Brown Bear! Polar Bear!

By Razib Khan | March 18, 2013 2:31 am

Bears are big deal today. I’ve talked about this before, so I won’t belabor the point in this post. Rather, I want to persuade you that there’s a really interesting paper out in PLOS Genetics right now, Genomic Evidence for Island Population Conversion Resolves Conflicting Theories of Polar Bear Evolution. I know that seems like a mouthful, and despite the fact that I nodded to the reality that this is highly relevant in part because of policy concerns, the paper itself makes salient the reality that oftentimes we are confronted with the juxtposition between useful abstractions and the empirical shape of the world. In this case the abstraction is that of species, the one taxonomic category which many people find to be a natural kind, so to speak. These sorts of confusions of our expectations are often highly informative. They illustrate the limits of our abstractions, and drive us toward more complex and/or elegant formalisms which are capable of modeling nature as it is, rather than as it we wish it would be.


The peculiar result is that a few years ago some researchers began to report that brown bears were a paraphyletic species. That just means that the last common ancestor of all modern brown bears has descendants who are not brown bears. In this case, polar bears. Specifically, these results were derived using mtDNA, and they showed that the brown bears of the ABC islands in Alaska seem to cluster with polar bears, and not other brown bears. The figure below from a 2010 paper outlines the lay of the land.

 

Look at the timeline above. If it’s right then polar bears are a very recently derived lineage out of the genetic background of brown bears. But there’s a problem. The nuclear DNA, which is most of the DNA, tell a different story. You can follow all the gory details on the Wikipedia page. Let’s get to the author summary of the PLOS paper:

The evolutionary genetic relationship between polar bears (Ursus maritimus) and brown bears (U. arctos) is a subject of continuing controversy. To address this we generated genome-wide sequence data for seven polar bears, two brown bears (including one from the enigmatic ABC Islands population), and a black bear (U. americanus). These data reveal remarkable genetic homogeneity within polar bears and clear evidence of past hybridization with brown bears. Hybridization, however, appears to be limited to habitat islands, where isolated populations of polar bears are gradually converted into brown bears via male-mediated dispersal and sex-biased gene flow. Our simplified and comprehensive model for the origin and evolution of polar bears resolves conflicting interpretations of mitochondrial and nuclear genetic data, and highlights the potential effect of natural climate change on long-term evolutionary processes.

 

That answers the discordant results between mtDNA and autosomal results easy enough. If gene flow is overwhelmingly male mediated then little of the polar bear mtDNA will be replaced, since that is passed only through the mothers. And interestingly the X chromosome of the ABC brown bears still has a signature of polar bear ancestry! Actually, that’s not interesting, it strongly argues for the plausibility of the above model, because male mediated gene flow will replace ancestral X chromosomes more slowly (2/3 of X chromosomes are found in females in a sex balanced scenario). All this is not a very shocking model. This seems to have occurred with Argentina. A predominantly white nation, it turns out Argentines have a very high frequency of Amerindian mtDNA.

What does this have to with abstractions and empirical reality? Ultimately it goes back to folk biology, and adherence to a Platonic species concept. In many domains this is useful and sane. Clear and distinct ideas with boundaries are necessary for thought. But when thinking on an evolutionary genetic scale excessive focus on a Platonic species concept can mislead. The same applies to other scientific domains. One speaks of “solid” matter, but on a molecular scale most of the solidity of the matter is not a function of material (i.e., subatomic particles), but the electromagnetic force. But in most situations the abstraction is useful. We simply have to always be careful not to confuse our useful shorthand for the real state of affairs.

Similarly, species as a concept has stood the time. Even though the term is obviously anthropocentric. It makes no sense for asexual organisms. And even plants, which hybridize promiscuously, are often ill-served by it. Nevertheless for many purposes the biological species concept works fine in the contexts which are relevant and important to us.  The key is not to confuse a useful abstraction for reality. Speaking of abstraction, mathematics is useful for science, but it isn’t science (by this, I mean I think it can be a science, but science itself is not pure mathematics).

When it comes to charismatic fauna and their natural history I often imagine a dramatis personæ, with characters coming onto the scene, and sometimes fading. But these points in space and time which we fix upon as the hinges of the narrative arc are subject to a thick and complex scaffold of dynamics and forces, of which only the distinct phenotypes we have in mind are the final outcome In the case of the polar bear, it has become totemic of great arctic fauna under threat by climate change. So they have always been, so they are, and hopefully so they shall always be. But the results above show that reality was likely always more complicated, as brown bears and polar bears impinged upon each other’s territory, and may have been involved in gene flow over the course of millions of years. The realty may be a complex and hidden back story which we are only now becoming privy to. Fixating upon distinct and clear species categories is one of the best ways to keep this hidden structure masked, as well explain away the “anomalies.”

Citation: Cahill JA, Green RE, Fulton TL, Stiller M, Jay F, et al. (2013) Genomic Evidence for Island Population Conversion Resolves Conflicting Theories of Polar Bear Evolution. PLoS Genet 9(3): e1003345. doi:10.1371/journal.pgen.1003345

CATEGORIZED UNDER: Genetics, Genomics
  • http://www.facebook.com/karl.zimmerman Karl Zimmerman

    Wolves are another great example, as it seems that the wolf/coyote populations in North America, despite varying morphologies, interbreed readily in the wild, to the point that red wolves and eastern wolves have substantial coyote ancestry.

    Oddly, conservation efforts have identified hybridization with coyotes as one of the principle threats of extinction for both groups. this makes little sense, because even assuming a total blending of the wolf/coyote phenotype, the genes for wolves would be in the mix, and presuming selective pressure for wolves rose again, the body form could easily reassert itself.

  • tonywaters

    “Clear and distinct ideas with boundaries are necessary for thought. But when thinking on an evolutionary genetic scale excessive focus on a Platonic species concept can mislead. The same applies to other scientific domains.”

    Razib: Sounds like you are pushing into some post-modern ideas here. But I do appreciate your openness to such definitional issues!

    • razibkhan

      then i’ve been pushing them for 10 years. if you work with statistical data platonic models are obviously stupid, if sometimes useful. this doesn’t require much reflection.

      • tonywaters

        Well, I guess you are the first post-modernist who doesn’t wallow in self-reflection. I thought it was a hazard of the sub-species, so to speak.

        • razibkhan

          the post modernists engage in topics which open themselves up to qualitative verbal deconstruction. and that is an opening for an eternal loop of critique and deconstruction, to the point where the ultimate aim of inquiry becomes marginalized. my primary focus is on issues which have some concrete and often quantitizable form. scientists are well aware that their categories and abstracts are not perfect fits for these forms. some philosophy-of-science is aimed toward resolving/clarifying these issues. but at no point do we forget that the concepts and abstracts are ultimately less important than the underlying reality. the linguistic structures we we utilize never become the objects of ‘discourse,’ because the failing is always in the humans, not in nature.

          a domain like literature does not lend itself to such a neat resolution, because literature is human product, so analysis of humans is warranted, though to what extent is debatable. i think the study of humans is more tractable because humans are just complex animals. some of your colleagues (perhaps you) seem to disagree, and treat human cultural phenomena as if they were of the same class as a james joyce novel.

          • tonywaters

            The James Joyce novel is indeed a cultural phenomenon and the nature of the phenomenon itself is open to systematic inquiry.

            Where I think you would bump up against me, is with the assertion that there is an “underlying reality” which is ultimately measurable in a positivistic fashion. Certainly positivism, and assumptions about the existence of reality have their utility–including the wonderful things wrought by the genetic revolution. But from a philosophical level, all categories are still “social constructions.”

            A lot can be learned about humans by assuming that they are complex animals. Other things can be learned by assuming that because humans are products of their own ideas, they are indeed different.

            Admittedly, there are a number of philosophical dilemma, conundrums, and paradoxes embedded in all this. But taht is what makes the chase more interesting, in my view!

          • razibkhan

            But from a philosophical level, all categories are still “social constructions.”

            yes. but civil engineers build bridges, and gene therapy is finally getting off the ground after the disasters of the late 1990s. not bad for “constructions.” and that i think is the problem that some humanists have. without secondary concrete applications it seems that excessive chattering without getting to the ‘heart of the matter’ proliferates. the old model where there were Great Works of literature which were self-evidently and objectively good was priggish, but at least it kept the chattering focused and on point.

            ultimately the position that all categories are social constructions is a trivial assertion if you aren’t some sort of idealist. the better question is whether a given construction is *useful* and *informative*

          • tonywaters

            Not much disagreement from me on what you write above. I hope that you can continue to bring such an attitude to your study of genetics.

            The one point to quibble with is about your dismissal of idealism, The strength and weaknesses of particular ideals are still necessary to give direction to those engineers and geneticists about where “the good” which they define as “utility.” There are tensions in how such values emerge across time, and such changes tend to be addressed best through the humanities, including literature, and are still very much a legitimate subject for inquiry.

          • razibkhan

            I hope that you can continue to bring such an attitude to your study of genetics.

            pretty much all pop geneticists think like this. one of my major quibbles at this point interacting with people on your blog is that you guys don’t seem to know what some scientists really seem to think about their field, but create projections. you should do some on-the-ground ethnography.

          • tonywaters

            LOL. I will pass along your message to Michael who, I think is currently doing just that!

          • tonywaters

            Here is a post from Michael from his work on DIY Bio labs:

            http://www.ethnography.com/2013/01/why-a-diybio-lab-is-the-new-darkroom/

          • razibkhan

            embedding in an DIY bio lab is NOT the same thing as actually understanding what pop geneticists are doing/thinking. his comments are evo-devo etc., are a joke, for example (actually, they repeat stuff you see among those who don’t know, but if he’s a scholar that’s no excuse). his caricatures of what population geneticists think is totally unrecognizable.

            i’ve interacted with the DIY bio scene in the bay…. http://blogs.discovermagazine.com/gnxp/2011/03/d-i-y-bio-power-to-the-people/

  • stevesailer

    What sounds like a problem in epistemology is actually a huge issue in the Endangered Species Act. The billion dollar Ahmanson Ranch development was blocked in part by the finding on the property of the San Fernando Spineflower, a dime-sized weed that no naturalist had written about in generations. Does that mean it’s endangered? Or is the San Fernando Spineflower just a local variant of the common San Gabriel Spineflower? A billion dollar investment was on the line!

  • razibkhan

    the greeks didn’t invent species. it’s a natural intuitive ‘kind.’ when we think about biological taxonomy we’re natural ‘platonists.’

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

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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