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

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 an...

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Autores principales: Rands, Chris M, Darling, Aaron, Fujita, Matthew, Kong, Lesheng, Webster, Matthew T, Clabaut, Céline, Emes, Richard D, Heger, Andreas, Meader, Stephen, Hawkins, Michael Brent, Eisen, Michael B, Teiling, Clotilde, Affourtit, Jason, Boese, Benjamin, Grant, Peter R, Grant, Barbara Rosemary, Eisen, Jonathan A, Abzhanov, Arhat, Ponting, Chris P
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575239/
https://www.ncbi.nlm.nih.gov/pubmed/23402223
http://dx.doi.org/10.1186/1471-2164-14-95
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author Rands, Chris M
Darling, Aaron
Fujita, Matthew
Kong, Lesheng
Webster, Matthew T
Clabaut, Céline
Emes, Richard D
Heger, Andreas
Meader, Stephen
Hawkins, Michael Brent
Eisen, Michael B
Teiling, Clotilde
Affourtit, Jason
Boese, Benjamin
Grant, Peter R
Grant, Barbara Rosemary
Eisen, Jonathan A
Abzhanov, Arhat
Ponting, Chris P
author_facet Rands, Chris M
Darling, Aaron
Fujita, Matthew
Kong, Lesheng
Webster, Matthew T
Clabaut, Céline
Emes, Richard D
Heger, Andreas
Meader, Stephen
Hawkins, Michael Brent
Eisen, Michael B
Teiling, Clotilde
Affourtit, Jason
Boese, Benjamin
Grant, Peter R
Grant, Barbara Rosemary
Eisen, Jonathan A
Abzhanov, Arhat
Ponting, Chris P
author_sort Rands, Chris M
collection PubMed
description 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.
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spelling pubmed-35752392013-02-19 Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence Rands, Chris M Darling, Aaron Fujita, Matthew Kong, Lesheng Webster, Matthew T Clabaut, Céline Emes, Richard D Heger, Andreas Meader, Stephen Hawkins, Michael Brent Eisen, Michael B Teiling, Clotilde Affourtit, Jason Boese, Benjamin Grant, Peter R Grant, Barbara Rosemary Eisen, Jonathan A Abzhanov, Arhat Ponting, Chris P BMC Genomics Research Article 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. BioMed Central 2013-02-12 /pmc/articles/PMC3575239/ /pubmed/23402223 http://dx.doi.org/10.1186/1471-2164-14-95 Text en Copyright ©2013 Rands et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 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.
spellingShingle Research Article
Rands, Chris M
Darling, Aaron
Fujita, Matthew
Kong, Lesheng
Webster, Matthew T
Clabaut, Céline
Emes, Richard D
Heger, Andreas
Meader, Stephen
Hawkins, Michael Brent
Eisen, Michael B
Teiling, Clotilde
Affourtit, Jason
Boese, Benjamin
Grant, Peter R
Grant, Barbara Rosemary
Eisen, Jonathan A
Abzhanov, Arhat
Ponting, Chris P
Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence
title Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence
title_full Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence
title_fullStr Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence
title_full_unstemmed Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence
title_short Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence
title_sort insights into the evolution of darwin’s finches from comparative analysis of the geospiza magnirostris genome sequence
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575239/
https://www.ncbi.nlm.nih.gov/pubmed/23402223
http://dx.doi.org/10.1186/1471-2164-14-95
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