each species, although the estimation procedure failed under insufficient marker polymorphism, limited sample size, or inappropriate sampling area. Estimates generally suffered low precision and were affected by assumptions regarding the effective population density. Averaging estimates over data sets, the extent of gene dispersal ranged from 150 m to 1200 m according to species. Smaller gene dispersal estimates were obtained in species with heavy diaspores, which are presumably not well dispersed, and in populations with high local adult density. We suggest that limited seed dispersal could indirectly limit effective pollen dispersal by creating higher local tree densities, thereby increasing the positive correlation between pollen and seed dispersal distances. We discuss the potential and limitations of our indirect estimation procedure and suggest guidelines for future studies
ISSN: 0962-1083

hal-01031603
https://hal.archives-ouvertes.fr/hal-01031603
DOI : 10.1111/j.1365-294X.2005.02785.x

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : The diversity and functional identity of organisms are known to be relevant to the maintenance of ecosystem processes but can be variable in different environments. Particularly, it is uncertain whether ecosystem processes are driven by complementary effects or by dominant groups of species. We investigated how community structure (i.e., the diversity and relative abundance of biological entities) explains the community-level contribution of Neotropical ant communities to different ecosystem processes in different environments. Ants were attracted with food resources representing six ant-mediated ecosystem processes in four environments: ground and vegetation strata in cropland and forest habitats. The exploitation frequencies of the baits were used to calculate the taxonomic and trophic structures of ant communities and their contribution to ecosystem processes considered individually or in combination (i.e., multifunctionality). We then investigated whether community structure variables could predict ecosystem processes and whether such relationships were affected by the environment. We found that forests presented a greater biodiversity and trophic complementarity and lower dominance than croplands, but this did not affect ecosystem processes. In contrast, trophic complementarity was greater on the ground than on vegetation and was followed by greater resource exploitation levels. Although ant participation in ecosystem processes can be predicted by means of trophic-based indices, we found that variations in community structure and performance in ecosystem processes were best explained by environment. We conclude that determining the extent to which the dominance and complementarity of communities affect ecosystem processes in different environments requires a better understanding of resource availability to different species.
ISSN: 0029-8549

hal-01606497
https://hal.archives-ouvertes.fr/hal-01606497
DOI : 10.1007/s00442-016-3741-z
PRODINRA : 407457

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 Wiley
Résumé : Understanding the mechanisms generating species distributions remains a challenge, especially in hyperdiverse tropical forests. We evaluated the role of rainfall variation, soil gradients and herbivory on seedling mortality, and how variation in seedling performance along these gradients contributes to habitat specialisation. In a 4-year experiment, replicated at the two extremes of the Amazon basin, we reciprocally transplanted 4638 tree seedlings of 41 habitat-specialist species from seven phylogenetic lineages among the three most important forest habitats of lowland Amazonia. Rainfall variation, flooding and soil gradients strongly influenced seedling mortality, whereas herbivory had negligible impact. Seedling mortality varied strongly among habitats, consistent with predictions for habitat specialists in most lineages. This suggests that seedling performance is a primary determinant of the habitat associations of adult trees across Amazonia. It further suggests that tree diversity, currently mostly harboured in terra firme forests, may be strongly impacted by the predicted climate changes in Amazonia.
ISSN: 1461-023X

hal-01531751
https://hal.archives-ouvertes.fr/hal-01531751
DOI : 10.1111/ele.12661
PRODINRA : 387284

Éditeur(s) : HAL CCSD Wiley
Résumé :  
absent
ISSN: 0307-6946

hal-01032107
https://hal.archives-ouvertes.fr/hal-01032107
DOI : 10.1111/j.1365-2311.2011.01265.x