Supplementary information for "Demography, ecology and selection interact with species’ historical biogeography to shape intraspecific genetic variation in a Tibetan bird"

Elucidating the formation of intraspecific genetic variation remains challenging. A powerful but rarely-used approach is to decipher the drivers of demographic dynamics, habitat suitability and linked selection within the context of species’ historical biogeography. We did so using whole genome and fecundity data from 37 populations across the range of a Tibetan bird, the ground tit Pseudopodoces humilis. The spatial pattern of genetic diversity aligned with refugium, bottleneck and founder events experienced by different ground tit populations since the Quaternary glaciation. Contemporary habitat suitability promoted genetic diversity only in highly-isolated regions where populations experienced historical bottlenecks and fragmented habitats, but not in less-isolated regions where refugium and founder populations persisted, highlighting the role of gene flow in maintaining mutation-drift equilibrium. The genetic diversity of neutral loci coupled with fecundity-associated genes declined from refugium to founder populations along a gradient of increased environmental harshness. Our study reveals that present-day genetic diversity is deeply rooted in historical biogeography and offers a general framework for evaluating the macroevolution of intraspecific genetic variation.