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Oury N, Noël C, Mona S, Aurelle D, Magalon H. From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals. Mol Phylogenet Evol 2023; 184:107803. [PMID: 37120114 DOI: 10.1016/j.ympev.2023.107803] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/06/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
With the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data is available due to the small number of currently available markers and obscures species boundaries. Difficulties in inferring gene trees and morphological incongruences further blur the study and conservation of these organisms. Yet, can genomics alone be used to delimit species? Here, focusing on the coral genus Pocillopora, whose colonies play key roles in Indo-Pacific reef ecosystems but have challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNP) were first used to resolve Pocillopora phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to other lines of evidence based on genetic, morphology, biogeography and symbiont associations. Out of 21 species hypotheses delimited by genomics, 13 were strongly supported by all approaches, while six could represent either undescribed species or nominal species that have been synonymised incorrectly. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine Pocillopora species boundaries, (2) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, (3) the requirement of molecular identification when species identity of colonies is absolutely necessary to interpret results, as morphology can blur species identification in the field, and (4) the need for a taxonomic revision of the genus Pocillopora. These results give new insights into the usefulness of multiple criteria for resolving Pocillopora, and more widely, scleractinian species boundaries, and will ultimately contribute to the taxonomic revision of this genus and the conservation of its species.
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Affiliation(s)
- Nicolas Oury
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, St Denis, La Réunion, France; Laboratoire Cogitamus, Paris, France.
| | - Cyril Noël
- IFREMER - IRSI - Service de Bioinformatique (SeBiMER), Plouzané, France
| | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, EPHE-PSL, Université PSL, CNRS, SU, UA, Paris, France; EPHE, PSL Research University, Paris, France; Laboratoire d'Excellence CORAIL, Perpignan, France
| | - Didier Aurelle
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, EPHE-PSL, Université PSL, CNRS, SU, UA, Paris, France; Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, St Denis, La Réunion, France; Laboratoire Cogitamus, Paris, France; Laboratoire d'Excellence CORAIL, Perpignan, France
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2
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Coelho MAG, Pearson GA, Boavida JRH, Paulo D, Aurelle D, Arnaud‐Haond S, Gómez‐Gras D, Bensoussan N, López‐Sendino P, Cerrano C, Kipson S, Bakran‐Petricioli T, Ferretti E, Linares C, Garrabou J, Serrão EA, Ledoux J. Not out of the Mediterranean: Atlantic populations of the gorgonian Paramuricea clavata are a separate sister species under further lineage diversification. Ecol Evol 2023; 13:e9740. [PMID: 36789139 PMCID: PMC9912747 DOI: 10.1002/ece3.9740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/31/2023] Open
Abstract
The accurate delimitation of species boundaries in nonbilaterian marine taxa is notoriously difficult, with consequences for many studies in ecology and evolution. Anthozoans are a diverse group of key structural organisms worldwide, but the lack of reliable morphological characters and informative genetic markers hampers our ability to understand species diversification. We investigated population differentiation and species limits in Atlantic (Iberian Peninsula) and Mediterranean lineages of the octocoral genus Paramuricea previously identified as P. clavata. We used a diverse set of molecular markers (microsatellites, RNA-seq derived single-copy orthologues [SCO] and mt-mutS [mitochondrial barcode]) at 49 locations. Clear segregation of Atlantic and Mediterranean lineages was found with all markers. Species-tree estimations based on SCO strongly supported these two clades as distinct, recently diverged sister species with incomplete lineage sorting, P. cf. grayi and P. clavata, respectively. Furthermore, a second putative (or ongoing) speciation event was detected in the Atlantic between two P. cf. grayi color morphotypes (yellow and purple) using SCO and supported by microsatellites. While segregating P. cf. grayi lineages showed considerable geographic structure, dominating circalittoral communities in southern (yellow) and western (purple) Portugal, their occurrence in sympatry at some localities suggests a degree of reproductive isolation. Overall, our results show that previous molecular and morphological studies have underestimated species diversity in Paramuricea occurring in the Iberian Peninsula, which has important implications for conservation planning. Finally, our findings validate the usefulness of phylotranscriptomics for resolving evolutionary relationships in octocorals.
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Affiliation(s)
- Márcio A. G. Coelho
- Centre for Marine Sciences (CCMAR)University of AlgarveFaroPortugal,MARE – Marine and Environmental Sciences CentreISPA‐Instituto UniversitárioLisboaPortugal
| | | | | | - Diogo Paulo
- Centre for Marine Sciences (CCMAR)University of AlgarveFaroPortugal
| | - Didier Aurelle
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIOMarseilleFrance,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRSSorbonne UniversitéParisFrance
| | - Sophie Arnaud‐Haond
- MARBEC (Marine Biodiversity, Exploitation and Conservation)Univ. Montpellier, IFREMER, CNRS, IRDSète CedexFrance
| | - Daniel Gómez‐Gras
- Hawai‘i Institute of Marine BiologyUniversity of Hawai‘i at MānoaKaneoheHawaiiUSA,Departament de Biologia Evolutiva, Ecologia i Ciències AmbientalsUniversitat de Barcelona (UB)BarcelonaSpain,Institut de Recerca de la Biodiversitat (IRBio)Universitat de Barcelona (UB)BarcelonaSpain
| | - Nathaniel Bensoussan
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIOMarseilleFrance,Departament de Biologia MarinaInstitut de Ciències del Mar (CSIC)BarcelonaSpain
| | - Paula López‐Sendino
- Departament de Biologia MarinaInstitut de Ciències del Mar (CSIC)BarcelonaSpain
| | - Carlo Cerrano
- Dipartimento di Scienze della Vita e dell’Ambiente (DiSVA)Università Politecnica delle MarcheAnconaItaly,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomeItaly,Stazione Zoologica Anton DohrnNaplesItaly,Fano Marine CenterFanoItaly
| | - Silvija Kipson
- Department of Biology, Faculty of ScienceUniversity of ZagrebZagrebCroatia,SEAFAN – Marine Research & ConsultancyZagrebCroatia
| | | | - Eliana Ferretti
- Studio Associato GAIA s.n.c.GenoaItaly,Institute of Marine ScienceThe University of AucklandAucklandNew Zealand
| | - Cristina Linares
- Departament de Biologia Evolutiva, Ecologia i Ciències AmbientalsUniversitat de Barcelona (UB)BarcelonaSpain,Institut de Recerca de la Biodiversitat (IRBio)Universitat de Barcelona (UB)BarcelonaSpain
| | - Joaquim Garrabou
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIOMarseilleFrance,Departament de Biologia MarinaInstitut de Ciències del Mar (CSIC)BarcelonaSpain
| | - Ester A. Serrão
- Centre for Marine Sciences (CCMAR)University of AlgarveFaroPortugal,CIBIO/InBIO‐Centro de Investigação em Biodiversidade e Recursos GenéticosVairãoPortugal
| | - Jean‐Baptiste Ledoux
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e AmbientalUniversidade do PortoPortoPortugal
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Aurelle D, Thomas S, Albert C, Bally M, Bondeau A, Boudouresque C, Cahill AE, Carlotti F, Chenuil A, Cramer W, Davi H, De Jode A, Ereskovsky A, Farnet A, Fernandez C, Gauquelin T, Mirleau P, Monnet A, Prévosto B, Rossi V, Sartoretto S, Van Wambeke F, Fady B. Biodiversity, climate change, and adaptation in the Mediterranean. Ecosphere 2022. [DOI: 10.1002/ecs2.3915] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Didier Aurelle
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO Marseille France
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS Sorbonne Université, EPHE Paris France
| | - Séverine Thomas
- Aix Marseille Université, Labex‐OT‐Med Aix‐en‐Provence France
| | - Cécile Albert
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | - Marc Bally
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO Marseille France
| | - Alberte Bondeau
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | | | | | - François Carlotti
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO Marseille France
| | - Anne Chenuil
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | - Wolfgang Cramer
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | - Hendrik Davi
- INRAE, Ecologie des Forêts Méditerranéennes (URFM) Avignon France
| | - Aurélien De Jode
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
- Department of Marine Sciences‐Tjärnö University of Gothenburg, Tjärnö Marine Laboratory Gothenburg Sweden
| | - Alexander Ereskovsky
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
- Saint‐Petersburg State University St. Petersburg Russia
| | - Anne‐Marie Farnet
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | | | - Thierry Gauquelin
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | - Pascal Mirleau
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE Marseille France
| | | | | | - Vincent Rossi
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO Marseille France
| | | | - France Van Wambeke
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO Marseille France
| | - Bruno Fady
- INRAE, Ecologie des Forêts Méditerranéennes (URFM) Avignon France
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Reynes L, Thibaut T, Mauger S, Blanfuné A, Holon F, Cruaud C, Couloux A, Valero M, Aurelle D. Genomic signatures of clonality in the deep water kelp Laminaria rodriguezii. Mol Ecol 2021; 30:1806-1822. [PMID: 33629449 DOI: 10.1111/mec.15860] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/17/2022]
Abstract
The development of population genomic approaches in non-model species allows for renewed studies of the impact of reproductive systems and genetic drift on population diversity. Here, we investigate the genomic signatures of partial clonality in the deep water kelp Laminaria rodriguezii, known to reproduce by both sexual and asexual means. We compared these results with the species Laminaria digitata, a closely related species that differs by different traits, in particular its reproductive mode (no clonal reproduction). We analysed genome-wide variation with dd-RAD sequencing using 4,077 SNPs in L. rodriguezii and 7,364 SNPs in L. digitata. As predicted for partially clonal populations, we show that the distribution of FIS within populations of L. rodriguezii is shifted toward negative values, with a high number of loci showing heterozygote excess. This finding is the opposite of what we observed within sexual populations of L. digitata, characterized by a generalized deficit in heterozygotes. Furthermore, we observed distinct distributions of FIS among populations of L. rodriguezii, which is congruent with the predictions of theoretical models for different levels of clonality and genetic drift. These findings highlight that the empirical distribution of FIS is a promising feature for the genomic study of asexuality in natural populations. Our results also show that the populations of L. rodriguezii analysed here are genetically differentiated and probably isolated. Our study provides a conceptual framework to investigate partial clonality on the basis of RAD-sequencing SNPs. These results could be obtained without any reference genome, and are therefore of interest for various non-model species.
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Affiliation(s)
- Lauric Reynes
- CNRS, IRD, MIO, Aix Marseille Université, Université de Toulon, Marseille, France
| | - Thierry Thibaut
- CNRS, IRD, MIO, Aix Marseille Université, Université de Toulon, Marseille, France
| | - Stéphane Mauger
- IRL 3614, Evolutionary Biology and Ecology of Algae, CNRS, UC, UACH, Sorbonne Université, Roscoff, France
| | - Aurélie Blanfuné
- CNRS, IRD, MIO, Aix Marseille Université, Université de Toulon, Marseille, France
| | | | - Corinne Cruaud
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Arnaud Couloux
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Myriam Valero
- IRL 3614, Evolutionary Biology and Ecology of Algae, CNRS, UC, UACH, Sorbonne Université, Roscoff, France
| | - Didier Aurelle
- CNRS, IRD, MIO, Aix Marseille Université, Université de Toulon, Marseille, France
- Institut de Systématique Évolution Biodiversité (ISYEB, UMR 7205), Muséum National d'Histoire Naturelle, CNRS, EPHE, Sorbonne Université, Paris, France
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Aurelle D, Pante E, Ledoux JB, Sartoretto S. Advances on the phylogenetic placement of the enigmatic octocoral Dendrobrachia Brook 1889. Zootaxa 2019; 4674:zootaxa.4674.1.6. [PMID: 31716023 DOI: 10.11646/zootaxa.4674.1.6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Indexed: 11/04/2022]
Abstract
The monogeneric family Dendrobrachiidae has been a taxonomic curiosity since its original description in 1889. Using one nuclear (18S) and two mitochondrial (mtMutS and cox1) genes, the phylogenetic placement of Dendrobrachiidae within the Octocorallia was investigated based on recently-collected specimens and museum collections. In particular, the relationship between Dendrobrachia and its suspected close allies from the Chrysogorgiidae and Ifalukellidae was examined. Phylogenetic inferences based on nuclear 18S sequences were inconclusive. On the basis of mitochondrial cox1 and mtMutS, the hypothesis that Dendrobrachia is closely related to the Chrysogorgiidae or the Ifalukellidae could be rejected with confidence. Dendrobrachia appeared distantly related to all octocoral groups considered here. However, the phylogenetic placement of Dendrobrachia could not be further clearly resolved.
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Affiliation(s)
- Didier Aurelle
- Aix Marseille Univ., Universite de Toulon, CNRS, IRD, MIO UM 110 , 13288, Marseille, France. Aix Marseille Univ, Avignon Universit, CNRS, IRD, IMBE, Marseille, France.
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Ody A, Thibaut T, Berline L, Changeux T, André JM, Chevalier C, Blanfuné A, Blanchot J, Ruitton S, Stiger-Pouvreau V, Connan S, Grelet J, Aurelle D, Guéné M, Bataille H, Bachelier C, Guillemain D, Schmidt N, Fauvelle V, Guasco S, Ménard F. From In Situ to satellite observations of pelagic Sargassum distribution and aggregation in the Tropical North Atlantic Ocean. PLoS One 2019; 14:e0222584. [PMID: 31527915 PMCID: PMC6748567 DOI: 10.1371/journal.pone.0222584] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 09/03/2019] [Indexed: 11/18/2022] Open
Abstract
The present study reports on observations carried out in the Tropical North Atlantic in summer and autumn 2017, documenting Sargassum aggregations using both ship-deck observations and satellite sensor observations at three resolutions (MSI-10 m, OLCI-300 m, VIIRS-750 m and MODIS-1 km). Both datasets reported that in summer, Sargassum aggregations were mainly observed off Brazil and near the Caribbean Islands, while they accumulated near the African coast in autumn. Based on in situ observations, we propose a five-class typology allowing standardisation of the description of in situ Sargassum raft shapes and sizes. The most commonly observed Sargassum raft type was windrows, but large rafts composed of a quasi-circular patch hundreds of meters wide were also observed. Satellite imagery showed that these rafts formed larger Sargassum aggregations over a wide range of scales, with smaller aggregations (of tens of m2 area) nested within larger ones (of hundreds of km2). Match-ups between different satellite sensors and in situ observations were limited for this dataset, mainly because of high cloud cover during the periods of observation. Nevertheless, comparisons between the two datasets showed that satellite sensors successfully detected Sargassum abundance and aggregation patterns consistent with in situ observations. MODIS and VIIRS sensors were better suited to describing the Sargassum aggregation distribution and dynamics at Atlantic scale, while the new sensors, OLCI and MSI, proved their ability to detect Sargassum aggregations and to describe their (sub-) mesoscale nested structure. The high variability in raft shape, size, thickness, depth and biomass density observed in situ means that caution is called for when using satellite maps of Sargassum distribution and biomass estimation. Improvements would require additional in situ and airborne observations or very high-resolution satellite imagery.
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Affiliation(s)
- Anouck Ody
- Aix-Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Thierry Thibaut
- Aix-Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Léo Berline
- Aix-Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Thomas Changeux
- Aix-Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Jean-Michel André
- Aix-Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Cristèle Chevalier
- Aix-Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Aurélie Blanfuné
- Aix-Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Jean Blanchot
- Aix-Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Sandrine Ruitton
- Aix-Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Valérie Stiger-Pouvreau
- Université de Bretagne Occidentale (UBO), Institut Universitaire Européen de la Mer (IUEM), LEMAR UMR 6539, Technopôle Brest-Iroise, Plouzané, France
| | - Solène Connan
- Université de Bretagne Occidentale (UBO), Institut Universitaire Européen de la Mer (IUEM), LEMAR UMR 6539, Technopôle Brest-Iroise, Plouzané, France
| | - Jacques Grelet
- IRD DR-OUEST, US191 IMAGO, Technopole de Brest-Iroise—Site de la Pointe du Diable, Plouzané, France
| | - Didier Aurelle
- Aix-Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Mathilde Guéné
- Université des Antilles, UMR BOREA, Campus de Fouillole, BP 592, Pointe-à-Pitre, Guadeloupe, France
| | | | - Céline Bachelier
- IRD DR-OUEST, US191 IMAGO, Technopole de Brest-Iroise—Site de la Pointe du Diable, Plouzané, France
| | - Dorian Guillemain
- Aix Marseille Univ, CNRS, IRD, IRSTEA, OSU PYTHEAS, Marseille, France
| | - Natascha Schmidt
- Aix-Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Vincent Fauvelle
- Aix-Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Sophie Guasco
- Aix-Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Frédéric Ménard
- Aix-Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
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Brener-Raffalli K, Clerissi C, Vidal-Dupiol J, Adjeroud M, Bonhomme F, Pratlong M, Aurelle D, Mitta G, Toulza E. Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato. Microbiome 2018; 6:39. [PMID: 29463295 PMCID: PMC5819220 DOI: 10.1186/s40168-018-0423-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 02/11/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Although the term holobiont has been popularized in corals with the advent of the hologenome theory of evolution, the underlying concepts are still a matter of debate. Indeed, the relative contribution of host and environment and especially thermal regime in shaping the microbial communities should be examined carefully to evaluate the potential role of symbionts for holobiont adaptation in the context of global changes. We used the sessile, long-lived, symbiotic and environmentally sensitive reef-building coral Pocillopora damicornis to address these issues. RESULTS We sampled Pocillopora damicornis colonies corresponding to two different mitochondrial lineages in different geographic areas displaying different thermal regimes: Djibouti, French Polynesia, New Caledonia, and Taiwan. The community composition of bacteria and the algal endosymbiont Symbiodinium were characterized using high-throughput sequencing of 16S rRNA gene and internal transcribed spacer, ITS2, respectively. Bacterial microbiota was very diverse with high prevalence of Endozoicomonas, Arcobacter, and Acinetobacter in all samples. While Symbiodinium sub-clade C1 was dominant in Taiwan and New Caledonia, D1 was dominant in Djibouti and French Polynesia. Moreover, we also identified a high background diversity (i.e., with proportions < 1%) of A1, C3, C15, and G Symbiodinum sub-clades. Using redundancy analyses, we found that the effect of geography was very low for both communities and that host genotypes and temperatures differently influenced Symbiodinium and bacterial microbiota. Indeed, while the constraint of host haplotype was higher than temperatures on bacterial composition, we showed for the first time a strong relationship between the composition of Symbiodinium communities and minimal sea surface temperatures. CONCLUSION Because Symbiodinium assemblages are more constrained by the thermal regime than bacterial communities, we propose that their contribution to adaptive capacities of the holobiont to temperature changes might be higher than the influence of bacterial microbiota. Moreover, the link between Symbiodinium community composition and minimal temperatures suggests low relative fitness of clade D at lower temperatures. This observation is particularly relevant in the context of climate change, since corals will face increasing temperatures as well as much frequent abnormal cold episodes in some areas of the world.
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Affiliation(s)
- Kelly Brener-Raffalli
- IHPE, UMR 5244, University of Perpignan Via Domitia, CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Camille Clerissi
- IHPE, UMR 5244, University of Perpignan Via Domitia, CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Jeremie Vidal-Dupiol
- IHPE, UMR 5244, University of Perpignan Via Domitia, CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Mehdi Adjeroud
- ENTROPIE, UMR 9220 & Laboratoire d’Excellence CORAIL, IRD, University of Perpignan Via Domitia, Perpignan, France
| | - François Bonhomme
- ISEM, UMR 5554, CNRS, University of Montpellier, IRD, EPHE, Sète, France
| | - Marine Pratlong
- IMBE, UMR 7263, Aix Marseille University, CNRS, IRD, Avignon University, Marseille, France
| | - Didier Aurelle
- IMBE, UMR 7263, Aix Marseille University, CNRS, IRD, Avignon University, Marseille, France
| | - Guillaume Mitta
- IHPE, UMR 5244, University of Perpignan Via Domitia, CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Eve Toulza
- IHPE, UMR 5244, University of Perpignan Via Domitia, CNRS, IFREMER, University of Montpellier, Perpignan, France
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8
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Cahill AE, De Jode A, Dubois S, Bouzaza Z, Aurelle D, Boissin E, Chabrol O, David R, Egea E, Ledoux JB, Mérigot B, Weber AAT, Chenuil A. A multispecies approach reveals hot spots and cold spots of diversity and connectivity in invertebrate species with contrasting dispersal modes. Mol Ecol 2017; 26:6563-6577. [PMID: 29087018 DOI: 10.1111/mec.14389] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 09/18/2017] [Indexed: 12/18/2022]
Abstract
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.
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Affiliation(s)
- Abigail E Cahill
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France.,Biology Department, Albion College, Albion, MI, USA
| | - Aurélien De Jode
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Sophie Dubois
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Zoheir Bouzaza
- Département de Biologie, Faculté des Sciences de la Nature et de la Vie, Université Abdelhamid Ibn Badis, Mostaganem, Algérie
| | - Didier Aurelle
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
| | - Olivier Chabrol
- CNRS, Centrale Marseille, I2M, UMR7373, Aix-Marseille Université, Marseille, France
| | - Romain David
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Emilie Egea
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Jean-Baptiste Ledoux
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal.,Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Bastien Mérigot
- UMR MARBEC (CNRS, Ifremer, IRD, UM), Université de Montpellier, Sète, France
| | - Alexandra Anh-Thu Weber
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France.,Zoological Institute, University of Basel, Basel, Switzerland
| | - Anne Chenuil
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
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9
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Poliseno A, Feregrino C, Sartoretto S, Aurelle D, Wörheide G, McFadden CS, Vargas S. Comparative mitogenomics, phylogeny and evolutionary history of Leptogorgia (Gorgoniidae). Mol Phylogenet Evol 2017; 115:181-189. [PMID: 28782594 DOI: 10.1016/j.ympev.2017.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/05/2017] [Accepted: 08/03/2017] [Indexed: 10/19/2022]
Abstract
Molecular analyses of the ecologically important gorgonian octocoral genus Leptogorgia are scant and mostly deal with few species from restricted geographical regions. Here we explore the phylogenetic relationships and the evolutionary history of Leptogorgia using the complete mitochondrial genomes of six Leptogorgia species from different localities in the Atlantic, Mediterranean and eastern Pacific as well as four other genera of Gorgoniidae and Plexauridae. Our mitogenomic analyses showed high inter-specific diversity, variable nucleotide substitution rates and, for some species, novel genomic features such as ORFs of unknown function. The phylogenetic analyses using complete mitogenomes and an extended mtMutS dataset recovered Leptogorgia as polyphyletic, and the species considered in the analyses were split into two defined groups corresponding to different geographic regions, namely the eastern Pacific and the Atlantic-Mediterranean. Our phylogenetic analysis based on mtMutS also showed a clear separation between the eastern Atlantic and South African Leptogorgia, suggesting the need of a taxonomic revision for these forms. A time-calibrated phylogeny showed that the separation of eastern Pacific and western Atlantic species started ca. 20Mya and suggested a recent divergence for eastern Pacific species and for L. sarmentosa-L. capverdensis. Our results also revealed high inter-specific diversity among eastern Atlantic and South African species, highlighting a potential role of the geographical diversification processes and geological events occurring during the last 30Ma in the Atlantic on the evolutionary history of these organisms.
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Affiliation(s)
- Angelo Poliseno
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Straße 10, 80333 München, Germany.
| | - Christian Feregrino
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Straße 10, 80333 München, Germany.
| | - Stéphane Sartoretto
- IFREMER, Z.P: de Brègaillon, CS 20330, 83507 La Seyne-sur-mer Cedex, France.
| | - Didier Aurelle
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, 13007 Marseille, France.
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Straße 10, 80333 München, Germany; GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Straße 10, 80333 München, Germany; Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Straße 10, 80333 München, Germany.
| | | | - Sergio Vargas
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Straße 10, 80333 München, Germany.
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10
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Marzouk Z, Aurelle D, Said K, Chenuil A. Cryptic lineages and high population genetic structure in the exploited marine snail Hexaplex trunculus (Gastropoda: Muricidae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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11
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Crisci C, Ledoux JB, Mokhtar-Jamaï K, Bally M, Bensoussan N, Aurelle D, Cebrian E, Coma R, Féral JP, La Rivière M, Linares C, López-Sendino P, Marschal C, Ribes M, Teixidó N, Zuberer F, Garrabou J. Regional and local environmental conditions do not shape the response to warming of a marine habitat-forming species. Sci Rep 2017; 7:5069. [PMID: 28698582 PMCID: PMC5505982 DOI: 10.1038/s41598-017-05220-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 05/25/2017] [Indexed: 11/20/2022] Open
Abstract
The differential response of marine populations to climate change remains poorly understood. Here, we combine common garden thermotolerance experiments in aquaria and population genetics to disentangle the factors driving the population response to thermal stress in a temperate habitat-forming species: the octocoral Paramuricea clavata. Using eight populations separated from tens of meters to hundreds of kilometers, which were differentially impacted by recent mortality events, we identify 25 °C as a critical thermal threshold. After one week of exposure at this temperature, seven of the eight populations were affected by tissue necrosis and after 30 days of exposure at this temperature, the mean % of affected colonies increased gradually from 3 to 97%. We then demonstrate the weak relation between the observed differential phenotypic responses and the local temperature regimes experienced by each population. A significant correlation was observed between these responses and the extent of genetic drift impacting each population. Local adaptation may thus be hindered by genetic drift, which seems to be the main driver of the differential response. Accordingly, conservation measures should promote connectivity and control density erosion in order to limit the impact of genetic drift on marine populations facing climate change.
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Affiliation(s)
- C Crisci
- Polo de Desarrollo Universitario Modelización y Análisis de Recursos Naturales, Centro Universitario Regional del Este, Universidad de la República, Rocha, 27000, Uruguay.
| | - J-B Ledoux
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, 4050-123, Portugal
- Institute of Marine Sciences (ICM-CSIC), Barcelona, 08003, Spain
| | - K Mokhtar-Jamaï
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, Station Marine d'Endoume, Marseille, 13007, France
| | - M Bally
- Aix-Marseille Université, Mediterranean Institute of Oceanography (M I O), Université de Toulon, CNRS/IRD, Marseille, France
| | - N Bensoussan
- IPSO FACTO, SCOPArl, Pole Océanologie, Marseille, 13001, France
| | - D Aurelle
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, Station Marine d'Endoume, Marseille, 13007, France
| | - E Cebrian
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, 17300, Spain
- Departament de Ciències Ambientals, Facultat de Ciències, Universitat de Girona, Girona, 17071, Spain
| | - R Coma
- Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, 17300, Spain
| | - J-P Féral
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, Station Marine d'Endoume, Marseille, 13007, France
| | - M La Rivière
- Aix-Marseille Université, Mediterranean Institute of Oceanography (M I O), Université de Toulon, CNRS/IRD, Marseille, France
| | - C Linares
- Departament d'Ecologia, Universitat de Barcelona, Barcelona, 08028, Spain
| | - P López-Sendino
- Institute of Marine Sciences (ICM-CSIC), Barcelona, 08003, Spain
| | - C Marschal
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, Station Marine d'Endoume, Marseille, 13007, France
| | - M Ribes
- Institute of Marine Sciences (ICM-CSIC), Barcelona, 08003, Spain
| | - N Teixidó
- Stazione Zoologica Anton Dohrn, Villa Dohrn-Benthic Ecology Center, Punta San Pietro, Ischia, Naples, 80077, Italy
| | - F Zuberer
- Institut Pytheas, UMS 3470, CNRS, Marseille, 13013, France
| | - J Garrabou
- Institute of Marine Sciences (ICM-CSIC), Barcelona, 08003, Spain
- Aix-Marseille Université, Mediterranean Institute of Oceanography (M I O), Université de Toulon, CNRS/IRD, Marseille, France
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12
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Aurelle D, Pivotto ID, Malfant M, Topçu NE, Masmoudi MB, Chaoui L, Kara HM, Coelho MA, Castilho R, Haguenauer A. Fuzzy species limits in Mediterranean gorgonians (Cnidaria, Octocorallia): inferences on speciation processes. ZOOL SCR 2017. [DOI: 10.1111/zsc.12245] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Didier Aurelle
- Aix Marseille Univ; Univ Avignon; CNRS, IRD, IMBE; Station Marine d'Endoume 13007 Marseille France
| | - Isabelle D. Pivotto
- Aix Marseille Univ; Univ Avignon; CNRS, IRD, IMBE; Station Marine d'Endoume 13007 Marseille France
- Department of Computer Science and Operations Research (DIRO); University of Montreal; Montréal QC 2194 Canada
| | - Marine Malfant
- Aix Marseille Univ; Univ Avignon; CNRS, IRD, IMBE; Station Marine d'Endoume 13007 Marseille France
- Lab. « Adaptation et Diversité en Milieu Marin »; Team Div&Co; Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7144; 29682 Roscoff France
| | - Nur E. Topçu
- Fisheries Faculty; Istanbul University; Ordu Cad No 200 34130 Laleli Istanbul Turkey
| | - Mauatassem B. Masmoudi
- Aix Marseille Univ; Univ Avignon; CNRS, IRD, IMBE; Station Marine d'Endoume 13007 Marseille France
- Laboratoire Bioressources Marines; Université d'Annaba Badji Mokhtar; BP 230 Oued Kouba Annaba 23008 Algeria
| | - Lamya Chaoui
- Laboratoire Bioressources Marines; Université d'Annaba Badji Mokhtar; BP 230 Oued Kouba Annaba 23008 Algeria
| | - Hichem M. Kara
- Laboratoire Bioressources Marines; Université d'Annaba Badji Mokhtar; BP 230 Oued Kouba Annaba 23008 Algeria
| | - Márcio A.G. Coelho
- Aix Marseille Univ; Univ Avignon; CNRS, IRD, IMBE; Station Marine d'Endoume 13007 Marseille France
- Centre for Marine Sciences; CCMAR-CIMAR Laboratório Associado; Universidade do Algarve; Campus do Gambelas 8005-139 Faro Portugal
| | - Rita Castilho
- Centre for Marine Sciences; CCMAR-CIMAR Laboratório Associado; Universidade do Algarve; Campus do Gambelas 8005-139 Faro Portugal
- Graduate Program in Evolution, Ecology and Behavior; University at Buffalo; Buffalo NY 14260 USA
| | - Anne Haguenauer
- Aix Marseille Univ; Univ Avignon; CNRS, IRD, IMBE; Station Marine d'Endoume 13007 Marseille France
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13
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Pratlong M, Haguenauer A, Chenesseau S, Brener K, Mitta G, Toulza E, Bonabaud M, Rialle S, Aurelle D, Pontarotti P. Evidence for a genetic sex determination in Cnidaria, the Mediterranean red coral ( Corallium rubrum). R Soc Open Sci 2017. [PMID: 28405374 DOI: 10.5061/dryad.rs7bm] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Sexual reproduction is widespread among eukaryotes, and the sex-determining processes vary greatly among species. While genetic sex determination (GSD) has been intensively described in bilaterian species, no example has yet been recorded among non-bilaterians. However, the quasi-ubiquitous repartition of GSD among multicellular species suggests that similar evolutionary forces can promote this system, and that these forces could occur also in non-bilaterians. Studying sex determination across the range of Metazoan diversity is indeed important to understand better the evolution of this mechanism and its lability. We tested the existence of sex-linked genes in the gonochoric red coral (Corallium rubrum, Cnidaria) using restriction site-associated DNA sequencing. We analysed 27 461 single nucleotide polymorphisms (SNPs) in 354 individuals from 12 populations including 53 that were morphologically sexed. We found a strong association between the allele frequencies of 472 SNPs and the sex of individuals, suggesting an XX/XY sex-determination system. This result was confirmed by the identification of 435 male-specific loci. An independent test confirmed that the amplification of these loci enabled us to identify males with absolute certainty. This is the first demonstration of a GSD system among non-bilaterian species and a new example of its convergence in multicellular eukaryotes.
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Affiliation(s)
- M Pratlong
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France; Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
| | - A Haguenauer
- Aix Marseille Univ, Avignon Université , CNRS, IRD, IMBE , Marseille , France
| | - S Chenesseau
- Aix Marseille Univ, Avignon Université , CNRS, IRD, IMBE , Marseille , France
| | - K Brener
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER , Montpellier Université , Perpignan , France
| | - G Mitta
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER , Montpellier Université , Perpignan , France
| | - E Toulza
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER , Montpellier Université , Perpignan , France
| | - M Bonabaud
- UMS BioCampus- MGX Montpellier GenomiX , Institut de Génomique Fonctionelle , 141 rue de la Cardonnille, 34094 Montpellier Cedex 05 , France
| | - S Rialle
- UMS BioCampus- MGX Montpellier GenomiX , Institut de Génomique Fonctionelle , 141 rue de la Cardonnille, 34094 Montpellier Cedex 05 , France
| | - D Aurelle
- Aix Marseille Univ, Avignon Université , CNRS, IRD, IMBE , Marseille , France
| | - P Pontarotti
- Aix Marseille Univ , CNRS, Centrale Marseille, I2M , Marseille , France
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14
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Pratlong M, Haguenauer A, Chenesseau S, Brener K, Mitta G, Toulza E, Bonabaud M, Rialle S, Aurelle D, Pontarotti P. Evidence for a genetic sex determination in Cnidaria, the Mediterranean red coral ( Corallium rubrum). R Soc Open Sci 2017; 4:160880. [PMID: 28405374 PMCID: PMC5383831 DOI: 10.1098/rsos.160880] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/01/2017] [Indexed: 05/29/2023]
Abstract
Sexual reproduction is widespread among eukaryotes, and the sex-determining processes vary greatly among species. While genetic sex determination (GSD) has been intensively described in bilaterian species, no example has yet been recorded among non-bilaterians. However, the quasi-ubiquitous repartition of GSD among multicellular species suggests that similar evolutionary forces can promote this system, and that these forces could occur also in non-bilaterians. Studying sex determination across the range of Metazoan diversity is indeed important to understand better the evolution of this mechanism and its lability. We tested the existence of sex-linked genes in the gonochoric red coral (Corallium rubrum, Cnidaria) using restriction site-associated DNA sequencing. We analysed 27 461 single nucleotide polymorphisms (SNPs) in 354 individuals from 12 populations including 53 that were morphologically sexed. We found a strong association between the allele frequencies of 472 SNPs and the sex of individuals, suggesting an XX/XY sex-determination system. This result was confirmed by the identification of 435 male-specific loci. An independent test confirmed that the amplification of these loci enabled us to identify males with absolute certainty. This is the first demonstration of a GSD system among non-bilaterian species and a new example of its convergence in multicellular eukaryotes.
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Affiliation(s)
- M. Pratlong
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
| | - A. Haguenauer
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
| | - S. Chenesseau
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
| | - K. Brener
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER, Montpellier Université, Perpignan, France
| | - G. Mitta
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER, Montpellier Université, Perpignan, France
| | - E. Toulza
- Perpignan Via Domitia Univ, IHPE UMR 5244, CNRS, IFREMER, Montpellier Université, Perpignan, France
| | - M. Bonabaud
- UMS BioCampus- MGX Montpellier GenomiX, Institut de Génomique Fonctionelle, 141 rue de la Cardonnille, 34094 Montpellier Cedex 05, France
| | - S. Rialle
- UMS BioCampus- MGX Montpellier GenomiX, Institut de Génomique Fonctionelle, 141 rue de la Cardonnille, 34094 Montpellier Cedex 05, France
| | - D. Aurelle
- Aix Marseille Univ, Avignon Université, CNRS, IRD, IMBE, Marseille, France
| | - P. Pontarotti
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
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15
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Masmoudi MB, Chaoui L, Topçu NE, Hammami P, Kara MH, Aurelle D. Contrasted levels of genetic diversity in a benthic Mediterranean octocoral: Consequences of different demographic histories? Ecol Evol 2016; 6:8665-8678. [PMID: 28035258 PMCID: PMC5192949 DOI: 10.1002/ece3.2490] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 08/17/2016] [Accepted: 08/18/2016] [Indexed: 01/17/2023] Open
Abstract
Understanding the factors explaining the observed patterns of genetic diversity is an important question in evolutionary biology. We provide the first data on the genetic structure of a Mediterranean octocoral, the yellow gorgonian Eunicella cavolini, along with insights into the demographic history of this species. We sampled populations in four areas of the Mediterranean Sea: continental France, Algeria, Turkey, and the Balearic and Corsica islands. Along French coasts, three sites were sampled at two depths (20 and 40 m). We demonstrated a high genetic structure in this species (overall FST = 0.13), and most pairwise differentiation tests were significant. We did not detect any difference between depths at the same site. Clustering analyses revealed four differentiated groups corresponding to the main geographical areas. The levels of allelic richness and heterozygosity were significantly different between regions, with highest diversity in Algeria and lowest levels in Turkey. The highest levels of private allelic richness were observed in Algeria followed by Turkey. Such contrasted patterns of genetic diversity were not observed in other Mediterranean octocorals and could be the result of different evolutionary histories. We also provide new empirical evidence of contrasting results between tests and model‐based studies of demographic history. Our results have important consequences for the management of this species.
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Affiliation(s)
- Moutassem Billah Masmoudi
- Aix Marseille Univ Univ Avignon CNRS IRD IMBE Marseille France; Laboratoire Bioressources Marines Université d'Annaba Badji Mokhtar Annaba Algérie
| | - Lamya Chaoui
- Laboratoire Bioressources Marines Université d'Annaba Badji Mokhtar Annaba Algérie
| | - Nur Eda Topçu
- İstanbul Üniversitesi Su Ürünleri Fakültesi İstanbul Turkey
| | - Pachka Hammami
- Aix Marseille UnivUniv Avignon CNRS IRD IMBE Marseille France; CIRAD UMR CMAEE Montpellier France
| | - Mohamed Hichem Kara
- Laboratoire Bioressources Marines Université d'Annaba Badji Mokhtar Annaba Algérie
| | - Didier Aurelle
- Aix Marseille Univ Univ Avignon CNRS IRD IMBE Marseille France
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16
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Affiliation(s)
- Marine Pratlong
- Aix Marseille Univ; Univ Avignon; CNRS; IRD; IMBE; Marseille France
- Aix Marseille Univ; CNRS; Centrale Marseille, I2M, Equipe Evolution Biologique et Modélisation; Marseille France
| | - Corinne Rancurel
- INRA; University Nice Sophia Antipolis; CNRS; UMR 1355-7254 Institut Sophia Agrobiotech; Sophia Antipolis France
| | - Pierre Pontarotti
- Aix Marseille Univ; CNRS; Centrale Marseille, I2M, Equipe Evolution Biologique et Modélisation; Marseille France
| | - Didier Aurelle
- Aix Marseille Univ; Univ Avignon; CNRS; IRD; IMBE; Marseille France
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17
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Boavida J, Paulo D, Aurelle D, Arnaud-Haond S, Marschal C, Reed J, Gonçalves JMS, Serrão EA. A Well-Kept Treasure at Depth: Precious Red Coral Rediscovered in Atlantic Deep Coral Gardens (SW Portugal) after 300 Years. PLoS One 2016; 11:e0147228. [PMID: 26800449 PMCID: PMC4730840 DOI: 10.1371/journal.pone.0147228] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/30/2015] [Indexed: 11/18/2022] Open
Abstract
Background The highly valuable red coral Corallium rubrum is listed in several Mediterranean Conventions for species protection and management since the 1980s. Yet, the lack of data about its Atlantic distribution has hindered its protection there. This culminated in the recent discovery of poaching activities harvesting tens of kg of coral per day from deep rocky reefs off SW Portugal. Red coral was irregularly exploited in Portugal between the 1200s and 1700s, until the fishery collapsed. Its occurrence has not been reported for the last 300 years. Results Here we provide the first description of an Atlantic red coral assemblage, recently rediscovered dwelling at 60–100 m depth in southern Portugal. We report a very slow growth rate (0.23 mm year-1), comparable to Mediterranean specimens. In comparison with most of the Mediterranean reports, the population reaches much larger sizes, estimated to be over one century old, and has a more complex coral branch architecture that promotes a rich assemblage of associated species, with boreal and Mediterranean affinities. Atlantic red coral is genetically distinct, yet mitochondrial analyses suggest that red corals from the Atlantic may have introgressed the Mediterranean ones after migration via the Algeria current. Our underwater surveys, using advanced mixed-gas diving, retrieved lost fishing gear in all coral sites. Besides illegal harvesting, the use and loss of fishing gears, particularly nets, by local fisheries are likely sources of direct impacts on these benthic assemblages. Conclusions We extended the knowledge on the distribution of C. rubrum in the Atlantic, discovered its genetic distinctiveness, and reveal a rich deep-dwelling fauna associated to these coral assemblages. These findings support a barrier role of the Atlantic-Mediterranean transition zone, but reveal also hints of connectivity along its southern margin. The results highlight the genetic and demographic uniqueness of red coral populations from SW Iberia. However, we also report threats to these vulnerable populations by direct and indirect fishing activities and argue that its protection from any mechanically destructive activities is urgent as a precautionary approach. This study advances our understanding of phylogeographic barriers and range edge genetic diversity, and serves as a baseline against which to monitor future human and environmental disturbances to Atlantic C. rubrum.
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Affiliation(s)
- Joana Boavida
- CCMAR, Centro de Ciências do Mar, Universidade do Algarve, Campus of Gambelas, 8005-139, Faro, Portugal
- * E-mail:
| | - Diogo Paulo
- CCMAR, Centro de Ciências do Mar, Universidade do Algarve, Campus of Gambelas, 8005-139, Faro, Portugal
| | - Didier Aurelle
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, 13007, Marseille, France
| | - Sophie Arnaud-Haond
- Ifremer, UMR MARBEC (Marine Biodiversity, Exploitation and Conservation) Bd Jean Monnet, BP 171, F-34203, Sète, France
| | - Christian Marschal
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, 13007, Marseille, France
| | - John Reed
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, United States of America
| | - Jorge M. S. Gonçalves
- CCMAR, Centro de Ciências do Mar, Universidade do Algarve, Campus of Gambelas, 8005-139, Faro, Portugal
| | - Ester A. Serrão
- CCMAR, Centro de Ciências do Mar, Universidade do Algarve, Campus of Gambelas, 8005-139, Faro, Portugal
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Manel S, Perrier C, Pratlong M, Abi-Rached L, Paganini J, Pontarotti P, Aurelle D. Genomic resources and their influence on the detection of the signal of positive selection in genome scans. Mol Ecol 2015; 25:170-84. [DOI: 10.1111/mec.13468] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 11/06/2015] [Accepted: 11/07/2015] [Indexed: 12/16/2022]
Affiliation(s)
- S. Manel
- CEFE UMR 5175; CNRS - Université de Montpellier - Université Paul-Valéry Montpellier -EPHE; laboratoire Biogéographie et écologie des vertébrés; 1919 route de Mende 34293 Montpellier Cedex 5 France
| | - C. Perrier
- CEFE UMR 5175; CNRS - Université de Montpellier - Université Paul-Valéry Montpellier -EPHE; laboratoire Biogéographie et écologie des vertébrés; 1919 route de Mende 34293 Montpellier Cedex 5 France
| | - M. Pratlong
- Aix Marseille Université; CNRS; IRD; Avignon Université, IMBE UMR 7263; Station Marine d'Endoume, 13007; Marseille France
- Aix Marseille Université; CNRS; Centrale Marseille; I2M UMR 7373; Evolution Biologique Modélisation; 3 Place Victor Hugo, 13331 Marseille Cedex Case 19 France
| | - L. Abi-Rached
- Equipe ATIP; URMITE UM 63 CNRS 7278 IRD 198 Inserm U1095; IHU Méditerranée Infection; Aix-Marseille Université; 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05 France
| | - J. Paganini
- XEGEN SAS; 15 Rue de la République 13420 Gemenos France
| | - P. Pontarotti
- Aix Marseille Université; CNRS; Centrale Marseille; I2M UMR 7373; Evolution Biologique Modélisation; 3 Place Victor Hugo, 13331 Marseille Cedex Case 19 France
| | - D. Aurelle
- Aix Marseille Université; CNRS; IRD; Avignon Université, IMBE UMR 7263; Station Marine d'Endoume, 13007; Marseille France
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Gagnaire PA, Broquet T, Aurelle D, Viard F, Souissi A, Bonhomme F, Arnaud-Haond S, Bierne N. Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era. Evol Appl 2015; 8:769-86. [PMID: 26366195 PMCID: PMC4561567 DOI: 10.1111/eva.12288] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/05/2015] [Indexed: 12/14/2022] Open
Abstract
Estimating the rate of exchange of individuals among populations is a central concern to evolutionary ecology and its applications to conservation and management. For instance, the efficiency of protected areas in sustaining locally endangered populations and ecosystems depends on reserve network connectivity. The population genetics theory offers a powerful framework for estimating dispersal distances and migration rates from molecular data. In the marine realm, however, decades of molecular studies have met limited success in inferring genetic connectivity, due to the frequent lack of spatial genetic structure in species exhibiting high fecundity and dispersal capabilities. This is especially true within biogeographic regions bounded by well-known hotspots of genetic differentiation. Here, we provide an overview of the current methods for estimating genetic connectivity using molecular markers and propose several directions for improving existing approaches using large population genomic datasets. We highlight several issues that limit the effectiveness of methods based on neutral markers when there is virtually no genetic differentiation among samples. We then focus on alternative methods based on markers influenced by selection. Although some of these methodologies are still underexplored, our aim was to stimulate new research to test how broadly they are applicable to nonmodel marine species. We argue that the increased ability to apply the concepts of cline analyses will improve dispersal inferences across physical and ecological barriers that reduce connectivity locally. We finally present how neutral markers hitchhiking with selected loci can also provide information about connectivity patterns within apparently well-mixed biogeographic regions. We contend that one of the most promising applications of population genomics is the use of outlier loci to delineate relevant conservation units and related eco-geographic features across which connectivity can be measured.
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Affiliation(s)
- Pierre-Alexandre Gagnaire
- Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France
| | - Thomas Broquet
- CNRS team Diversity and connectivity of coastal marine landscapes, Station Biologique de Roscoff Roscoff, France ; Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff Roscoff, France
| | - Didier Aurelle
- Aix Marseille Université, CNRS-IRD-Avignon Université, IMBE UMR 7263 Marseille, France
| | - Frédérique Viard
- CNRS team Diversity and connectivity of coastal marine landscapes, Station Biologique de Roscoff Roscoff, France ; Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff Roscoff, France
| | | | - François Bonhomme
- Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France
| | - Sophie Arnaud-Haond
- Université de Montpellier Montpellier, France ; Ifremer, UMR "Ecosystèmes Marins Exploités" Sète, France
| | - Nicolas Bierne
- Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France
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20
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Pivotto ID, Nerini D, Masmoudi M, Kara H, Chaoui L, Aurelle D. Highly contrasted responses of Mediterranean octocorals to climate change along a depth gradient. R Soc Open Sci 2015; 2:140493. [PMID: 26064654 PMCID: PMC4453260 DOI: 10.1098/rsos.140493] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/10/2015] [Indexed: 06/04/2023]
Abstract
Climate change has a strong impact on marine ecosystems, including temperate species. Analysing the diversity of thermotolerance levels within species along with their genetic structure enables a better understanding of their potential response to climate change. We performed this integrative study on the Mediterranean octocoral Eunicella cavolini, with samples from different depths and by means of a common garden experiment. This species does not host photosynthetic Symbiodinium, enabling us to focus on the cnidarian response. We compared the thermotolerance of individuals from 20 m and 40 m depths from the same site and with replicates from the same colony. On the basis of an innovative statistical analysis of necrosis kinetics and risk, we demonstrated the occurrence of a very different response between depths at this local scale, with lower thermotolerance of deep individuals. Strongly thermotolerant individuals were observed at 20 m with necrosis appearing at higher temperatures than observed in situ. On the basis of nine microsatellite loci, we showed that these marked thermotolerance differences occur within a single population. This suggests the importance of acclimatization processes in adaptation to these different depths. In addition, differences between replicates demonstrated the occurrence of a variability of response between fragments from the same colony with the possibility of an interaction with a tank effect. Our results provide a basis for studying adaptation and acclimatization in Mediterranean octocorals in a heterogeneous environment.
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Affiliation(s)
- I. D. Pivotto
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, Marseille 13397, France
| | - D. Nerini
- Aix Marseille Université, CNRS, Université de Toulon, IRD, MIO UMR 7294, Marseille 13288, France
| | - M. Masmoudi
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, Marseille 13397, France
- Laboratoire Bioressources Marines – Université d'Annaba, Badji Mokhtar, BP 230, Oued Kouba, Annaba 23008, Algeria
| | - H. Kara
- Laboratoire Bioressources Marines – Université d'Annaba, Badji Mokhtar, BP 230, Oued Kouba, Annaba 23008, Algeria
| | - L. Chaoui
- Laboratoire Bioressources Marines – Université d'Annaba, Badji Mokhtar, BP 230, Oued Kouba, Annaba 23008, Algeria
| | - D. Aurelle
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, Marseille 13397, France
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21
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Pratlong M, Haguenauer A, Chabrol O, Klopp C, Pontarotti P, Aurelle D. The red coral (Corallium rubrum) transcriptome: a new resource for population genetics and local adaptation studies. Mol Ecol Resour 2015; 15:1205-15. [PMID: 25648864 DOI: 10.1111/1755-0998.12383] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 01/22/2015] [Accepted: 01/26/2015] [Indexed: 12/20/2022]
Abstract
The question of species survival and evolution in heterogeneous environments has long been a subject for study. Indeed, it is often difficult to identify the molecular basis of adaptation to contrasted environments, and nongenetic effects increase the difficulty to disentangle fixed effects, such as genetic adaptation, from variable effects, such as individual phenotypic plasticity, in adaptation. Nevertheless, this question is also of great importance for understanding the evolution of species in a context of climate change. The red coral (Corallium rubrum) lives in the Mediterranean Sea, where at depths ranging from 5 to 600 m, it meets very contrasted thermal conditions. The shallowest populations of this species suffered from mortality events linked with thermal anomalies that have highlighted thermotolerance differences between individuals. We provide here a new transcriptomic resource, as well as candidate markers for the study of local adaptation. We sequenced the transcriptome of six individuals from 5 m and six individuals from 40 m depth at the same site of the Marseilles bay, after a period of common garden acclimatization. We found differential expression maintained between the two depths even after common garden acclimatization, and we analysed the polymorphism pattern of these samples. We highlighted contigs potentially implicated in the response to thermal stress, which could be good candidates for the study of thermal adaptation for the red coral. Some of these genes are also involved in the response to thermal stress in other corals. Our method enables the identification of candidate loci of local adaptation useful for other nonmodel organisms.
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Affiliation(s)
- M Pratlong
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, 13397, Marseille, France.,Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, Equipe Evolution Biologique et Modélisation, 13453, Marseille, France
| | - A Haguenauer
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, 13397, Marseille, France
| | - O Chabrol
- Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, Equipe Evolution Biologique et Modélisation, 13453, Marseille, France
| | - C Klopp
- Plateforme Bioinformatique Toulouse Midi-Pyrénées, UR 875 UMIAT, INRA, Auzeville Castanet-Tolosan, France
| | - P Pontarotti
- Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, Equipe Evolution Biologique et Modélisation, 13453, Marseille, France
| | - D Aurelle
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, 13397, Marseille, France
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22
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Ledoux JB, Aurelle D, Bensoussan N, Marschal C, Féral JP, Garrabou J. Potential for adaptive evolution at species range margins: contrasting interactions between red coral populations and their environment in a changing ocean. Ecol Evol 2015; 5:1178-92. [PMID: 25859324 PMCID: PMC4377262 DOI: 10.1002/ece3.1324] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 10/21/2014] [Accepted: 10/22/2014] [Indexed: 01/17/2023] Open
Abstract
Studying population-by-environment interactions (PEIs) at species range margins offers the opportunity to characterize the responses of populations facing an extreme regime of selection, as expected due to global change. Nevertheless, the importance of these marginal populations as putative reservoirs of adaptive genetic variation has scarcely been considered in conservation biology. This is particularly true in marine ecosystems for which the deep refugia hypothesis proposes that disturbed shallow and marginal populations of a given species can be replenished by mesophotic ones. This hypothesis therefore assumes that identical PEIs exist between populations, neglecting the potential for adaptation at species range margins. Here, we combine reciprocal transplant and common garden experiments with population genetics analyses to decipher the PEIs in the red coral, Corallium rubrum. Our analyses reveal partially contrasting PEIs between shallow and mesophotic populations separated by approximately one hundred meters, suggesting that red coral populations may potentially be locally adapted to their environment. Based on the effective population size and connectivity analyses, we posit that genetic drift may be more important than gene flow in the adaptation of the red coral. We further investigate how adaptive divergence could impact population viability in the context of warming and demonstrate differential phenotypic buffering capacities against thermal stress. Our study questions the relevance of the deep refugia hypothesis and highlights the conservation value of marginal populations as a putative reservoir of adaptive genetic polymorphism.
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Affiliation(s)
- Jean-Baptiste Ledoux
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigacção Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 177 4050-123, Porto, Portugal ; Institut de Ciencies del Mar CSIC, Passeig Maritim de la Barceloneta 37-49 Barcelona, Spain ; Aix Marseille Universite, CNRS, IRD, Avignon Université, IMBE, UMR 7263 13397, Marseille, France
| | - Didier Aurelle
- Aix Marseille Universite, CNRS, IRD, Avignon Université, IMBE, UMR 7263 13397, Marseille, France
| | - Nathaniel Bensoussan
- IPSO FACTO, SCOPARL, Pôle Océanologie et Limnologie, 37 rue Saint-Sebastien F-13006, Marseille, France
| | - Christian Marschal
- Aix Marseille Universite, CNRS, IRD, Avignon Université, IMBE, UMR 7263 13397, Marseille, France
| | - Jean-Pierre Féral
- Aix Marseille Universite, CNRS, IRD, Avignon Université, IMBE, UMR 7263 13397, Marseille, France
| | - Joaquim Garrabou
- Aix Marseille Universite, CNRS, IRD, Avignon Université, IMBE, UMR 7263 13397, Marseille, France ; Institut de Ciencies del Mar CSIC, Passeig Maritim de la Barceloneta 37-49 Barcelona, Spain
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23
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Pante E, Puillandre N, Viricel A, Arnaud-Haond S, Aurelle D, Castelin M, Chenuil A, Destombe C, Forcioli D, Valero M, Viard F, Samadi S. Species are hypotheses: avoid connectivity assessments based on pillars of sand. Mol Ecol 2015; 24:525-44. [DOI: 10.1111/mec.13048] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/06/2014] [Accepted: 12/13/2014] [Indexed: 01/31/2023]
Affiliation(s)
- Eric Pante
- Littoral, Environnement et Sociétés (LIENSs); UMR 7266 CNRS - Université de La Rochelle; 2 rue Olympe de Gouges 17042 La Rochelle France
| | - Nicolas Puillandre
- ISYEB - UMR 7205 - CNRS, MNHN; UPMC (University Paris 06); EPHE - Muséum national d'Histoire naturelle; Sorbonne Universités; CP26, 57 rue Cuvier F-75231 Paris Cedex 05 France
| | - Amélia Viricel
- Littoral, Environnement et Sociétés (LIENSs); UMR 7266 CNRS - Université de La Rochelle; 2 rue Olympe de Gouges 17042 La Rochelle France
| | | | - Didier Aurelle
- Aix Marseille Université; CNRS, IRD; Avignon Université, IMBE UMR 7263; 13397 Marseille France
| | - Magalie Castelin
- Aquatic Animal Health Section; Fisheries and Oceans Canada; Pacific Biological Station; 3190 Hammond Bay Road Nanaimo BC Canada V9T 6N7
| | - Anne Chenuil
- Aix Marseille Université; CNRS, IRD; Avignon Université, IMBE UMR 7263; 13397 Marseille France
| | - Christophe Destombe
- Sorbonne Universités; UPMC; University Paris 06; Station Biologique de Roscoff F-29680 Roscoff France
- CNRS, Laboratory Evolutionary Biology and Ecology of Algae; Sorbonne Universités; Université Pierre et Marie Curie (UPMC) Univ Paris 06, UMI 3614, UPMC, PUCCh, UACh; Station Biologique de Roscoff F-29680 Roscoff France
| | - Didier Forcioli
- Faculté des Sciences; Université Nice-Sophia-Antipolis, Equipe Symbiose Marine UMR 7138; Parc Valrose 06108 Nice Cedex 2 France
- UMR 7138 Evolution Paris Seine; Université Pierre et Marie Curie - CNRS; 7 Quai St Bernard 75252 Paris Cedex 05 France
| | - Myriam Valero
- Sorbonne Universités; UPMC; University Paris 06; Station Biologique de Roscoff F-29680 Roscoff France
- CNRS, Laboratory Evolutionary Biology and Ecology of Algae; Sorbonne Universités; Université Pierre et Marie Curie (UPMC) Univ Paris 06, UMI 3614, UPMC, PUCCh, UACh; Station Biologique de Roscoff F-29680 Roscoff France
| | - Frédérique Viard
- Sorbonne Universités; UPMC; University Paris 06; Station Biologique de Roscoff F-29680 Roscoff France
- Centre National de la Recherche Scientifique (CNRS); Laboratory Adaptation and Diversity in the Marine Environment; Team Diversity and Connectivity in Coastal Marine Landscapes, UMR 7144; Station Biologique de Roscoff F-29680 Roscoff France
| | - Sarah Samadi
- ISYEB - UMR 7205 - CNRS, MNHN; UPMC (University Paris 06); EPHE - Muséum national d'Histoire naturelle; Sorbonne Universités; CP26, 57 rue Cuvier F-75231 Paris Cedex 05 France
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24
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Van Ofwegen LP, Aurelle D, Sartoretto S. A new genus of soft coral (Cnidaria, Octocorallia) from the Republic of Congo (Pointe-Noire Region). Zookeys 2015:1-10. [PMID: 25589850 PMCID: PMC4284428 DOI: 10.3897/zookeys.462.8533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 10/06/2014] [Indexed: 11/12/2022] Open
Abstract
A new genus of soft coral from the Republic of Congo is described, Complexumgen. n. Nine West African octocoral species previously described in the genus Alcyonium by Tixier-Durivault (1955) are referred to this new genus, and a new species is described and figured, Complexumpusillumsp. n. The new species is characterized by having encrusting growth form and abundant spiny clubs in the surface of the polyparium. It colonizes shallow calcareous rocky banks (5 to 20 m depth) existing in coastal water of the region of Pointe-Noire. Based on molecular phylogeny this new genus is well separated from Alcyonium species.
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Affiliation(s)
- Leen P Van Ofwegen
- Naturalis Biodiversity Center, P.O. Box 9517, NL-2300 RA Leiden, The Netherlands
| | - Didier Aurelle
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE UMR 7263, 13397, Marseille, France
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25
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Gérard K, Guilloton E, Arnaud-Haond S, Aurelle D, Bastrop R, Chevaldonné P, Derycke S, Hanel R, Lapègue S, Lejeusne C, Mousset S, Ramšak A, Remerie T, Viard F, Féral JP, Chenuil A. PCR survey of 50 introns in animals: cross-amplification of homologous EPIC loci in eight non-bilaterian, protostome and deuterostome phyla. Mar Genomics 2013; 12:1-8. [PMID: 24184205 DOI: 10.1016/j.margen.2013.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 10/03/2013] [Accepted: 10/07/2013] [Indexed: 11/28/2022]
Abstract
Exon Primed Intron Crossing (EPIC) markers provide molecular tools that are susceptible to be variable within species while remaining amplifiable by PCR using potentially universal primers. In this study we tested the possibility of obtaining PCR products from 50 EPIC markers on 23 species belonging to seven different phyla (Porifera, Cnidaria, Arthropoda, Nematoda, Mollusca, Annelida, Echinodermata) using 70 new primer pairs. A previous study had identified and tested those loci in a dozen species, including another phylum, Urochordata (Chenuil et al., 2010). Results were contrasted among species. The best results were achieved with the oyster (Mollusca) where 28 loci provided amplicons susceptible to contain an intron according to their size. This was however not the case with the other mollusk Crepidula fornicata, which seems to have undergone a reduction in intron number or intron size. In the Porifera, 13 loci appeared susceptible to contain an intron, a surprisingly high number for this phylum considering its phylogenetic distance with genomic data used to design the primers. For two cnidarian species, numerous loci (24) were obtained. Ecdysozoan phyla (arthropods and nematodes) proved less successful than others as expected considering reports of their rapid rate of genome evolution and the worst results were obtained for several arthropods. Some general patterns among phyla arose, and we discuss how the results of this EPIC survey may give new insights into genome evolution of the study species. This work confirms that this set of EPIC loci provides an easy-to-use toolbox to identify genetic markers potentially useful for population genetics, phylogeography or phylogenetic studies for a large panel of metazoan species. We then argue that obtaining diploid sequence genotypes for these loci became simple and affordable owing to Next-Generation Sequencing development. Species surveyed in this study belong to several genera (Acanthaster, Alvinocaris, Aplysina, Aurelia, Crepidula, Eunicella, Hediste, Hemimysis, Litoditis, Lophelia, Mesopodopsis, Mya, Ophiocten, Ophioderma, Ostrea, Pelagia, Platynereis, Rhizostoma, Rimicaris), two of them, belonging to the family Vesicomydae and Eunicidae, could not be determined at the genus level.
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Affiliation(s)
- K Gérard
- Laboratorio Ecología Molecular, las Palmeras 3425, Ñuñoa, Santiago, Chile.
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Mokhtar-Jamaï K, Coma R, Wang J, Zuberer F, Féral JP, Aurelle D. Role of evolutionary and ecological factors in the reproductive success and the spatial genetic structure of the temperate gorgonian Paramuricea clavata. Ecol Evol 2013; 3:1765-79. [PMID: 23789084 PMCID: PMC3686208 DOI: 10.1002/ece3.588] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 04/08/2013] [Accepted: 04/09/2013] [Indexed: 12/05/2022] Open
Abstract
Dispersal and mating features strongly influence the evolutionary dynamics and the spatial genetic structure (SGS) of marine populations. For the first time in a marine invertebrate, we examined individual reproductive success, by conducting larval paternity assignments after a natural spawning event, combined with a small-scale SGS analysis within a population of the gorgonian Paramuricea clavata. Thirty four percent of the larvae were sired by male colonies surrounding the brooding female colonies, revealing that the bulk of the mating was accomplished by males from outside the studied area. Male success increased with male height and decreased with increasing male to female distance. The parentage analyses, with a strong level of self-recruitment (25%), unveiled the occurrence of a complex family structure at a small spatial scale, consistent with the limited larval dispersal of this species. However, no evidence of small scale SGS was revealed despite this family structure. Furthermore, temporal genetic structure was not observed, which appears to be related to the rather large effective population size. The low level of inbreeding found suggests a pattern of random mating in this species, which disagrees with expectations that limited larval dispersal should lead to biparental inbreeding. Surface brooding and investment in sexual reproduction in P. clavata contribute to multiple paternity (on average 6.4 fathers were assigned per brood), which enhance genetic diversity of the brood. Several factors may have contributed to the lack of biparental inbreeding in our study such as (i) the lack of sperm limitation at a small scale, (ii) multiple paternity, and (iii) the large effective population size. Thus, our results indicate that limited larval dispersal and complex family structure do not necessarily lead to biparental inbreeding and SGS. In the framework of conservation purposes, our results suggested that colony size, proximity among colonies and the population size should be taken into consideration for restoration projects.
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Affiliation(s)
- Kenza Mokhtar-Jamaï
- Institut National de Recherche Halieutique (INRH)2 rue Tiznit, Casablanca, Morocco
- CNRS, UMR 7263 IMBE, Aix-Marseille UniversitéStation Marine d'Endoume, Chemin de la Batterie des Lions, 13007, Marseille, France
| | - Rafel Coma
- Centre d'Estudis Avançats de Blanes (CEAB-CSIC)Accés Cala Sant Francesc 14, 17300, Blanes, Girona, Catalonia, Spain
| | - Jinliang Wang
- Institute of Zoology, Zoological Society of LondonRegent's Park, London, NW1 4RY, U.K
| | - Frederic Zuberer
- CNRS, UMS 3470 Pythéas, Aix-Marseille UniversitéStation Marine d'Endoume, Chemin de la Batterie des Lions, 13007, Marseille, France
| | - Jean-Pierre Féral
- CNRS, UMR 7263 IMBE, Aix-Marseille UniversitéStation Marine d'Endoume, Chemin de la Batterie des Lions, 13007, Marseille, France
| | - Didier Aurelle
- CNRS, UMR 7263 IMBE, Aix-Marseille UniversitéStation Marine d'Endoume, Chemin de la Batterie des Lions, 13007, Marseille, France
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Fadhlaoui-Zid K, Knittweis L, Aurelle D, Nafkha C, Ezzeddine S, Fiorentino F, Ghmati H, Ceriola L, Jarboui O, Maltagliati F. Genetic structure of Octopus vulgaris (Cephalopoda, Octopodidae) in the central Mediterranean Sea inferred from the mitochondrial COIII gene. C R Biol 2012. [DOI: 10.1016/j.crvi.2012.10.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Mokhtar-Jamaï K, Pascual M, Ledoux JB, Coma R, Féral JP, Garrabou J, Aurelle D. From global to local genetic structuring in the red gorgonian Paramuricea clavata: the interplay between oceanographic conditions and limited larval dispersal. Mol Ecol 2011; 20:3291-305. [PMID: 21762434 DOI: 10.1111/j.1365-294x.2011.05176.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Defining the scale of connectivity among marine populations and identifying the barriers to gene flow are tasks of fundamental importance for understanding the genetic structure of populations and for the design of marine reserves. Here, we investigated the population genetic structure at three spatial scales of the red gorgonian Paramuricea clavata (Cnidaria, Octocorallia), a key species dwelling in the coralligenous assemblages of the Mediterranean Sea. Colonies of P. clavata were collected from 39 locations across the Mediterranean Sea from Morocco to Turkey and analysed using microsatellite loci. Within three regions (Medes, Marseille and North Corsica), sampling was obtained from multiple locations and at different depths. Three different approaches (measures of genetic differentiation, Bayesian clustering and spatially explicit maximum-difference algorithm) were used to determine the pattern of genetic structure. We identified genetic breaks in the spatial distribution of genetic diversity, which were concordant with oceanographic conditions in the Mediterranean Sea. We revealed a high level of genetic differentiation among populations and a pattern of isolation by distance across the studied area and within the three regions, underlining short effective larval dispersal in this species. We observed genetic differentiation among populations in the same locality dwelling at different depths, which may be explained by local oceanographic conditions and which may allow a process of local adaptation of the populations to their environment. We discuss the implications of our results for the conservation of the species, which is exposed to various threats.
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Affiliation(s)
- K Mokhtar-Jamaï
- Aix-Marseille Université, CNRS UMR 6540 DIMAR, Centre d'Océanologie de Marseille, Station Marine d'Endoume, Chemin de la Batterie des Lions, 13007 Marseille, France.
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Ledoux JB, Garrabou J, Bianchimani O, Drap P, Féral JP, Aurelle D. Fine-scale genetic structure and inferences on population biology in the threatened Mediterranean red coral, Corallium rubrum. Mol Ecol 2010; 19:4204-16. [PMID: 20854271 DOI: 10.1111/j.1365-294x.2010.04814.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Identifying microevolutionary processes acting in populations of marine species with larval dispersal is a challenging but crucial task because of its conservation implications. In this context, recent improvements in the study of spatial genetic structure (SGS) are particularly promising because they allow accurate insights into the demographic and evolutionary processes at stake. Using an exhaustive sampling and a combination of image processing and population genetics, we highlighted significant SGS between colonies of Corallium rubrum over an area of half a square metre, which sheds light on a number of aspects of its population biology. Based on this SGS, we found the mean dispersal range within sites to be between 22.6 and 32.1 cm, suggesting that the surveyed area approximately corresponded to a breeding unit. We then conducted a kinship analysis, which revealed a complex half-sib family structure and allowed us to quantify the level of self-recruitment and to characterize aspects of the mating system of this species. Furthermore, significant temporal variations in allele frequencies were observed, suggesting low genetic drift. These results have important conservation implications for the red coral and further our understanding of the microevolutionary processes acting within populations of sessile marine species with a larval phase.
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Affiliation(s)
- J-B Ledoux
- Aix-Marseille Université, CNRS UMR 6540 DIMAR, Centre d'Océanologie de Marseille, Station Marine d'Endoume, Chemin de la Batterie des Lions, 13007 Marseille, FranceEcole d'ingénieur de Luminy, CNRS UMR 6168 LSIS Avenue de Luminy 13288 Marseille Cedex 09, France
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Chenuil A, Hoareau TB, Egea E, Penant G, Rocher C, Aurelle D, Mokhtar-Jamai K, Bishop JDD, Boissin E, Diaz A, Krakau M, Luttikhuizen PC, Patti FP, Blavet N, Mousset S. An efficient method to find potentially universal population genetic markers, applied to metazoans. BMC Evol Biol 2010; 10:276. [PMID: 20836842 PMCID: PMC2949868 DOI: 10.1186/1471-2148-10-276] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 09/13/2010] [Indexed: 12/27/2022] Open
Abstract
Background Despite the impressive growth of sequence databases, the limited availability of nuclear markers that are sufficiently polymorphic for population genetics and phylogeography and applicable across various phyla restricts many potential studies, particularly in non-model organisms. Numerous introns have invariant positions among kingdoms, providing a potential source for such markers. Unfortunately, most of the few known EPIC (Exon Primed Intron Crossing) loci are restricted to vertebrates or belong to multigenic families. Results In order to develop markers with broad applicability, we designed a bioinformatic approach aimed at avoiding multigenic families while identifying intron positions conserved across metazoan phyla. We developed a program facilitating the identification of EPIC loci which allowed slight variation in intron position. From the Homolens databases we selected 29 gene families which contained 52 promising introns for which we designed 93 primer pairs. PCR tests were performed on several ascidians, echinoderms, bivalves and cnidarians. On average, 24 different introns per genus were amplified in bilaterians. Remarkably, five of the introns successfully amplified in all of the metazoan genera tested (a dozen genera, including cnidarians). The influence of several factors on amplification success was investigated. Success rate was not related to the phylogenetic relatedness of a taxon to the groups that most influenced primer design, showing that these EPIC markers are extremely conserved in animals. Conclusions Our new method now makes it possible to (i) rapidly isolate a set of EPIC markers for any phylum, even outside the animal kingdom, and thus, (ii) compare genetic diversity at potentially homologous polymorphic loci between divergent taxa.
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Affiliation(s)
- Anne Chenuil
- Aix-Marseille Université, Laboratoire DIMAR, CNRS UMR6540, rue de la batterie des Lions, 13007 Marseille, France.
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Aurelle D, Baker AJ, Bottin L, Brouat C, Caccone A, Chaix A, Dhakal P, Ding Y, Duplantier JM, Fiedler W, Fietz J, Fong Y, Forcioli D, Freitas TRO, Gunnarsson GH, Haddrath O, Hadziabdic D, Hauksdottir S, Havill NP, Heinrich M, Heinz T, Hjorleifsdottir S, Hong Y, Hreggvidsson GO, Huchette S, Hurst J, Kane M, Kane NC, Kawakami T, Ke W, Keith RA, Klauke N, Klein JL, Kun JFJ, Li C, Li GQ, Li JJ, Loiseau A, Lu LZ, Lucas M, Martins-Ferreira C, Mokhtar-Jamaï K, Olafsson K, Pampoulie C, Pan L, Pooler MR, Ren JD, Rinehart TA, Roussel V, Santos MO, Schaefer HM, Scheffler BE, Schmidt A, Segelbacher G, Shen JD, Skirnisdottir S, Sommer S, Tao ZR, Taubert R, Tian Y, Tomiuk J, Trigiano RN, Ungerer MC, Van Wormhoudt A, Wadl PA, Wang DQ, Weis-Dootz T, Xia Q, Yuan QY. Permanent Genetic Resources added to the Molecular Ecology Resources Database 1 February 2010-31 March 2010. Mol Ecol Resour 2010; 10:751-4. [PMID: 21565086 DOI: 10.1111/j.1755-0998.2010.02871.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
This article documents the addition of 228 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anser cygnoides, Apodemus flavicollis, Athene noctua, Cercis canadensis, Glis glis, Gubernatrix cristata, Haliotis tuberculata, Helianthus maximiliani, Laricobius nigrinus, Laricobius rubidus, Neoheligmonella granjoni, Nephrops norvegicus, Oenanthe javanica, Paramuricea clavata, Pyrrhura orcesi and Samanea saman. These loci were cross-tested on the following species: Apodemus sylvaticus, Laricobius laticollis and Laricobius osakensis (a proposed new species currently being described).
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Affiliation(s)
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- Aix-Marseille Université, Centre d'Océanologie de Marseille, CNRS-UMR 6540 DIMAR, rue de la Batterie des Lions, 13007 Marseille, France
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Ledoux JB, Mokhtar-Jamaï K, Roby C, Féral JP, Garrabou J, Aurelle D. Genetic survey of shallow populations of the Mediterranean red coral [Corallium rubrum (Linnaeus, 1758)]: new insights into evolutionary processes shaping nuclear diversity and implications for conservation. Mol Ecol 2010; 19:675-90. [PMID: 20074314 DOI: 10.1111/j.1365-294x.2009.04516.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Combined action from over-harvesting and recent mass mortality events potentially linked to ongoing climate changes has led to new concerns for the conservation of shallow populations (5-60 m) of Corallium rubrum, an octocorallian that is mainly found in the Mediterranean Sea. The present study was designed to analyse population structure and relationships at different spatial scales (from 10s of meters to 100s of kilometres) with a focus on dispersal pattern. We also performed the first analysis of the distribution of genetic diversity using a comparative approach between regional-clusters and samples. Forty populations dwelling in four distinct regions between 14 and 60 m in depth were genotyped using 10 microsatellites. Our main results indicate (i) a generalized pair-sample differentiation combined with a weak structure between regional-clusters; (ii) the occurrence of isolation by distance at the global scale, but also within two of the three analysed regional-clusters; (iii) a high level of genetic diversity over the surveyed area with a heterogeneous distribution from regional-cluster to sample levels. The evolutionary consequences of these results are discussed and their management implications are provided.
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Affiliation(s)
- J-B Ledoux
- Aix-Marseille Université, CNRS UMR 6540 DIMAR, Centre d'Océanologie de Marseille, Station Marine d'Endoume, Chemin de la Batterie des Lions, 13007 Marseille, France.
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Lemer S, Aurelle D, Vigliola L, Durand JD, Borsa P. Cytochrome b barcoding, molecular systematics and geographic differentiation in rabbitfishes (Siganidae). C R Biol 2006; 330:86-94. [PMID: 17241952 DOI: 10.1016/j.crvi.2006.09.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2006] [Revised: 08/31/2006] [Accepted: 09/06/2006] [Indexed: 11/27/2022]
Abstract
The fish genus Siganus (Siganidae) is widely distributed in the coastal habitats of all the tropical Indo-Pacific, with 28 nominal species recognized so far, based on general morphology and coloration patterns. A mitochondrial phylogeny of 16 Siganidae species, based on the partial nucleotide sequences of the cytochome b gene, was produced. Individual haplotypes of given nominal species generally clustered at the extremity of long branches, thus validating the current taxonomy. However, S. lineatus haplotypes formed a paraphyletic group including S. guttatus, while S. fuscescens haplotypes were apparently splitted in two groups, calling for further investigation. S. woodlandi and S. argenteus formed a monophyletic group, as expected from their close morphological relatedness, although they were separated by a substantial, 14.5-16.3% nucleotide distance. Among eight species sampled from different locations across the Indo-West Pacific, S. argenteus and S. spinus showed the lowest degree of geographic differentiation, a result that correlated well with their extended pelagic larval stage. Fixation index estimates were high in all six other species tested (S. doliatus, S. fuscescens, S. lineatus, S. puellus, S. punctatus, S. vulpinus). The cytochrome b gene fragment chosen here proved useful as a barcode in Siganidae.
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Affiliation(s)
- Sarah Lemer
- Institut de recherche pour le développement (IRD), UR 128, 98848 Nouméa, New Caledonia
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Aurelle D, Guillemaud T, Afonso P, Morato T, Wirtz P, Santos RS, Cancela ML. Genetic study of Coris julis (Osteichthyes, Perciformes, Labridae) evolutionary history and dispersal abilities. C R Biol 2003; 326:771-85. [PMID: 14608697 DOI: 10.1016/j.crvi.2003.08.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Microsatellite markers have been used to study the genetic variability of rainbow wrasse (Coris julis) Mediterranean and Atlantic populations. Differentiation tests failed to reveal any significant genetic differentiation among samples from continental Portugal and the Azores, despite more than 1800 km of geographical separation. Preliminary results tended to indicate a significant genetic differentiation among Atlantic and Mediterranean samples. It also supported the specific status of Cape Verde populations (Coris atlantica). We compare these results with previous mtDNA analyses and propose a biogeographic scenario that could explain our results.
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Aurelle D, Cattaneo-Berrebi G, Berrebi P. Natural and artificial secondary contact in brown trout (Salmo trutta, L.) in the French western Pyrenees assessed by allozymes and microsatellites. Heredity (Edinb) 2002; 89:171-83. [PMID: 12209387 DOI: 10.1038/sj.hdy.6800120] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2001] [Accepted: 04/23/2001] [Indexed: 11/09/2022] Open
Abstract
Analysis of allozyme polymorphism in brown trout (Salmo trutta) populations from south-western France shows that two genetically differentiated wild forms (characterised by the LDH-C1*100 and 90 alleles) introgress in this area. As allozymes could not evaluate the impact of stocking in the Atlantic basin, microsatellites have been necessary to detect the influence of hatchery fish and to confirm that the observed structure was natural. Microsatellites confirm the distinctness of the two wild forms based on allozyme loci. This situation provides a new example of secondary contact for this species in the Atlantic basin, with various levels of mixing being seen between the two population groups. The origin of these forms is discussed in the light of previous studies concerning modern and ancestral Atlantic trout (Hamilton et al, 1989) and lineages stemming from different glacial refuges (Garcia Marin et al, 1999; Weiss et al, 2000). This local analysis provides new insights in defining the evolutionary history of this species and confirms the important role of glaciation events in this history.
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Affiliation(s)
- D Aurelle
- Laboratoire Génome, Populations et Interactions, CNRS UMR 5000, cc063, Université Montpellier 2, place E. Bataillon, 34095 Montpellier, cedex 05, France
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Aurelle D, Berrebi P. Genetic structure of brown trout (Salmo trutta, L.) populations from south-western France: data from mitochondrial control region variability. Mol Ecol 2001; 10:1551-61. [PMID: 11412375 DOI: 10.1046/j.1365-294x.2001.01293.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The genetic relationships between several French Atlantic populations of brown trout were analysed using polymerase chain reaction-single-strand conformation polymorphism and sequencing of two parts of the mitochondrial control region. Ten mitochondrial haplotypes were identified, separated by a small number of mutations. The distribution of these haplotypes confirmed our hypothesis of the existence of two genetically well-differentiated groups of populations in this area, which has already been suggested using nuclear markers. Nuclear and mitochondrial markers, however, show different patterns of genetic differentiation: some populations which belong to one group according to allozyme results appear to be part of the other when using mitochondrial DNA. The origin of these different forms is discussed; they seem to belong to the Atlantic grouping. Nevertheless, the hypothesis of an ancestral and a modern form suggested for northern populations does not appear valid in this particular case.
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Affiliation(s)
- D Aurelle
- Laboratoire Génome et Populations, CNRS UPR 9060, Université Montpellier II, France
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Aurelle D, Lek S, Giraudel JL, Berrebi P. Microsatellites and artificial neural networks: tools for the discrimination between natural and hatchery brown trout (Salmo trutta, L.) in Atlantic populations. Ecol Modell 1999. [DOI: 10.1016/s0304-3800(99)00111-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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