Genome-wide SNP analyses reveal population structure of Portunus pelagicus along Vietnam coastline
The blue swimming crab (Portunus pelagicus Linnaeus, 1758) is one of the commercially exploited crab fishery resources in Vietnam. This is the first study to provide a broad survey of genetic diversity, population structure and migration patterns of P. pelagicus along the Vietnamese coastline. The c...
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| Veröffentlicht in: | PloS one 2019-11, Vol.14 (11), p.e0224473-e0224473 |
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| description | The blue swimming crab (Portunus pelagicus Linnaeus, 1758) is one of the commercially exploited crab fishery resources in Vietnam. This is the first study to provide a broad survey of genetic diversity, population structure and migration patterns of P. pelagicus along the Vietnamese coastline. The crab samples were collected from northern, central and southern Vietnam. Here, we used a panel of single nucleotide polymorphisms (SNPs) generated from restriction site-associated DNA sequencing (RADseq). After removing 32 outlier loci, 306 putatively neutral SNPs from 96 individuals were used to assess fine-scale population structure of blue swimming crab. The mean observed heterozygosity (Ho) and expected heterozygosity (He) per locus was 0.196 and 0.223, respectively. Pairwise Fst and hierarchical AMOVA supported significant differentiation of central and northern from southern populations (P |
| doi_str_mv | 10.1371/journal.pone.0224473 |
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This is the first study to provide a broad survey of genetic diversity, population structure and migration patterns of P. pelagicus along the Vietnamese coastline. The crab samples were collected from northern, central and southern Vietnam. Here, we used a panel of single nucleotide polymorphisms (SNPs) generated from restriction site-associated DNA sequencing (RADseq). After removing 32 outlier loci, 306 putatively neutral SNPs from 96 individuals were used to assess fine-scale population structure of blue swimming crab. The mean observed heterozygosity (Ho) and expected heterozygosity (He) per locus was 0.196 and 0.223, respectively. Pairwise Fst and hierarchical AMOVA supported significant differentiation of central and northern from southern populations (P<0.01). Population structure analyses revealed that P. pelagicus in the south is a separate fisheries unit from the north and center. Contemporary migration patterns supported high migration between northern and central populations and restricted genetic exchange within the southern population. In contrast, historic gene flow provides strong evidence for single panmictic population. The results are useful for understanding current status of P. pelagicus in the wild under an environment changing due to natural and anthropogenic stresses, with implications for fisheries management.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0224473</identifier><identifier>PMID: 31689298</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Animals ; Anthropogenic factors ; Arthropods ; Biodiversity ; Biology ; Biology and Life Sciences ; Biotechnology ; Brachyura - genetics ; Chromosomes ; Climate change ; Coastlines ; Coasts ; Connectivity ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; Female ; Fisheries ; Fisheries - statistics & numerical data ; Fisheries management ; Fishery management ; Fishery resources ; Gene Flow ; Gene sequencing ; Genes ; Genetic aspects ; Genetic diversity ; Genetic polymorphisms ; Genetic research ; Genomes ; Genomics ; Heterozygosity ; Hydrology ; Loci ; Male ; Medicine and Health Sciences ; Mitochondrial DNA ; Nucleotides ; Ocean circulation ; Oceanography ; Outliers (statistics) ; People and Places ; Polymorphism, Single Nucleotide ; Population ; Population Dynamics - statistics & numerical data ; Population genetics ; Population structure ; Populations ; Portunus pelagicus ; Sequence Analysis, DNA ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Social Sciences ; Swimming ; Vietnam</subject><ispartof>PloS one, 2019-11, Vol.14 (11), p.e0224473-e0224473</ispartof><rights>COPYRIGHT 2019 Public Library of Science</rights><rights>2019 Dang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2019 Dang et al 2019 Dang et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-212dd431514946f06f862e2a283c5890a94eee151e06ee8e5414ee3317afbe763</citedby><cites>FETCH-LOGICAL-c692t-212dd431514946f06f862e2a283c5890a94eee151e06ee8e5414ee3317afbe763</cites><orcidid>0000-0002-7666-8029 ; 0000-0002-8961-7319</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6830773/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6830773/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2100,2926,23865,27923,27924,53790,53792,79371,79372</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31689298$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Palsson, Arnar</contributor><creatorcontrib>Dang, Binh Thuy</creatorcontrib><creatorcontrib>Rahman, Muhammad Arifur</creatorcontrib><creatorcontrib>Tran, Sang Quang</creatorcontrib><creatorcontrib>Glenner, Henrik</creatorcontrib><title>Genome-wide SNP analyses reveal population structure of Portunus pelagicus along Vietnam coastline</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The blue swimming crab (Portunus pelagicus Linnaeus, 1758) is one of the commercially exploited crab fishery resources in Vietnam. This is the first study to provide a broad survey of genetic diversity, population structure and migration patterns of P. pelagicus along the Vietnamese coastline. The crab samples were collected from northern, central and southern Vietnam. Here, we used a panel of single nucleotide polymorphisms (SNPs) generated from restriction site-associated DNA sequencing (RADseq). After removing 32 outlier loci, 306 putatively neutral SNPs from 96 individuals were used to assess fine-scale population structure of blue swimming crab. The mean observed heterozygosity (Ho) and expected heterozygosity (He) per locus was 0.196 and 0.223, respectively. Pairwise Fst and hierarchical AMOVA supported significant differentiation of central and northern from southern populations (P<0.01). Population structure analyses revealed that P. pelagicus in the south is a separate fisheries unit from the north and center. Contemporary migration patterns supported high migration between northern and central populations and restricted genetic exchange within the southern population. In contrast, historic gene flow provides strong evidence for single panmictic population. The results are useful for understanding current status of P. pelagicus in the wild under an environment changing due to natural and anthropogenic stresses, with implications for fisheries management.</description><subject>Animals</subject><subject>Anthropogenic factors</subject><subject>Arthropods</subject><subject>Biodiversity</subject><subject>Biology</subject><subject>Biology and Life Sciences</subject><subject>Biotechnology</subject><subject>Brachyura - genetics</subject><subject>Chromosomes</subject><subject>Climate change</subject><subject>Coastlines</subject><subject>Coasts</subject><subject>Connectivity</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>Female</subject><subject>Fisheries</subject><subject>Fisheries - statistics & numerical data</subject><subject>Fisheries management</subject><subject>Fishery management</subject><subject>Fishery resources</subject><subject>Gene Flow</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>Genetic polymorphisms</subject><subject>Genetic research</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Heterozygosity</subject><subject>Hydrology</subject><subject>Loci</subject><subject>Male</subject><subject>Medicine and Health Sciences</subject><subject>Mitochondrial DNA</subject><subject>Nucleotides</subject><subject>Ocean circulation</subject><subject>Oceanography</subject><subject>Outliers (statistics)</subject><subject>People and Places</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Population</subject><subject>Population Dynamics - statistics & numerical data</subject><subject>Population genetics</subject><subject>Population structure</subject><subject>Populations</subject><subject>Portunus pelagicus</subject><subject>Sequence Analysis, DNA</subject><subject>Single nucleotide polymorphisms</subject><subject>Single-nucleotide polymorphism</subject><subject>Social Sciences</subject><subject>Swimming</subject><subject>Vietnam</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNk01v1DAQhiMEoqXwDxBEQkJw2MVfcZILUlVBWamiFYVeLa8zybry2sF2Cv33OGxabVAPyAdb42feGY9nsuwlRktMS_zh2g3eSrPsnYUlIoSxkj7KDnFNyYITRB_vnQ-yZyFcI1TQivOn2QHFvKpJXR1m61OwbguLX7qB_PLrRS6T5m2AkHu4AWny3vWDkVE7m4foBxUHD7lr8wvn42CHkPdgZKdVOknjbJdfaYhWbnPlZIhGW3iePWmlCfBi2o-yH58_fT_5sjg7P12dHJ8tFK9JXBBMmoZRXGBWM94i3lacAJGkoqqoaiRrBgDpGhAHqKBgOBkoxaVs11ByepS93un2xgUxlScIQnEqTkXrkVjtiMbJa9F7vZX-VjipxV-D852QPmplQKwL1aI1L7nCJQOOK05LVqc8eNsUDWVJ6-MUbVhvoVFgo5dmJjq_sXojOncjeEVRWdIk8G4S8O7nACGKrQ4KjJEW3LDLuyhwQXFC3_yDPvy6iepkeoC2rUtx1SgqjjliVcE4H_NePkCl1cBWq9RLrU72mcP7mUNiIvyOnRxCEKvLb__Pnl_N2bd77Cb1WtwEZ4ax1cIcZDtQeReCh_a-yBiJcRTuqiHGURDTKCS3V_sfdO901_v0D-_dA2w</recordid><startdate>20191105</startdate><enddate>20191105</enddate><creator>Dang, Binh Thuy</creator><creator>Rahman, Muhammad Arifur</creator><creator>Tran, Sang Quang</creator><creator>Glenner, Henrik</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-7666-8029</orcidid><orcidid>https://orcid.org/0000-0002-8961-7319</orcidid></search><sort><creationdate>20191105</creationdate><title>Genome-wide SNP analyses reveal population structure of Portunus pelagicus along Vietnam coastline</title><author>Dang, Binh Thuy ; Rahman, Muhammad Arifur ; Tran, Sang Quang ; Glenner, Henrik</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-212dd431514946f06f862e2a283c5890a94eee151e06ee8e5414ee3317afbe763</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Animals</topic><topic>Anthropogenic factors</topic><topic>Arthropods</topic><topic>Biodiversity</topic><topic>Biology</topic><topic>Biology and Life Sciences</topic><topic>Biotechnology</topic><topic>Brachyura - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Dang, Binh Thuy</au><au>Rahman, Muhammad Arifur</au><au>Tran, Sang Quang</au><au>Glenner, Henrik</au><au>Palsson, Arnar</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-wide SNP analyses reveal population structure of Portunus pelagicus along Vietnam coastline</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2019-11-05</date><risdate>2019</risdate><volume>14</volume><issue>11</issue><spage>e0224473</spage><epage>e0224473</epage><pages>e0224473-e0224473</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The blue swimming crab (Portunus pelagicus Linnaeus, 1758) is one of the commercially exploited crab fishery resources in Vietnam. This is the first study to provide a broad survey of genetic diversity, population structure and migration patterns of P. pelagicus along the Vietnamese coastline. The crab samples were collected from northern, central and southern Vietnam. Here, we used a panel of single nucleotide polymorphisms (SNPs) generated from restriction site-associated DNA sequencing (RADseq). After removing 32 outlier loci, 306 putatively neutral SNPs from 96 individuals were used to assess fine-scale population structure of blue swimming crab. The mean observed heterozygosity (Ho) and expected heterozygosity (He) per locus was 0.196 and 0.223, respectively. Pairwise Fst and hierarchical AMOVA supported significant differentiation of central and northern from southern populations (P<0.01). Population structure analyses revealed that P. pelagicus in the south is a separate fisheries unit from the north and center. Contemporary migration patterns supported high migration between northern and central populations and restricted genetic exchange within the southern population. In contrast, historic gene flow provides strong evidence for single panmictic population. The results are useful for understanding current status of P. pelagicus in the wild under an environment changing due to natural and anthropogenic stresses, with implications for fisheries management.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>31689298</pmid><doi>10.1371/journal.pone.0224473</doi><tpages>e0224473</tpages><orcidid>https://orcid.org/0000-0002-7666-8029</orcidid><orcidid>https://orcid.org/0000-0002-8961-7319</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Animals Anthropogenic factors Arthropods Biodiversity Biology Biology and Life Sciences Biotechnology Brachyura - genetics Chromosomes Climate change Coastlines Coasts Connectivity Deoxyribonucleic acid DNA DNA sequencing Female Fisheries Fisheries - statistics & numerical data Fisheries management Fishery management Fishery resources Gene Flow Gene sequencing Genes Genetic aspects Genetic diversity Genetic polymorphisms Genetic research Genomes Genomics Heterozygosity Hydrology Loci Male Medicine and Health Sciences Mitochondrial DNA Nucleotides Ocean circulation Oceanography Outliers (statistics) People and Places Polymorphism, Single Nucleotide Population Population Dynamics - statistics & numerical data Population genetics Population structure Populations Portunus pelagicus Sequence Analysis, DNA Single nucleotide polymorphisms Single-nucleotide polymorphism Social Sciences Swimming Vietnam |
| title | Genome-wide SNP analyses reveal population structure of Portunus pelagicus along Vietnam coastline |
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