title: Evolution of Darwin's finches and their beaks revealed by genome sequencing.
abstract: Darwin's finches, inhabiting the Galápagos archipelago and Cocos Island, constitute an iconic model for studies of speciation and adaptive evolution. Here we report the results of whole-genome re-sequencing of 120 individuals representing all of the Darwin's finch species and two close relatives. Phylogenetic analysis reveals important discrepancies with the phenotype-based taxonomy. We find extensive evidence for interspecific gene flow throughout the radiation. Hybridization has given rise to species of mixed ancestry. A 240 kilobase haplotype encompassing the ALX1 gene that encodes a transcription factor affecting craniofacial development is strongly associated with beak shape diversity across Darwin's finch species as well as within the medium ground finch (Geospiza fortis), a species that has undergone rapid evolution of beak shape in response to environmental changes. The ALX1 haplotype has contributed to diversification of beak shapes among the Darwin's finches and, thereby, to an expanded utilization of food resources.
authors: Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden.
authors: Sangeet
authors: S
authors: Lamichhaney
authors: Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden.
authors: Jonas
authors: J
authors: Berglund
authors: Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden.
authors: Markus Sällman
authors: MS
authors: Almén
authors: Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden.
authors: Khurram
authors: K
authors: Maqbool
authors: Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden.
authors: Manfred
authors: M
authors: Grabherr
authors: Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden.
authors: Alvaro
authors: A
authors: Martinez-Barrio
authors: Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden.
authors: Marta
authors: M
authors: Promerová
authors: Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden.
authors: Carl-Johan
authors: CJ
authors: Rubin
authors: Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden.
authors: Chao
authors: C
authors: Wang
authors: 1] Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden [2] Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden.
authors: Neda
authors: N
authors: Zamani
authors: Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA.
authors: B Rosemary
authors: BR
authors: Grant
authors: Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA.
authors: Peter R
authors: PR
authors: Grant
authors: Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden.
authors: Matthew T
authors: MT
authors: Webster
authors: 1] Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden [2] Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden [3] Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA.
authors: Leif
authors: L
authors: Andersson
mesh_terms: D000818:Animals; D030161:Avian Proteins / Q000235:genetics / Q000378:metabolism; D001502:Beak / Q000033:anatomy & histology*; D004484:Ecuador; D019143:Evolution, Molecular; D005260:Female; D046369:Finches / Q000033:anatomy & histology* / Q000145:classification / Q000196:embryology / Q000235:genetics*; D051456:Gene Flow; D016678:Genome / Q000235:genetics; D006239:Haplotypes / Q000235:genetics; D006824:Hybridization, Genetic; D007195:Indian Ocean Islands; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D030161:Avian Proteins; D014157:Transcription Factors