Bearish wisdom!

By Razib Khan | July 12, 2011 1:11 am

ResearchBlogging.orgA 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

CATEGORIZED UNDER: Genetics, Genomics
  • Sandgroper

    I’ve been waiting for Paul to say “You see, polar bears are Irish too.”

  • http://lablemming.blogspot.com/ Lab Lemming

    “coalescence of more than 500 years as well.”
    You’re missing a ‘thousand’ here.

  • DK

    It doesn’t match the fossil record, which indicates the separation of polar and brown bears more than 500 thousand years ago.

    Wikipedia sites recent paper in PNAS that says: “the specimen was estimated to be 130–110 ky old, which is significantly older than any other known polar bear subfossils”. The paper itself suggest the split at around 150 kya.

  • pconroy

    Sandgroper,

    Woot!!!

    Polar Bears and the Irish share a common ancestor ;)

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    thanks for the catches guys!

  • Dallas

    I had the same feeling as you, Razib, when I first saw the press on this story, and I’ve seen it elsewhere. I’m currently working in a crocodilian systematics lab and one of our Ph.D. students recently published a paper on hybridization between Cuban crocs and American crocs living in Cuba (I believe you linked to this on here before). It got a reasonable amount of press and many of the news stories said the Cuban and American crocs in Cuba are now more closely related to each other than the American crocs in Cuba are to American crocs on the mainland. Only a few of them mentioned this was only in the mitochondrial DNA. I guess its semi-understandable, most people have no understanding of mitochondrial vs genomic inheritance, but it becomes disingenuous when its phrased that way, because it implies something so incredibly and drastically different. I think it aligns with something Jon Stewart is always talking about: the media is all about sensationalism and whatever sounds more dramatic and news worthy is better to publish, whether its true or not. And then there’s the possibility that the journalists in question are just don’t know enough to recognize the distinction.

  • http://forwhattheywereweare.blogspot.com/ Maju

    Reptiles are monophyletic (class: Reptilia, which includes now birds).

    The Terrestrial Vertebrates category is divided in two: Amphibians and Reptilomorpha, which is surely a category you can describe as “reptiles” in the broad sense.

    Reptilomorpha divides in several extinct groups and then Amniota.

    Amniota divides between Synapsida (mammals and extinct “reptile-like” relatives) and Reptilia (reptiles in the narrow sense, including birds and dinosaurs).

    Reptilia divides in Anapsida (leading to Testudina: turtles) and Romerida (leading to Diapsida, which includes all other reptiles and, of course, birds and dinosaurs).

    It is not that Reptilia or Reptilomorpha are not monophyletic, it is just that traditionally we decided that a widespread subclade was out of the group (birds and mammals respectively).

    Similarly brown bears are monophyletic in the graphic above, if anything it is polar bears, a subclade of brown bears it seems, which are not.

  • http://backseatdriving.blogspot.com/ Brian Schmidt

    If by affecting “conservation status” Razib means “legal conservation status”, the answer would be not really, at least not in the US. As I’ve mentioned before, the US Endangered Species Act protects not only species but subspecies and “distinct population segments” (DPS) of vertebrates in order to preserve genetic diversity, and apparently in prejudice against invertebrates.

    A citation, although they’re easy to find:

    “Under the original ESA, a species was defined to
    include ‘‘any subspecies of fish or wildlife or plants
    and any other group of fish or wildlife of the same
    species or smaller taxa in common spatial arrangement that interbreed when mature’’ (ESA, Section
    3(15)). In 1978, the Act was amended to eliminate
    this language and replace it with the current DPS
    concept. The new definition provides that a species
    includes ‘‘any subspecies of fish or wildlife or plants,
    and any distinct population segment of any species
    of vertebrate fish or wildlife which interbreeds when
    mature’’ (ESA, Section 4)”

    http://www.bearbiology.com/fileadmin/tpl/Downloads/URSUS/Vol_18/U18_1_Rosen.pdf

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About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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