Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene

Species that evolved in temperate regions during the Pleistocene experienced periods of extreme climatic transitions.  Consequent population fragmentation and dynamics had the potential to generate small, isolated populations where the influence of genetic drift would be expected to be strong.  We use comparative genomics to assess the evolutionary influence of historical demographics and natural selection through a series of transitions associated with the formation of the genus Capreolus, speciation within this genus during the Quaternary and during divergence among European roe deer (C. capreolus) populations. Our analyses were facilitated by the generation of a new high-coverage reference genome for the Siberian roe deer (Capreolus pygargus).  We find progressive reductions in effective population size (Ne), despite very large census sizes in modern C. capreolus populations and show that low Ne has impacted the C. capreolus genome, reducing diversity and increasing linkage disequili...