title: Adaptive radiation of Darwin's finches revisited using whole genome sequencing.
abstract: We recently used genome sequencing to study the evolutionary history of the Darwin's finches. A prominent feature of our data was that different polymorphic sites in the genome tended to indicate different genetic relationships among these closely related species. Such patterns are expected in recently diverged genomes as a result of incomplete lineage sorting. However, we uncovered conclusive evidence that these patterns have also been influenced by interspecies hybridisation, a process that has likely played an important role in the radiation of Darwin's finches. A major discovery was that segregation of two haplotypes at the ALX1 locus underlies variation in beak shape among the Darwin's finches, and that differences between the two haplotypes in a 240 kb region in blunt and pointed beaked birds involve both coding and regulatory changes. As we review herein, the evolution of such adaptive haplotypes comprising multiple causal changes appears to be an important mechanism contributing to the evolution of biodiversity.
authors.affiliation: Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Markus Sällman
authors.initials: MS
authors.lastname: Almén
authors.affiliation: Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Sangeet
authors.initials: S
authors.lastname: Lamichhaney
authors.affiliation: Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Jonas
authors.initials: J
authors.lastname: Berglund
authors.affiliation: Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
authors.forename: B Rosemary
authors.initials: BR
authors.lastname: Grant
authors.affiliation: Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
authors.forename: Peter R
authors.initials: PR
authors.lastname: Grant
authors.affiliation: Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Webster
authors.affiliation: Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.|Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.|Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, USA.
authors.forename: Leif
authors.initials: L
authors.lastname: Andersson
mesh_terms: D000818:Animals; D001483:Base Sequence; D001502:Beak / Q000033:anatomy & histology; D005075:Biological Evolution; D046369:Finches / Q000033:anatomy & histology / Q000235:genetics*; D016678:Genome; D006239:Haplotypes; D010802:Phylogeny
keywords: adaptation; evolution; gene flow; genome sequencing