Signatures of genetic adaptation to extremely varied Australian environments in introduced European house sparrows

Abstract

Due to its history of multiple introductions to novel environments worldwide, the house sparrow has been used as a model species to study local adaption in invasive avian species. New genomic resources such as a custom 200K SNP array and a house sparrow reference genome provide great prospects for studying rapid local adaptation in this invasive species. Here, we analyse high-density genomewide genetic data collected across an extensive range of temperate, arid and tropical climates, in Australian populations that were introduced from Europe 150 years ago. We used two population differentiation (PD) and two ecological association (EA) methods to identify putative loci subject to selection across these varied climates. A majority of the outlier SNPs were identified through the use of the latent factor mixed models (LFMM) EA method, but the BayeScEnv EA method had the strongest overlap with the outliers from the two PD methods. Out of all the 971 outliers identified across the different methods, 38.3% were physically linked (within 20 kbps) to 575 known protein-coding regions in the house sparrow reference genome. Interestingly, some outlier genes had been previously identified in genome scan studies of broadly distributed species or had strong links to traits that are expected to be important to local adaptation, for example, heat-shock proteins, immune response and HOX genes. However, many outliers still have unknown relevance and some outliers can be false positives. Our results identify an opportunity to use the house sparrow model to further study local adaptation in an invasive species.