Genetic differentiation and delimitation between ecologically diverged Populus euphratica and P. pruinosa
The fixed genetic differences between ecologically divergent species were found to change greatly depending on the markers examined. With such species it is difficult to differentiate between shared ancestral polymorphisms and past introgressions between the diverging species. In order to disentangl...
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| description | The fixed genetic differences between ecologically divergent species were found to change greatly depending on the markers examined. With such species it is difficult to differentiate between shared ancestral polymorphisms and past introgressions between the diverging species. In order to disentangle these possibilities and provide a further case for DNA barcoding of plants, we examine genetic differentiation between two ecologically divergent poplar species, Populus euphratica Oliver and P. pruinosa Schrenk using three different types of genetic marker.
We genotyped 290 individuals from 29 allopatric and sympatric populations, using chloroplast (cp) DNA, nuclear (nr) ITS sequences and eight simple sequence repeat (SSR) loci. Three major cpDNA haplotypes were widely shared between the two species and between-species cpDNA differentiation (F(CT)) was very low, even lower than among single species populations. The average SSR F(CT) values were higher. Bayesian clustering analysis of all loci allowed a clear delineation of the two species. Gene flow, determined by examining all SSR loci, was obvious but only slightly asymmetrical. However, the two species were almost fixed for two different nrITS genotypes that had the highest F(CT), although a few introgressed individuals were detected both in allopatric and sympatric populations.
The two species shared numerous ancestral polymorphisms at cpDNA and a few SSR loci. Both ITS and a combination of nuclear SSR data could be used to differentiate between the two species. Introgressions and gene flow were obvious between the two species either during or after their divergence. Our findings underscore the complex genetic differentiations between ecologically diverged species and highlight the importance of nuclear DNA (especially ITS) differentiation for delimiting closely related plant species. |
| doi_str_mv | 10.1371/journal.pone.0026530 |
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We genotyped 290 individuals from 29 allopatric and sympatric populations, using chloroplast (cp) DNA, nuclear (nr) ITS sequences and eight simple sequence repeat (SSR) loci. Three major cpDNA haplotypes were widely shared between the two species and between-species cpDNA differentiation (F(CT)) was very low, even lower than among single species populations. The average SSR F(CT) values were higher. Bayesian clustering analysis of all loci allowed a clear delineation of the two species. Gene flow, determined by examining all SSR loci, was obvious but only slightly asymmetrical. However, the two species were almost fixed for two different nrITS genotypes that had the highest F(CT), although a few introgressed individuals were detected both in allopatric and sympatric populations.
The two species shared numerous ancestral polymorphisms at cpDNA and a few SSR loci. Both ITS and a combination of nuclear SSR data could be used to differentiate between the two species. Introgressions and gene flow were obvious between the two species either during or after their divergence. Our findings underscore the complex genetic differentiations between ecologically diverged species and highlight the importance of nuclear DNA (especially ITS) differentiation for delimiting closely related plant species.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0026530</identifier><identifier>PMID: 22028897</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Bar codes ; Bayesian analysis ; Bioinformatics ; Biology ; Chloroplast DNA ; Chloroplasts ; Cluster analysis ; Clustering ; Data analysis ; Deoxyribonucleic acid ; Desert Climate ; Deserts ; Differentiation ; Divergence ; DNA ; DNA, Chloroplast - genetics ; DNA, Ribosomal Spacer - genetics ; Ecological and Environmental Phenomena ; Ecology ; Ecumenism ; Evolution, Molecular ; Farming ; Gene flow ; Gene sequencing ; Genes ; Genetic aspects ; Genetic Loci - genetics ; Genetic markers ; Genetic Markers - genetics ; Genomics ; Genotypes ; Grasslands ; Haplotypes ; Hypotheses ; Integrated software ; Laboratories ; Leaves ; Loci ; Microsatellite Repeats - genetics ; Migration ; Nucleotide sequence ; Phylogeny ; Polymorphism, Genetic - genetics ; Poplar ; Population genetics ; Populations ; Populus - genetics ; Populus euphratica ; Populus pruinosa ; Software packages ; Species ; Sympatric populations</subject><ispartof>PloS one, 2011-10, Vol.6 (10), p.e26530</ispartof><rights>COPYRIGHT 2011 Public Library of Science</rights><rights>2011 Wang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://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>Wang et al. 2011</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c728t-b890f634f0737ff61e73ed83805983f65b19e60d720dfd4eaeb22d82440f38113</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3197521/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3197521/$$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/22028897$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-162361$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><contributor>DeSalle, Robert</contributor><creatorcontrib>Wang, Juan</creatorcontrib><creatorcontrib>Wu, Yuxia</creatorcontrib><creatorcontrib>Ren, Guangpeng</creatorcontrib><creatorcontrib>Guo, Qiuhong</creatorcontrib><creatorcontrib>Liu, Jianquan</creatorcontrib><creatorcontrib>Lascoux, Martin</creatorcontrib><title>Genetic differentiation and delimitation between ecologically diverged Populus euphratica and P. pruinosa</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The fixed genetic differences between ecologically divergent species were found to change greatly depending on the markers examined. With such species it is difficult to differentiate between shared ancestral polymorphisms and past introgressions between the diverging species. In order to disentangle these possibilities and provide a further case for DNA barcoding of plants, we examine genetic differentiation between two ecologically divergent poplar species, Populus euphratica Oliver and P. pruinosa Schrenk using three different types of genetic marker.
We genotyped 290 individuals from 29 allopatric and sympatric populations, using chloroplast (cp) DNA, nuclear (nr) ITS sequences and eight simple sequence repeat (SSR) loci. Three major cpDNA haplotypes were widely shared between the two species and between-species cpDNA differentiation (F(CT)) was very low, even lower than among single species populations. The average SSR F(CT) values were higher. Bayesian clustering analysis of all loci allowed a clear delineation of the two species. Gene flow, determined by examining all SSR loci, was obvious but only slightly asymmetrical. However, the two species were almost fixed for two different nrITS genotypes that had the highest F(CT), although a few introgressed individuals were detected both in allopatric and sympatric populations.
The two species shared numerous ancestral polymorphisms at cpDNA and a few SSR loci. Both ITS and a combination of nuclear SSR data could be used to differentiate between the two species. Introgressions and gene flow were obvious between the two species either during or after their divergence. Our findings underscore the complex genetic differentiations between ecologically diverged species and highlight the importance of nuclear DNA (especially ITS) differentiation for delimiting closely related plant species.</description><subject>Bar codes</subject><subject>Bayesian analysis</subject><subject>Bioinformatics</subject><subject>Biology</subject><subject>Chloroplast DNA</subject><subject>Chloroplasts</subject><subject>Cluster analysis</subject><subject>Clustering</subject><subject>Data analysis</subject><subject>Deoxyribonucleic acid</subject><subject>Desert Climate</subject><subject>Deserts</subject><subject>Differentiation</subject><subject>Divergence</subject><subject>DNA</subject><subject>DNA, Chloroplast - genetics</subject><subject>DNA, Ribosomal Spacer - genetics</subject><subject>Ecological and Environmental Phenomena</subject><subject>Ecology</subject><subject>Ecumenism</subject><subject>Evolution, Molecular</subject><subject>Farming</subject><subject>Gene flow</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic Loci - genetics</subject><subject>Genetic markers</subject><subject>Genetic Markers - genetics</subject><subject>Genomics</subject><subject>Genotypes</subject><subject>Grasslands</subject><subject>Haplotypes</subject><subject>Hypotheses</subject><subject>Integrated software</subject><subject>Laboratories</subject><subject>Leaves</subject><subject>Loci</subject><subject>Microsatellite Repeats - genetics</subject><subject>Migration</subject><subject>Nucleotide sequence</subject><subject>Phylogeny</subject><subject>Polymorphism, Genetic - genetics</subject><subject>Poplar</subject><subject>Population genetics</subject><subject>Populations</subject><subject>Populus - genetics</subject><subject>Populus euphratica</subject><subject>Populus pruinosa</subject><subject>Software packages</subject><subject>Species</subject><subject>Sympatric populations</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</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>eNqNk11rFDEUhgdRbK3-A9EBQRDcNR8zmcyNsFStC4UWP3obMpOT3ZTsZEwmrf33ZnenZQcUJBcJJ8_7zpyXnCx7idEc0wp_uHbRd9LOe9fBHCHCSooeZce4pmTGCKKPD85H2bMQrhEqKWfsaXZECCKc19VxZs6gg8G0uTJag4duMHIwrstlp3IF1mzMsC80MNwCdDm0zrqVaaW1d0l1A34FKr90fbQx5BD7tU-CVu4cLud576PpXJDPsyda2gAvxv0k-_nl84_Tr7Pzi7Pl6eJ81laED7OG10gzWmhU0UprhqGioDjlqKw51axscA0MqYogpVUBEhpCFCdFgTTlGNOT7PXet7cuiDGlIDBFNaspw0UilntCOXktem820t8JJ43YFZxfCelTCxYEABAOZa0bxYqmlVKqUjKsq0JpWgJKXu_3XuEW-thM3D6Zq8XOLUaBGUnfTvjH8ediswHVpry9tBPV9KYza7FyN4LiuirJ1uDNaODdrwhh-EeHI7WSqQnTaZfM2o0JrVgUFeOsKgqaqPlfqLQUbEybnpU2qT4RvJsIEjPA72ElYwhi-f3b_7MXV1P27QG7BmmHdXA2bt9dmILFHmy9C8GDfkgOI7Gdivs0xHYqxDgVSfbqMPUH0f0Y0D-qggnV</recordid><startdate>20111019</startdate><enddate>20111019</enddate><creator>Wang, Juan</creator><creator>Wu, Yuxia</creator><creator>Ren, Guangpeng</creator><creator>Guo, Qiuhong</creator><creator>Liu, Jianquan</creator><creator>Lascoux, Martin</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>5PM</scope><scope>ADTPV</scope><scope>AOWAS</scope><scope>DF2</scope><scope>DOA</scope></search><sort><creationdate>20111019</creationdate><title>Genetic differentiation and delimitation between ecologically diverged Populus euphratica and P. pruinosa</title><author>Wang, Juan ; Wu, Yuxia ; Ren, Guangpeng ; Guo, Qiuhong ; Liu, Jianquan ; Lascoux, Martin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c728t-b890f634f0737ff61e73ed83805983f65b19e60d720dfd4eaeb22d82440f38113</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Bar codes</topic><topic>Bayesian analysis</topic><topic>Bioinformatics</topic><topic>Biology</topic><topic>Chloroplast DNA</topic><topic>Chloroplasts</topic><topic>Cluster analysis</topic><topic>Clustering</topic><topic>Data analysis</topic><topic>Deoxyribonucleic acid</topic><topic>Desert Climate</topic><topic>Deserts</topic><topic>Differentiation</topic><topic>Divergence</topic><topic>DNA</topic><topic>DNA, Chloroplast - genetics</topic><topic>DNA, Ribosomal Spacer - genetics</topic><topic>Ecological and Environmental Phenomena</topic><topic>Ecology</topic><topic>Ecumenism</topic><topic>Evolution, Molecular</topic><topic>Farming</topic><topic>Gene flow</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genetic Loci - genetics</topic><topic>Genetic markers</topic><topic>Genetic Markers - genetics</topic><topic>Genomics</topic><topic>Genotypes</topic><topic>Grasslands</topic><topic>Haplotypes</topic><topic>Hypotheses</topic><topic>Integrated software</topic><topic>Laboratories</topic><topic>Leaves</topic><topic>Loci</topic><topic>Microsatellite Repeats - genetics</topic><topic>Migration</topic><topic>Nucleotide sequence</topic><topic>Phylogeny</topic><topic>Polymorphism, Genetic - genetics</topic><topic>Poplar</topic><topic>Population genetics</topic><topic>Populations</topic><topic>Populus - genetics</topic><topic>Populus euphratica</topic><topic>Populus pruinosa</topic><topic>Software packages</topic><topic>Species</topic><topic>Sympatric populations</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wang, Juan</creatorcontrib><creatorcontrib>Wu, Yuxia</creatorcontrib><creatorcontrib>Ren, Guangpeng</creatorcontrib><creatorcontrib>Guo, Qiuhong</creatorcontrib><creatorcontrib>Liu, Jianquan</creatorcontrib><creatorcontrib>Lascoux, Martin</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - 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With such species it is difficult to differentiate between shared ancestral polymorphisms and past introgressions between the diverging species. In order to disentangle these possibilities and provide a further case for DNA barcoding of plants, we examine genetic differentiation between two ecologically divergent poplar species, Populus euphratica Oliver and P. pruinosa Schrenk using three different types of genetic marker.
We genotyped 290 individuals from 29 allopatric and sympatric populations, using chloroplast (cp) DNA, nuclear (nr) ITS sequences and eight simple sequence repeat (SSR) loci. Three major cpDNA haplotypes were widely shared between the two species and between-species cpDNA differentiation (F(CT)) was very low, even lower than among single species populations. The average SSR F(CT) values were higher. Bayesian clustering analysis of all loci allowed a clear delineation of the two species. Gene flow, determined by examining all SSR loci, was obvious but only slightly asymmetrical. However, the two species were almost fixed for two different nrITS genotypes that had the highest F(CT), although a few introgressed individuals were detected both in allopatric and sympatric populations.
The two species shared numerous ancestral polymorphisms at cpDNA and a few SSR loci. Both ITS and a combination of nuclear SSR data could be used to differentiate between the two species. Introgressions and gene flow were obvious between the two species either during or after their divergence. Our findings underscore the complex genetic differentiations between ecologically diverged species and highlight the importance of nuclear DNA (especially ITS) differentiation for delimiting closely related plant species.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>22028897</pmid><doi>10.1371/journal.pone.0026530</doi><tpages>e26530</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Bar codes Bayesian analysis Bioinformatics Biology Chloroplast DNA Chloroplasts Cluster analysis Clustering Data analysis Deoxyribonucleic acid Desert Climate Deserts Differentiation Divergence DNA DNA, Chloroplast - genetics DNA, Ribosomal Spacer - genetics Ecological and Environmental Phenomena Ecology Ecumenism Evolution, Molecular Farming Gene flow Gene sequencing Genes Genetic aspects Genetic Loci - genetics Genetic markers Genetic Markers - genetics Genomics Genotypes Grasslands Haplotypes Hypotheses Integrated software Laboratories Leaves Loci Microsatellite Repeats - genetics Migration Nucleotide sequence Phylogeny Polymorphism, Genetic - genetics Poplar Population genetics Populations Populus - genetics Populus euphratica Populus pruinosa Software packages Species Sympatric populations |
| title | Genetic differentiation and delimitation between ecologically diverged Populus euphratica and P. pruinosa |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-26T03%3A52%3A13IST&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=Genetic%20differentiation%20and%20delimitation%20between%20ecologically%20diverged%20Populus%20euphratica%20and%20P.%20pruinosa&rft.jtitle=PloS%20one&rft.au=Wang,%20Juan&rft.date=2011-10-19&rft.volume=6&rft.issue=10&rft.spage=e26530&rft.pages=e26530-&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0026530&rft_dat=%3Cgale_plos_%3EA476867443%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=1309693614&rft_id=info:pmid/22028897&rft_galeid=A476867443&rft_doaj_id=oai_doaj_org_article_eee28e59fbd64bcaaad5a61f74df35e0&rfr_iscdi=true |