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Wagner I, Smolina I, Koop MEL, Bal T, Lizano AM, Choo LQ, Hofreiter M, Gennari E, de Sabata E, Shivji MS, Noble LR, Jones CS, Hoarau G. Genome analysis reveals three distinct lineages of the cosmopolitan white shark. Curr Biol 2024; 34:3582-3590.e4. [PMID: 39047735 DOI: 10.1016/j.cub.2024.06.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/22/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024]
Abstract
The white shark (Carcharodon carcharias) (Linnaeus, 1758), an iconic apex predator occurring in all oceans,1,2 is classified as Vulnerable globally3-with global abundance having dropped to 63% of 1970s estimates,4-and as Critically Endangered in Europe.5 Identification of evolutionary significant units and their management are crucial for conservation,6 especially as the white shark is facing various but often region-specific anthropogenic threats.7,8,9,10,11 Assessing connectivity in a cosmopolitan marine species requires worldwide sampling and high-resolution genetic markers.12 Both are lacking for the white shark, with studies to date typified by numerous but geographically limited sampling, and analyses relying largely on relatively small numbers of nuclear microsatellites,13,14,15,16,17,18,19 which can be plagued by various genotyping artefacts and thus require cautious interpretation.20 Sequencing and computational advances are finally allowing genomes21,22,23 to be leveraged into population studies,24,25,26,27 with datasets comprising thousands of single-nucleotide polymorphisms (SNPs). Here, combining target gene capture (TGC)28 sequencing (89 individuals, 4,000 SNPs) and whole-genome re-sequencing (17 individuals, 391,000 SNPs) with worldwide sampling across most of the distributional range, we identify three genetically distinct allopatric lineages (North Atlantic, Indo-Pacific, and North Pacific). These diverged 100,000-200,000 years ago during the Penultimate Glaciation, when low sea levels, different ocean currents, and water temperatures produced significant biogeographic barriers. Our results show that without high-resolution genomic analyses of samples representative of a species' range,12 the true extent of diversity, presence of past and contemporary barriers to gene flow, subsequent speciation, and local evolutionary events will remain enigmatic.
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Affiliation(s)
- Isabel Wagner
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Irina Smolina
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Martina E L Koop
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Thijs Bal
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Apollo M Lizano
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway; Marine Science Institute, University of the Philippines, Diliman Quezon City 1101, Philippines
| | - Le Qin Choo
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway; Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Enrico Gennari
- Oceans Research Institute, Mossel Bay 6500, South Africa
| | | | - Mahmood S Shivji
- Save Our Seas Shark Foundation Research Center and Guy Harvey Research Institute, Nova Southeastern University, Dania Beach, FL 33004, USA
| | - Leslie R Noble
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway; School of Biological Sciences, University of Aberdeen, Aberdeen, Scotland AB24 2TZ, UK.
| | - Catherine S Jones
- School of Biological Sciences, University of Aberdeen, Aberdeen, Scotland AB24 2TZ, UK.
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway.
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2
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Dolfo V, Boissin E, Lapinski M, Planes S. New insights into population structure, demographic history, and effective population size of the critically endangered blue shark Prionace glauca in the Mediterranean Sea. PLoS One 2024; 19:e0305608. [PMID: 38885253 PMCID: PMC11182550 DOI: 10.1371/journal.pone.0305608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/03/2024] [Indexed: 06/20/2024] Open
Abstract
The blue shark, Prionace glauca, is the most abundant pelagic shark in the open ocean but its vulnerability remains poorly understood while being one of the most fecund sharks. In the Mediterranean Sea, the blue shark is listed as Critically Endangered (CR) by the International Union for Conservation of Nature. The species is facing a strong decline due to fishing, and scientific data regarding its genetic structure and vulnerability are still lacking. Here, we investigated the genetic diversity, demographic history, and population structure of the blue shark within the Mediterranean Sea, from samples of the Gulf of Lion and Malta, using sequences of the mtDNA control region and 22 microsatellite markers. We also compared our mitochondrial data to previous studies to examine the Atlantic-Mediterranean population structure. We assessed the blue shark's genetic vulnerability in the Mediterranean basin by modelling its effective population size. Our results showed a genetic differentiation between the Atlantic and the Mediterranean basins, with limited gene flow between the two areas, and distinct demographic histories making the Mediterranean population an independent management unit. Within the Mediterranean Sea, no sign of population structure was detected, suggesting a single population across the Western and Central parts of the sea. The estimated effective population size was low and highlighted the high vulnerability of the Mediterranean blue shark population, as the estimated size we calculated might not be sufficient to ensure the long-term persistence of the population. Our data also provide additional evidence that the Gulf of Lion area acts as a nursery for P. glauca, where protection is essential for the conservation strategy of the species in the Mediterranean.
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Affiliation(s)
- Violaine Dolfo
- CRIOBE UAR3278, PSL Research University: EPHE–UPVD–CNRS, Perpignan, France
| | - Emilie Boissin
- CRIOBE UAR3278, PSL Research University: EPHE–UPVD–CNRS, Perpignan, France
- Laboratoire d’Excellence « CORAIL », PSL Research University: EPHE–UPVD–CNRS, Perpignan, France
| | - Matthieu Lapinski
- Association AILERONS, Université de Montpellier, Montpellier, France
| | - Serge Planes
- CRIOBE UAR3278, PSL Research University: EPHE–UPVD–CNRS, Perpignan, France
- Laboratoire d’Excellence « CORAIL », PSL Research University: EPHE–UPVD–CNRS, Perpignan, France
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Díaz-Arce N, Gagnaire PA, Richardson DE, Walter JF, Arnaud-Haond S, Fromentin JM, Brophy D, Lutcavage M, Addis P, Alemany F, Allman R, Deguara S, Fraile I, Goñi N, Hanke AR, Karakulak FS, Pacicco A, Quattro JM, Rooker JR, Arrizabalaga H, Rodríguez-Ezpeleta N. Unidirectional trans-Atlantic gene flow and a mixed spawning area shape the genetic connectivity of Atlantic bluefin tuna. Mol Ecol 2024; 33:e17188. [PMID: 37921120 DOI: 10.1111/mec.17188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/02/2023] [Accepted: 10/19/2023] [Indexed: 11/04/2023]
Abstract
The commercially important Atlantic bluefin tuna (Thunnus thynnus), a large migratory fish, has experienced notable recovery aided by accurate resource assessment and effective fisheries management efforts. Traditionally, this species has been perceived as consisting of eastern and western populations, spawning respectively in the Mediterranean Sea and the Gulf of Mexico, with mixing occurring throughout the Atlantic. However, recent studies have challenged this assumption by revealing weak genetic differentiation and identifying a previously unknown spawning ground in the Slope Sea used by Atlantic bluefin tuna of uncertain origin. To further understand the current and past population structure and connectivity of Atlantic bluefin tuna, we have assembled a unique dataset including thousands of genome-wide single-nucleotide polymorphisms (SNPs) from 500 larvae, young of the year and spawning adult samples covering the three spawning grounds and including individuals of other Thunnus species. Our analyses support two weakly differentiated but demographically connected ancestral populations that interbreed in the Slope Sea. Moreover, we also identified signatures of introgression from albacore (Thunnus alalunga) into the Atlantic bluefin tuna genome, exhibiting varied frequencies across spawning areas, indicating strong gene flow from the Mediterranean Sea towards the Slope Sea. We hypothesize that the observed genetic differentiation may be attributed to increased gene flow caused by a recent intensification of westward migration by the eastern population, which could have implications for the genetic diversity and conservation of western populations. Future conservation efforts should consider these findings to address potential genetic homogenization in the species.
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Affiliation(s)
- Natalia Díaz-Arce
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | | | - David E Richardson
- Northeast Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration (NOAA), Narragansett, Rhode Island, USA
| | - John F Walter
- Southeast Fisheries Sciences Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration (NOAA), Miami, Florida, USA
| | | | | | - Deirdre Brophy
- Marine and Freshwater Research Center, Atlantic Technological University (ATU), Galway City, Ireland
| | - Molly Lutcavage
- Large Pelagics Research Center, School for the Environment, University of Massachusetts Boston, Gloucester, Massachusetts, USA
| | - Piero Addis
- Department of Environmental and Life Science, University of Cagliari, Cagliari, Italy
| | - Francisco Alemany
- International Commission for the Conservation of Atlantic Tunas, GBYP, Madrid, Spain
| | - Robert Allman
- National Marine Fisheries Service, Southeast Fisheries Science Center, Panama City Laboratory, Panama City, Florida, USA
| | | | - Igaratza Fraile
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Spain
| | - Nicolas Goñi
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Spain
| | - Alex R Hanke
- St Andrews Biological Station, Fisheries and Oceans Canada, St. Andrews, New Brunswick, Canada
| | | | - Ashley Pacicco
- Cooperative Institute for Marine and Atmospheric Studies Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, Florida, USA
| | - Joseph M Quattro
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
| | - Jay R Rooker
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, Texas, USA
| | - Haritz Arrizabalaga
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Spain
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Humble E, Hosegood J, Carvalho G, de Bruyn M, Creer S, Stevens GMW, Armstrong A, Bonfil R, Deakos M, Fernando D, Froman N, Peel LR, Pollett S, Ponzo A, Stewart JD, Wintner S, Ogden R. Comparative population genomics of manta rays has global implications for management. Mol Ecol 2023. [PMID: 37994168 DOI: 10.1111/mec.17220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023]
Abstract
Understanding population connectivity and genetic diversity is of fundamental importance to conservation. However, in globally threatened marine megafauna, challenges remain due to their elusive nature and wide-ranging distributions. As overexploitation continues to threaten biodiversity across the globe, such knowledge gaps compromise both the suitability and effectiveness of management actions. Here, we use a comparative framework to investigate genetic differentiation and diversity of manta rays, one of the most iconic yet vulnerable groups of elasmobranchs on the planet. Despite their recent divergence, we show how oceanic manta rays (Mobula birostris) display significantly higher heterozygosity than reef manta rays (Mobula alfredi) and that M. birostris populations display higher connectivity worldwide. Through inferring modes of colonization, we reveal how both contemporary and historical forces have likely influenced these patterns, with important implications for population management. Our findings highlight the potential for fisheries to disrupt population dynamics at both local and global scales and therefore have direct relevance for international conservation of marine species.
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Affiliation(s)
- Emily Humble
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
- The Manta Trust, Catemwood House, Dorset, UK
| | - Jane Hosegood
- The Manta Trust, Catemwood House, Dorset, UK
- Molecular Ecology and Evolution Group, Bangor University, Bangor, UK
| | - Gary Carvalho
- Molecular Ecology and Evolution Group, Bangor University, Bangor, UK
| | - Mark de Bruyn
- Molecular Ecology and Evolution Group, Bangor University, Bangor, UK
- Australian Research Centre for Human Evolution, Griffith University, Nathan, Queensland, Australia
| | - Simon Creer
- Molecular Ecology and Evolution Group, Bangor University, Bangor, UK
| | | | - Amelia Armstrong
- School of Biomedical Sciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Ramon Bonfil
- Océanos Vivientes AC, Mexico City, Mexico
- Consejo Nacional de Humanidades Ciencia y Tecnología (CONAHCyT), Mexico City, Mexico
- El Colegio de la Frontera Sur, Unidad Chetumal, Chetumal, Mexico
| | - Mark Deakos
- Hawai'i Association for Marine Education and Research, Lahaina, USA
| | - Daniel Fernando
- The Manta Trust, Catemwood House, Dorset, UK
- Blue Resources Trust, Colombo, Sri Lanka
| | - Niv Froman
- The Manta Trust, Catemwood House, Dorset, UK
| | - Lauren R Peel
- The Manta Trust, Catemwood House, Dorset, UK
- Save Our Seas Foundation - D'Arros Research Centre, Geneva, Switzerland
- School of Biological Sciences, Oceans Institute and Oceans Graduate School, The University of Western Australia, Crawley, Western Australia, Australia
| | | | - Alessandro Ponzo
- Large Marine Vertebrates Research Institute Philippines, Jagna, Philippines
| | - Joshua D Stewart
- The Manta Trust, Catemwood House, Dorset, UK
- Ocean Ecology Lab, Marine Mammal Institute, Department of Fisheries, Wildlife & Conservation Sciences, Oregon State University, Newport, Oregon, USA
| | - Sabine Wintner
- KwaZulu-Natal Sharks Board, Umhlanga Rocks, South Africa
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
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Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations. Animals (Basel) 2023; 13:ani13061089. [PMID: 36978629 PMCID: PMC10044284 DOI: 10.3390/ani13061089] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023] Open
Abstract
Simple Summary In recent decades, societies, states and local authorities have become increasingly aware that for effective long-term management and protection of aquatic ecosystems and populations, it is necessary to take into account the genetic changes occurring in these populations. One type of high-resolution molecular marker suitable for studying the neutral and adaptive genetic diversity of populations is single nucleotide polymorphism (SNP). This review is an attempt to show the benefits of using SNPs to recognize natural populations of aquatic animals and detect the threats to them from accidentally or intentionally released farm animals, fishery and global climate changes. It is postulated that conservation actions should protect not only pristine natural populations that are endangered or overfished, but also protect populations of non-threatened species from unnecessarily released semi-domesticated animals. The enhancement of natural populations with farmed material usually reduces their genetic diversity. Experimental size-selective catches of artificially created populations have caused evolutionary changes in the life cycles of fishes. However, fishery-induced evolution in natural populations is difficult to observe. The negative measurable effects on populations can be expected when the number of breeding individuals is reduced below 100, which occurs very rarely in the sea and more often in fragmented freshwater streams, ponds and seasonal rivers. Abstract An increasing number of aquatic species have been studied for genetic polymorphism, which extends the knowledge on their natural populations. One type of high-resolution molecular marker suitable for studying the genetic diversity of large numbers of individuals is single nucleotide polymorphism (SNP). This review is an attempt to show the range of applications of SNPs in studies of natural populations of aquatic animals. In recent years, SNPs have been used in the genetic analysis of wild and enhanced fish and invertebrate populations in natural habitats, exploited migratory species in the oceans, migratory anadromous and freshwater fish and demersal species. SNPs have been used for the identification of species and their hybrids in natural environments, to study the genetic consequences of restocking for conservation purposes and the negative effects on natural populations of fish accidentally escaping from culture. SNPs are very useful for identifying genomic regions correlated with phenotypic variants relevant for wildlife protection, management and aquaculture. Experimental size-selective catches of populations created in tanks have caused evolutionary changes in life cycles of fishes. The research results have been discussed to clarify whether the fish populations in natural conditions can undergo changes due to selective harvesting targeting the fastest-growing fishes.
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