Evolution of Darwin’s finches and their beaks revealed by genome sequencing

• Published in: Nature (London) 2015-02, Vol.518 (7539), p.371-375
• Main Authors: Lamichhaney, Sangeet, Berglund, Jonas, Almén, Markus Sällman, Maqbool, Khurram, Grabherr, Manfred, Martinez-Barrio, Alvaro, Promerová, Marta, Rubin, Carl-Johan, Wang, Chao, Zamani, Neda, Grant, B. Rosemary, Grant, Peter R., Webster, Matthew T., Andersson, Leif
• Format: Article
• Language: English
• Subjects: 45/22; 45/23; 45/43; 45/77; 631/181/2474; Animals; Archipelagoes; Avian Proteins - genetics; Avian Proteins - metabolism; Beak - anatomy & histology; Birds; DNA sequencing; Ecuador; Environmental changes; Evolution; Evolution, Molecular; Female; Finches - anatomy & histology; Finches - classification; Finches - embryology; Finches - genetics; Food resources; Gene Flow; Genes; Genetic diversity; Genetic research; Genetics and Breeding; Genetik och förädling; Genome - genetics; Genomes; Haplotypes; Haplotypes - genetics; Humanities and Social Sciences; Hybridization; Hybridization, Genetic; Indian Ocean Islands; Islands; Male; Mitochondrial DNA; Molecular Sequence Data; Morphology; multidisciplinary; Nucleotide sequencing; Phylogenetics; Phylogeny; Science; Speciation; Species diversity; Taxonomy; Transcription Factors - genetics; Transcription Factors - metabolism
• ISSN: 0028-0836; 1476-4687; 1476-4687
• DOI: 10.1038/nature14181

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. Comprehensive genome sequencing of 120 individuals representing all of the Darwin’s finch species and two close relatives reveals important discrepancies with morphology-based taxonomy, widespread hybridization, and a gene, ALX1 , underlying variation in beak shape. Beak evolution genetics in Darwin's finches Darwin's finches, from the Galápagos archipelago and nearby Cocos Island, are the iconic model for studies of evolution and particularly of speciation. Comprehensive genome sequencing of 120 individuals, including all Darwin's finch species and two close relatives, reveals important discrepancies with morphology-based taxonomy, including evidence that hybridization has given rise to species of mixed ancestry. Beak shape has traditionally featured prominently in discussions of finch adaptation. The study shows how a haplotype encompassing the ALX1 gene — encoding a transcription factor affecting craniofacial development — is strongly associated with beak shape diversity across Darwin's finches and in the medium ground finch (a species that has undergone rapid evolution of beak shape in response to environmental changes).