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Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes

Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes

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Prüfsumme: MD5:15d50625801db1c245c1309d37a81406

ELMER, Kathryn, Shaohua FAN, Helen GUNTER, Julia JONES, S. BOEKHOFF, Shigehiro KURAKU, Axel MEYER, 2010. Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes. In: Molecular Ecology. 19, pp. 197-211. ISSN 0962-1083. eISSN 1365-294X

@article{Elmer2010-03Rapid-13566, title={Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes}, year={2010}, doi={10.1111/j.1365-294X.2009.04488.x}, volume={19}, issn={0962-1083}, journal={Molecular Ecology}, pages={197--211}, author={Elmer, Kathryn and Fan, Shaohua and Gunter, Helen and Jones, Julia and Boekhoff, S. and Kuraku, Shigehiro and Meyer, Axel} }

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. eng Meyer, Axel Elmer, Kathryn Kuraku, Shigehiro Elmer, Kathryn 2011-06-14T14:23:32Z First publ. in: Molecular Ecology ; 19 (2010), S1. - pp. 197-211, DOI: 10.1111/j.1365-294X.2009.04488.x Meyer, Axel Gunter, Helen 2011-06-14T14:23:32Z Kuraku, Shigehiro Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes 2010-03 Boekhoff, S. Jones, Julia Boekhoff, S. deposit-license Gunter, Helen Jones, Julia Fan, Shaohua Fan, Shaohua

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