When, how, and why, different lineages of the tree of life diverged has long been a preoccupation of evolutionary science. Now one must add to that a caveat that it seems a great deal of the story also has to do with the entanglement of branches which were long separated. Paleontology has looked at the macroevolutionary patterns, and attempted to move from description to formal models which scaffold the long progress of natural history. Phylogenetics has painted the branches of the tree in loving detail, and attempted to infer patterns from the shape and pulses of the diversification. Population genetics has focused upon the microevolutionary parameters which shape the flux of the genetic makeup of particular lineages; drift, mutation, and selection. Now you have new fields such as population genomics, which fuse 21st technologies with the questions and theoretical machinery of 20th century disciplines (in this case, population genetics, just as phylogenomics is an extension of phylogenetics).
Because of the monetary investment by organizations such as the NIH (among other factors) the -omics revolution has hit Homo sapiens first. But it is moving on, and that is important, because evolutionary science really can’t constrain itself purely to the human domain. Ultimate questions such as why there are so many species requires actually surveying the nature of variation in the world out there. Nevertheless, currently most of the post-human work seems to be occurring in the classical ‘model organisms’ (e.g., Drosophila), or charismatic creatures, especially big mammals. A new paper in Cell, of all journals, is in the second class, Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears. As you can infer from the title the paper looks at both the phylogenetic history of polar and brown bears, as well as the evolutionary genetic functional differences between the two distinct lineages. As you can see their sampling coverage was limited to particular populations, which is reasonable in light of finite sequencing resources. They had 10 brown bears and 79 polar bears, with good coverage on a lot of them (~30x not atypical). The inferences necessarily derive from these populations, though they admit in the text you can only go so far with their limited geographic coverage.
Using a variety of methods (IBS tracts and ∂a∂i) they found that polar bears and brown bears (or at least the ones in their sample) diverged on the order of ~500,000 years ago into two populations. More precisely 479-343,000 years ago. This overlaps with the fossil evidence. It translates to a separation between the ancestral populations about 20,000 generations ago. The authors state:
… the distinct adaptations of polar bears may have evolved in less than 20,500 generations; this is truly exceptional for a large mammal. In this limited amount of time, polar bears became uniquely adapted to the extremities of life out on the Arctic sea ice, enabling them to inhabit some of the world’s harshest climates and most inhospitable conditions.
This seems a little hyperbolic to me. In fact the Neandertal-modern human divergence is only about half as far back in the past in generation time, and one could argue that our two lineages were pretty diverged as well. That being said, obviously there are huge visible and physiological differences between polar and brown bears. They include in their model estimates of effective population declines in the past, presumably due to the exigencies of the Pleistocene glaciations. Using paleontological results already known they suggest that the emergence, and derivation of the polar bear lineage occurred during a period of separation from the ancestors of brown bears. In other words, allopatric speciation. In line with earlier work they also report evidence of long term gene flow between the two lineages, in particular, gene flow from polar bears to brown bears. This seems to be an old and continuous event which has become attenuated of late (they didn’t detect the sort of long haplotypes indicative recent admixture).
A note of caution again, as the samples here are geographically limited. But using measures such as D-statistics which attempt to infer patterns of admixture between populations it does seem that the initial conclusion about decreased effective population implies expansion from small initial founder groups for modern extant lineages. One wonders if this is a commonality with large mammals which have been shaped by repeated glaciation events. Obviously I’m including humans here, but for humans we have a lot of evidence that in fact there has been a lot of replacement due to ancient DNA.
Perhaps more thoroughly persuasive is the evidence they report in the paper that the polar bear exhibits lots of evolutionary change from their ancestors in particular functional regions. Polar bears are highly carnivorous, and exhibit lots of morphological and metabolic differences from brown bears. To be short it is as if brown bears were put on a very high fat diet. The functional regions which indicate signatures of selection in polar bears don’t have corresponding hits in brown bears, which isn’t surprising. They’re adapted to different conditions. Additionally a lot of these changes in polar bears are inferred to be harmful in humans. Fast evolution often occurs by breaking things; loss of function. So not surprising. The question is how polar bears function then? Also, I wonder if brown bears themselves are derived in a manner which we don’t understand yet (the sample here is skewed toward polar bears). Though brown bears are generalists, so I presume that they’re probably closer to the ancestral morphology.
They conclude intriguingly:
…Such a drastic genetic response to chronically elevated levels of fat and cholesterol in the diet has not previously been reported. It certainly encourages a move beyond the standard model organisms in our search for the underlying genetic causes of human cardiovascular diseases.
As Sydney Brenner would say, we’ve learned enough (or not) about mouse diseases.
Citation: Liu, Shiping, et al. “Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears.” Cell 157.4 (2014): 785-794.