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Polar Bears

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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).

Liu, Shiping, et al. "Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears." Cell 157.4 (2014): 785-794.

Liu, Shiping, et al. “Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears.” Cell 157.4 (2014): 785-794.

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.

 
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ResearchBlogging.org A few years ago a paper came out which suggested that the brown bears of the ABC Islands of southeastern Alaska were more closely related to polar bears than they were to other brown bears. More precisely, polar bears and ABC brown bears formed a distinct clade set apart from other brown bears, so that the class “brown bear” was not monophyletic. This meant that all the descendants of the hypothetical ancestral lineage of brown bears are not brown bears. Like reptiles, brown bears may then be paraphyletic. If this is correct polar bears can be thought of as a derived and specialized lineage of brown bears, despite all their morphological differences.

This is not just systematic arcana. The phylogenetic relationships of species has important implications for their conservation status, something all the more salient due to changes in the arctic habitat of the polar bear.

But there is a catch with the science: it focuses on mitochondrial lineages. In other words, the matriline, the female line of descent. There are technical reasons for this, primarily having to do with the tractability of generating phylogenetic trees from nonrecombining data sets of mtDNA as well as the ease of extractions of this genetic material (it’s abundant). And, in the case of ancient DNA abundance is still critical.

Last week a new paper in Current Biology reexamined the phylogenetic relationships of polar bears and brown bears using ancient DNA samples. Unfortunately it resulted in some weird titles: ‘Polar bear’s ancestor is Irish brown bear, study finds’. We’re revisiting the problem of ‘mitochondrial Eve’ all over, conflating mtDNA lineages with the total history of the species (granted, the fine print of the journalism usually alludes to this detail, but the headlines do not).

Let’s look at the paper itself. Ancient Hybridization and an Irish Origin for the Modern Polar Bear Matriline:

Results
We used a spatially explicit phylogeographic model to estimate the dynamics of 242 brown bear and polar bear matrilines sampled throughout the last 120,000 years and across their present and past geographic ranges. Our results show that the present distribution of these matrilines was shaped by a combination of regional stability and rapid, long-distance dispersal from ice-age refugia. In addition, hybridization between polar bears and brown bears may have occurred multiple times throughout the Late Pleistocene.

Conclusions
The reconstructed matrilineal history of brown and polar bears has two striking features. First, it is punctuated by dramatic and discrete climate-driven dispersal events. Second, opportunistic mating between these two species as their ranges overlapped has left a strong genetic imprint. In particular, a likely genetic exchange with extinct Irish brown bears forms the origin of the modern polar bear matriline. This suggests that interspecific hybridization not only may be more common than previously considered but may be a mechanism by which species deal with marginal habitats during periods of environmental deterioration.

In the methods they note that they “extracted DNA from 23 ancient Irish bears, 30 historic polar bears, four early Holocene (circa 8 kya) polar bears, and 17 modern polar bears.” The primary results of their phylogenetic analysis can be seen below:

As you can see, the Irish brown bear lineages now interpose themselves between the ABC brown bears and the polar bears. A tree of this sort shows the paraphyly of brown bears, as a whole side branch is given over to what is notionally another species, polar bears. This phylogenetic tree also shows approximate time until the coalescence of the mtDNA lineages (back to the last common ancestor). The maximum value is ~120,000 years. If these results are correct the polar bear lineages separated from the now extinct Irish brown bears ~30,000 years ago! This is problem. It doesn’t match the fossil record, which indicates the separation of polar and brown bears more than 100 thousand years ago. And, it doesn’t match their own nuclear analyses on 20 markers, which also indicates a coalescence of more than 500 thousand years.

Why the disjunction? The above tree was of mtDNA lineages. Below are a set of schematics which propose to explain at least some of the mtDNA results. In panel A you see a demographic scenario totally in line with the mtDNA, and contradicting the fossils and autosomal results. In this model polar bears emerged recently from brown bears. In B and C you see scenarios of hybridization, more or less complex, which illustrate how mtDNA can obscure more elaborated demographic processes, and substitute in their stead a spare tree:

I think it is clear that the authors lean toward one of the last two scenarios: the history of the polar bears and their relationship to brown bears is not captured by mtDNA alone. This is somewhat ironic, because the media representation has not spotlighted this at all.

The authors outline a natural history scenario where the ranges of polar and brown bears expanded and receded with the ice ages and interglacials, and where these two populations met there were periods of hybridization. For reasons of chance many mtDNA lineages are lost over time, and so it may be that the dominant matriline of polar bears just happens to be that of an ancient brown bear female (or, it could be natural selection of favored mitochondria). I don’t see why this is so surprising, the whole circumpolar zone is a potential point of contact.

More broadly, it may cause us to reflect on the nature of the historical genetic processes at play amongst geographically expansive mammals. Recall the famous ‘X-woman’, who later became the Denisovan hominin. The mtDNA of this individual was far more diverged from Neandertals than the total genome turned out to be. Why? There are various technical reasons, but let’s remember that in many ways ~500,000 years ago the situation with hominins wasn’t that different from brown and polar bears. Some of the same insights about hybridization between diverged lineages may be usefully applied.

Citation: Edwards CJ, Suchard MA, Lemey P, Welch JJ, Barnes I, Fulton TL, Barnett R, O’Connell TC, Coxon P, Monaghan N, Valdiosera CE, Lorenzen ED, Willerslev E, Baryshnikov GF, Rambaut A, Thomas MG, Bradley DG, & Shapiro B (2011). Ancient Hybridization and an Irish Origin for the Modern Polar Bear Matriline. Current biology : CB PMID: 21737280

Image credit: Alan Wilson

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Genetics, Genomics, Phylogenetics, Polar Bears 
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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"