title: Genomic variation at the tips of the adaptive radiation of Darwin's finches.
abstract: Adaptive radiation unfolds as selection acts on the genetic variation underlying functional traits. The nature of this variation can be revealed by studying the tips of an ongoing adaptive radiation. We studied genomic variation at the tips of the Darwin's finch radiation; specifically focusing on polymorphism within, and variation among, three sympatric species of the genus Geospiza. Using restriction site-associated DNA (RAD-seq), we characterized 32 569 single-nucleotide polymorphisms (SNPs), from which 11 outlier SNPs for beak and body size were uncovered by a genomewide association study (GWAS). Principal component analysis revealed that these 11 SNPs formed four statistically linked groups. Stepwise regression then revealed that the first PC score, which included 6 of the 11 top SNPs, explained over 80% of the variation in beak size, suggesting that selection on these traits influences multiple correlated loci. The two SNPs most strongly associated with beak size were near genes associated with beak morphology across deeper branches of the radiation: delta-like 1 homologue (DLK1) and high-mobility group AT-hook 2 (HMGA2). Our results suggest that (i) key adaptive traits are associated with a small fraction of the genome (11 of 32 569 SNPs), (ii) SNPs linked to the candidate genes are dispersed throughout the genome (on several chromosomes), and (iii) micro- and macro-evolutionary variation (roots and tips of the radiation) involve some shared and some unique genomic regions.
authors.affiliation: Department of Biology, University of Miami, Coral Gables, FL, 33146, USA. jachaves@usfq.edu.ec.|Universidad San Francisco de Quito, USFQ, Colegio de Ciencias Biológicas y Ambientales, y Extensión Galápagos, Campus Cumbayá, Quito, Ecuador. jachaves@usfq.edu.ec.
authors.forename: Jaime A
authors.initials: JA
authors.lastname: Chaves
authors.affiliation: Department of Biology, University of Miami, Coral Gables, FL, 33146, USA.|Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA.
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Cooper
authors.affiliation: Redpath Museum, Department of Biology, McGill University, Montréal, QC, Canada.
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Hendry
authors.affiliation: Department of Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Podos
authors.affiliation: Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), Ciudad del Saber, Panama, Panama.|Department of Biology, University of Massachusetts Boston, 100 Morrissey Blvd, Boston, MA, 02125, USA.
authors.forename: Luis F
authors.identifier: 0000-0001-9317-420X
authors.initials: LF
authors.lastname: De León
authors.affiliation: Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, B-3000, Leuven, Belgium.|Center for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, N-7491, Trondheim, Norway.
authors.forename: Joost A M
authors.initials: JA
authors.lastname: Raeymaekers
authors.affiliation: Smithsonian Tropical Research Institute, Panama, Panama.
authors.forename: W Owen
authors.initials: WO
authors.lastname: MacMillan
authors.affiliation: Department of Biology, University of Miami, Coral Gables, FL, 33146, USA.
authors.forename: J Albert C
authors.initials: JA
authors.lastname: Uy
mesh_terms: D000818:Animals; D001502:Beak; D005075:Biological Evolution; D049628:Body Size; D046369:Finches / Q000235:genetics*; D056726:Genetic Association Studies; D008040:Genetic Linkage; D023281:Genomics; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic
keywords: Darwin's finches; RAD-seq; adaptive radiation; beak size; genomic regions