Using genome scans to identify genes used repeatedly for adaptation

• Published in: Evolution 2023-03, Vol.77 (3), p.801-811
• Main Authors: Booker, Tom R, Yeaman, Sam, Whitlock, Michael C
• Format: Article
• Language: English
• Subjects: Adaptation, Physiological - genetics; Biological Evolution; Evolution, Molecular; Genome; Genomics
• ISSN: 0014-3820; 1558-5646
• DOI: 10.1093/evolut/qpac063

Adaptation occurring in similar genes or genomic regions in distinct lineages provides evolutionary biologists with a glimpse at the fundamental opportunities for and constraints to diversification. With the widespread availability of high-throughput sequencing technologies and the development of population genetic methods to identify the genetic basis of adaptation, studies have begun to compare the evidence for adaptation at the molecular level among distinct lineages. However, methods to study repeated adaptation are often oriented toward genome-wide testing to identify a set of genes with signatures of repeated use, rather than evaluating the significance at the level of an individual gene. In this study, we propose PicMin, a novel statistical method derived from the theory of order statistics that can test for repeated molecular evolution to estimate significance at the level of an individual gene, using the results of genome scans. This method is generalizable to any number of lineages and, indeed, statistical power to detect repeated adaptation increases with the number of lineages that have signals of repeated adaptation of a given gene in multiple lineages. An implementation of the method written for R can be downloaded from https://github.com/TBooker/PicMin.