title: Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence.
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.
authors: Department of Physiology, Anatomy, and Genetics, MRC Functional Genomics Unit, University of Oxford, Oxford, OX1 3PT, UK.
authors: Chris M
authors: CM
authors: Rands
authors: Aaron
authors: A
authors: Darling
authors: Matthew
authors: M
authors: Fujita
authors: Lesheng
authors: L
authors: Kong
authors: Matthew T
authors: MT
authors: Webster
authors: Céline
authors: C
authors: Clabaut
authors: Richard D
authors: RD
authors: Emes
authors: Andreas
authors: A
authors: Heger
authors: Stephen
authors: S
authors: Meader
authors: Michael Brent
authors: MB
authors: Hawkins
authors: Michael B
authors: MB
authors: Eisen
authors: Clotilde
authors: C
authors: Teiling
authors: Jason
authors: J
authors: Affourtit
authors: Benjamin
authors: B
authors: Boese
authors: Peter R
authors: PR
authors: Grant
authors: Barbara Rosemary
authors: BR
authors: Grant
authors: Jonathan A
authors: JA
authors: Eisen
authors: Arhat
authors: A
authors: Abzhanov
authors: Chris P
authors: CP
authors: Ponting
mesh_terms: D000222:Adaptation, Physiological; D000818:Animals; D019143:Evolution, Molecular; D005828:Genetics, Population; D023281:Genomics; D008957:Models, Genetic; D046109:Passeriformes / Q000235:genetics* / Q000502:physiology; D012689:Sequence Homology, Nucleic Acid
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D1077-81
references: 22064864
references: Mol Biol Cell. 2003 May;14(5):2041-56
references: 12802074
references: Nature. 2006 Aug 3;442(7102):563-7
references: 16885984
references: Proc Natl Acad Sci U S A. 1929 Sep 15;15(9):733-4
references: 16577229
references: Genome Res. 2007 Dec;17(12):1837-49
references: 17989258
references: Science. 2004 Sep 3;305(5689):1462-5
references: 15353802
references: Nucleic Acids Res. 2007 Jan;35(Database issue):D332-8
references: 17090588
references: PLoS Comput Biol. 2011 Dec;7(12):e1002269
references: 22144877
references: Genome Biol Evol. 2011;3:974-84
references: 21795750
references: Syst Biol. 2007 Aug;56(4):564-77
references: 17654362
references: Genes Genet Syst. 2008 Aug;83(4):331-8
references: 18931458
references: PLoS Biol. 2010 Sep 07;8(9):
references: 20838655
references: Science. 1992 Apr 10;256(5054):193-7
references: 17744718
references: Genomics. 2004 Nov;84(5):806-13
references: 15475259
references: Trends Immunol. 2003 Sep;24(9):512-7
references: 12967676
references: Mol Ecol. 2005 Sep;14(10):2943-57
references: 16101765
references: Mol Biol Evol. 2010 Aug;27(8):1759-67
references: 20207713
references: Nat Rev Genet. 2002 Feb;3(2):137-44
references: 11836507
references: PLoS Comput Biol. 2006 Jan;2(1):e5
references: 16410828
references: Mol Biol Evol. 2010 Oct;27(10):2257-67
references: 20447933
references: Nature. 2010 Apr 1;464(7289):757-62
references: 20360741
references: Hereditas. 1983;98(2):235-9
references: 6874394
references: J Mol Biol. 2000 Sep 8;302(1):205-17
references: 10964570
references: Trends Genet. 2012 Jul;28(7):342-50
references: 22520730
references: Genome Res. 2004 Apr;14(4):708-15
references: 15060014
references: Bioinformatics. 2005 Jun;21 Suppl 1:i351-8
references: 15961478
references: Annu Rev Genomics Hum Genet. 2009;10:285-311
references: 19630562
references: Genome Res. 2009 Feb;19(2):327-35
references: 19029536
references: Mol Biol Evol. 2011 Aug;28(8):2197-210
references: 21393604
references: Genome Inform. 2009 Oct;23(1):205-11
references: 20180275
references: Nature. 2004 Dec 9;432(7018):695-716
references: 15592404
references: Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6700-5
references: 19339501
references: Genome Res. 2012 Jan;22(1):51-63
references: 22006216
references: Nat Genet. 2000 May;25(1):25-9
references: 10802651
references: Mol Biol Evol. 2007 Aug;24(8):1586-91
references: 17483113
references: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D187-91
references: 16381842
references: PLoS Comput Biol. 2006 Sep 29;2(9):e133
references: 17009864
references: Genome Biol. 2010;11(6):R68
references: 20573239
references: Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9
references: 14500911
references: Proc Natl Acad Sci U S A. 2009 Sep 8;106(36):E95; author reply E96
references: 19805241
references: BMC Bioinformatics. 2005 Apr 27;6:108
references: 15857510
references: Hum Mol Genet. 2010 Mar 1;19(5):920-30
references: 20015954
references: Mol Biol Evol. 2005 Apr;22(4):1107-18
references: 15689528
references: Am J Physiol Endocrinol Metab. 2006 Jul;291(1):E128-36
references: 16464905
references: Cell Motil Cytoskeleton. 2002 Apr;51(4):197-212
references: 11977094
references: Nature. 2009 Apr 23;458(7241):987-92
references: 19363474
references: Proc Natl Acad Sci U S A. 2007 May 1;104(18):7489-94
references: 17449636
references: Mol Phylogenet Evol. 2006 Feb;38(2):499-509
references: 16112881
references: Proc Natl Acad Sci U S A. 2001 Nov 6;98(23):13225-30
references: 11687639
references: Gene. 2008 Sep 15;421(1-2):37-51
references: 18590805
references: Cell Death Differ. 2012 Jul;19(7):1117-26
references: 22240895
references: Cytogenet Genome Res. 2007;117(1-4):64-77
references: 17675846
references: Genome Res. 2010 Oct;20(10):1335-43
references: 20693480
references: Comput Appl Biosci. 1997 Oct;13(5):555-6
references: 9367129
references: Science. 2000 Oct 13;290(5490):331-3
references: 11030650
references: Nature. 1994 Dec 1;372(6505):464-7
references: 7984240
references: Mol Phylogenet Evol. 1996 Feb;5(1):182-7
references: 8673286
references: Genome Res. 2009 May;19(5):922-33
references: 19411606
references: Curr Opin Struct Biol. 1996 Jun;6(3):361-5
references: 8804822
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D267-70
references: 17933761
references: BMC Bioinformatics. 2004 Aug 19;5:113
references: 15318951
references: Nature. 1984 Jun 28-Jul 4;309(5971):787-9
references: 6738694
references: Mol Biol Evol. 2005 Dec;22(12):2472-9
references: 16107592
references: Science. 1990 Jul 20;249(4966):306-7
references: 17750115
references: Am J Hum Genet. 2008 Nov;83(5):547-58
references: 18950741
references: Evolution. 2002 Jun;56(6):1240-52
references: 12144023
references: Trends Cell Biol. 2011 Jan;21(1):29-37
references: 20951588
references: Cell. 1988 Nov 4;55(3):519-29
references: 2902928
references: Genetics. 2009 Feb;181(2):645-60
references: 19047416
references: Mech Ageing Dev. 2002 May;123(9):1245-55
references: 12020946
references: Evolution. 2009 Feb;63(2):301-5
references: 19215289
references: Gen Comp Endocrinol. 2001 Sep;123(3):244-53
references: 11589626
references: Mol Biol Evol. 2001 Mar;18(3):299-311
references: 11230531
references: Mol Biol Evol. 2011 Mar;28(3):1217-28
references: 21087944
references: Nature. 2012 Nov 29;491(7426):756-60
references: 23103876
references: Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):4057-62
references: 21368127
references: Genome Res. 2003 Jan;13(1):13-26
references: 12529302
references: Philos Trans R Soc Lond B Biol Sci. 2010 Apr 12;365(1543):1001-7
references: 20194163
references: Philos Trans R Soc Lond B Biol Sci. 2010 Apr 12;365(1543):1065-76
references: 20194169