Genomic variation at the tips of the adaptive radiation of Darwin's finches

Jaime A. Chaves, Elizabeth A. Cooper, Andrew P. Hendry, Jeffrey Podos, Luis F. De León, Joost A.M. Raeymaekers, W. Owen MacMillan, J. Albert C. Uy

Research output: Contribution to journalArticlepeer-review

72 Scopus citations


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.

Original languageEnglish
Pages (from-to)5282-5295
Number of pages14
JournalMolecular Ecology
Issue number21
StatePublished - 1 Nov 2016


  • Darwin's finches
  • RAD-seq
  • adaptive radiation
  • beak size
  • genomic regions


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