Data from: The adaptive genomic landscape of beak morphology in Darwin's finches

Beak shape in Darwin's ground finches (Geospiza) is emblematic of natural selection and adaptive radiation, yet our understanding of the genetic basis of beak shape variation, and thus the genetic target of natural selection, is still evolving. Here we reveal the genomic architecture of beak shape variation using genomewide comparisons of four closely related and hybridizing species across 13 islands subject to parallel natural selection. Pairwise contrasts among species were used to identify a large number of genomic loci that are consistently related to species differences across a complex landscape. These loci are associated with hundreds of genes that have enriched GO categories significantly associated with development. One genomic region of particular interest is a section of Chromosome 1A with many candidate genes and increased linkage. The distinct, pointed beak shape of the cactus finch is linked to an excess of intermediate frequency alleles and increased heterozygosity in significant SNPs, but not across the rest of the genome. Alleles associated with pointier beaks among species were associated with pointier-beaked populations within each species, thus establishing a common basis for natural selection, species divergence and adaptive radiation. The adaptive genomic landscape for Darwin's finches mirrors theoretical expectations based on morphological variation. The implication that a large number of genes are actively maintained to facilitate beak variation across parallel populations with documented interspecies admixture challenges our understanding of evolutionary processes in the wild.MLM_GLM_FortScanResults from G. fortis/G.scandens GLM and MLM contrasts, including ensembl and GO analysisMLM_GLM_FuligMagResults from G. fuliginosa/G. magnirostris GLM and MLM contrasts, including ensembl and GO analysisMLM_GLM_FortMagResults from G. fortis/G. magnirostris GLM and MLM contrasts, including ensembl and GO analysisMLM_GLM_FortFuligResults from G. fortis/G. fuliginosa GLM and MLM contrasts, including ensembl and GO analysis83Hapmap_simple2_filteredHapmap file of all SNPs for the four focal Geospiza species. Produced through Tassel pipelin