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1. Convergent Evolution and Structural Adaptation to the Deep Ocean in the Protein-Folding Chaperonin CCTα

Author

Andrew F. Hugall, Alexandra Anh-Thu Weber, and Timothy D. O'Hara

Subjects
AcademicSubjects/SCI01140, 0106 biological sciences, Oceans and Seas, Protein subunit, In silico, Adaptation, Biological, Biology, 010603 evolutionary biology, 01 natural sciences, Chaperonin, Starfish, TCP-1, 03 medical and health sciences, positive selection, protein folding, Convergent evolution, Genetics, Animals, Denaturation (biochemistry), 14. Life underwater, Selection, Genetic, Gene, Ecology, Evolution, Behavior and Systematics, pressure adaptation, 030304 developmental biology, 0303 health sciences, TC P-1, Protein Stability, AcademicSubjects/SCI01130, Biological Evolution, protein stability, Evolutionary biology, Protein folding, Chaperonin Containing TCP-1, Biogenesis, Extreme Environments, Research Article, Echinodermata
Abstract

The deep ocean is the largest biome on Earth and yet it is among the least studied environments of our planet. Life at great depths requires several specific adaptations; however, their molecular mechanisms remain understudied. We examined patterns of positive selection in 416 genes from four brittle star (Ophiuroidea) families displaying replicated events of deep-sea colonization (288 individuals from 216 species). We found consistent signatures of molecular convergence in functions related to protein biogenesis, including protein folding and translation. Five genes were recurrently positively selected, including chaperonin-containing TCP-1 subunit α (CCTα), which is essential for protein folding. Molecular convergence was detected at the functional and gene levels but not at the amino-acid level. Pressure-adapted proteins are expected to display higher stability to counteract the effects of denaturation. We thus examined in silico local protein stability of CCTα across the ophiuroid tree of life (967 individuals from 725 species) in a phylogenetically corrected context and found that deep-sea-adapted proteins display higher stability within and next to the substrate-binding region, which was confirmed by in silico global protein stability analyses. This suggests that CCTα displays not only structural but also functional adaptations to deep-water conditions. The CCT complex is involved in the folding of ∼10% of newly synthesized proteins and has previously been categorized as a “cold-shock” protein in numerous eukaryotes. We thus propose that adaptation mechanisms to cold and deep-sea environments may be linked and highlight that efficient protein biogenesis, including protein folding and translation, is a key metabolic deep-sea adaptation.

Published
2020
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2. Repeated Evolution Versus Common Ancestry: Sex Chromosome Evolution in the Haplochromine CichlidPseudocrenilabrus philander

Author

Andrin Riss, Alexandra Anh-Thu Weber, Astrid Böhne, Michael Rechsteiner, Bernd Egger, Walter Salzburger, and Jelena Rajkov

Subjects
Male, 0106 biological sciences, Species complex, Lineage (evolution), Population, sex determination, Population genetics, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Cichlid, Genetics, Animals, 14. Life underwater, species complex, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, teleost fish, 0303 health sciences, education.field_of_study, Sex Chromosomes, biology, Phylogenetic tree, Pseudocrenilabrus philander, population genetics, Cichlids, Sex Determination Processes, biology.organism_classification, Biological Evolution, genome sequencing, Haplochromine, speciation, Evolutionary biology, Female, Research Article
Abstract

Why sex chromosomes turn over and remain undifferentiated in some taxa, whereas they degenerate in others, is still an area of ongoing research. The recurrent occurrence of homologous and homomorphic sex chromosomes in distantly related taxa suggests their independent evolution or continued recombination since their first emergence. Fishes display a great diversity of sex-determining systems. Here, we focus on sex chromosome evolution in haplochromines, the most species-rich lineage of cichlid fishes. We investigate sex-specific signatures in the Pseudocrenilabrus philander species complex, which belongs to a haplochromine genus found in many river systems and ichthyogeographic regions in northern, eastern, central, and southern Africa. Using whole-genome sequencing and population genetic, phylogenetic, and read-coverage analyses, we show that one population of P. philander has an XX–XY sex-determining system on LG7 with a large region of suppressed recombination. However, in a second bottlenecked population, we did not find any sign of a sex chromosome. Interestingly, LG7 also carries an XX–XY system in the phylogenetically more derived Lake Malawi haplochromine cichlids. Although the genomic regions determining sex are the same in Lake Malawi cichlids and P. philander, we did not find evidence for shared ancestry, suggesting that LG7 evolved as sex chromosome at least twice in haplochromine cichlids. Hence, our work provides further evidence for the labile nature of sex determination in fishes and supports the hypothesis that the same genomic regions can repeatedly and rapidly be recruited as sex chromosomes in more distantly related lineages.

Published
2019
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3. Immigrant and extrinsic hybrid inviability contribute to reproductive isolation between lake and river cichlid ecotypes

Author

Jelena, Rajkov, Alexandra Anh-Thu, Weber, Walter, Salzburger, and Bernd, Egger

Subjects
Ecotype, Male, Competitive Behavior, Reproductive Isolation, Behavior, Animal, Genetic Speciation, Reproduction, Cichlids, Lakes, Genetics, Population, Rivers, Animals, Hybridization, Genetic, Female, Ecosystem
Abstract

Understanding how reproductive barriers evolve and which barriers contribute to speciation requires the examination of organismal lineages that are still in the process of diversification and the study of the full range of reproductive barriers acting at different life stages. Lake and river ecotypes of the East African cichlid fish Astatotilapia burtoni show habitat-specific adaptations, despite different levels of genetic differentiation, and thus represent an ideal model to study the evolution of reproductive barriers. To evaluate the degree of reproductive isolation between genetically divergent lake and river populations, we performed a mesocosm mating experiment in a semi-natural setting at Lake Tanganyika. We assessed reproductive isolation in the presence of male-male competition by analyzing survival and growth rates of introduced adults and their reproductive success from genetic parentage of surviving offspring. The genetically divergent river population showed reduced fitness in terms of survival, growth rate, and mating success in a lake-like environment. Hybrid offspring between different populations showed intermediate survival consistent with extrinsic postzygotic reproductive barriers. Our results suggest that both prezygotic (immigrant inviability) and postzygotic reproductive barriers contribute to divergence, and highlight the value of assessing multiple reproductive barriers acting at different stages and in natural contexts to understand speciation mechanisms.

Published
2018

4. A multispecies approach reveals hot spots and cold spots of diversity and connectivity in invertebrate species with contrasting dispersal modes

Author

Bastien Mérigot, Anne Chenuil, Sophie Dubois, Jean-Baptiste Ledoux, Emilie Boissin, Abigail E. Cahill, Didier Aurelle, Alexandra Anh-Thu Weber, Zoheir Bouzaza, Emilie Egea, Olivier Chabrol, Aurélien De Jode, Romain David, CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Evolutionary Biology and Ecology of Algae (EBEA), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Pontificia Universidad Católica de Chile (UC)-Universidad Austral de Chile-Centre National de la Recherche Scientifique (CNRS), Université Abdelhamid Ibn Badis de Mostaganem, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), Institut de Mathématiques de Marseille (I2M), Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Aix Marseille Université (AMU), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Centro Interdisciplinar de Investigação Marinha e Ambiental (CIMAR/CIIMAR), Universidade do Porto, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de Recherche pour le Développement (IRD [France-Ouest]), University of Basel (Unibas), Aix-Marseille Université, Fundação para a Ciência e a Tecnologia (Portugal), Université Abdelhamid Ibn Badis Mostaganem, European Commission, Institut méditerranéen de biodiversité et d'écologie marine et continentale ( IMBE ), Université d'Avignon et des Pays de Vaucluse ( UAPV ) -Aix Marseille Université ( AMU ) -Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique ( CNRS ), Evolutionary Biology and Ecology of Algae ( EBEA ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Pontificia Universidad Católica de Chile-Universidad Austral de Chile-Centre National de la Recherche Scientifique ( CNRS ), Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de recherches insulaires et observatoire de l'environnement ( CRIOBE ), Université de Perpignan Via Domitia ( UPVD ) -École pratique des hautes études ( EPHE ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'Excellence CORAIL ( LabEX CORAIL ), Institut de Recherche pour le Développement ( IRD ) -Université des Antilles et de la Guyane ( UAG ) -École des hautes études en sciences sociales ( EHESS ) -École pratique des hautes études ( EPHE ) -Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ) -Université de la Réunion ( UR ) -Université de la Polynésie Française ( UPF ) -Université de Nouvelle Calédonie-Institut d'écologie et environnement, Institut de Mathématiques de Marseille ( I2M ), Aix Marseille Université ( AMU ) -Ecole Centrale de Marseille ( ECM ) -Centre National de la Recherche Scientifique ( CNRS ), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] ( ICM ), Consejo Superior de Investigaciones Científicas [Spain] ( CSIC ), Centro Interdisciplinar de Investigação Marinha e Ambiental ( CIMAR/CIIMAR ), Universidade do Porto [Porto], MARine Biodiversity Exploitation and Conservation ( UMR MARBEC ), Institut de Recherche pour le Développement ( IRD ) -Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Centre National de la Recherche Scientifique ( CNRS ), Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ), Institut de Recherche pour le Développement ( IRD [France-Ouest] ), University of Basel ( Unibas ), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Universidade do Porto = University of Porto, Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Universidad Austral de Chile-Centre National de la Recherche Scientifique (CNRS)-Pontificia Universidad Católica de Chile (UC), Université des Antilles (UA)-Institut d'écologie et environnement-Université de la Nouvelle-Calédonie (UNC)-Université de la Polynésie Française (UPF)-Université de La Réunion (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Université des Antilles et de la Guyane (UAG)-Institut de Recherche pour le Développement (IRD)

Subjects
0106 biological sciences, Aquatic Organisms, Population, Biology, Population structure, 010603 evolutionary biology, 01 natural sciences, Population density, Genetic diversity, Larvae, Mediterranean Sea, Genetics, Animals, 14. Life underwater, education, Species genetic diversity correlation, Ecology, Evolution, Behavior and Systematics, Invertebrate, education.field_of_study, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Geography, Ecology, Marine invertebrates, 010604 marine biology & hydrobiology, Marine larval ecology, Genetic Variation, Species diversity, Biodiversity, Dispersal, 15. Life on land, Invertebrates, [ SDV.GEN.GPO ] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Genetics, Population, 13. Climate action, Larva, Genetic structure, Biological dispersal, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Animal Distribution, human activities
Abstract

Cahill, Abigail E. ... et al.-- 15 pages, 5 figures, 4 tables, supporting information https://dx.doi.org/10.1111/mec.14389, data accessibility in GenBank (accession nos MG063882–MG064453), DataDryad https://doi.org/10.5061/dryad.dv4 mg, GitHub https://github.com/chaby/dana, Genetic diversity is crucial for species’ maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes via dispersal of gametes and larvae. Species with a larval period are expected to have more connected populations than those without larval dispersal. We assessed the relationship between measures of species and genetic diversity, and between dispersal ability and connectivity. We compiled data on genetic patterns and life history traits in nine species across five phyla. Sampling sites spanned 600 km in the northwest Mediterranean Sea and focused on a 50-km area near Marseilles, France. Comparative population genetic approaches yielded three main results. (i) Species without larvae showed higher levels of genetic structure than species with free-living larvae, but the role of larval type (lecithotrophic or planktotrophic) was negligible. (ii) A narrow area around Marseilles, subject to offshore advection, limited genetic connectivity in most species. (iii) We identified sites with significant positive contributions to overall genetic diversity across all species, corresponding with areas near low human population densities. In contrast, high levels of human activity corresponded with a negative contribution to overall genetic diversity. Genetic diversity within species was positively and significantly linearly related to local species diversity. Our study suggests that local contribution to overall genetic diversity should be taken into account for future conservation strategies, Funding was provided by DEVOTES (DEVelopment Of innovative Tools for understanding marine biodiversity and assessing good Environmental Status), funded by the European Union under the 7th FRAMEWORK Programme, “The Ocean of Tomorrow” (grant agreement no. 308392), www.devotes-project.eu, and by La Faculté des Sciences de la Nature et de la Vie de l’Université Abdelhamid Ibn Badis, Mostaganem, Algeria (ZB) and the Portuguese Foundation for Science and Technology (Fundação para a Ciência e a Tecnologia; FCT; Postdoctoral grant SFRH/BPD/74400/2010; JBL). This work is a contribution to Labex OT-Med (n° ANR-11-LABX-0061) and has received funding from Excellence Initiative of Aix-Marseille University - A*MIDEX, a French “Investissements d’Avenir” programme”

Published
2017
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5. Positive selection on sperm ion channels in a brooding brittle star: consequence of life-history traits evolution

Author

Nicolas Galtier, Anne Chenuil, Juan I. Montoya-Burgos, Laurent Abi-Rached, Aurélien Bernard, Alexandra Anh-Thu Weber, Institut de recherche sur la biologie de l'insecte ( IRBI ), Université de Tours-Centre National de la Recherche Scientifique ( CNRS ), Institut méditerranéen de biodiversité et d'écologie marine et continentale ( IMBE ), Université d'Avignon et des Pays de Vaucluse ( UAPV ) -Aix Marseille Université ( AMU ) -Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique ( CNRS ), University of Basel (Unibas), Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), University of Geneva [Switzerland], Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université de Genève = University of Geneva (UNIGE), and Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, 0301 basic medicine, Male, Species complex, Reproductive Isolation, sperm chemotaxis, Biology, Sperm chemotaxis, 010603 evolutionary biology, 01 natural sciences, sperm competition, Ion Channels, 03 medical and health sciences, ddc:590, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, marine invertebrate, Genetics, Animals, Selection, Genetic, education, Sperm competition, Ecology, Evolution, Behavior and Systematics, Sperm motility, education.field_of_study, Natural selection, Competition, Marine invertebrate, Genetic Variation, Reproductive isolation, Sperm receptor, Sperm, Spermatozoa, [ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Sympatry, 030104 developmental biology, Evolutionary biology, Fertilization, ion channel, Female, Ion channel, Transcriptome, transcriptome, Echinodermata
Abstract

International audience; Closely related species are key models to investigate mechanisms leading to reproductive isolation and early stages of diversification, also at the genomic level. The brittle star cryptic species complex Ophioderma longicauda encompasses the sympatric broadcast-spawning species C3 and the internal brooding species C5. Here, we used de novo transcriptome sequencing and assembly in two closely related species displaying contrasting reproductive modes to compare their genetic diversity and to investigate the role of natural selection in reproductive isolation. We reconstructed 20 146 and 22 123 genes for C3 and C5, respectively, and characterized a set of 12 229 orthologs. Genetic diversity was 1.5-2 times higher in C3 compared to C5, confirming that species with low parental investment display higher levels of genetic diversity. Forty-eight genes were the targets of positive diversifying selection during the evolution of the two species. Notably, two genes (NHE and TetraKCNG) are sperm-specific ion channels involved in sperm motility. Ancestral sequence reconstructions show that natural selection targeted the two genes in the brooding species. This may result from an adaptation to the novel environmental conditions surrounding sperm in the brooding species, either directly affecting sperm or via an increase in male/female conflict. This phenomenon could have promoted prezygotic reproductive isolation between C3 and C5. Finally, the sperm receptors to egg chemoattractants differed between C3 and C5 in the ligand-binding region. We propose that mechanisms of species-specific gamete recognition in brittle stars occur during sperm chemotaxis (sperm attraction towards the eggs), contrary to other marine invertebrates where prezygotic barriers to interspecific hybridization typically occur before sperm-egg fusion.

Published
2016
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6. Influence of the larval phase on connectivity: strong differences in the genetic structure of brooders and broadcasters in the Ophioderma longicauda species complex

Author

Sophie Valière, Bastien Mérigot, Anne Chenuil, Alexandra Anh-Thu Weber, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), European Project: 227799,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2008-1,ASSEMBLE(2009), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD)

Subjects
Genetic Markers, Species complex, life history evolution, Genotype, population genetics - empirical, education, Biology, DNA barcoding, DNA, Mitochondrial, Genetic variation, Genetics, Mediterranean Sea, Animals, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, Genetic diversity, Greece, Ecology, Marine larval ecology, Reproduction, echinoderms, Genetic Variation, Sequence Analysis, DNA, Biological Evolution, Introns, Phylogeography, Genetics, Population, Evolutionary biology, Genetic marker, Sympatric speciation, Larva, Genetic structure, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Transcriptome, Animal Distribution, human activities, Echinodermata
Abstract

International audience; Closely related species with divergent life history traits are excellent models to infer the role of such traits in genetic diversity and connectivity. Ophioderma longicauda is a brittle star species complex composed of different genetic clusters, including brooders and broadcasters. These species diverged very recently and some of them are sympatric and ecologically syntopic, making them particularly suitable to study the consequences of their trait differences. At the scale of the geographic distribution of the broadcasters (Mediterranean Sea and northeastern Atlantic), we sequenced the mitochondrial marker COI and genotyped an intron (i51) for 788 individuals. In addition, we sequenced 10 nuclear loci newly developed from transcriptome sequences, for six sympatric populations of brooders and broadcasters from Greece. At the large scale, we found a high genetic structure within the brooders (COI: 0.07 \textless F-ST \textless 0.65) and no polymorphism at the nuclear locus i51. In contrast, the broadcasters displayed lower genetic structure (0 \textless F-ST \textless 0.14) and were polymorphic at locus i51. At the regional scale, the multilocus analysis confirmed the contrasting genetic structure between species, with no structure in the broadcasters (global F-ST \textless 0.001) and strong structure in the brooders (global F-ST = 0.49), and revealed a higher genetic diversity in broadcasters. Our study showed that the lecithotrophic larval stage allows on average a 50-fold increase in migration rates, a 280-fold increase in effective size and a threefold to fourfold increase in genetic diversity. Our work, investigating complementary genetic markers on sympatric and syntopic taxa, highlights the strong impact of the larval phase on connectivity and genetic diversity.

Published
2015
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7. Genetic data, reproduction season and reproductive strategy data support the existence of biological species in Ophioderma longicauda

Author

Sabine Stöhr, Alexandra Anh-Thu Weber, Anne Chenuil, Swedish Museum of Natural History, Swedish Museum of Natural History (NRM), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), and Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS)

Subjects
Gene Flow, Male, Species complex, Mitochondrial DNA, Genotype, Lineage (evolution), media_common.quotation_subject, education, Zoology, Biology, DNA, Mitochondrial, General Biochemistry, Genetics and Molecular Biology, Gene flow, Monophyly, Brittle star, Sous-unité I de la cytochrome oxydase, Mediterranean Sea, Animals, 14. Life underwater, Ophiuroidea, Gonads, Espèces cryptiques, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Phylogeny, media_common, Cytochrome oxidase subunit I, General Immunology and Microbiology, Greece, Reproduction, General Medicine, Sequence Analysis, DNA, Brooding species, biology.organism_classification, Introns, Espèce incubante, [SDU]Sciences of the Universe [physics], Sympatric speciation, Fertilization, Cryptic species, Female, France, Seasons, EPIC, General Agricultural and Biological Sciences, Echinodermata
Abstract

Cryptic species are numerous in the marine environment. The brittle star Ophioderma longicauda is composed of six mitochondrial lineages, encompassing brooders, which form a monophyletic group, and broadcasters, from which the brooders are derived. To clarify the species limits within O. longicauda, we compared the reproductive status of the sympatric lineages L1 and L3 (defined after sequencing a portion of the mitochondrial gene COI) during the month of May in Greece. In addition, we genotyped a nuclear marker, intron i51. Each L3 female was brooding, whereas all L1 specimens displayed full gonads, suggesting temporal pre-zygotic isolation between brooders and broadcasters. Statistical differences were found among lineages in morphology and bathymetric distribution. Finally, the intron i51 was polymorphic in L1 (60 individuals), but monomorphic in L3 (109 individuals), confirming the absence of gene flow between brooders and broadcasters. In conclusion, the broadcasting lineage L1 and the brooding lineage L3 are different biological species., Les espèces cryptiques sont nombreuses dans l’environnement marin. L’ophiure Ophioderma longicauda est composée de six lignées mitochondriales, comprenant des incubants, qui forment un groupe monophylétique, et des individus à larves, desquels les incubants sont dérivés. Afin de clarifier les limites d’espèces chez O. longicauda, nous avons comparé l’état de reproduction des lignées sympatriques L1 et L3 (définies après séquençage d’une partie du gène mitochondrial COI) durant le mois de mai en Grèce. De plus, nous avons génotypé un marqueur nucléaire, l’intron i51. Chaque femelle L3 était incubante tandis que tous les individus L1 avaient les gonades pleines, suggérant un isolement pré-zygotique temporel entre les incubants et les individus à larves. Des différences statistiques de morphologie et de distribution bathymétrique ont été trouvées entre lignées. Finalement, l’intron i51 était polymorphe chez L1 (60 individus), mais monomorphe chez L3 (109 individus), confirmant l’absence de flux de gènes entre les incubants et dispersants. En conclusion, la lignée à larves L1 et la lignée incubante L3 sont des espèces biologiques différentes.

Published
2014
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8. Comparative population genomics in animals uncovers the determinants of genetic diversity

Author

Ylenia Chiari, Khalid Belkhir, Jonathan Romiguier, Sylvain Glémin, Nicolas Galtier, Alexandra Anh-Thu Weber, Nicolas Bierne, Georgia Tsagkogeorga, Lucy A. Weinert, Rémy Dernat, Camille Roux, Marion Ballenghien, Joao M. Lourenco, Philippe Gayral, Nicolas Faivre, Vincent Cahais, Benoit Nabholz, Etienne Loire, Laurent Duret, Anne Chenuil, Aurélien Bernard, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Lipides - Nutrition - Cancer (U866) (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon (ENSBANA), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Universidade do Porto, Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre d'économie de la Sorbonne (CES), Université Paris 1 Panthéon-Sorbonne (UP1)-Centre National de la Recherche Scientifique (CNRS), Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire d'Imagerie Biomédicale (LIB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Université Pierre et Marie Curie - Paris 6 (UPMC)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Service de Radiologie Vasculaire [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], School of Biological and Chemical Sciences, Queen Mary University of London (QMUL), Université Montpellier 2 - Sciences et Techniques (UM2), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Universidade do Porto = University of Porto, Laboratoire d'Imagerie Biomédicale [Paris] (LIB), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Centro de Investigac¸ao em Biodiversidade e Recursos Genéticos, Universidade do Porto, Centro de Investigaçao em Biodiversidade e Recursos Genéticos, Centre National de la Recherche Scientifique (CNRS)-Université Panthéon-Sorbonne (UP1), Inst Sci Evolut, Université Pierre et Marie Curie - Paris 6 (UPMC)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Pitié-Salpêtrière [APHP], Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Institut des Sciences de l'Evolution de Montpellier ( ISEM ), Université de Montpellier ( UM ) -Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique ( CNRS ), Institut de recherche sur la biologie de l'insecte ( IRBI ), Université de Tours-Centre National de la Recherche Scientifique ( CNRS ), Lipides - Nutrition - Cancer (U866) ( LNC ), Université de Bourgogne ( UB ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon ( ENSBANA ), Institut méditerranéen de biodiversité et d'écologie marine et continentale ( IMBE ), Centre National de la Recherche Scientifique ( CNRS ) -Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université ( AMU ) -Université d'Avignon et des Pays de Vaucluse ( UAPV ), Centre d'économie de la Sorbonne ( CES ), Université Panthéon-Sorbonne ( UP1 ) -Centre National de la Recherche Scientifique ( CNRS ), Ecole Polytechnique Fédérale de Lausanne ( EPFL ), Université Montpellier 2 - Sciences et Techniques ( UM2 ), Laboratoire d'Imagerie Biomédicale ( LIB ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition ( ICAN ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Assistance publique - Hôpitaux de Paris (AP-HP)-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -CHU Pitié-Salpêtrière [APHP], Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Pitié-Salpêtrière [APHP], Queen Mary University of London ( QMUL ), Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bourgogne (UB)-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon (ENSBANA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement

Subjects
0106 biological sciences, Conservation genetics, Species complex, Population, Population genetics, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, 010603 evolutionary biology, 01 natural sciences, Population genomics, Evolution, Molecular, 03 medical and health sciences, Animals, Genetic variability, education, Phylogeny, 030304 developmental biology, [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, 0303 health sciences, education.field_of_study, Genetic diversity, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Multidisciplinary, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Genome, Ecology, Genetic Variation, Genomics, L10 - Génétique et amélioration des animaux, [ SDV.GEN.GPO ] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Genetics, Population, Evolutionary biology, L20 - Écologie animale, Gene pool, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, human activities
Abstract

International audience; Genetic diversity is the amount of variation observed between DNA sequences from distinct individuals of a given species. This pivotal concept of population genetics has implications for species health, domest-ication, management and conservation. Levels of genetic diversity seem to vary greatly in natural populations and species, but the determinants of this variation, and particularly the relative influences of species biology and ecology versus population history, are still largely mysterious 1,2. Here we show that the diversity of a species is predictable , and is determined in the first place by its ecological strategy. We investigated the genome-wide diversity of 76 non-model animal species by sequencing the transcriptome of two to ten individuals in each species. The distribution of genetic diversity between species revealed no detectable influence of geographic range or invasive status but was accurately predicted by key species traits related to parental investment: long-lived or low-fecundity species with brooding ability were genetically less diverse than short-lived or highly fecund ones. Our analysis demonstrates the influence of long-term life-history strategies on species response to short-term environmental perturbations, a result with immediate implications for conservation policies. Since the early studies of evolutionary genetics, there has been no understanding of how and why genetic diversity levels vary between species. This old puzzle, considered four decades ago as 'the central problem in population genetics'

Published
2014
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9. Thermotolerance and regeneration in the brittle star species complex Ophioderma longicauda: A preliminary study comparing lineages and Mediterranean basins

Author

Alexandra Anh-Thu Weber, Anne Chenuil, Sam Dupont, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), and Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Mediterranean climate, Species complex, Hot Temperature, Survival, Lineage (evolution), Biology, Global Warming, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Starfish, Mediterranean sea, Brittle star, Animals, Regeneration, 14. Life underwater, Regeneration (ecology), [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Geography, Greece, General Immunology and Microbiology, Resistance (ecology), Mediterranean Region, Ecology, 010604 marine biology & hydrobiology, Temperature, General Medicine, biology.organism_classification, Kinetics, [SDU]Sciences of the Universe [physics], France, General Agricultural and Biological Sciences, Autotomy, Algorithms
Abstract

International audience; Global warming is expected to change marine species distributions; it is thus critical to understand species current thermotolerance. The brittle star species complex Ophioderma longicauda comprises a broadcast spawning lineage L1 and a brooding lineage L3. We collected L1 specimens from Marseilles and Crete, and L3 specimens from Crete. We monitored survival, autotomy and arm regeneration at 17,26 and 30 degrees C during 14 weeks. Globally O. longicauda showed good resistance to elevated temperatures compared to other published studies on ophiuroids. The L3 sample displayed a better thermotolerance than L1 samples. Yet, more research is needed to establish whether these differences are due to lineages, geographic origin, or random effects. We provided for the first time individual regeneration trajectories, and showed that regeneration followed a growth curve and was highly influenced by temperature in both lineages. Our results highlight the importance of taking into account the presence of cryptic species when studying the potential effects of global warming. (C) 2013 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved.

Published
2013
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