Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence

BMC Genomics

Research Article

Clotilde Teiling¹  Benjamin Boese¹  Jason Affourtit²  Michael B Eisen³  Chris M Rands⁴  Chris P Ponting⁴  Stephen Meader⁴  Andreas Heger⁴  Lesheng Kong⁴  Matthew Fujita⁵  Arhat Abzhanov⁶  Michael Brent Hawkins⁶  Barbara Rosemary Grant⁷  Peter R Grant⁷  Richard D Emes⁸  Matthew T Webster⁹  Céline Clabaut^1,10  Aaron Darling^1,10  Jonathan A Eisen^1,11 

[1] 454 Life Sciences, a Roche Company, Branford, CT, USA;454 Life Sciences, a Roche Company, Branford, CT, USA;Life Technologies, South San Francisco, CA, USA;Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA;Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA;Department of Physiology, Anatomy, and Genetics, MRC Functional Genomics Unit, University of Oxford, OX1 3PT, Oxford, UK;Department of Physiology, Anatomy, and Genetics, MRC Functional Genomics Unit, University of Oxford, OX1 3PT, Oxford, UK;Harvard University, Organismic and Evolutionary Biology, 02138-2020, Cambridge, MA, USA;Harvard University, Organismic and Evolutionary Biology, 02138-2020, Cambridge, MA, USA;Princeton University, Ecology and Evolutionary Biology, 08544-2016, Princeton, NJ, USA;School of Veterinary Medicine and Science, University of Nottingham, LE12 5RD, Leicestershire, UK;Advanced Data Analysis Centre, University of Nottingham, Nottingham, UK;Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23, Uppsala, Sweden;UC Davis Genome Center, University of California Davis, Davis, CA, USA;UC Davis Genome Center, University of California Davis, Davis, CA, USA;Department of Evolution and Ecology, University of California Davis, Davis, CA, USA;Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA;

关键词: Genomics;    Evolution;    Darwin’s finches;    Large ground finch;    Geospiza magnirostris;   

DOI  :  10.1186/1471-2164-14-95

 received in 2012-10-19, accepted in 2013-01-23,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundA classical example of repeated speciation coupled with ecological diversification is the evolution of 14 closely related species of Darwin’s (Galápagos) finches (Thraupidae, Passeriformes). Their adaptive radiation in the Galápagos archipelago took place in the last 2–3 million years and some of the molecular mechanisms that led to their diversification are now being elucidated. Here we report evolutionary analyses of genome of the large ground finch, Geospiza magnirostris.Results13,291 protein-coding genes were predicted from a 991.0 Mb G. magnirostris genome assembly. We then defined gene orthology relationships and constructed whole genome alignments between the G. magnirostris and other vertebrate genomes. We estimate that 15% of genomic sequence is functionally constrained between G. magnirostris and zebra finch. Genic evolutionary rate comparisons indicate that similar selective pressures acted along the G. magnirostris and zebra finch lineages suggesting that historical effective population size values have been similar in both lineages. 21 otherwise highly conserved genes were identified that each show evidence for positive selection on amino acid changes in the Darwin's finch lineage. Two of these genes (Igf2r and Pou1f1) have been implicated in beak morphology changes in Darwin’s finches. Five of 47 genes showing evidence of positive selection in early passerine evolution have cilia related functions, and may be examples of adaptively evolving reproductive proteins.ConclusionsThese results provide insights into past evolutionary processes that have shaped G. magnirostris genes and its genome, and provide the necessary foundation upon which to build population genomics resources that will shed light on more contemporaneous adaptive and non-adaptive processes that have contributed to the evolution of the Darwin’s finches.

【 授权许可】

Unknown   
© Rands et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.