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

Rands, CM; Darling, A; Fujita, M; Kong, L; Webster, MT; Clabaut, C; Emes, RD; Heger, A; Meader, S; Hawkins, MB; Eisen, MB; Teiling, C; Affourtit, J; Boese, B; Grant, PR; Grant, BR; Eisen, JA; Abzhanov, A; Ponting, CP

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

Rands, CM Darling, A

Fujita, M Kong, L Webster, MT Clabaut, C Emes, RD Heger, A Meader, S Hawkins, MB Eisen, MB Teiling, C Affourtit, J Boese, B Grant, PR Grant, BR Eisen, JA Abzhanov, A Ponting, CP

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Publication Type:: Journal Article
Citation:: BMC Genomics, 2013, 14 (1)
Issue Date:: 2013-02-12

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Field	Value	Language
dc.contributor.author	Rands, CM	en_US
dc.contributor.author	Darling, A https://orcid.org/0000-0003-2397-7925	en_US
dc.contributor.author	Fujita, M	en_US
dc.contributor.author	Kong, L	en_US
dc.contributor.author	Webster, MT	en_US
dc.contributor.author	Clabaut, C	en_US
dc.contributor.author	Emes, RD	en_US
dc.contributor.author	Heger, A	en_US
dc.contributor.author	Meader, S	en_US
dc.contributor.author	Hawkins, MB	en_US
dc.contributor.author	Eisen, MB	en_US
dc.contributor.author	Teiling, C	en_US
dc.contributor.author	Affourtit, J	en_US
dc.contributor.author	Boese, B	en_US
dc.contributor.author	Grant, PR	en_US
dc.contributor.author	Grant, BR	en_US
dc.contributor.author	Eisen, JA	en_US
dc.contributor.author	Abzhanov, A	en_US
dc.contributor.author	Ponting, CP	en_US
dc.date.available	2013-01-23	en_US
dc.date.issued	2013-02-12	en_US
dc.identifier.citation	BMC Genomics, 2013, 14 (1)	en_US
dc.identifier.uri	http://hdl.handle.net/10453/23585
dc.description.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. © 2013 Rands et al.; licensee BioMed Central Ltd.	en_US
dc.relation.ispartof	BMC Genomics	en_US
dc.relation.isbasedon	10.1186/1471-2164-14-95	en_US
dc.subject.classification	Bioinformatics	en_US
dc.subject.mesh	Animals	en_US
dc.subject.mesh	Passeriformes	en_US
dc.subject.mesh	Genetics, Population	en_US
dc.subject.mesh	Genomics	en_US
dc.subject.mesh	Adaptation, Physiological	en_US
dc.subject.mesh	Evolution, Molecular	en_US
dc.subject.mesh	Sequence Homology, Nucleic Acid	en_US
dc.subject.mesh	Models, Genetic	en_US
dc.title	Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence	en_US
dc.type	Journal Article
utslib.citation.volume	1	en_US
utslib.citation.volume	14	en_US
utslib.for	0604 Genetics	en_US
utslib.for	06 Biological Sciences	en_US
utslib.for	08 Information and Computing Sciences	en_US
utslib.for	11 Medical and Health Sciences	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - ithree - Institute of Infection, Immunity and Innovation
utslib.copyright.status	open_access
pubs.issue	1	en_US
pubs.publication-status	Published	en_US
pubs.volume	14	en_US

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. © 2013 Rands et al.; licensee BioMed Central Ltd.

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http://hdl.handle.net/10453/23585