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 Oxford University Press
Résumé : International audience
It was recently reported that the sizes of many mRNAs change when budding yeast cells exit mitosis and enter the meiotic differentiation pathway. These differences were attributed to length variations of their untranslated regions. The function of UTRs in protein translation is well established. However, the mechanism controlling the expression of distinct transcript isoforms during mitotic growth and meiotic development is unknown. In this study, we order developmentally regulated transcript isoforms according to their expression at specific stages during meiosis and gametogenesis, as compared to vegetative growth and starvation. We employ regulatory motif prediction, in vivo protein-DNA binding assays, genetic analyses and monitoring of epigenetic amino acid modification patterns to identify a novel role for Rpd3 and Ume6, two components of a histone deacetylase complex already known to repress early meiosis-specific genes in dividing cells, in mitotic repression of meiosis-specific transcript isoforms. Our findings classify developmental stage-specific early, middle and late meiotic transcript isoforms, and they point to a novel HDAC-dependent control mechanism for flexible transcript architecture during cell growth and differentiation. Since Rpd3 is highly conserved and ubiquitously expressed in many tissues, our results are likely relevant for development and disease in higher eukaryotes.
ISSN: 0305-1048

Droits : http://creativecommons.org/licenses/by/
hal-01122128
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01122128
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01122128/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01122128/file/The%20conserved%20histone%20deacetylase.pdf
DOI : 10.1093/nar/gku1185

Éditeur(s) : Wiley-blackwell
Résumé : In bird species that have a high movement capacity, dispersal may connect subpopulations over vast geographical regions, with important consequences for the design of conservation management strategies. Here we used a molecular approach to infer the patterns and rates of dispersal among eight Mediterranean subpopulations of the endangered Bonelli's Eagle, based on 245 individuals screened at 17 microsatellite loci. There was moderate genetic differentiation between subpopulations sampled in the western (Iberia and Morocco) and eastern (Cyprus) Mediterranean, whereas differentiation among subpopulations in the former region was weak to moderate and followed a pattern of isolation by distance. Within the western Mediterranean, the small, peripheral and ecologically unique population of southwest Portugal had the lowest genetic diversity and the highest differentiation. The remaining subpopulations formed two loose clusters, one including Morocco and southwest and eastern Spain, and the other northeast Portugal and western and central Spain. Few recent migrants were detected, and they originated primarily from adjacent subpopulations. Our findings suggest that western Mediterranean Bonelli's Eagles may have a large-scale metapopulation structure, with subpopulations connected to some extent by distance-dependent dispersal, probably influenced by natal philopatry and the geographical configuration of subpopulations. The combination of marked ecological and genetic divergence suggests that the peripheral subpopulation of southwest Portugal may be regarded as a distinct management unit.
Ibis (0019-1019) (Wiley-blackwell), 2013-07 , Vol. 155 , N. 3 , P. 485-498

Droits : 2013 British Ornithologists’ Union
http://archimer.ifremer.fr/doc/00148/25924/24018.pdf
DOI:10.1111/ibi.12065
http://archimer.ifremer.fr/doc/00148/25924/

Éditeur(s) : HAL CCSD
Résumé : International audience
Semantic web standards, tools, ontologies and related technologies have considerably matured in the recent years. Nowadays, accessing a wide catalogue of biological, social, environmental, and ecological data sources helps stakeholders working on biodiversity to answer their complex questions. Will the real time access to web resources effectively support the definition of strategies to conserve and manage biodiversity? How might semantic web technologies help us to handle the complex and heterogeneous big data related to biodiversity? The workshop aims to identify the key challenges faced by the bioinformatics community, discuss potential solutions and identify the opportunities emerging from the trans-disciplinary interactions between Plant Science and Informatics experts. Therefore, we expect the bioinformatics experts to explain how they apply semantic web standards and tools to their scientific topic, from biology, agriculture, agro-ecology, genomics, environmental studies, to social sciences, citizen sciences. Research papers presenting various aspects of semantic web technologies applied to biodiversity data, ranging from position papers to implemented systems descriptions and their evaluation, will be selected. We are particularly interested in the use of the semantic technologies to design and develop systems that supports research on agricultural and wild biodiversity conservation and management for food security. Examples may include strategies for resilience to climate change pressures, sustainability of productive ecosystems, ecosystems services monitoring or territories management, rather than systems supporting only research on climate patterns or soil erosion.
http://hal-lirmm.ccsd.cnrs.fr/lirmm-00831757

lirmm-00831757
http://hal-lirmm.ccsd.cnrs.fr/lirmm-00831757
http://hal-lirmm.ccsd.cnrs.fr/lirmm-00831757/document

Éditeur(s) : HAL CCSD Thai Society of Higher Education Institutes on Environment
Résumé : International audience
Due to the high level of endemic species that they support and the high threats they are facing, such as unsustainable limestone quarrying, hunting and urbanization, limestone karsts are recognized as biodiversity hotspots needing urgent protection. The first aim of our study was to investigate the mammal rodent diversity of Thai limestone karsts. Our second aim was to examine the diversity at a finer scale than the species level (intraspecific biodiversity) using phylogeographic approaches. Therefore, we studied the phylogeographic structure of a threatened rodent, endemic to limestone karsts of Thailand, the Murinae Leopoldamys neilli. We sampled 76 limestone karsts in whole Thailand and live-trapped 444 rodents including 115 Leopoldamys neilli. Our study revealed an important rodent diversity in Thai limestone karsts. Besides endemic rodent species, karsts also host typical forest species to which they provide forest refugia in deforested regions. At the intraspecific level, our study revealed an unexpected high level of genetic differentiation within the rodent species L. neilli. As each limestone area of Thailand is characterized by a particular genetic lineage of L. neilli, the destruction of these karsts would lead to the disappearance of unique intraspecific strains not found elsewhere. Our results highlight the importance of protecting limestone habitats to preserve not only their interspecific but also intraspecific rodent diversity that is highly threatened as more than 20% of limestone karsts in Thailand have already been quarried. Management plans of limestone, a non-renewable resource, should urgently take into account this high biological importance of karsts.
The 1st EnvironmentAsia International Conference on "Environmental Supporting in Food and Energy Security: Crisis and Opportunity"
Bangkok, Thailand

ird-00714455
http://hal.ird.fr/ird-00714455
http://hal.ird.fr/ird-00714455/document
IRD : fdi:010056152

Éditeur(s) : HAL CCSD PeerJ
Résumé : International audience
The tiger shark Galeocerdo cuvier (Carcharhinidae) is a large elasmobranch suspected to have, as other apex predators, a keystone function in marine ecosystems and is currently considered Near Threatened (Red list IUCN). Knowledge on its ecology, which is crucial to design proper conservation and management plans, is very scarce. Here we describe the isolation of eight polymorphic microsatellite loci using 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries. Their characteristics were tested on a population of tiger shark (n = 101) from Reunion Island (SouthWestern Indian Ocean). All loci were polymorphic with a number of alleles ranging from two to eight. No null alleles were detected and no linkage disequilibrium was detected after Bonferroni correction. Observed and expected heterozygosities ranged from 0.03 to 0.76 and from 0.03 to 0.77, respectively. No locus deviated from Hardy-Weinberg equilibrium and the global F IS of the population was of 0.04 NS. Some of the eight loci developed here successfully cross-amplified in the bull shark Carcharhinus leucas (one locus), the spinner shark Carcharhinus brevipinna (four loci), the sandbar shark Carcharhinus plumbeus (five loci) and the scalloped hammerhead shark Sphyrna lewini (two loci). We also designed primers to amplify and sequence a mitochondrial marker, the control region. We sequenced 862 bp and found a low genetic diversity, with four polymorphic sites, a haplotype diversity of 0.15 and a nucleotide diversity of 2 × 10 −4 .
ISSN: 2167-8359

hal-01317961
https://hal.archives-ouvertes.fr/hal-01317961
https://hal.archives-ouvertes.fr/hal-01317961/document
https://hal.archives-ouvertes.fr/hal-01317961/file/Pirog_2016PeerJ_microsat_tiger_shark.pdf
DOI : 10.7717/peerj.2041

Éditeur(s) : HAL CCSD
Résumé : International audience
The epigenetic mark 5-hydroxymethylcytosine (5hmC) is a cytosine modification that is abundant in the central nervous system of mammals and which results from 5-methylcytosine oxidation by TET enzymes. Such a mark is suggested to play key roles in the regulation of chromatin structure and gene expression. However, its precise functions still remain poorly understood and information about its distribution in non-mammalian species is still lacking. Here, the distribution of 5hmC was investigated in the brain of adult zebrafish, African claw frog, and mouse in a comparative manner. We show that zebrafish neurons are endowed with high levels of 5hmC, whereas quiescent or proliferative neural progenitors show low to undetectable levels of the modified cytosine. In the brain of larval and juvenile Xenopus, 5hmC is also detected in neurons, while ventricular proliferative cells do not display this epigenetic mark. Similarly, 5hmC is enriched in neurons compared to neural progenitors of the ventricular zone in the mouse developing cortex. Interestingly, 5hmC colocalized with the methylated DNA binding protein MeCP2 and with the active chromatin histone modification H3K4me2 in mouse neurons. Taken together, our results show an evolutionarily conserved cerebral distribution of 5hmC between fish and tetrapods and reinforce the idea that 5hmC fulfills major functions in the control of chromatin activity in vertebrate neurons. J. Comp. Neurol. 525:478-497, 2017. © 2016 Wiley Periodicals, Inc.
Journal of Comparative Neurology

hal-01439354
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01439354
DOI : 10.1002/cne.24077
PUBMED : 27414756

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Vertebrate genomes contain around 20,000 protein-encoding genes, of which a large fraction is still not associated with specific functions. A major task in future genomics will thus be to assign physiological roles to all open reading frames revealed by genome sequencing. Here we show that C2orf62, a highly conserved protein with little homology to characterized proteins, is strongly expressed in testis in zebrafish and mammals, and in various types of ciliated cells during zebrafish development. By yeast two hybrid and GST pull-down, C2orf62 was shown to interact with TTC17, another uncharacterized protein. Depletion of either C2orf62 or TTC17 in human ciliated cells interferes with actin polymerization and reduces the number of primary cilia without changing their length. Zebrafish embryos injected with morpholinos against C2orf62 or TTC17, or with mRNA coding for the C2orf62 C-terminal part containing a RII dimerization/docking (R2D2) - like domain show morphological defects consistent with imperfect ciliogenesis. We provide here the first evidence for a C2orf62-TTC17 axis that would regulate actin polymerization and ciliogenesis.
ISSN: 1932-6203

hal-00955242
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00955242
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00955242/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00955242/file/C2orf62_and_TTC17-accepted.pdf
DOI : 10.1371/journal.pone.0086476

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Amelotin (AMTN) is an ameloblast-secreted protein that belongs to the secretory calcium-binding phosphoprotein family, which also includes the enamel matrix proteins amelogenin, ameloblastin and enamelin. Although AMTN is supposed to play an important role in enamel formation, data were long limited to the rodents, in which it is expressed during the maturation stage. Recent comparative studies in sauropsids and amphibians revealed that (i) AMTN was expressed earlier, i.e. as soon as ameloblasts are depositing the enamel matrix, and (ii) AMTN structure was different, a change which mostly resulted from an intraexonic splicing in the large exon 8 of an ancestral mammal. The present study was performed to know whether the differences in AMTN structure and expression in rodents compared to non-mammalian tetrapods dated back to an early ancestral mammal or were acquired later in mammalian evolution. We sequenced, assembled and screened the jaw transcriptome of a neonate opossum Monodelphis domestica, a marsupial. We found two AMTN transcripts. Variant 1, representing 70.8% of AMTN transcripts, displayed the structure known in rodents, whereas variant 2 (29.2%) exhibited the nonmammalian tetrapod structure. Then, we studied AMTN expression during amelogenesis in a neonate specimen. We obtained similar data as those reported in rodents. These findings indicate that more than 180 million years ago, before the divergence of marsupials and placentals, changes occurred in AMTN function and structure. The spatiotemporal expression was delayed to the maturation stage of amelogenesis and the intraexonic splicing gave rise to isoform 1, encoded by variant 1 and lacking the RGD motif. The ancestral isoform 2, housing the RGD, was initially conserved, as demonstrated here in a marsupial, then secondarily lost in the placental lineages. These findings bring new elements towards our understanding of the non-prismatic to prismatic enamel transition that occurred at the onset of mammals.
ISSN: 1932-6203

Droits : http://creativecommons.org/licenses/by/
hal-01233552
https://hal.archives-ouvertes.fr/hal-01233552
https://hal.archives-ouvertes.fr/hal-01233552/document
https://hal.archives-ouvertes.fr/hal-01233552/file/journal.pone.0133314.pdf
DOI : 10.1371/journal.pone.0133314

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
While the populations of large herbivores are being depleted in many tropical rainforests, the importance of their trophic role in the ecological functioning and biodiversity of these ecosystems is still not well evaluated. This is due to the outstanding plant diversity that they feed upon and the inherent difficulties involved in observing their elusive behaviour. Classically, the diet of elusive tropical herbivores is studied through the observation of browsing signs and macroscopic analysis of faeces or stomach contents. In this study, we illustrate that the original coupling of classic methods with genetic and ethnobotanical approaches yields information both about the diet diversity, the foraging modalities and the potential impact on vegetation of the largest terrestrial mammal of Amazonia, the lowland tapir. The study was conducted in the Guianan shield, where the ecology of tapirs has been less investigated. We identified 92 new species, 51 new genera and 13 new families of plants eaten by tapirs. We discuss the relative contribution of our different approaches, notably the contribution of genetic barcoding, used for the first time to investigate the diet of a large tropical mammal, and how local traditional ecological knowledge is accredited and valuable for research on the ecology of elusive animals.
ISSN: 1932-6203

halsde-00676374
https://hal.archives-ouvertes.fr/halsde-00676374
DOI : 10.1371/journal.pone.0025850
PUBMED : 21991372

Éditeur(s) : HAL CCSD CSIRO Publishing
Résumé : International audience
The present study assessed the occurrence of multiple paternity in four litters of bull shark Carcharhinus leucas (n¼5, 8, 9 and 11 embryos) sampled at Reunion Island in the Western Indian Ocean. Using 21 microsatellite loci, we revealed that two litters were generated from two sires each, demonstrating for the first time multiple paternity for this species. We also reported a high paternal skew (10 : 1 in Litter 1 and 7 : 1 in Litter 3), which may be because of postcopulatory or post-zygotic selection processes. These results contribute to a better understanding of the reproductive behaviour of the bull shark, which remains poorly documented. The present study must be expanded to assess the frequency of multiple paternity in this species, and to test for genetic or cryptic benefits (convenience polyandry), which is important for long-term conservation and management plans.
ISSN: 1323-1650

hal-01253775
https://hal.archives-ouvertes.fr/hal-01253775
https://hal.archives-ouvertes.fr/hal-01253775/document
https://hal.archives-ouvertes.fr/hal-01253775/file/Pirog%20et%20al.%20-%202015%20-%20First%20evidence%20of%20multiple%20paternity%20in%20the%20bull%20s_hal.pdf
DOI : 10.1071/mf15255

Éditeur(s) : HAL CCSD Springer
Résumé : International audience
We isolated and characterized 16 polymorphic microsatellite loci for Lytocarpia brevirostris (Aglaophe- niidae), a hydrozoan common in the tropical Indo-Pacific region. Four to 34 alleles per locus were detected at the Indo-Pacific scale. At the population level, observed (Ho) and expected (He) heterozygosities ranged across 0.100–0.625 and 0.097–0.597, respectively. Three markers showed significant deviation from Hardy–Weinberg equi- librium, all of them presenting null alleles. Linkage dis- equilibrium was detected in three pairs of loci among 120. These primers provide powerful tools for studying popu- lation genetic diversity and the implication of life cycle strategies on population differentiation in tropical hydro- zoans. This will be valuable for the conservation of coral reefs biodiversity and the design of marine protected areas.
ISSN: 1877-7252

hal-01185722
https://hal.archives-ouvertes.fr/hal-01185722
https://hal.archives-ouvertes.fr/hal-01185722/document
https://hal.archives-ouvertes.fr/hal-01185722/file/Postaire%20et%20al.%20-%202015%20-%20Isolation%20and%20characterisation%20of%2016%20microsatellit_hal.pdf
DOI : 10.1007/s12686-014-0407-1