Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes
Identifieur interne : 000820 ( Main/Merge ); précédent : 000819; suivant : 000821Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes
Auteurs : K. R. Elmer [Allemagne] ; S. Fan [Allemagne] ; H. M. Gunter [Allemagne] ; J. C. Jones [Allemagne] ; S. Boekhoff [Allemagne] ; S. Kuraku [Allemagne] ; A. Meyer [Allemagne]Source :
- Molecular Ecology [ 0962-1083 ] ; 2010-03.
Descripteurs français
- Wicri :
- geographic : Nicaragua.
English descriptors
- KwdEn :
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.
Url:
DOI: 10.1111/j.1365-294X.2009.04488.x
Links toward previous steps (curation, corpus...)
- to stream Istex, to step Corpus: 001061
- to stream Istex, to step Curation: 001059
- to stream Istex, to step Checkpoint: 000331
Links to Exploration step
ISTEX:10D571EE02C077D62E29302D5598003429CB5045Le document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes</title>
<author><name sortKey="Elmer, K R" sort="Elmer, K R" uniqKey="Elmer K" first="K. R." last="Elmer">K. R. Elmer</name>
</author>
<author><name sortKey="Fan, S" sort="Fan, S" uniqKey="Fan S" first="S." last="Fan">S. Fan</name>
</author>
<author><name sortKey="Gunter, H M" sort="Gunter, H M" uniqKey="Gunter H" first="H. M." last="Gunter">H. M. Gunter</name>
</author>
<author><name sortKey="Jones, J C" sort="Jones, J C" uniqKey="Jones J" first="J. C." last="Jones">J. C. Jones</name>
</author>
<author><name sortKey="Boekhoff, S" sort="Boekhoff, S" uniqKey="Boekhoff S" first="S." last="Boekhoff">S. Boekhoff</name>
</author>
<author><name sortKey="Kuraku, S" sort="Kuraku, S" uniqKey="Kuraku S" first="S." last="Kuraku">S. Kuraku</name>
</author>
<author><name sortKey="Meyer, A" sort="Meyer, A" uniqKey="Meyer A" first="A." last="Meyer">A. Meyer</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">ISTEX</idno>
<idno type="RBID">ISTEX:10D571EE02C077D62E29302D5598003429CB5045</idno>
<date when="2010" year="2010">2010</date>
<idno type="doi">10.1111/j.1365-294X.2009.04488.x</idno>
<idno type="url">https://api.istex.fr/document/10D571EE02C077D62E29302D5598003429CB5045/fulltext/pdf</idno>
<idno type="wicri:Area/Istex/Corpus">001061</idno>
<idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">001061</idno>
<idno type="wicri:Area/Istex/Curation">001059</idno>
<idno type="wicri:Area/Istex/Checkpoint">000331</idno>
<idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Checkpoint">000331</idno>
<idno type="wicri:doubleKey">0962-1083:2010:Elmer K:rapid:evolution:and</idno>
<idno type="wicri:Area/Main/Merge">000820</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes</title>
<author><name sortKey="Elmer, K R" sort="Elmer, K R" uniqKey="Elmer K" first="K. R." last="Elmer">K. R. Elmer</name>
<affiliation wicri:level="4"><country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz</wicri:regionArea>
<placeName><region type="land" nuts="1">Bade-Wurtemberg</region>
<region type="district" nuts="2">District de Fribourg-en-Brisgau</region>
<settlement type="city">Constance (Allemagne)</settlement>
</placeName>
<orgName type="university">Université de Constance</orgName>
</affiliation>
</author>
<author><name sortKey="Fan, S" sort="Fan, S" uniqKey="Fan S" first="S." last="Fan">S. Fan</name>
<affiliation wicri:level="4"><country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz</wicri:regionArea>
<placeName><region type="land" nuts="1">Bade-Wurtemberg</region>
<region type="district" nuts="2">District de Fribourg-en-Brisgau</region>
<settlement type="city">Constance (Allemagne)</settlement>
</placeName>
<orgName type="university">Université de Constance</orgName>
</affiliation>
</author>
<author><name sortKey="Gunter, H M" sort="Gunter, H M" uniqKey="Gunter H" first="H. M." last="Gunter">H. M. Gunter</name>
<affiliation wicri:level="4"><country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz</wicri:regionArea>
<placeName><region type="land" nuts="1">Bade-Wurtemberg</region>
<region type="district" nuts="2">District de Fribourg-en-Brisgau</region>
<settlement type="city">Constance (Allemagne)</settlement>
</placeName>
<orgName type="university">Université de Constance</orgName>
</affiliation>
</author>
<author><name sortKey="Jones, J C" sort="Jones, J C" uniqKey="Jones J" first="J. C." last="Jones">J. C. Jones</name>
<affiliation wicri:level="4"><country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz</wicri:regionArea>
<placeName><region type="land" nuts="1">Bade-Wurtemberg</region>
<region type="district" nuts="2">District de Fribourg-en-Brisgau</region>
<settlement type="city">Constance (Allemagne)</settlement>
</placeName>
<orgName type="university">Université de Constance</orgName>
</affiliation>
</author>
<author><name sortKey="Boekhoff, S" sort="Boekhoff, S" uniqKey="Boekhoff S" first="S." last="Boekhoff">S. Boekhoff</name>
<affiliation wicri:level="4"><country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz</wicri:regionArea>
<placeName><region type="land" nuts="1">Bade-Wurtemberg</region>
<region type="district" nuts="2">District de Fribourg-en-Brisgau</region>
<settlement type="city">Constance (Allemagne)</settlement>
</placeName>
<orgName type="university">Université de Constance</orgName>
</affiliation>
</author>
<author><name sortKey="Kuraku, S" sort="Kuraku, S" uniqKey="Kuraku S" first="S." last="Kuraku">S. Kuraku</name>
<affiliation wicri:level="4"><country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz</wicri:regionArea>
<placeName><region type="land" nuts="1">Bade-Wurtemberg</region>
<region type="district" nuts="2">District de Fribourg-en-Brisgau</region>
<settlement type="city">Constance (Allemagne)</settlement>
</placeName>
<orgName type="university">Université de Constance</orgName>
</affiliation>
</author>
<author><name sortKey="Meyer, A" sort="Meyer, A" uniqKey="Meyer A" first="A." last="Meyer">A. Meyer</name>
<affiliation wicri:level="4"><country xml:lang="fr">Allemagne</country>
<wicri:regionArea>Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz</wicri:regionArea>
<placeName><region type="land" nuts="1">Bade-Wurtemberg</region>
<region type="district" nuts="2">District de Fribourg-en-Brisgau</region>
<settlement type="city">Constance (Allemagne)</settlement>
</placeName>
<orgName type="university">Université de Constance</orgName>
</affiliation>
</author>
</analytic>
<monogr></monogr>
<series><title level="j">Molecular Ecology</title>
<idno type="ISSN">0962-1083</idno>
<idno type="eISSN">1365-294X</idno>
<imprint><publisher>Blackwell Publishing Ltd</publisher>
<pubPlace>Oxford, UK</pubPlace>
<date type="published" when="2010-03">2010-03</date>
<biblScope unit="volume">19</biblScope>
<biblScope unit="supplement">s1</biblScope>
<biblScope unit="page" from="197">197</biblScope>
<biblScope unit="page" to="211">211</biblScope>
</imprint>
<idno type="ISSN">0962-1083</idno>
</series>
<idno type="istex">10D571EE02C077D62E29302D5598003429CB5045</idno>
<idno type="DOI">10.1111/j.1365-294X.2009.04488.x</idno>
<idno type="ArticleID">MEC4488</idno>
</biblStruct>
</sourceDesc>
<seriesStmt><idno type="ISSN">0962-1083</idno>
</seriesStmt>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Nicaragua</term>
<term>Roche 454 GS FLX</term>
<term>adaptive radiation</term>
<term>comparative genomics</term>
<term>expressed sequence tags</term>
<term>natural selection</term>
<term>pyrosequencing</term>
<term>substitutional mutation rate</term>
</keywords>
<keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>Nicaragua</term>
</keywords>
</textClass>
<langUsage><language ident="en">en</language>
</langUsage>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml: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.</div>
</front>
</TEI>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Eau/explor/EsturgeonV1/Data/Main/Merge
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000820 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Merge/biblio.hfd -nk 000820 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Wicri/Eau |area= EsturgeonV1 |flux= Main |étape= Merge |type= RBID |clé= ISTEX:10D571EE02C077D62E29302D5598003429CB5045 |texte= Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes }}
![]() | This area was generated with Dilib version V0.6.27. | ![]() |