Disentangling the relative roles of geographical and ecological factors in driving genomic variations of a widely distributed bird across a longitudinal gradient

Unraveling geographical modes of speciation processes has been a longstanding topic in biogeography. Divergence can be driven by factors operating on multiple spatial scales, such as geographical distance (isolation by distance, IBD), landscape resistance (isolation by resistance, IBR) and environmental heterogeneity (isolation by environment, IBE). However, it is challenging to assess the relative contributions of such factors, which are usually autocorrelated with each other. On the basis of similar to 294 K nuclear single-nucleotide polymorphisms from 53 samples, we integrated population genomics, geographical information and environmental variables to delineate genetic differentiation in the common pheasant Phasianus colchicus across a longitudinal gradient in northern China. Generalized dissimilarity modeling (GDM) was used to analyze the relative importance of IBD, IBR and IBE. We found that the common pheasant in northern China was grouped into six genetic clusters, which was consistent with the taxonomic affinities. Genetic diversity changed along the longitudinal gradient, reaching its lowest level at the eastern edge of the Qinghai-Tibetan Plateau (QTP). The spatial pattern of gene flow suggested that the mountains surrounding the QTP and the mountains in central China have acted as geographical barriers impeding common pheasant dispersal. GDM analysis indicated that environmental heterogeneity is the most important driver explaining the lineage divergence, which supports the IBE model. These results suggest that multiple isolation mechanisms shaped genetic diversity and genomic divergence in this wide-ranging bird species. Together, our results underscore the importance of leveraging genome-wide variations and ecological modeling to facilitate a deeper understanding of population divergence processes.