Many aspects of the environment that are critical for the species survival can vary through time, from day to day changes, to those across years or over geological periods. They not only modify the selective pressures acting on populations but also change the size and distribution of the populations themselves, isolating or connecting them. Such changes may result in extinction but alternatively can lead to diversification processes. In this context, our theoretical investigations have shown that rapid evolutionary processes may be triggered by population isolation and reconnection events occurring over a large time-scale, as these generate a transient excess of genetic diversity in populations providing the required raw material for rapid evolution. Accordingly, we have demonstrated that successive population isolation and reconnection events occurring during the quaternary climate cycles are associated with high diversification rates in animal clades and intricate patterns of genetic diversity in African hippopotamus. Importantly, these events leave distinguishable genomic signatures on SFS and as well as on common summary statistics of DNA variation in populations. Using these theoretical results and full genome polymorphism data we infer the recent evolutionary history of human immunodeficiency virus (HIV-1) in Asia and South America and successfully retrieve the successive HIV subtype colonization events in these regions.