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Klein JD, Maduna SN, Dicken ML, da Silva C, Soekoe M, McCord ME, Potts WM, Hagen SB, Bester‐van der Merwe AE. Local adaptation with gene flow in a highly dispersive shark. Evol Appl 2024; 17:e13628. [PMID: 38283610 PMCID: PMC10810256 DOI: 10.1111/eva.13628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/06/2023] [Accepted: 11/27/2023] [Indexed: 01/30/2024] Open
Abstract
Adaptive divergence in response to environmental clines are expected to be common in species occupying heterogeneous environments. Despite numerous advances in techniques appropriate for non-model species, gene-environment association studies in elasmobranchs are still scarce. The bronze whaler or copper shark (Carcharhinus brachyurus) is a large coastal shark with a wide distribution and one of the most exploited elasmobranchs in southern Africa. Here, we assessed the distribution of neutral and adaptive genomic diversity in C. brachyurus across a highly heterogeneous environment in southern Africa based on genome-wide SNPs obtained through a restriction site-associated DNA method (3RAD). A combination of differentiation-based genome-scan (outflank) and genotype-environment analyses (redundancy analysis, latent factor mixed models) identified a total of 234 differentiation-based outlier and candidate SNPs associated with bioclimatic variables. Analysis of 26,299 putatively neutral SNPs revealed moderate and evenly distributed levels of genomic diversity across sites from the east coast of South Africa to Angola. Multivariate and clustering analyses demonstrated a high degree of gene flow with no significant population structuring among or within ocean basins. In contrast, the putatively adaptive SNPs demonstrated the presence of two clusters and deep divergence between Angola and all other individuals from Namibia and South Africa. These results provide evidence for adaptive divergence in response to a heterogeneous seascape in a large, mobile shark despite high levels of gene flow. These results are expected to inform management strategies and policy at the national and regional level for conservation of C. brachyurus populations.
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Affiliation(s)
- Juliana D. Klein
- Molecular Breeding and Biodiversity Research Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
| | - Simo N. Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy Research—NIBIOSvanvikNorway
| | - Matthew L. Dicken
- KwaZulu‐Natal Sharks BoardUmhlanga RocksSouth Africa
- Institute for Coastal and Marine Research (CMR), Ocean Sciences CampusNelson Mandela UniversityGqeberhaSouth Africa
| | - Charlene da Silva
- Department of Forestry, Fisheries and EnvironmentRogge BaySouth Africa
| | - Michelle Soekoe
- Division of Marine ScienceReel Science CoalitionCape TownSouth Africa
| | - Meaghen E. McCord
- South African Shark ConservancyHermanusSouth Africa
- Canadian Parks and Wilderness SocietyVancouverBritish ColumbiaCanada
| | - Warren M. Potts
- Department of Ichthyology and Fisheries ScienceRhodes UniversityMakhandaSouth Africa
- South African Institute for Aquatic BiodiversityMakhandaSouth Africa
| | - Snorre B. Hagen
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy Research—NIBIOSvanvikNorway
| | - Aletta E. Bester‐van der Merwe
- Molecular Breeding and Biodiversity Research Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
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Investigating an Unknown Biodiversity: Evidence of Distinct Lineages of the Endemic Chola Guitarfish Pseudobatos percellens Walbaum, 1792 in the Western Atlantic Ocean. DIVERSITY 2023. [DOI: 10.3390/d15030344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Anthropogenic actions have affected marine species for a long time, through overexploitation of natural stocks and habitat degradation, influencing the life strategies of several taxa, especially rays and sharks, which have suffered significant population declines in recent years. Therefore, conservation actions and stock management have become paramount. In this regard, chola guitarfish, Pseudobatos percellens, distributed throughout the Brazilian coast, is often commercially fished by local artisanal fleets or as by-catch in shrimp trawl fisheries. Therefore, this study aimed to understand the genetic diversity of P. percellens throughout the Brazilian coast, using single nucleotide polymorphisms (SNPs). Genetic analyses employing 3329 SNPs revealed a hidden biodiversity within P. percellens, with at least one lineage occurring in the Northern and Northeastern regions and another distributed in the Southeastern/Southern Brazilian coast, with high genetic differentiation between them. However, the Discriminant Analysis of Principal Components (DAPC) indicated the presence of in fact three lineages distributed in these regions that must still be better investigated. Therefore, to ensure adequate conservation of chola guitarfish biodiversity, populations must be managed separately along the Brazilian coast. Furthermore, the need for a taxonomic review for this group is noted.
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Lesturgie P, Lainé H, Suwalski A, Chifflet-Belle P, Maisano Delser P, Clua E, Jaquemet S, Magalon H, Mona S. Ecological and biogeographic features shaped the complex evolutionary history of an iconic apex predator (Galeocerdo cuvier). BMC Ecol Evol 2022; 22:147. [PMID: 36526977 PMCID: PMC9758794 DOI: 10.1186/s12862-022-02100-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The tiger shark (Galeocerdo cuvier) is a large iconic marine predator inhabiting worldwide tropical and subtropical waters. So far, only mitochondrial markers and microsatellites studies have investigated its worldwide historical demography with inconclusive outcomes. Here, we assessed for the first time the genomic variability of tiger shark based on RAD-seq data for 50 individuals from five sampling sites in the Indo-Pacific (IP) and one in the Atlantic Ocean (AO) to decipher the extent of the species' global connectivity and its demographic history. RESULTS Clustering algorithms (PCA and NMF), FST and an approximate Bayesian computation framework revealed the presence of two clusters corresponding to the two oceanic basins. By modelling the two-dimensional site frequency spectrum, we tested alternative isolation/migration scenarios between these two identified populations. We found the highest support for a divergence time between the two ocean basins of ~ 193,000 years before present (B.P) and an ongoing but limited asymmetric migration ~ 176 times larger from the IP to the AO (Nm ~ 3.9) than vice versa (Nm ~ 0.02). CONCLUSIONS The two oceanic regions are isolated by a strong barrier to dispersal more permeable from the IP to the AO through the Agulhas leakage. We finally emphasized contrasting recent demographic histories for the two regions, with the IP characterized by a recent bottleneck around 2000 years B.P. and the AO by an expansion starting 6000 years B.P. The large differentiation between the two oceanic regions and the absence of population structure within each ocean basin highlight the need for two large management units and call for future conservation programs at the oceanic rather than local scale, particularly in the Indo-Pacific where the population is declining.
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Affiliation(s)
- Pierre Lesturgie
- grid.503191.f0000 0001 0143 5055Institut de Systématique, Evolution, Biodiversité (ISYEB), EPHE-PSL, Université PSL, MNHN, CNRS, SU, UA, Paris, France
| | - Hugo Lainé
- grid.503191.f0000 0001 0143 5055Institut de Systématique, Evolution, Biodiversité (ISYEB), EPHE-PSL, Université PSL, MNHN, CNRS, SU, UA, Paris, France
| | - Arnaud Suwalski
- grid.503191.f0000 0001 0143 5055Institut de Systématique, Evolution, Biodiversité (ISYEB), EPHE-PSL, Université PSL, MNHN, CNRS, SU, UA, Paris, France ,grid.424469.90000 0001 2195 5365EPHE, PSL Research University, Paris, France
| | - Pascaline Chifflet-Belle
- grid.503191.f0000 0001 0143 5055Institut de Systématique, Evolution, Biodiversité (ISYEB), EPHE-PSL, Université PSL, MNHN, CNRS, SU, UA, Paris, France ,grid.424469.90000 0001 2195 5365EPHE, PSL Research University, Paris, France
| | | | - Eric Clua
- grid.424469.90000 0001 2195 5365EPHE, PSL Research University, Paris, France ,Laboratoire d’Excellence CORAIL, Papetoai, French Polynesia
| | - Sébastien Jaquemet
- grid.11642.300000 0001 2111 2608UMR ENTROPIE (Université de La Réunion/IRD/CNRS), Université de La Réunion, Saint Denis, France
| | - Hélène Magalon
- Laboratoire d’Excellence CORAIL, Papetoai, French Polynesia ,grid.11642.300000 0001 2111 2608UMR ENTROPIE (Université de La Réunion/IRD/CNRS), Université de La Réunion, Saint Denis, France
| | - Stefano Mona
- grid.503191.f0000 0001 0143 5055Institut de Systématique, Evolution, Biodiversité (ISYEB), EPHE-PSL, Université PSL, MNHN, CNRS, SU, UA, Paris, France ,grid.424469.90000 0001 2195 5365EPHE, PSL Research University, Paris, France ,Laboratoire d’Excellence CORAIL, Papetoai, French Polynesia
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