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Spatial coalescent connectivity through multi-generation dispersal modelling predicts gene flow across marine phyla. Nat Commun 2022; 13:5861. [PMID: 36195609 PMCID: PMC9532449 DOI: 10.1038/s41467-022-33499-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 09/21/2022] [Indexed: 11/08/2022] Open
Abstract
Gene flow governs the contemporary spatial structure and dynamic of populations as well as their long-term evolution. For species that disperse using atmospheric or oceanic flows, biophysical models allow predicting the migratory component of gene flow, which facilitates the interpretation of broad-scale spatial structure inferred from observed allele frequencies among populations. However, frequent mismatches between dispersal estimates and observed genetic diversity prevent an operational synthesis for eco-evolutionary projections. Here we use an extensive compilation of 58 population genetic studies of 47 phylogenetically divergent marine sedentary species over the Mediterranean basin to assess how genetic differentiation is predicted by Isolation-By-Distance, single-generation dispersal and multi-generation dispersal models. Unlike previous approaches, the latter unveil explicit parents-to-offspring links (filial connectivity) and implicit links among siblings from a common ancestor (coalescent connectivity). We find that almost 70 % of observed variance in genetic differentiation is explained by coalescent connectivity over multiple generations, significantly outperforming other models. Our results offer great promises to untangle the eco-evolutionary forces that shape sedentary population structure and to anticipate climate-driven redistributions, altogether improving spatial conservation planning.
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Ledoux J, Ghanem R, Horaud M, López‐Sendino P, Romero‐Soriano V, Antunes A, Bensoussan N, Gómez‐Gras D, Linares C, Machordom A, Ocaña O, Templado J, Leblois R, Ben Souissi J, Garrabou J. Gradients of genetic diversity and differentiation across the distribution range of a Mediterranean coral: Patterns, processes and conservation implications. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Jean‐Baptiste Ledoux
- CIIMAR/CIMAR Centro Interdisciplinar de Investigação Marinha e Ambiental Universidade do Porto Porto Portugal
- Institut de Ciències del Mar CSIC Barcelona Spain
| | - Raouia Ghanem
- Institut National Agronomique de Tunisie Université de Carthage Tunis Tunisie
- Laboratoire de Biodiversité, Biotechnologies et Changements Climatiques (LR11ES09) Université Tunis El Manar Tunis Tunisie
| | | | | | | | - Agostinho Antunes
- CIIMAR/CIMAR Centro Interdisciplinar de Investigação Marinha e Ambiental Universidade do Porto Porto Portugal
- Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
| | | | | | - Cristina Linares
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals Institut de Recerca de la Biodiversitat (IRBIO) Universitat de Barcelona Barcelona Spain
| | - Annie Machordom
- Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
| | - Oscar Ocaña
- Departamento de Oceanografía Biológica y Biodiversidad Fundación Museo del Mar de Ceuta Ceuta Spain
| | - José Templado
- Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
| | - Raphaêl Leblois
- CBGP INRAE CIRAD IRD Montpellier SupAgro University of Montpellier Montpellier France
- Institut de Biologie Computationnelle University of Montpellier Montpellier France
| | - Jamila Ben Souissi
- Institut National Agronomique de Tunisie Université de Carthage Tunis Tunisie
- Laboratoire de Biodiversité, Biotechnologies et Changements Climatiques (LR11ES09) Université Tunis El Manar Tunis Tunisie
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Aichelman HE, Barshis DJ. Adaptive divergence, neutral panmixia, and algal symbiont population structure in the temperate coral Astrangia poculata along the Mid-Atlantic United States. PeerJ 2020; 8:e10201. [PMID: 33240603 PMCID: PMC7680023 DOI: 10.7717/peerj.10201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/27/2020] [Indexed: 12/11/2022] Open
Abstract
Astrangia poculata is a temperate scleractinian coral that exists in facultative symbiosis with the dinoflagellate alga Breviolum psygmophilum across a range spanning the Gulf of Mexico to Cape Cod, Massachusetts. Our previous work on metabolic thermal performance of Virginia (VA) and Rhode Island (RI) populations of A. poculata revealed physiological signatures of cold (RI) and warm (VA) adaptation of these populations to their respective local thermal environments. Here, we used whole-transcriptome sequencing (mRNA-Seq) to evaluate genetic differences and identify potential loci involved in the adaptive signature of VA and RI populations. Sequencing data from 40 A. poculata individuals, including 10 colonies from each population and symbiotic state (VA-white, VA-brown, RI-white, and RI-brown), yielded a total of 1,808 host-associated and 59 algal symbiont-associated single nucleotide polymorphisms (SNPs) post filtration. Fst outlier analysis identified 66 putative high outlier SNPs in the coral host and 4 in the algal symbiont. Differentiation of VA and RI populations in the coral host was driven by putatively adaptive loci, not neutral divergence (Fst = 0.16, p = 0.001 and Fst = 0.002, p = 0.269 for outlier and neutral SNPs respectively). In contrast, we found evidence of neutral population differentiation in B. psygmophilum (Fst = 0.093, p = 0.001). Several putatively adaptive host loci occur on genes previously associated with the coral stress response. In the symbiont, three of four putatively adaptive loci are associated with photosystem proteins. The opposing pattern of neutral differentiation in B. psygmophilum, but not the A. poculata host, reflects the contrasting dynamics of coral host and algal symbiont population connectivity, dispersal, and gene by environment interactions.
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Affiliation(s)
- Hannah E Aichelman
- Department of Biology, Boston University, Boston, MA, USA.,Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA
| | - Daniel J Barshis
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA
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Sromek L, Forcioli D, Lasota R, Furla P, Wolowicz M. Next-generation phylogeography of the cockle Cerastoderma glaucum: Highly heterogeneous genetic differentiation in a lagoon species. Ecol Evol 2019; 9:4667-4682. [PMID: 31031934 PMCID: PMC6476780 DOI: 10.1002/ece3.5070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 01/30/2019] [Accepted: 02/25/2019] [Indexed: 11/10/2022] Open
Abstract
AIM Coastal lagoons form an intriguing example of fragmented marine habitats. Restricted gene flow among isolated populations of lagoon species may promote their genetic divergence and may thus provide a first step toward speciation. In the present study, the population genetic structure of the lagoon cockle Cerastoderma glaucum has been investigated to clarify the complex phylogeographic pattern found in previous studies, to localize major genetic breaks, and to discuss their origin and maintenance. LOCATION The Atlantic and Mediterranean coasts, including the Baltic, North Sea, and Black Sea. METHODS A total of 204 C. glaucum individuals from 14 populations were genotyped using restriction site-associated DNA sequencing (RADseq). The genetic diversity, divergence, and structure were analyzed using genome-wide single nucleotide polymorphisms (SNPs). Phylogenetic relationships were inferred under a coalescent model using svdquartets. RESULTS The RADseq approach allowed inferring phylogeographic relationships with an unprecedented resolution. Three deeply divergent lineages were identified within C. glaucum that are separated by many genetic barriers: one lineage in the Aegean-Black Sea region, one in the Ionian Sea, and the last one widely distributed from the Western Mediterranean to the Baltic Sea. The nested branching pattern displayed on the species tree largely agrees with the likely scenario of C. glaucum postglacial expansion from the Mediterranean to the Baltic Sea. MAIN CONCLUSION The genetic differentiations between geographically separated lagoons proved to be strong, highlighting the evolutionary influence of these naturally fragmented habitats. The postglacial expansion created complex patterns of spatial segregation of genetic diversity with allele frequency gradients in many outlier loci, but also discrepancies between the nuclear and mitochondrial genetic markers that probably arose from genetic surfing of mitochondrial variation.
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Affiliation(s)
- Ludmila Sromek
- Department of Marine Ecosystems Functioning, Institute of Oceanography, Faculty of Oceanography and Geography University of Gdansk Gdynia Poland
- UPMC Université Paris 06, Université Antilles, Université Nice Sophia Antipolis, CNRS, Laboratoire Evolution Paris Seine, Institut de Biologie Paris Seine (EPS-IBPS) Sorbonne Universités Paris France
| | - Didier Forcioli
- UPMC Université Paris 06, Université Antilles, Université Nice Sophia Antipolis, CNRS, Laboratoire Evolution Paris Seine, Institut de Biologie Paris Seine (EPS-IBPS) Sorbonne Universités Paris France
| | - Rafal Lasota
- Department of Marine Ecosystems Functioning, Institute of Oceanography, Faculty of Oceanography and Geography University of Gdansk Gdynia Poland
| | - Paola Furla
- UPMC Université Paris 06, Université Antilles, Université Nice Sophia Antipolis, CNRS, Laboratoire Evolution Paris Seine, Institut de Biologie Paris Seine (EPS-IBPS) Sorbonne Universités Paris France
| | - Maciej Wolowicz
- Department of Marine Ecosystems Functioning, Institute of Oceanography, Faculty of Oceanography and Geography University of Gdansk Gdynia Poland
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5
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Costantini F, Rugiu L, Cerrano C, Abbiati M. Living upside down: patterns of red coral settlement in a cave. PeerJ 2018; 6:e4649. [PMID: 29844950 PMCID: PMC5967367 DOI: 10.7717/peerj.4649] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/29/2018] [Indexed: 11/20/2022] Open
Abstract
Background Larval settlement and intra-specific interactions during the recruitment phase are crucial in determining the distribution and density of sessile marine populations. Marine caves are confined and stable habitats. As such, they provide a natural laboratory to study the settlement and recruitment processes in sessile invertebrates, including the valuable Mediterranean red coral Corallium rubrum. In the present study, the spatial and temporal variability of red coral settlers in an underwater cave was investigated by demographic and genetic approaches. Methods Sixteen PVC tiles were positioned on the walls and ceiling of the Colombara Cave, Ligurian Sea, and recovered after twenty months. A total of 372 individuals of red coral belonging to two different reproductive events were recorded. Basal diameter, height, and number of polyps were measured, and seven microsatellites loci were used to evaluate the genetic relationships among individuals and the genetic structure. Results Significant differences in the colonization rate were observed both between the two temporal cohorts and between ceiling and walls. No genetic structuring was observed between cohorts. Overall, high levels of relatedness among individuals were found. Conclusion The results show that C. rubrumindividuals on tiles are highly related at very small spatial scales, suggesting that nearby recruits are likely to be sibs. Self-recruitment and the synchronous settlement of clouds of larvae could be possible explanations for the observed pattern.
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Affiliation(s)
- Federica Costantini
- Department of Biological, Geological and Environmental Sciences (BiGEA), University of Bologna, Ravenna, Italy.,Centro Interdipartimentale di Ricerca per le Scienze Ambientali (CIRSA), Ravenna, Italy.,CoNISMa, Roma, Italy
| | - Luca Rugiu
- Section of Ecology, Department of Biology, University of Turku, Turku, Finland
| | - Carlo Cerrano
- CoNISMa, Roma, Italy.,Department of Life and Environmental Science (DiSVA), Università Politecnica delle Marche, Ancona, Italy
| | - Marco Abbiati
- Centro Interdipartimentale di Ricerca per le Scienze Ambientali (CIRSA), Ravenna, Italy.,CoNISMa, Roma, Italy.,Istituto di Scienze Marine (ISMAR), Consiglio Nazionale delle Ricerche, Bologna, Italy.,Department of Cultural Heritage, University of Bologna, Ravenna, Italy
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6
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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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] [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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Contrasting patterns of population structure and gene flow facilitate exploration of connectivity in two widely distributed temperate octocorals. Heredity (Edinb) 2017; 119:35-48. [PMID: 28295035 PMCID: PMC5520136 DOI: 10.1038/hdy.2017.14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 02/03/2017] [Accepted: 02/17/2017] [Indexed: 12/13/2022] Open
Abstract
Connectivity is an important component of metapopulation dynamics in marine systems and can influence population persistence, migration rates and conservation decisions associated with Marine Protected Areas (MPAs). In this study, we compared the genetic diversity, gene flow and population structure of two octocoral species, Eunicella verrucosa and Alcyonium digitatum, in the northeast Atlantic (ranging from the northwest of Ireland and the southern North Sea, to southern Portugal), using two panels of 13 and 8 microsatellite loci, respectively. Our results identified regional genetic structure in E. verrucosa partitioned between populations from southern Portugal, northwest Ireland and Britain/France; subsequent hierarchical analysis of population structure also indicated reduced gene flow between southwest Britain and northwest France. However, over a similar geographical area, A. digitatum showed little evidence of population structure, suggesting high gene flow and/or a large effective population size; indeed, the only significant genetic differentiation detected in A. digitatum occurred between North Sea samples and those from the English Channel/northeast Atlantic. In both species the vast majority of gene flow originated from sample sites within regions, with populations in southwest Britain being the predominant source of contemporary exogenous genetic variants for the populations studied. Overall, historical patterns of gene flow appeared more complex, though again southwest Britain appeared to be an important source of genetic variation for both species. Our findings have major conservation implications, particularly for E. verrucosa, a protected species in UK waters and listed by the IUCN as ‘Vulnerable’, and for the designation and management of European MPAs.
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Postaire B, Gélin P, Bruggemann JH, Magalon H. One species for one island? Unexpected diversity and weak connectivity in a widely distributed tropical hydrozoan. Heredity (Edinb) 2017; 118:385-394. [PMID: 28177325 DOI: 10.1038/hdy.2016.126] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 10/03/2016] [Accepted: 11/05/2016] [Indexed: 11/09/2022] Open
Abstract
Isolation by distance (IBD) is one of the main modes of differentiation in marine species, above all in species presenting low dispersal capacities. This study reports the genetic structuring in the tropical hydrozoan Lytocarpia brevirostris α (sensu Postaire et al, 2016b), a brooding species, from 13 populations in the Western Indian Ocean (WIO) and one from New Caledonia (Tropical Southwestern Pacific). At the local scale, populations rely on asexual propagation at short distance, which was not found at larger scales; identical genotypes were restricted to single populations. After the removal of repeated genotypes, all populations presented significant positive FIS values (between 0.094*** and 0.335***). Gene flow was extremely low at all spatial scales, between sites within islands (<10 km distance) and among islands (100 to>11 000 km distance), with significant pairwise FST values (between 0.012*** and 0.560***). A general pattern of IBD was found at the Indo-Pacific scale, but also within sampled ecoregions of the WIO province. Clustering analyses identified each sampled island as an independent population, whereas analysis of molecular variance indicated that population genetic differentiation was significant at small (within island) and intermediate (among islands within province) spatial scales. The high population differentiation might reflect the life cycle of this brooding hydrozoan, possibly preventing regular dispersal at distances more than a few kilometres and probably leading to high cryptic diversity, each island housing an independent evolutionary lineage.
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Affiliation(s)
- B Postaire
- Université de La Réunion, UMR ENTROPIE Université de La Réunion-CNRS-IRD, Saint Denis, France.,Laboratoire d'Excellence CORAIL, Perpignan, France
| | - P Gélin
- Université de La Réunion, UMR ENTROPIE Université de La Réunion-CNRS-IRD, Saint Denis, France.,Laboratoire d'Excellence CORAIL, Perpignan, France
| | - J H Bruggemann
- Université de La Réunion, UMR ENTROPIE Université de La Réunion-CNRS-IRD, Saint Denis, France.,Laboratoire d'Excellence CORAIL, Perpignan, France
| | - H Magalon
- Université de La Réunion, UMR ENTROPIE Université de La Réunion-CNRS-IRD, Saint Denis, France.,Laboratoire d'Excellence CORAIL, Perpignan, France
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Postaire B, Magalon H, Bourmaud CAF, Bruggemann JH. Molecular species delimitation methods and population genetics data reveal extensive lineage diversity and cryptic species in Aglaopheniidae (Hydrozoa). Mol Phylogenet Evol 2016; 105:36-49. [DOI: 10.1016/j.ympev.2016.08.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 08/16/2016] [Accepted: 08/21/2016] [Indexed: 01/04/2023]
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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] [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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12
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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] [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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Arizmendi-Mejía R, Linares C, Garrabou J, Antunes A, Ballesteros E, Cebrian E, Díaz D, Ledoux JB. Combining genetic and demographic data for the conservation of a Mediterranean marine habitat-forming species. PLoS One 2015; 10:e0119585. [PMID: 25774522 PMCID: PMC4361678 DOI: 10.1371/journal.pone.0119585] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 01/14/2015] [Indexed: 11/19/2022] Open
Abstract
The integration of ecological and evolutionary data is highly valuable for conservation planning. However, it has been rarely used in the marine realm, where the adequate design of marine protected areas (MPAs) is urgently needed. Here, we examined the interacting processes underlying the patterns of genetic structure and demographic strucuture of a highly vulnerable Mediterranean habitat-forming species (i.e. Paramuricea clavata (Risso, 1826)), with particular emphasis on the processes of contemporary dispersal, genetic drift, and colonization of a new population. Isolation by distance and genetic discontinuities were found, and three genetic clusters were detected; each submitted to variations in the relative impact of drift and gene flow. No founder effect was found in the new population. The interplay of ecology and evolution revealed that drift is strongly impacting the smallest, most isolated populations, where partial mortality of individuals was highest. Moreover, the eco-evolutionary analyses entailed important conservation implications for P. clavata. Our study supports the inclusion of habitat-forming organisms in the design of MPAs and highlights the need to account for genetic drift in the development of MPAs. Moreover, it reinforces the importance of integrating genetic and demographic data in marine conservation.
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Affiliation(s)
- Rosana Arizmendi-Mejía
- Departament d´Ecologia, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 643, 08028, Barcelona, Spain
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Cristina Linares
- Departament d´Ecologia, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 643, 08028, Barcelona, Spain
| | - Joaquim Garrabou
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Agostinho Antunes
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 177, 4050-123, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Enric Ballesteros
- Centre d’Estudis Avançats de Blanes (CSIC), Accés Cala St. Francesc 14, 17300, Blanes, Spain
| | - Emma Cebrian
- Centre d’Estudis Avançats de Blanes (CSIC), Accés Cala St. Francesc 14, 17300, Blanes, Spain
| | - David Díaz
- Instituto Español de Oceanografia, C/ Moll de Ponent s/n, 07015, Palma de Mallorca, Spain
| | - Jean-Baptiste Ledoux
- Institut de Ciències del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 177, 4050-123, Porto, Portugal
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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: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [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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15
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Wang H, Liu H, Yang M, Bao L, Ge J. Phylogeographic study of Chinese seabuckthorn (Hippophae rhamnoides subsp. sinensis Rousi) reveals two distinct haplotype groups and multiple microrefugia on the Qinghai-Tibet Plateau. Ecol Evol 2014; 4:4370-9. [PMID: 25540697 PMCID: PMC4267874 DOI: 10.1002/ece3.1295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/13/2014] [Accepted: 10/01/2014] [Indexed: 11/16/2022] Open
Abstract
Historical climate change can shape the genetic pattern of a species. Studies on this phenomenon provide great advantage in predicting the response of species to current and future global climate change. Chinese seabuckthorn (Hippophae rhamnoides subsp. sinensis) is one of the most important cultivated plants in Northwest China. However, the subspecies history and the potential genetic resources within the subspecies range remain unclear. In this study, we utilized two intergenic chloroplast regions to characterize the spatial genetic distribution of the species. We found 19 haplotypes in total, 12 of which were unique to the Chinese seabuckthorn. The populations observed on the Qinghai-Tibet Plateau (QTP) consisted of most of the haplotypes, while in the northeast of the range of the subspecies, an area not on the QTP, only four haplotypes were detected. Our study also revealed two distinct haplotype groups of the subspecies with a sharp transition region located in the south of the Zoige Basin. 89.96% of the genetic variation located between the regions. Mismatch analysis indicated old expansions of these two haplotype groups, approximately around the early stage of Pleistocene. Additional morphological proofs from existing studies and habitat differentiation supported a long independent colonization history among the two regions. Potential adaptation probably occurred but needs more genome and morphology data in future. Chinese seabuckthorn have an older population expansion compared with subspecies in Europe. The lack of large land ice sheets and the heterogeneous landscape of the QTP could have provided extensive microrefugia for Chinese seabuckthorn during the glaciation period. Multiple localities sustaining high-frequency private haplotypes support this hypothesis. Our study gives clear insight into the distribution of genetic resources and the evolutionary history of Chinese seabuckthorn.
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Affiliation(s)
- Hongfang Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology & College of Life Sciences, Beijing Normal University Beijing, 100875, China
| | - Han Liu
- State Key Laboratory of Earth Surface Processes and Resource Ecology & College of Life Sciences, Beijing Normal University Beijing, 100875, China
| | - Mingbo Yang
- State Key Laboratory of Earth Surface Processes and Resource Ecology & College of Life Sciences, Beijing Normal University Beijing, 100875, China
| | - Lei Bao
- State Key Laboratory of Earth Surface Processes and Resource Ecology & College of Life Sciences, Beijing Normal University Beijing, 100875, China
| | - Jianping Ge
- State Key Laboratory of Earth Surface Processes and Resource Ecology & College of Life Sciences, Beijing Normal University Beijing, 100875, China
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16
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Wirshing HH, Feldheim KA, Baker AC. Vectored dispersal of Symbiodinium by larvae of a Caribbean gorgonian octocoral. Mol Ecol 2014; 22:4413-32. [PMID: 23980762 DOI: 10.1111/mec.12405] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Revised: 05/17/2013] [Accepted: 05/21/2013] [Indexed: 11/28/2022]
Abstract
The ability of coral reefs to recover from natural and anthropogenic disturbance is difficult to predict, in part due to uncertainty regarding the dispersal capabilities and connectivity of their reef inhabitants. We developed microsatellite markers for the broadcast spawning gorgonian octocoral Eunicea (Plexaura) flexuosa (four markers) and its dinoflagellate symbiont, Symbiodinium B1 (five markers), and used them to assess genetic connectivity, specificity and directionality of gene flow among sites in Florida, Panama, Saba and the Dominican Republic. Bayesian analyses found that most E. flexuosa from the Florida reef tract, Saba and the Dominican Republic were strongly differentiated from many E. flexuosa in Panama, with the exception of five colonies from Key West that clustered with colonies from Panama. In contrast, Symbiodinium B1 was more highly structured. At least seven populations were detected that showed patterns of isolation by distance. The symbionts in the five unusual Key West colonies also clustered with symbionts from Panama, suggesting these colonies are the result of long-distance dispersal. Migration rate tests indicated a weak signal of northward immigration from the Panama population into the lower Florida Keys. As E. flexuosa clonemates only rarely associated with the same Symbiodinium B1 genotype (and vice versa), these data suggest a dynamic host-symbiont relationship in which E. flexuosa is relatively well dispersed but likely acquires Symbiodinium B1 from highly structured natal areas prior to dispersal. Once vectored by host larvae, these symbionts may then spread through the local population, and/or host colonies may acquire different local symbiont genotypes over time.
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Affiliation(s)
- Herman H Wirshing
- Division of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbaker Causeway, Miami, FL 33149, USA.
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17
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Haye PA, Muñoz-Herrera NC. Isolation with differentiation followed by expansion with admixture in the tunicate Pyura chilensis. BMC Evol Biol 2013; 13:252. [PMID: 24238017 PMCID: PMC3840596 DOI: 10.1186/1471-2148-13-252] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Accepted: 10/29/2013] [Indexed: 11/21/2022] Open
Abstract
Background Pyura chilensis, a tunicate commercially exploited as food resource in Chile, is subject to management strategies, including restocking. The goal of this study was to examine the genetic structure of P. chilensis using information from a mitochondrial gene (Cytochrome Oxidase I, COI) and a nuclear gene (Elongation 1 alpha, EF1a), to characterize the geographic distribution of genetic diversity and differentiation, and to identify the main processes that have shaped it. We analyzed 268 and 208 sequences of COI and EF1a, respectively, from samples of eight local populations covering ca. 1800 km. Results For Pyura chilensis, partial sequences of the gene COI revealed three highly supported haplogroups that diverged 260000 to 470000 years ago. Two haplogroups currently are widely distributed and sympatric, while one is dominant only in Los Molinos (LM, 39°50′S). The two widespread COI haplogroups underwent a geographic expansion during an interglacial period of the Late Pleistocene ca. 100000 years ago. The nuclear gene was less divergent and did not resolve the COI haplogroups. Bayesian clustering of the nuclear gene’s SNPs revealed that individuals from the two widespread COI haplogroups were mostly assigned to two of the three detected clusters and had a marked degree of admixture. The third cluster predominated in LM and showed low admixture. Haplotypic diversity of both genes was very high, there was no isolation by distance, and most localities were genetically undifferentiated; only LM was consistently differentiated with both genes analyzed. Conclusions Pyura chilensis has less genetic structure than expected given its life history, which could be a consequence of dispersal on ship hulls. The only differentiated local population analyzed was LM. Coincidentally, it is the one furthest away from main maritime routes along the coast of Chile. The use of mitochondrial and nuclear markers allowed detection of divergent mitochondrial haplogroups in P. chilensis, two of which revealed nuclear admixture. The genetic structure of P. chilensis has likely been shaped by Pleistocene’s climatic effect on sea level leading to population contraction with isolation, followed by geographic range expansions with concomitant secondary contact and admixture.
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Affiliation(s)
- Pilar A Haye
- Laboratorio de Diversidad Molecular, Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Casilla 117, Coquimbo, Chile.
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Costantini F, Carlesi L, Abbiati M. Quantifying spatial genetic structuring in mesophotic populations of the precious coral Corallium rubrum. PLoS One 2013; 8:e61546. [PMID: 23646109 PMCID: PMC3640028 DOI: 10.1371/journal.pone.0061546] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 03/11/2013] [Indexed: 11/18/2022] Open
Abstract
While shallow water red coral populations have been overharvested in the past, nowadays, commercial harvesting shifted its pressure on mesophotic organisms. An understanding of red coral population structure, particularly larval dispersal patterns and connectivity among harvested populations is paramount to the viability of the species. In order to determine patterns of genetic spatial structuring of deep water Corallium rubrum populations, for the first time, colonies found between 58–118 m depth within the Tyrrhenian Sea were collected and analyzed. Ten microsatellite loci and two regions of mitochondrial DNA (mtMSH and mtC) were used to quantify patterns of genetic diversity within populations and to define population structuring at spatial scales from tens of metres to hundreds of kilometres. Microsatellites showed heterozygote deficiencies in all populations. Significant levels of genetic differentiation were observed at all investigated spatial scales, suggesting that populations are likely to be isolated. This differentiation may by the results of biological interactions, occurring within a small spatial scale and/or abiotic factors acting at a larger scale. Mitochondrial markers revealed significant genetic structuring at spatial scales greater then 100 km showing the occurrence of a barrier to gene flow between northern and southern Tyrrhenian populations. These findings provide support for the establishment of marine protected areas in the deep sea and off-shore reefs, in order to effectively maintain genetic diversity of mesophotic red coral populations.
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Affiliation(s)
- Federica Costantini
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Centro Interdipartimentale di Ricerca per le Scienze Ambientali, Università di Bologna, CoNISMa, Ravenna, Italy.
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19
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Interplay between isolation by distance and genetic clusters in the red coral Corallium rubrum: insights from simulated and empirical data. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0464-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Molecular forensics in the precious Mediterranean red coral, Corallium rubrum: testing DNA extraction and microsatellite genotyping using dried colonies. CONSERV GENET RESOUR 2012. [DOI: 10.1007/s12686-012-9795-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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