Data from: Climate change promotes allopatric divergence and ecological adaptation in a tropical montane bird. SNP data used to analyse the demographic history of Amblyornis papuensis.

Environmental heterogeneity and Pleistocene glaciations have largely contributed to speciation and adaptation processes that have promoted genetic diversity of montane birds in temperate regions, but how these processes have influenced montane species in tropical regions is less known. We study these processes using a chromosome-level genome and comparative population genomics in Archbold's bowerbird (Amblyornis papuensis), a rare and poorly known montane bird in New Guinea. The analyses showed a deep divergence between the populations isolated in the eastern and western parts of the New Guinea Highlands, respectively. Using demographic model inference, we estimated that the two populations were part of the same population until ca. 140,000 years ago. They then diverged as the warmer climate in the Eemian interglacial forced them to retreat to higher elevations, which also led to decreasing population sizes. Subsequently, the two isolated populations evolved considerable phenotypic differences, particularly in body size, and in accordance with this, we observed strong divergent selection in genes related to body development. The phenotypic and genomic differences are likely a response to heterogenic environmental conditions in their respective habitats.