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Bertram A, Fairclough D, Sandoval‐Castillo J, Brauer C, Fowler A, Wellenreuther M, Beheregaray LB. Fisheries genomics of snapper (
Chrysophrys auratus
) along the west Australian coast. Evol Appl 2022; 15:1099-1114. [PMID: 35899251 PMCID: PMC9309437 DOI: 10.1111/eva.13439] [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: 01/18/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/28/2022] Open
Abstract
The efficacy of fisheries management strategies depends on stock assessment and management actions being carried out at appropriate spatial scales. This requires understanding of spatial and temporal population structure and connectivity, which is challenging in weakly structured and highly connected marine populations. We carried out a population genomics study of the heavily exploited snapper (Chrysophrys auratus) along ~2600 km of the Australian coastline, with a focus on Western Australia (WA). We used 10,903 filtered SNPs in 341 individuals from eight sampling locations to characterize population structure and connectivity in snapper across WA and to assess if current spatial scales of stock assessment and management agree with evidence from population genomics. Our dataset also enabled us to investigate temporal stability in population structure as well as connectivity between WA and its nearest, eastern jurisdictional neighbour. As expected for a species influenced by the extensive ocean boundary current in the region, low genetic differentiation and high connectivity were uncovered across WA. However, we did detect strong isolation by distance and genetic discontinuities in the mid‐west and south‐east. The discontinuities correlate with boundaries between biogeographic regions, influenced by on‐shelf oceanography, and the sites of important spawning aggregations. We also detected temporal instability in genetic structure at one of our sites, possibly due to interannual variability in recruitment in adjacent regions. Our results partly contrast with the current spatial management of snapper in WA, indicating the likely benefits of a review. This study supports the value of population genomic surveys in informing the management of weakly structured and wide‐ranging marine fishery resources.
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Affiliation(s)
- Andrea Bertram
- Molecular Ecology Laboratory, College of Science and Engineering Flinders University Bedford Park SA Australia
| | - David Fairclough
- Aquatic Sciences and Assessment, Department of Primary Industries and Regional Development, Hillarys WA Australia
| | - Jonathan Sandoval‐Castillo
- Molecular Ecology Laboratory, College of Science and Engineering Flinders University Bedford Park SA Australia
| | - Chris Brauer
- Molecular Ecology Laboratory, College of Science and Engineering Flinders University Bedford Park SA Australia
| | - Anthony Fowler
- Aquatic Sciences South Australian Research and Development Institute SA Australia
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Limited Nelson New Zealand
- The School of Biological Sciences University of Auckland Auckland New Zealand
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering Flinders University Bedford Park SA Australia
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Population genetics reveals divergent lineages and ongoing hybridization in a declining migratory fish species complex. Heredity (Edinb) 2022; 129:137-151. [PMID: 35665777 PMCID: PMC9338086 DOI: 10.1038/s41437-022-00547-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 11/08/2022] Open
Abstract
Deciphering the effects of historical and recent demographic processes responsible for the spatial patterns of genetic diversity and structure is a key objective in evolutionary and conservation biology. Using population genetic analyses, we investigated the demographic history, the contemporary genetic diversity and structure, and the occurrence of hybridization and introgression of two species of anadromous fish with contrasting life history strategies and which have undergone recent demographic declines, the allis shad (Alosa alosa) and the twaite shad (Alosa fallax). We genotyped 706 individuals from 20 rivers and 5 sites at sea in Southern Europe at thirteen microsatellite markers. Genetic structure between populations was lower for the nearly semelparous species A. alosa, which disperses greater distances compared to the iteroparous species, A. fallax. Individuals caught at sea were assigned at the river level for A. fallax and at the region level for A. alosa. Using an approximate Bayesian computation framework, we inferred that the most likely long term historical divergence scenario between both species and lineages involved historical separation followed by secondary contact accompanied by strong population size decline. Accordingly, we found evidence for contemporary hybridization and bidirectional introgression due to gene flow between both species and lineages. Moreover, our results support the existence of at least one distinct species in the Mediterrannean sea: A. agone in Golfe du Lion area, and another divergent lineage in Corsica. Overall, our results shed light on the interplay between historical and recent demographic processes and life history strategies in shaping population genetic diversity and structure of closely related species. The recent demographic decline of these species' populations and their hybridization should be carefully considered while implementing conservation programs.
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Tran Lu Y A, Ruault S, Daguin-Thiébaut C, Castel J, Bierne N, Broquet T, Wincker P, Perdereau A, Arnaud-Haond S, Gagnaire PA, Jollivet D, Hourdez S, Bonhomme F. Subtle limits to connectivity revealed by outlier loci within two divergent metapopulations of the deep-sea hydrothermal gastropod Ifremeria nautilei. Mol Ecol 2022; 31:2796-2813. [PMID: 35305041 DOI: 10.1111/mec.16430] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 02/14/2022] [Accepted: 03/01/2022] [Indexed: 11/30/2022]
Abstract
Hydrothermal vents form archipelagos of ephemeral deep-sea habitats that raise interesting questions about the evolution and dynamics of the associated endemic fauna, constantly subject to extinction-recolonization processes. These metal-rich environments are coveted for the mineral resources they harbor, thus raising recent conservation concerns. The evolutionary fate and demographic resilience of hydrothermal species strongly depend on the degree of connectivity among and within their fragmented metapopulations. In the deep sea, however, assessing connectivity is difficult and usually requires indirect genetic approaches. Improved detection of fine-scale genetic connectivity is now possible based on genome-wide screening for genetic differentiation. Here, we explored population connectivity in the hydrothermal vent snail Ifremeria nautilei across its species range encompassing five distinct back-arc basins in the Southwest Pacific. The global analysis, based on 10 570 single nucleotide polymorphism (SNP) markers derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), depicted two semi-isolated and homogeneous genetic clusters. Demo-genetic modeling suggests that these two groups began to diverge about 70 000 generations ago, but continue to exhibit weak and slightly asymmetrical gene flow. Furthermore, a careful analysis of outlier loci showed subtle limitations to connectivity between neighboring basins within both groups. This finding indicates that migration is not strong enough to totally counterbalance drift or local selection, hence questioning the potential for demographic resilience at this latter geographical scale. These results illustrate the potential of large genomic datasets to understand fine-scale connectivity patterns in hydrothermal vents and the deep sea.
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Affiliation(s)
- Adrien Tran Lu Y
- ISEM, Institut des Sciences de l'Evolution, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Stéphanie Ruault
- Sorbonne Université, CNRS, UMR 7144, 'Dynamique de la Diversité Marine' (DyDiv) Lab, Station biologique de Roscoff, Place G. Teissier, 29680, Roscoff, France
| | - Claire Daguin-Thiébaut
- Sorbonne Université, CNRS, UMR 7144, 'Dynamique de la Diversité Marine' (DyDiv) Lab, Station biologique de Roscoff, Place G. Teissier, 29680, Roscoff, France
| | - Jade Castel
- Sorbonne Université, CNRS, UMR 7144, 'Dynamique de la Diversité Marine' (DyDiv) Lab, Station biologique de Roscoff, Place G. Teissier, 29680, Roscoff, France
| | - Nicolas Bierne
- ISEM, Institut des Sciences de l'Evolution, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Thomas Broquet
- Sorbonne Université, CNRS, UMR 7144, 'Dynamique de la Diversité Marine' (DyDiv) Lab, Station biologique de Roscoff, Place G. Teissier, 29680, Roscoff, France
| | - Patrick Wincker
- Génomique Métabolique, Génoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Aude Perdereau
- Génomique Métabolique, Génoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Sophie Arnaud-Haond
- MARBEC, Marine Biodiversity Exploitation and Conservation, Univ Montpellier, CNRS, IFREMER, IRD, Sète, France
| | | | - Didier Jollivet
- Sorbonne Université, CNRS, UMR 7144, 'Dynamique de la Diversité Marine' (DyDiv) Lab, Station biologique de Roscoff, Place G. Teissier, 29680, Roscoff, France
| | - Stéphane Hourdez
- Sorbonne Université, CNRS, UMR 8222, Laboratoire d'Ecogéochimie des Environnements Benthiques, Observatoire Océanologique de Banyuls, Avenue Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | - François Bonhomme
- ISEM, Institut des Sciences de l'Evolution, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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