Parallel Signatures of Diet Adaptation in the Invasive Common Myna Genome

Abstract

Invasive species offer uniquely replicated model systems to study rapid adaptation. The common myna (Acridotheres tristis) has been introduced to over a dozen countries and is classified as one of the most invasive birds in the world. Their multiple invasions provide an opportunity to identify repeated adaptation, as invasive populations originated from multiple source populations. We compared whole-genome resequencing data from 80 individuals from four native and seven invasive populations, representing two independent introduction pathways. Results from two different selection scan methods were combined and identified a strongly selected region on chromosome 8 that spans two copies of AMY2A, part of the alpha-amylase gene family, a putative ncRNA and an insertion–deletion structural variant (SV) that contains an ERVK transposable element (TE). Outlier SNPs and the SV are polymorphic in native populations, but fixed or close-to-fixed in the two invasive pathways, with the fixation of the same alleles in two independent lineages providing evidence for parallel selection on standing variation. Intriguingly, the second copy of AMY2A has a non-conservative missense mutation at a phylogenetically conserved site. This mutation, alongside variation in the SV, TE and ncRNA, provide possible routes for changes to protein function or expression. AMY2A has been associated with human commensalism in house sparrows, and genes in this family have been linked to adaptation to high-starch diets in humans and dogs. This study illustrates the value of replicated analyses within and across species to understand rapid adaptation at the molecular level.