Data from: 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 disequilibrium.  Even so, we find evidence for
natural selection shared among C. capreolus populations, including a
population that has been through a severe bottleneck. During each period
of transition there is evidence for selection, including at loci
associated with diapause (delayed embryonic development), a phenotype
restricted to this genus among the even-toed ungulates.  Together
these data allow us to assess expectations for the origin and
diversification of a mammalian genus during a period of extreme
environmental change.