Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes
Identifieur interne : 001061 ( Istex/Corpus ); précédent : 001060; suivant : 001062Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes
Auteurs : K. R. Elmer ; S. Fan ; H. M. Gunter ; J. C. Jones ; S. Boekhoff ; S. Kuraku ; A. MeyerSource :
- Molecular Ecology [ 0962-1083 ] ; 2010-03.
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Abstract
Crater lakes provide a natural laboratory to study speciation of cichlid fishes by ecological divergence. Up to now, there has been a dearth of transcriptomic and genomic information that would aid in understanding the molecular basis of the phenotypic differentiation between young species. We used next‐generation sequencing (Roche 454 massively parallel pyrosequencing) to characterize the diversity of expressed sequence tags between ecologically divergent, endemic and sympatric species of cichlid fishes from crater lake Apoyo, Nicaragua: benthic Amphilophus astorquii and limnetic Amphilophus zaliosus. We obtained 24 174 A. astorquii and 21 382 A. zaliosus high‐quality expressed sequence tag contigs, of which 13 106 pairs are orthologous between species. Based on the ratio of nonsynonymous to synonymous substitutions, we identified six sequences exhibiting signals of strong diversifying selection (Ka/Ks > 1). These included genes involved in biosynthesis, metabolic processes and development. This transcriptome sequence variation may be reflective of natural selection acting on the genomes of these young, sympatric sister species. Based on Ks ratios and p‐distances between 3′‐untranslated regions (UTRs) calibrated to previously published species divergence times, we estimated a neutral transcriptome‐wide substitutional mutation rate of ∼1.25 × 10−6 per site per year. We conclude that next‐generation sequencing technologies allow us to infer natural selection acting to diversify the genomes of young species, such as crater lake cichlids, with much greater scope than previously possible.
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DOI: 10.1111/j.1365-294X.2009.04488.x
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This transcriptome sequence variation may be reflective of natural selection acting on the genomes of these young, sympatric sister species. Based on Ks ratios and p‐distances between 3′‐untranslated regions (UTRs) calibrated to previously published species divergence times, we estimated a neutral transcriptome‐wide substitutional mutation rate of ∼1.25 × 10−6 per site per year. 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Up to now, there has been a dearth of transcriptomic and genomic information that would aid in understanding the molecular basis of the phenotypic differentiation between young species. We used next‐generation sequencing (Roche 454 massively parallel pyrosequencing) to characterize the diversity of expressed sequence tags between ecologically divergent, endemic and sympatric species of cichlid fishes from crater lake Apoyo, Nicaragua: benthic Amphilophus astorquii and limnetic Amphilophus zaliosus. We obtained 24 174 A. astorquii and 21 382 A. zaliosus high‐quality expressed sequence tag contigs, of which 13 106 pairs are orthologous between species. Based on the ratio of nonsynonymous to synonymous substitutions, we identified six sequences exhibiting signals of strong diversifying selection (Ka/Ks > 1). These included genes involved in biosynthesis, metabolic processes and development. This transcriptome sequence variation may be reflective of natural selection acting on the genomes of these young, sympatric sister species. Based on Ks ratios and p‐distances between 3′‐untranslated regions (UTRs) calibrated to previously published species divergence times, we estimated a neutral transcriptome‐wide substitutional mutation rate of ∼1.25 × 10−6 per site per year. We conclude that next‐generation sequencing technologies allow us to infer natural selection acting to diversify the genomes of young species, such as crater lake cichlids, with much greater scope than previously possible.</p></abstract><textClass xml:lang="en"><keywords scheme="keyword"><list><head>keywords</head><item><term>adaptive radiation</term></item><item><term>comparative genomics</term></item><item><term>expressed sequence tags</term></item><item><term>natural selection</term></item><item><term>pyrosequencing</term></item><item><term>Roche 454 GS FLX</term></item><item><term>substitutional mutation rate</term></item><item><term>Nicaragua</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="2010-03">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/document/10D571EE02C077D62E29302D5598003429CB5045/fulltext/txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Wiley, elements deleted: body"><istex:xmlDeclaration>version="1.0" encoding="UTF-8" standalone="yes"</istex:xmlDeclaration><istex:document><component version="2.0" type="serialArticle" xml:lang="en"><header><publicationMeta level="product"><publisherInfo><publisherName>Blackwell Publishing Ltd</publisherName><publisherLoc>Oxford, UK</publisherLoc></publisherInfo><doi origin="wiley" registered="yes">10.1111/(ISSN)1365-294X</doi><issn type="print">0962-1083</issn><issn type="electronic">1365-294X</issn><idGroup><id type="product" value="MEC"></id><id type="publisherDivision" value="ST"></id></idGroup><titleGroup><title type="main" sort="MOLECULAR ECOLOGY">Molecular Ecology</title></titleGroup></publicationMeta><publicationMeta level="part" position="03001"><doi origin="wiley">10.1111/mec.2010.19.issue-s1</doi><titleGroup><title type="specialIssueTitle">Next Generation Molecular Ecology</title></titleGroup><numberingGroup><numbering type="journalVolume" number="19">19</numbering><numbering type="supplement">s1</numbering></numberingGroup><coverDate startDate="2010-03">March 2010</coverDate></publicationMeta><publicationMeta level="unit" type="article" position="16" status="forIssue"><doi origin="wiley">10.1111/j.1365-294X.2009.04488.x</doi><idGroup><id type="unit" value="MEC4488"></id></idGroup><countGroup><count type="pageTotal" number="15"></count></countGroup><titleGroup><title type="tocHeading1">ORIGINAL ARTICLES</title></titleGroup><copyright>© 2010 Blackwell Publishing Ltd</copyright><eventGroup><event type="firstOnline" date="2010-02-10"></event><event type="publishedOnlineFinalForm" date="2010-02-10"></event><event type="xmlConverted" agent="Converter:BPG_TO_WML3G version:2.4 mode:FullText source:FullText result:FullText" date="2010-12-14"></event><event type="xmlConverted" agent="Converter:WILEY_ML3G_TO_WILEY_ML3GV2 version:4.0.1" date="2014-03-20"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.1.7 mode:FullText,remove_FC" date="2014-10-31"></event></eventGroup><numberingGroup><numbering type="pageFirst" number="197">197</numbering><numbering type="pageLast" number="211">211</numbering></numberingGroup><correspondenceTo>Axel Meyer, Fax: +49 7531 88 3018;
E‐mail: <email normalForm="axel.meyer@uni-konstanz.de">axel.meyer@uni‐konstanz.de</email></correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:MEC.MEC4488.pdf"></link></linkGroup></publicationMeta><contentMeta><unparsedEditorialHistory>Received 15 July 2009; revision received 6 October 2009; accepted 9 October 2009</unparsedEditorialHistory><countGroup><count type="figureTotal" number="4"></count><count type="tableTotal" number="2"></count></countGroup><titleGroup><title type="main">Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes</title><title type="shortAuthors">K. R. ELMER <i>ET AL.</i></title><title type="short">CRATER LAKE CICHLID TRANSCRIPTOME VARIATION</title></titleGroup><creators><creator creatorRole="author" xml:id="cr1" affiliationRef="#aff-1-1"><personName><givenNames>K. R.</givenNames><familyName>ELMER</familyName></personName></creator><creator creatorRole="author" xml:id="cr2" affiliationRef="#aff-1-1"><personName><givenNames>S.</givenNames><familyName>FAN</familyName></personName></creator><creator creatorRole="author" xml:id="cr3" affiliationRef="#aff-1-1"><personName><givenNames>H. M.</givenNames><familyName>GUNTER</familyName></personName></creator><creator creatorRole="author" xml:id="cr4" affiliationRef="#aff-1-1"><personName><givenNames>J. C.</givenNames><familyName>JONES</familyName></personName></creator><creator creatorRole="author" xml:id="cr5" affiliationRef="#aff-1-1"><personName><givenNames>S.</givenNames><familyName>BOEKHOFF</familyName></personName></creator><creator creatorRole="author" xml:id="cr6" affiliationRef="#aff-1-1"><personName><givenNames>S.</givenNames><familyName>KURAKU</familyName></personName></creator><creator creatorRole="author" xml:id="cr7" affiliationRef="#aff-1-1"><personName><givenNames>A.</givenNames><familyName>MEYER</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="aff-1-1" countryCode="DE"><unparsedAffiliation>Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz, Germany</unparsedAffiliation></affiliation></affiliationGroup><keywordGroup xml:lang="en"><keyword xml:id="k1">adaptive radiation</keyword><keyword xml:id="k2">comparative genomics</keyword><keyword xml:id="k3">expressed sequence tags</keyword><keyword xml:id="k4">natural selection</keyword><keyword xml:id="k5">pyrosequencing</keyword><keyword xml:id="k6">Roche 454 GS FLX</keyword><keyword xml:id="k7">substitutional mutation rate</keyword><keyword xml:id="k8">Nicaragua</keyword></keywordGroup><abstractGroup><abstract type="main" xml:lang="en"><title type="main">Abstract</title><p>Crater lakes provide a natural laboratory to study speciation of cichlid fishes by ecological divergence. Up to now, there has been a dearth of transcriptomic and genomic information that would aid in understanding the molecular basis of the phenotypic differentiation between young species. We used next‐generation sequencing (Roche 454 massively parallel pyrosequencing) to characterize the diversity of expressed sequence tags between ecologically divergent, endemic and sympatric species of cichlid fishes from crater lake Apoyo, Nicaragua: benthic <i>Amphilophus astorquii</i> and limnetic <i>Amphilophus zaliosus</i>. We obtained 24 174 <i>A. astorquii</i> and 21 382 <i>A. zaliosus</i> high‐quality expressed sequence tag contigs, of which 13 106 pairs are orthologous between species. Based on the ratio of nonsynonymous to synonymous substitutions, we identified six sequences exhibiting signals of strong diversifying selection (<i>K</i><sub>a</sub>/<i>K</i><sub>s</sub> > 1). These included genes involved in biosynthesis, metabolic processes and development. This transcriptome sequence variation may be reflective of natural selection acting on the genomes of these young, sympatric sister species. Based on <i>K</i>s ratios and p‐distances between 3′‐untranslated regions (UTRs) calibrated to previously published species divergence times, we estimated a neutral transcriptome‐wide substitutional mutation rate of ∼1.25 × 10<sup>−6</sup> per site per year. We conclude that next‐generation sequencing technologies allow us to infer natural selection acting to diversify the genomes of young species, such as crater lake cichlids, with much greater scope than previously possible.</p></abstract></abstractGroup></contentMeta><noteGroup><note xml:id="fn1"><p>The Meyer Laboratory (AM, KRE, JCJ, HGM, SF) is interested in the molecular basis of the vast ecological adaptations and evolutionary radiations of cichlid fishes, both African and neotropical. The Kuraku Laboratory (SK, SB) studies the evolution of gene repertoires, especially in early vertebrates, and the integration of bioinformatics and molecular evolutionary developmental biology.</p></note></noteGroup></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>CRATER LAKE CICHLID TRANSCRIPTOME VARIATION</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes</title></titleInfo><name type="personal"><namePart type="given">K. R.</namePart><namePart type="family">ELMER</namePart><affiliation>Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz, Germany</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">S.</namePart><namePart type="family">FAN</namePart><affiliation>Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz, Germany</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">H. M.</namePart><namePart type="family">GUNTER</namePart><affiliation>Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz, Germany</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">J. C.</namePart><namePart type="family">JONES</namePart><affiliation>Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz, Germany</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">S.</namePart><namePart type="family">BOEKHOFF</namePart><affiliation>Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz, Germany</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">S.</namePart><namePart type="family">KURAKU</namePart><affiliation>Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz, Germany</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">A.</namePart><namePart type="family">MEYER</namePart><affiliation>Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz, Germany</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article"></genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><place><placeTerm type="text">Oxford, UK</placeTerm></place><dateIssued encoding="w3cdtf">2010-03</dateIssued><edition>Received 15 July 2009; revision received 6 October 2009; accepted 9 October 2009</edition><copyrightDate encoding="w3cdtf">2010</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType><extent unit="figures">4</extent><extent unit="tables">2</extent></physicalDescription><abstract lang="en">Crater lakes provide a natural laboratory to study speciation of cichlid fishes by ecological divergence. Up to now, there has been a dearth of transcriptomic and genomic information that would aid in understanding the molecular basis of the phenotypic differentiation between young species. We used next‐generation sequencing (Roche 454 massively parallel pyrosequencing) to characterize the diversity of expressed sequence tags between ecologically divergent, endemic and sympatric species of cichlid fishes from crater lake Apoyo, Nicaragua: benthic Amphilophus astorquii and limnetic Amphilophus zaliosus. We obtained 24 174 A. astorquii and 21 382 A. zaliosus high‐quality expressed sequence tag contigs, of which 13 106 pairs are orthologous between species. Based on the ratio of nonsynonymous to synonymous substitutions, we identified six sequences exhibiting signals of strong diversifying selection (Ka/Ks > 1). These included genes involved in biosynthesis, metabolic processes and development. This transcriptome sequence variation may be reflective of natural selection acting on the genomes of these young, sympatric sister species. Based on Ks ratios and p‐distances between 3′‐untranslated regions (UTRs) calibrated to previously published species divergence times, we estimated a neutral transcriptome‐wide substitutional mutation rate of ∼1.25 × 10−6 per site per year. We conclude that next‐generation sequencing technologies allow us to infer natural selection acting to diversify the genomes of young species, such as crater lake cichlids, with much greater scope than previously possible.</abstract><subject lang="en"><genre>keywords</genre><topic>adaptive radiation</topic><topic>comparative genomics</topic><topic>expressed sequence tags</topic><topic>natural selection</topic><topic>pyrosequencing</topic><topic>Roche 454 GS FLX</topic><topic>substitutional mutation rate</topic><topic>Nicaragua</topic></subject><relatedItem type="host"><titleInfo><title>Molecular Ecology</title></titleInfo><genre type="journal">journal</genre><identifier type="ISSN">0962-1083</identifier><identifier type="eISSN">1365-294X</identifier><identifier type="DOI">10.1111/(ISSN)1365-294X</identifier><identifier type="PublisherID">MEC</identifier><part><date>2010</date><detail type="title"><title>Next Generation Molecular Ecology</title></detail><detail type="volume"><caption>vol.</caption><number>19</number></detail><detail type="supplement"><caption>Suppl. no.</caption><number>s1</number></detail><extent unit="pages"><start>197</start><end>211</end><total>15</total></extent></part></relatedItem><identifier type="istex">10D571EE02C077D62E29302D5598003429CB5045</identifier><identifier type="DOI">10.1111/j.1365-294X.2009.04488.x</identifier><identifier type="ArticleID">MEC4488</identifier><accessCondition type="use and reproduction" contentType="copyright">© 2010 Blackwell Publishing Ltd</accessCondition><recordInfo><recordContentSource>WILEY</recordContentSource><recordOrigin>Blackwell Publishing Ltd</recordOrigin></recordInfo></mods></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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