Population genetic studies revealed local adaptation in a high gene-flow marine fish, the small yellow croaker (Larimichthys polyactis)
The genetic differentiation of many marine fish species is low. Yet local adaptation may be common in marine fish species as the vast and changing marine environment provides more chances for natural selection. Here, we used anonymous as well as known protein gene linked microsatellites and mitochon...
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| description | The genetic differentiation of many marine fish species is low. Yet local adaptation may be common in marine fish species as the vast and changing marine environment provides more chances for natural selection. Here, we used anonymous as well as known protein gene linked microsatellites and mitochondrial DNA to detect the population structure of the small yellow croaker (Larimichthys polyactis) in the Northwest Pacific marginal seas. Among these loci, we detected at least two microsatellites, anonymous H16 and HSP27 to be clearly under diversifying selection in outlier tests. Sequence cloning and analysis revealed that H16 was located in the intron of BAHCC1 gene. Landscape genetic analysis showed that H16 mutations were significantly associated with temperature, which further supported the diversifying selection at this locus. These marker types presented different patterns of population structure: (i) mitochondrial DNA phylogeny showed no evidence of genetic divergence and demonstrated only one glacial linage; (ii) population differentiation using putatively neutral microsatellites presented a pattern of high gene flow in the L. polyactis. In addition, several genetic barriers were identified; (iii) the population differentiation pattern revealed by loci under diversifying selection was rather different from that revealed by putatively neutral loci. The results above suggest local adaptation in the small yellow croaker. In summary, population genetic studies based on different marker types disentangle the effects of demographic history, migration, genetic drift and local adaptation on population structure and also provide valuable new insights for the design of management strategies in L. polyactis. |
| doi_str_mv | 10.1371/journal.pone.0083493 |
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Yet local adaptation may be common in marine fish species as the vast and changing marine environment provides more chances for natural selection. Here, we used anonymous as well as known protein gene linked microsatellites and mitochondrial DNA to detect the population structure of the small yellow croaker (Larimichthys polyactis) in the Northwest Pacific marginal seas. Among these loci, we detected at least two microsatellites, anonymous H16 and HSP27 to be clearly under diversifying selection in outlier tests. Sequence cloning and analysis revealed that H16 was located in the intron of BAHCC1 gene. Landscape genetic analysis showed that H16 mutations were significantly associated with temperature, which further supported the diversifying selection at this locus. These marker types presented different patterns of population structure: (i) mitochondrial DNA phylogeny showed no evidence of genetic divergence and demonstrated only one glacial linage; (ii) population differentiation using putatively neutral microsatellites presented a pattern of high gene flow in the L. polyactis. In addition, several genetic barriers were identified; (iii) the population differentiation pattern revealed by loci under diversifying selection was rather different from that revealed by putatively neutral loci. The results above suggest local adaptation in the small yellow croaker. In summary, population genetic studies based on different marker types disentangle the effects of demographic history, migration, genetic drift and local adaptation on population structure and also provide valuable new insights for the design of management strategies in L. polyactis.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0083493</identifier><identifier>PMID: 24349521</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Adaptation ; Adaptation, Physiological - genetics ; Analysis ; Animal behavior ; Animals ; Cloning ; Clupea harengus ; Commercial fishing ; Coryphaenoides rupestris ; Demographics ; Deoxyribonucleic acid ; Differentiation ; Divergence ; DNA ; DNA structure ; DNA, Mitochondrial - genetics ; Fish ; Fisheries management ; Fishery sciences ; Fishes ; Fishing ; Gene flow ; Gene Flow - physiology ; Genes ; Genetic analysis ; Genetic aspects ; Genetic drift ; Genetic Loci - physiology ; Geology ; Heat shock proteins ; Hsp27 protein ; Laboratories ; Larimichthys polyactis ; Life sciences ; Loci ; Marine environment ; Marine fish ; Microsatellite Repeats - genetics ; Microsatellites ; Migration ; Mitochondrial DNA ; Mutation ; Natural selection ; Perciformes - genetics ; Phylogeny ; Population ; Population differentiation ; Population genetics ; Population structure ; Population studies ; Strategic planning (Business) ; Studies</subject><ispartof>PloS one, 2013-12, Vol.8 (12), p.e83493-e83493</ispartof><rights>COPYRIGHT 2013 Public Library of Science</rights><rights>2013 Wang 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>2013 Wang et al 2013 Wang et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c758t-c9f40175c2241292d7b79d94ee466128ef178c3a33df97d86b5835d96a34517b3</citedby><cites>FETCH-LOGICAL-c758t-c9f40175c2241292d7b79d94ee466128ef178c3a33df97d86b5835d96a34517b3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3861527/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3861527/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24349521$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Yao, Yong-Gang</contributor><creatorcontrib>Wang, Le</creatorcontrib><creatorcontrib>Liu, Shufang</creatorcontrib><creatorcontrib>Zhuang, Zhimeng</creatorcontrib><creatorcontrib>Guo, Liang</creatorcontrib><creatorcontrib>Meng, Zining</creatorcontrib><creatorcontrib>Lin, Haoran</creatorcontrib><title>Population genetic studies revealed local adaptation in a high gene-flow marine fish, the small yellow croaker (Larimichthys polyactis)</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The genetic differentiation of many marine fish species is low. Yet local adaptation may be common in marine fish species as the vast and changing marine environment provides more chances for natural selection. Here, we used anonymous as well as known protein gene linked microsatellites and mitochondrial DNA to detect the population structure of the small yellow croaker (Larimichthys polyactis) in the Northwest Pacific marginal seas. Among these loci, we detected at least two microsatellites, anonymous H16 and HSP27 to be clearly under diversifying selection in outlier tests. Sequence cloning and analysis revealed that H16 was located in the intron of BAHCC1 gene. Landscape genetic analysis showed that H16 mutations were significantly associated with temperature, which further supported the diversifying selection at this locus. These marker types presented different patterns of population structure: (i) mitochondrial DNA phylogeny showed no evidence of genetic divergence and demonstrated only one glacial linage; (ii) population differentiation using putatively neutral microsatellites presented a pattern of high gene flow in the L. polyactis. In addition, several genetic barriers were identified; (iii) the population differentiation pattern revealed by loci under diversifying selection was rather different from that revealed by putatively neutral loci. The results above suggest local adaptation in the small yellow croaker. In summary, population genetic studies based on different marker types disentangle the effects of demographic history, migration, genetic drift and local adaptation on population structure and also provide valuable new insights for the design of management strategies in L. polyactis.</description><subject>Adaptation</subject><subject>Adaptation, Physiological - genetics</subject><subject>Analysis</subject><subject>Animal behavior</subject><subject>Animals</subject><subject>Cloning</subject><subject>Clupea harengus</subject><subject>Commercial fishing</subject><subject>Coryphaenoides rupestris</subject><subject>Demographics</subject><subject>Deoxyribonucleic acid</subject><subject>Differentiation</subject><subject>Divergence</subject><subject>DNA</subject><subject>DNA structure</subject><subject>DNA, Mitochondrial - genetics</subject><subject>Fish</subject><subject>Fisheries management</subject><subject>Fishery sciences</subject><subject>Fishes</subject><subject>Fishing</subject><subject>Gene flow</subject><subject>Gene Flow - physiology</subject><subject>Genes</subject><subject>Genetic analysis</subject><subject>Genetic aspects</subject><subject>Genetic drift</subject><subject>Genetic Loci - physiology</subject><subject>Geology</subject><subject>Heat shock proteins</subject><subject>Hsp27 protein</subject><subject>Laboratories</subject><subject>Larimichthys polyactis</subject><subject>Life sciences</subject><subject>Loci</subject><subject>Marine environment</subject><subject>Marine fish</subject><subject>Microsatellite Repeats - genetics</subject><subject>Microsatellites</subject><subject>Migration</subject><subject>Mitochondrial DNA</subject><subject>Mutation</subject><subject>Natural selection</subject><subject>Perciformes - genetics</subject><subject>Phylogeny</subject><subject>Population</subject><subject>Population differentiation</subject><subject>Population genetics</subject><subject>Population structure</subject><subject>Population studies</subject><subject>Strategic planning (Business)</subject><subject>Studies</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</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>eNqNk12L1DAUhoso7rr6D0QDguyCMzZNP5IbYVn8GBhY8es2pOlJmzXTdJt0dX6Bf9t0prtMZS-kFy3J875J33NOFD3H8RKTAr-9skPfCrPsbAvLOKYkZeRBdIwZSRZ5EpOHB99H0RPnruI4IzTPH0dHSRroLMHH0Z_PthuM8Nq2qIYWvJbI-aHS4FAPNyAMVMhYKQwSlej8ntQtEqjRdbPTLJSxv9BG9LoFpLRr3iDfAHIbYQzaghl3ZW_FT-jR6TpgGy0b32wd6qzZCum1O3saPVLCOHg2vU-i7x_ef7v4tFhfflxdnK8XssioX0im0hgXmUySFCcsqYqyYBVLAdI8xwkFhQsqiSCkUqyoaF5mlGQVywVJM1yU5CR6ufftjHV8ytBxnOaUJSywgVjticqKK96F24p-y63QfLdg-5qLPsRkgDOR0IxksVCjPcSlgkopmiqSlaoUELzeTacN5QYqCa3vhZmZznda3fDa3vBQJ5wlRTA4nQx6ez2A83yjnQyRihbssLs3ywmjDAf01T_o_X83UXWoLNetsuFcOZry87SgBMcFY4Fa3kOFp4JQu9BwSof1meBsJgiMh9--FoNzfPX1y_-zlz_m7OsDtgnt6BtnzTB2oZuD6R4MjeZcD-ouZBzzcV5u0-DjvPBpXoLsxWGB7kS3A0L-AhZ4EfI</recordid><startdate>20131212</startdate><enddate>20131212</enddate><creator>Wang, Le</creator><creator>Liu, Shufang</creator><creator>Zhuang, Zhimeng</creator><creator>Guo, Liang</creator><creator>Meng, Zining</creator><creator>Lin, Haoran</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>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></search><sort><creationdate>20131212</creationdate><title>Population genetic studies revealed local adaptation in a high gene-flow marine fish, the small yellow croaker (Larimichthys polyactis)</title><author>Wang, Le ; Liu, Shufang ; Zhuang, Zhimeng ; Guo, Liang ; Meng, Zining ; Lin, Haoran</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c758t-c9f40175c2241292d7b79d94ee466128ef178c3a33df97d86b5835d96a34517b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Adaptation</topic><topic>Adaptation, Physiological - 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Yet local adaptation may be common in marine fish species as the vast and changing marine environment provides more chances for natural selection. Here, we used anonymous as well as known protein gene linked microsatellites and mitochondrial DNA to detect the population structure of the small yellow croaker (Larimichthys polyactis) in the Northwest Pacific marginal seas. Among these loci, we detected at least two microsatellites, anonymous H16 and HSP27 to be clearly under diversifying selection in outlier tests. Sequence cloning and analysis revealed that H16 was located in the intron of BAHCC1 gene. Landscape genetic analysis showed that H16 mutations were significantly associated with temperature, which further supported the diversifying selection at this locus. These marker types presented different patterns of population structure: (i) mitochondrial DNA phylogeny showed no evidence of genetic divergence and demonstrated only one glacial linage; (ii) population differentiation using putatively neutral microsatellites presented a pattern of high gene flow in the L. polyactis. In addition, several genetic barriers were identified; (iii) the population differentiation pattern revealed by loci under diversifying selection was rather different from that revealed by putatively neutral loci. The results above suggest local adaptation in the small yellow croaker. In summary, population genetic studies based on different marker types disentangle the effects of demographic history, migration, genetic drift and local adaptation on population structure and also provide valuable new insights for the design of management strategies in L. polyactis.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>24349521</pmid><doi>10.1371/journal.pone.0083493</doi><tpages>e83493</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Adaptation Adaptation, Physiological - genetics Analysis Animal behavior Animals Cloning Clupea harengus Commercial fishing Coryphaenoides rupestris Demographics Deoxyribonucleic acid Differentiation Divergence DNA DNA structure DNA, Mitochondrial - genetics Fish Fisheries management Fishery sciences Fishes Fishing Gene flow Gene Flow - physiology Genes Genetic analysis Genetic aspects Genetic drift Genetic Loci - physiology Geology Heat shock proteins Hsp27 protein Laboratories Larimichthys polyactis Life sciences Loci Marine environment Marine fish Microsatellite Repeats - genetics Microsatellites Migration Mitochondrial DNA Mutation Natural selection Perciformes - genetics Phylogeny Population Population differentiation Population genetics Population structure Population studies Strategic planning (Business) Studies |
| title | Population genetic studies revealed local adaptation in a high gene-flow marine fish, the small yellow croaker (Larimichthys polyactis) |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-28T22%3A19%3A20IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Population%20genetic%20studies%20revealed%20local%20adaptation%20in%20a%20high%20gene-flow%20marine%20fish,%20the%20small%20yellow%20croaker%20(Larimichthys%20polyactis)&rft.jtitle=PloS%20one&rft.au=Wang,%20Le&rft.date=2013-12-12&rft.volume=8&rft.issue=12&rft.spage=e83493&rft.epage=e83493&rft.pages=e83493-e83493&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0083493&rft_dat=%3Cgale_plos_%3EA478310799%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1468929835&rft_id=info:pmid/24349521&rft_galeid=A478310799&rft_doaj_id=oai_doaj_org_article_9a285350afa345e0bfedff84f35bfbae&rfr_iscdi=true |