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

Additional files

Additional file 1:

The origin of the Darwin's Finch genome project.

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Additional file 2:

Histograms showing the divergence of transposable element (TE) sequences relative to their consensus sequences for (a) G. magnirostris TEs and (b) zebra finch TEs. Those that are more diverged are more likely to be older. (a) contains TEs defined using a library constructed from the G. magnirostris genome assembly, whereas (b) contains TEs defined by RepeatMasker [91]. The paucity of lowly diverged TEs in the G. magnirostris genome assembly indicates that it is likely to be most incomplete within repetitive sequence. The figures were generated using scripts from Juan Caballero available at https://github.com/caballero/RepeatLandscape webcite.

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Additional file 3:

GC content distribution in G. magnirostris. Panel (A) shows the variation of GC content in 3Kb windows along scaffold 10304, the largest scaffold in the assembly. Panel (B) shows the third codon position GC content (GC3) and the equilibrium GC3 (GC3*) content in different vertebrate lineages. The predicted increase in GC content along the Darwin's finch lineage is consistent with the maintenance of GC-rich isochores.

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Additional file 4:

Base composition properties of G. magnirostris positively selected genes. The genes in bold show a high rate of AT→GC changes. The equilibrium GC content (GC*) was calculated as described by Axelsson et al.[92].

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Additional file 5:

Positively selected genes along the passerine branch. P-values of less than 0.01 are highlighted in bold.

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Additional file 6:

Gene Ontology enrichments for positively selected genes along the passerine branch.

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Additional file 7:

Details of 454 Sequencing Runs including length distributions of high quality reads.

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Additional file 8:

Amount of aligning and indel-purified sequence shared between different avian species pairs.

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Additional file 9:

Frequency histograms of inter-gap segments lengths inferred from the G. gallus to G. magnirostris alignment.

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Additional file 10:

Frequency histograms of inter-gap segments lengths inferred from the T. guttata to G. magnirostris alignment.

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Additional file 11:

Frequency histograms of inter-gap segments lengths inferred from the G. gallus to T. guttata alignment.

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