Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
The Hedgehog (Hh) family of secreted proteins act as morphogens to control embryonic patterning and development in a variety of organ systems. Post-translational covalent attachment of cholesterol and palmitate to Hh proteins are critical for multimerization and long range signaling potency. However, the biological impact of lipid modifications on Hh ligand distribution and signal reception in humans remains unclear. In the present study, we report a unique case of autosomal recessive syndromic 46,XY Disorder of Sex Development (DSD) with testicular dysgenesis and chondrodysplasia resulting from a homozygous G287V missense mutation in the hedgehog acyl-transferase (HHAT) gene. This mutation occurred in the conserved membrane bound O-acyltransferase (MBOAT) domain and experimentally disrupted the ability of HHAT to palmitoylate Hh proteins such as DHH and SHH. Consistent with the patient phenotype, HHAT was found to be expressed in the somatic cells of both XX and XY gonads at the time of sex determination, and Hhat loss of function in mice recapitulates most of the testicular, skeletal, neuronal and growth defects observed in humans. In the developing testis, HHAT is not required for Sertoli cell commitment but plays a role in proper testis cord formation and the differentiation of fetal Leydig cells. Altogether, these results shed new light on the mechanisms of action of Hh proteins. Furthermore, they provide the first clinical evidence of the essential role played by lipid modification of Hh proteins in human testicular organogenesis and embryonic development.
ISSN: 1553-7390

hal-01063929
https://hal.archives-ouvertes.fr/hal-01063929
DOI : 10.1371/journal.pgen.1004340
PUBMED : 24784881

Éditeur(s) : HAL CCSD Wiley
Résumé : Over the past three decades, many small-scale floristic studies of white-sand forests across the Amazon basin have been published. Nonetheless, a basin-wide description of both taxonomic and phylogenetic alpha and beta diversity at regional scales has never been achieved. We present a complete floristic analysis of white-sand forests across the Amazon basin including both taxonomic and phylogenetic diversity. We found strong regional differences in the signal of phylogenetic community structure with both overall and regional Net Relatedness Index and Nearest Taxon Index values found to be significantly positive leading to a pattern of phylogenetic clustering. Additionally, we found high taxonomic dissimilarity but low phylogenetic dissimilarity in pairwise community comparisons. These results suggest that recent diversification has played an important role in the assembly of white-sand forests causing geographic neo-endemism patterns at the regional scale.
ISSN: 0006-3606

hal-01532549
https://hal.archives-ouvertes.fr/hal-01532549
DOI : 10.1111/btp.12298
PRODINRA : 353398

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Geographical distribution of parasite species can provide insights into the evolution and diversity of parasiticcommunities. Biogeography of marine parasites is poorly known, especially because it requires anunderstanding of host-parasite interactions, information that is rare, especially over large spatial scales.Here, we have studied the biogeographical patterns of dactylogyrid parasites of chaetodontids, one of themost well-studied fish families, in the tropical Indo-west Pacific region. Dactylogyrid parasites were collectedfrom gills of 34 butterflyfish species (n = 560) at nine localities within an approximate area of62 million km2. Thirteen dactylogyrid species were identified, with richness ranging from 6 to 12 speciesat individual localities. Most dactylogyrid communities were dominated by Haliotrema angelopterum orHaliotrema aurigae, for which relative abundance was negatively correlated (q = !0.59). Parasite richnessand diversity were highest in French Polynesia and the Great Barrier Reef (Australia) and lowest in Palau.Three biogeographic regions were identified based on dactylogyrid dissimilarities: French Polynesia,characterised by the dominance of H. angelopterum, the western Pacific region dominated by H. aurigae,and Ningaloo Reef (Australia), dominated by Euryhaliotrema berenguelae. Structure of host assemblageswas the main factor explaining the dissimilarity (turnover and nestedness components of the Bray-Curtis dissimilarity and overall Bray-Curtis dissimilarity) of parasite communities between localities,while environment was only significant in the turnover of parasite communities and overall dissimilarity.Spatial structure of localities explained only 10% of the turnover of parasite communities. The interactionof the three factors (host assemblages, environment and spatial structure), however, explained the highestamounts of variance of the dactylogyrid communities, indicating a strong colinearity between the factors.Our findings show that spatial arrangement of chaetodontid dactylogyrids in the tropical Indo-westPacific is primarily characterised by the turnover of the main Haliotrema spp., which is mainly explainedby the structure of host assemblages.
ISSN: 0020-7519

hal-01562156
https://hal-univ-perp.archives-ouvertes.fr/hal-01562156
DOI : 10.1016/j.ijpara.2017.01.006

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 Wiley
Résumé : International audience
ISSN: 1354-1013

hal-01107919
https://hal-agroparistech.archives-ouvertes.fr/hal-01107919
DOI : 10.1111/j.1365-2486.2011.02432.x

Éditeur(s) : HAL CCSD CRC Press
Résumé : International audience
Biology of European Sea Bass

hal-01122043
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01122043
DOI : 10.1201/b16043-8

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
ISSN: 2047-217X

hal-01429002
https://hal.archives-ouvertes.fr/hal-01429002
DOI : 10.1186/s13742-016-0118-5

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Resolving the early diversification of animal lineages has proven difficult, even using genome-scale datasets. Several phylogenomic studies have supported the classical scenario in which sponges (Porifera) are the sister group to all other animals (''Porifera-sister''3 hypothesis), consistent with a single origin of the gut, nerve cells, and muscle cells in the stem lineage of eumetazoans (bilaterians + ctenophores + cnidarians). In contrast, several other studies have recovered an alternative topology in which ctenophores are the sister group to all other animals (including sponges). The ``Ctenophora-sister'' hypothesis implies that eumetazoan-specific traits, such as neurons and muscle cells, either evolved once along the metazoan stem lineage and were then lost in sponges and placozoans or evolved at least twice independently in Ctenophora and in Cnidaria + Bilateria. Here, we report on our reconstruction of deep metazoan relationships using a 1,719-gene dataset with dense taxonomic sampling of non-bilaterian animals that was assembled using a semi-automated procedure, designed to reduce known error sources. Our dataset outperforms previous metazoan gene superalignments in terms of data quality and quantity. Analyses with a best-fitting site-heterogeneous evolutionary model provide strong statistical support for placing sponges as the sister-group to all other metazoans, with ctenophores emerging as the second-earliest branching animal lineage. Only those methodological settings that exacerbated long-branch attraction artifacts yielded Ctenophora-sister. These results show that methodological issues must be carefully addressed to tackle difficult phylogenetic questions and pave the road to a better understanding of how fundamental features of animal body plans have emerged.
ISSN: 0960-9822

hal-01681528
https://hal.archives-ouvertes.fr/hal-01681528
DOI : 10.1016/j.cub.2017.02.031

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : The Amazon basin harbors a diverse ecological community that has a critical role in the maintenance of the biosphere. Although plant and animal communities have received much attention, basic information is lacking for fungal or prokaryotic communities. This is despite the fact that recent ecological studies have suggested a prominent role for interactions with soil fungi in structuring the diversity and abundance of tropical rainforest trees. In this study, we characterize soil fungal communities across three major tropical forest types in the western Amazon basin (terra firme, seasonally flooded and white sand) using 454 pyrosequencing. Using these data, we examine the relationship between fungal diversity and tree species richness, and between fungal community composition and tree species composition, soil environment and spatial proximity. We find that the fungal community in these ecosystems is diverse, with high degrees of spatial variability related to forest type. We also find strong correlations between alpha- and beta-diversity of soil fungi and trees. Both fungal and plant community beta-diversity were also correlated with differences in environmental conditions. The correlation between plant and fungal richness was stronger in fungal lineages known for biotrophic strategies (for example, pathogens, mycorrhizas) compared with a lineage known primarily for saprotrophy (yeasts), suggesting that this coupling is, at least in part, due to direct plant-fungal interactions. These data provide a much-needed look at an understudied dimension of the biota in an important ecosystem and supports the hypothesis that fungal communities are involved in the regulation of tropical tree diversity.
ISSN: 1751-7362

hal-01032405
https://hal.archives-ouvertes.fr/hal-01032405
DOI : 10.1038/ismej.2013.66

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The extent of the global human footprint [ 1 ] limits our understanding of what is natural in the marine environment. Remote, near-pristine areas provide some baseline expectations for biomass [ 2, 3 ] and suggest that predators dominate, producing an inverted biomass pyramid. The southern pass of Fakarava atoll—a biosphere reserve in French Polynesia—hosts an average of 600 reef sharks, two to three times the biomass per hectare documented for any other reef shark aggregations [ 4 ]. This huge biomass of predators makes the trophic pyramid inverted. Bioenergetics models indicate that the sharks require ∼90 tons of fish per year, whereas the total fish production in the pass is ∼17 tons per year. Energetic theory shows that such trophic structure is maintained through subsidies [ 5–9 ], and empirical evidence suggests that sharks must engage in wide-ranging foraging excursions to meet energy needs [ 9, 10 ]. We used underwater surveys and acoustic telemetry to assess shark residency in the pass and feeding behavior and used bioenergetics models to understand energy flow. Contrary to previous findings, our results highlight that sharks may overcome low local energy availability by feeding on fish spawning aggregations, which concentrate energy from other local trophic pyramids. Fish spawning aggregations are known to be targeted by sharks, but they were previously believed to play a minor role representing occasional opportunistic supplements. This research demonstrates that fish spawning aggregations can play a significant role in the maintenance of local inverted pyramids in pristine marine areas. Conservation of fish spawning aggregations can help conserve shark populations, especially if combined with shark fishing bans.
ISSN: 0960-9822

hal-01359391
https://hal-univ-perp.archives-ouvertes.fr/hal-01359391
DOI : 10.1016/j.cub.2016.05.058

Éditeur(s) : Monachii ; Lipsiae : apud R. Oldenbourg in comm.
Extrait de : Flora brasiliensis : enumeratio plantarum in Brasilia hactenus detectarum quas suis aliorumque botanicorum studiis descriptas et methodo naturali digestas partim icone illustratas
Résumé : Édition : 1840-1906
Siècle(s) traité(s) : 19
Droits : Domaine public
Provenance : Université Toulouse III - Paul Sabatier. Service Commun de la Documentation
Permalien : http://www.manioc.org/patrimon/TLS17055
TLS17055

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: Amelotin (AMTN) is an ameloblast-secreted protein that belongs to the secretory calcium-binding phosphoprotein (SCPP) family, which originated in early vertebrates. In rodents, AMTN is expressed during the maturation stage of amelogenesis only. This expression pattern strongly differs from the spatiotemporal expression of other ameloblast-secreted SCPPs, such as the enamel matrix proteins (EMPs). Furthermore, AMTN was characterized in rodents only. In this study, we applied various approaches, including in silico screening of databases, PCRs and transcriptome sequencing to characterize AMTN sequences in sauropsids and amphibians, and compared them to available mammalian and coelacanth sequences. Results: We showed that (i) AMTN is tooth (enamel) specific and underwent pseudogenization in toothless turtles and birds, and (ii) the AMTN structure changed during tetrapod evolution. To infer AMTN function, we studied spatiotemporal expression of AMTN during amelogenesis in a salamander and a lizard, and compared the results with available expression data from mouse. We found that AMTN is expressed throughout amelogenesis in non-mammalian tetrapods, in contrast to its expression limited to enamel maturation in rodents. Conclusions: Taken together our findings suggest that AMTN was primarily an EMP. Its functions were conserved in amphibians and sauropsids while a change occurred early in the mammalian lineage, modifying its expression pattern during amelogenesis and its gene structure. These changes likely led to a partial loss of AMTN function and could have a link with the emergence of prismatic enamel in mammals.
ISSN: 1471-2148

Droits : http://creativecommons.org/licenses/by/
hal-01212821
http://hal.upmc.fr/hal-01212821
http://hal.upmc.fr/hal-01212821/document
http://hal.upmc.fr/hal-01212821/file/s12862-015-0329-x.pdf
DOI : 10.1186/s12862-015-0329-x

Éditeur(s) : HAL CCSD Royal Society, The
Résumé : International audience
Individuals can play different roles in maintaining connectivity and socialcohesion in animal populations and thereby influence population robustnessto perturbations.We performed a social network analysis in a reef shark populationto assess the vulnerability of the global network to node removal underdifferent scenarios. We found that the network was generally robust to theremoval of nodes with high centrality. The network appeared also highlyrobust to experimental fishing. Individual shark catchability decreased as afunction of experience, as revealed by comparing capture frequency and sitepresence. Altogether, these features suggest that individuals learnt to avoidcapture, which ultimately increased network robustness to experimentalcatch-and-release. Our results also suggest that some caution must be takenwhen using capture–recapture models often used to assess population sizeas assumptions (such as equal probabilities of capture and recapture) maybe violated by individual learning to escape recapture.
EISSN: 1471-2954

hal-01561754
https://hal-univ-perp.archives-ouvertes.fr/hal-01561754
DOI : 10.1098/rsbl.2016.0824

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 : The analysis of fine-scale spatial genetic structure (FSGS) within populations can provide insights into eco-evolutionary processes. Restricted dispersal and locally occurring genetic drift are the primary causes for FSGS at equilibrium, as described in the isolation by distance (IBD) model. Beyond IBD expectations, spatial, environmental or historical factors can affect FSGS. We examined FSGS in seven African and Neotropical populations of the late-successional rain forest tree Symphonia globulifera L. f. (Clusiaceae) to discriminate the influence of drift-dispersal vs. landscape/ecological features and historical processes on FSGS. We used spatial principal component analysis and Bayesian clustering to assess spatial genetic heterogeneity at SSRs and examined its association with plastid DNA and habitat features. African populations (from Cameroon and São Tomé) displayed a stronger FSGS than Neotropical populations at both marker types (mean Sp = 0.025 vs. Sp = 0.008 at SSRs) and had a stronger spatial genetic heterogeneity. All three African populations occurred in pronounced altitudinal gradients, possibly restricting animal-mediated seed dispersal. Cyto-nuclear disequilibria in Cameroonian populations also suggested a legacy of biogeographic history to explain these genetic patterns. Conversely, Neotropical populations exhibited a weaker FSGS, which may reflect more efficient wide-ranging seed dispersal by Neotropical bats and other dispersers. The population from French Guiana displayed an association of plastid haplotypes with two morphotypes characterized by differential habitat preferences. Our results highlight the importance of the microenvironment for eco-evolutionary processes within persistent tropical tree populations.
ISSN: 1932-6203

hal-01608324
https://hal.archives-ouvertes.fr/hal-01608324
DOI : 10.1371/journal.pone.0182515
PRODINRA : 403154
PUBMED : 28771629

Éditeur(s) : HAL CCSD BioMed Central
Résumé :  
absent
ISSN: 1471-2148

hal-01032078
https://hal.archives-ouvertes.fr/hal-01032078
DOI : 10.1186/1471-2148-10-202

Éditeur(s) : Hamburg, Paris, Milano : The Albatross
Siècle(s) traité(s) : 20
Provenance : Université Caen Normandie. Service commun de la documentation
Permalien : http://www.manioc.org/patrimon/CAE19035
CAE19035

Éditeur(s) : HAL CCSD Cold Spring Harbor Laboratory Press
Résumé : International audience
The genome of male germ cells is actively transcribed during spermatogenesis to produce phase-specific protein-coding mRNAs and a considerable amount of different noncoding RNAs. Ribonucleoprotein (RNP) granule-mediated RNA regulation provides a powerful means to secure the quality and correct expression of the requisite transcripts. Haploid spermatids are characterized by a unique, unusually large cytoplasmic granule, the chromatoid body (CB), which emerges during the switch between the meiotic and post-meiotic phases of spermatogenesis. To better understand the role of the CB in male germ cell differentiation, we isolated CBs from mouse testes and revealed its full RNA and protein composition. We showed that the CB is mainly composed of RNA-binding proteins and other proteins involved RNA regulation. The CB was loaded with RNA, including pachytene piRNAs, a diverse set of mRNAs, and a number of uncharacterized long noncoding transcripts. The CB was demonstrated to accumulate nascent RNA during all the steps of round spermatid differentiation. Our results revealed the CB as a large germ cell-specific RNP platform that is involved in the control of the highly complex transcriptome of haploid male germ cells.
ISSN: 1355-8382

hal-00985894
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00985894
DOI : 10.1261/rna.043729.113
PUBMED : 24554440

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BACKGROUND: Homologous recombination is the key process that generates genetic diversity and drives evolution. SPO11 protein triggers recombination by introducing DNA double stranded breaks at discreet areas of the genome called recombination hotspots. The hotspot locations are largely determined by the DNA binding specificity of the PRDM9 protein in human, mice and most other mammals. In budding yeast Saccharomyces cerevisae, which lacks a Prdm9 gene, meiotic breaks are formed opportunistically in the regions of accessible chromatin, primarily at gene promoters. The genome-wide distribution of hotspots in this organism can be altered by tethering Spo11 protein to Gal4 recognition sequences in the strain expressing Spo11 attached to the DNA binding domain of the Gal4 transcription factor. To establish whether similar re-targeting of meiotic breaks can be achieved in PRDM9-containing organisms we have generated a Gal4BD-Spo11 mouse that expresses SPO11 protein joined to the DNA binding domain of yeast Gal4. RESULTS: We have mapped the genome-wide distribution of the recombination initiation sites in the Gal4BD-Spo11 mice. More than two hundred of the hotspots in these mice were novel and were likely defined by Gal4BD, as the Gal4 consensus motif was clustered around the centers in these hotspots. Surprisingly, meiotic DNA breaks in the Gal4BD-Spo11 mice were significantly depleted near the ends of chromosomes. The effect is particularly striking at the pseudoautosomal region of the X and Y chromosomes -- normally the hottest region in the genome. CONCLUSIONS: Our data suggest that specific, yet-unidentified factors influence the initiation of meiotic recombination at subtelomeric chromosomal regions.
ISSN: 1471-2164

inserm-00849779
http://www.hal.inserm.fr/inserm-00849779
http://www.hal.inserm.fr/inserm-00849779/document
http://www.hal.inserm.fr/inserm-00849779/file/1471-2164-14-493.pdf
DOI : 10.1186/1471-2164-14-493

Éditeur(s) : HAL CCSD Wiley
Résumé : The intensification of the hydrological cycle, with an observed and modeled increase in drought incidence and severity, underscores the need to quantify drought effects on carbon cycling and the terrestrial sink. FLUXNET, a global network of eddy covariance towers, provides dense data streams of meteorological data, and through flux partitioning and gap filling algorithms, estimates of net ecosystem productivity (FNEP), gross ecosystem productivity (P), and ecosystem respiration (R). We analyzed the functional relationship of these three carbon fluxes relative to evaporative fraction (EF), an index of drought and site water status, using monthly data records from 238 micrometeorological tower sites distributed globally across 11 biomes. The analysis was based on relative anomalies of both EF and carbon fluxes and focused on drought episodes by biome and climatic season. Globally P was ≈50% more sensitive to a drought event than R. Network-wide drought-induced decreases in carbon flux averaged −16.6 and −9.3 g C m−2 month−1 for P and R, i.e., drought events induced a net decline in the terrestrial sink. However, in evergreen forests and wetlands drought was coincident with an increase in P or R during parts of the growing season. The most robust relationships between carbon flux and EF occurred during climatic spring for FNEP and in climatic summer for P and R. Upscaling flux sensitivities to a global map showed that spatial patterns for all three carbon fluxes were linked to the distribution of croplands. Agricultural areas exhibited the highest sensitivity whereas the tropical region had minimal sensitivity to drought. Combining gridded flux sensitivities with their uncertainties and the spatial grid of FLUXNET revealed that a more robust quantification of carbon flux response to drought requires additional towers in all biomes of Africa and Asia as well as in the cropland, shrubland, savannah, and wetland biomes globally.
ISSN: 1354-1013

hal-01032076
https://hal.archives-ouvertes.fr/hal-01032076
DOI : 10.1111/j.1365-2486.2009.01991.x