Genomic signatures of rapid adaptive divergence in a tropical montane species

This dataset contains data from a study described in the paper: Ericson, P.G.P., Irestedt, M., She, H., and Qu, Y. (2021) "Genomic signatures of rapid adaptive divergence in a tropical montane species". Biology Letters (in print).

The study investigates allopatric divergence and selection in Archbold’s Bowerbird (Amblyornis papuensis), an iconic bird living in a tropical mountain region in New Guinea, using a novel chromosome-level genome and population genomic comparisons.

Our results show that the two populations inhabiting the eastern and western Central Range became isolated ca 11,800 years ago, probably because the suitable habitats for this cold-tolerating bird decreased when the climate got warmer. Our genomic scans detect that genes in highly divergent genomic regions are over-represented in developmental processes, which is likely associated with the observed differences in body size between the populations. Overall, our results suggest that environmental differences between eastern and western Central Range likely drive adaptive divergence between them.

Methods
We generated a nearly chromosome-level genome of the closely related Ailuroedus stonii and extracted DNA from toepads of taxonomically well-identified and vouchered museum study skins of Amblyornis papuensis collected between 1938 and 1961. Phylogenetic relationships were inferred by a Bayesian analysis of 80,157 randomly drawn SNPs and we estimated genetic population structure with principal component analysis (PCA). We compared the historical demography of the populations and tested for environmental heterogeneity between their core distributions in the highlands of New Guinea. We also studied the landscape of genomic divergence between the two populations and searched for evidence of selective sweeps.