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Open Access Highly Accessed Research article

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

Chris M Rands1, Aaron Darling2, Matthew Fujita13, Lesheng Kong1, Matthew T Webster4, Céline Clabaut2, Richard D Emes56, Andreas Heger1, Stephen Meader1, Michael Brent Hawkins3, Michael B Eisen78, Clotilde Teiling9, Jason Affourtit109, Benjamin Boese9, Peter R Grant11, Barbara Rosemary Grant11, Jonathan A Eisen12132*, Arhat Abzhanov3* and Chris P Ponting1*

Author Affiliations

1 Department of Physiology, Anatomy, and Genetics, MRC Functional Genomics Unit, University of Oxford, Oxford, OX1 3PT, UK

2 UC Davis Genome Center, University of California Davis, Davis, CA, USA

3 Harvard University, Organismic and Evolutionary Biology, Cambridge, MA, 02138-2020, USA

4 Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, 751 23, Sweden

5 School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, LE12 5RD, UK

6 Advanced Data Analysis Centre, University of Nottingham, Nottingham, UK

7 Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA

8 Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA

9 454 Life Sciences, a Roche Company, Branford, CT, USA

10 Life Technologies, South San Francisco, CA, USA

11 Princeton University, Ecology and Evolutionary Biology, Princeton, NJ, 08544-2016, USA

12 Department of Evolution and Ecology, University of California Davis, Davis, CA, USA

13 Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA

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BMC Genomics 2013, 14:95  doi:10.1186/1471-2164-14-95

Published: 12 February 2013

Abstract

Background

A 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.

Results

13,291 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.

Conclusions

These 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.

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