Interestingly, polar bears are now providing us with a wonderful example of this process in action. It has been abundantly clear for a while now, that polar bears are an arctic-adapted form of non-polar bears, bow how far back in time can there evolutionary relationship be pushed?
A new open access paper in PNAS answers this question:
We first used a simple isolation model (15), comparing pairs of genomes under the assumption of allopatric speciation. However, for all comparisons, we obtained estimates of very recent split times and very large ancestral effective population sizes (Ne ), consistent with mis-specification of the demographic model and suggesting that the true demographics involved are not simple splits but instead initial splits followed by prolonged periods with structured populations and gene flow. WWe therefore applied an extended model estimating an initial split time followed by a period of gene flow before a complete split (SI Appendix). We estimated an initial split between black bears and their sister lineage 4 to 5 Mya followed by gene flow until 100 to 200 kya (Fig. 3)There you have it: low split times/high effective sizes are inferred in a tree model ("simple isolation model"), but when one does not take into account gene flow between the diverged populations, split times balloon and effective sizes shrink.
Of course in this case, we actually do have extant brown/black/polar samples to work with. But, leaving zoology and going back to anthropology, we only have on extant species (H. sapiens) within the genus Homo and only two (H. Neandertalensis and "Denisovans") of several archaic hominins that once roamed the planet, in some cases, apparently until very recently. Both the cases we do have indicate differential admixture levels with modern human groups.
I think we need to open ourselves to the possibility that shallow divergence times and higher effective population sizes in some human populations may not be the result of Biblical-level bottlenecks as small tribes of humans "conquered the earth", but of thorough and long-term gene flow between populations within the genus Homo.
PNAS doi: 10.1073/pnas.1210506109
Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change
Webb Miller et al.
Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000- to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska's Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5–10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4–5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.