Do “polar bears” exist?

Since 1996 it’s been known that, according to mitochondrial-DNA-based phylogenies, polar bears (Ursus maritimus) are actually nested within brown bears (Ursus arctos) rather than being a separate lineage.  In other words, the mtDNA of some populations of brown bears—in particular, those from the Admiralty, Baranof, and Chichagof (ABC) islands of southwest Alaska—is more closely related to the mtDNA of polar bears than to the mtDNA of other brown bears.

This makes brown bears “paraphyletic” with respect to polar bears.  That is, the brown bear species U. arctos does not include all of the descendants of its most recent common ancestor, since some of these descendants are placed within polar bears.

This conclusion was just confirmed by complete mtDNA sequencing of the bears. A new study in PNAS by Lindqvist et al. used “fossil DNA” from a subfossil polar bear jaw to look at the evolution of polar bears vis-à-vis their relatives.  The jaw, from Norway, was estimated at about 130,000-110,000 years old, and was sufficiently well preserved that a complete polar bear mtDNA genome could be extracted and sequenced.

This sequence was compared to mtDNA sequences from two living individual polar bears and four living brown bears.  The phylogeny based on this sequence is given below.  The main result is that this jawbone came from a polar bear living about the time (estimated at 152,000 years ago) when the ancestors of modern polar bears diverged from those of brown bears.  The authors also did stable carbon-isotope analysis of a tooth from the subfossil’s jaw, and found that the isotope values for carbon-13 were close to that of modern polar bears, suggesting to the authors that the individual engaged in “marine feeding,” i.e., ate seals.

The figure below also confirms the results of earlier phylogenies, using smaller segments of mtDNA, showing that brown bears—at least these three brown bears—from the ABC islands are more closely related to polar bears than to brown bears from other places.  Again, brown bears seem to be paraphyletic.

Fig. 1 (Fig. 3 of Lindqvist et al.)  A. Maximum clade probability tree of bear mtDNA using BEAST anaysis. B.  Phylogenetic network of complete mtDNA genomes. Note that brown bears from the “Adm” (Admiralty) and “Baranof” populations are more closely related to polar bears (including the subfossil specimen shown in red) than to other brown bears.

The authors conclude:

The stable isotope data, phylogenetic analysis, and the geological and molecular age estimates of the Poolepynten specimen indicate that ancient polar bears adapted extremely rapidly both morphologically and physiologically to their current and unique ecology within only 10–30 ky following their split from a brown bear precursor and, subsequently, within the course of ~100 ky, spread to the full perimeter of the polar basin. As such, the polar bear is an excellent example of evolutionary opportunism within a widespread mammalian lineage (33). Moreover, the extreme proximity of the Poolepynten specimen to the polar bear ancestor provides a unique case of a morphologically and molecularly validated fossil link between living mammal species.

Now this is pretty interesting, but I don’t find it terribly exciting.  I think its acceptance in PNAS is based more on the novelty of using subfossil DNA than on any new and pentrating insight into bear evolution.  But I want to discuss the “paraphyly” of brown bears highlighted here and in previous work.

If this DNA-based tree really reflected the species tree, then the ancestry of the groups shows true “species paraphyly“: that is, some living populations of brown bears are more closely related to living polar bears than to other living populations of brown bears.  And if that were the case, then hardcore cladists, who employ a species concept based only on “monophyly,” would not recognize the two species “brown bears” and “polar bears.”  They would have to lump them together into a single species of bear.  We would no longer have polar bears.

Of course, cladists aren’t rushing to do this, even though the paraphyly has been known for 14 years.  Why not? Well, a lot of cladists aren’t interested in “alpha taxonomy,” the practice of naming species. But anyone who’d lump polar with brown bears would also be derided.  That’s because, regardless of the genetic ancestry of these groups, the two species now seem to be independent evolutionary units, presumably isolated from each other by reproductive isolating barriers such as habitat and mate preference.

But if this is true “species paraphyly,” how could it have come about?  How could one or a few populations of species X be more genetically related to members of species Y than to members of its own named species? Well, it’s possible that the ancestor of all polar bears came from only one geographic population of brown bears (that population represented by the ABC  localities), and so the ancestry of polar bears reflects this origin.  If gene flow were sufficiently restricted among all populations of brown bears, then the species phylogeny (which, after all, is only a formalization of evolutionary history) could reflect this localized origin.

This probably happens quite commonly, as it cannot be all that rare for a widespread species to bud off a new descendant from only one or a few of its populations. (Migration of a few individuals to an island or a distant new habitat, for example, must involve such a process.) Usually, however, gene flow among members of that big, interbreeding species would soon efface this history.

But all this presupposes that the mtDNA phyogeny gives us the true species phylogeny—the evolutionary history of the populations themselves rather than just that of  mtDNA segments.  Does the “gene tree” of mtDNA—which, since all the DNA in a mitochondrion is physically linked, behaves as if it were a single gene—reflect the “species tree” of bears?

It may not.  We’ve known for a while that hybridization between species can occasionally move DNA between them, even after they’re formed, if reproductive barriers aren’t complete. And, for reasons we don’t understand, mitochondrial DNA (or chloroplast DNA) seems to move between species more easily than does nuclear DNA. If the ABC populations of brown bears exchanged, some time in the past, mitochondria with polar bears, though rare hybridization (and this is known to occur between the species), then sequencing mtDNA might tell us, erroneously, that for all genes, ABC populations are more closely related to polar bears than to other brown bears. And, importantly, such hybridization, which might have occurred after the polar and brown bear lineages diverged, would give us an erroneous idea of when the lineages diverged.

Such hybridization isn’t rare. There are lots of cases—Allen Orr and I list many of them in the appendix of our book Speciation (Sinauer, 2004)—in which mitochondrial-DNA based trees give a false diagnosis of paraphyly, while nuclear DNA, consisting of lots of independent genes and not just one, shows a nonparaphyletic tree.  This is true for oak trees, birds, fruit flies, and many other species. Sometimes, as in the Drosophila species I work on, movement of mtDNA between different species makes them seem genetically identical, while independent nuclear genes show well-demarcated species. Hybridization between species can make it very risky to use just one gene to reconstruct their history.

Yet somehow people continue to accept mtDNA trees as equivalent to species trees.  To be sure, Lindqvist et al. formally recognize that hybridization between polar and brown bears could produce an illusory species paraphyly, although they, like earlier authors, don’t give the possibility much weight (the PNAS paper gives the caveat,”Although mtDNA capture cannot be excluded to have happened between ABC bears and polar bears, these estimates nevertheless affirm with strong support a very recent divergence of polar bears from brown bears.”)  But it’s time for biologists to stop calling species paraphyletic when what they mean is that genes (e.g., mtDNA) are paraphyletic.

To determine if brown bears are really paraphyletic with respect to polar bears, and thus whether cladists would designate (brown + polar) bears as a single (very variable!) species, we’d have to look at a lot more genes—and genes from the nucleus.  If the consensus phylogeny from all these genes still shows the paraphyly, then systematists can worry about nomenclature. (But even if there were true species paraphyly, I’d still vote on retaining the two named species of bears, since I adhere to the “biological species concept” that is based not on phylogenies but the presence of reproductive barriers.)

For now, brown and polar bears are phylogenetically safe. But I wish that systematists would worry more about the problem of equating gene trees with species trees, and would stop relying solely on mitochondrial DNA when they can also use nuclear DNA. The more genes the better!

_____________

Lindqvist, C. et al. 2010.  Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proc. Nat. Acad. Sci. USA 107:5053-5057,

Shields, G. F., D. Adams, G. Garner, M. Labelle, J. Pietsch, M. Ramsay, C. Schwartz, K. Titus, and S. Williamson. 2000. Phylogeography of mitochondrial DNA variation in brown bears and polar bears. Molecular Phylogenetics and Evolution 15:319-326.

Talbot, S. L., and G. F. Shields. 1996. Phylogeography of brown bears (Ursus arctos) of Alaska and paraphyly within the Ursidae. Molecular Phylogenetics and Evolution 5:477-494.

31 Comments

  1. newenglandbob
    Posted March 17, 2010 at 1:33 pm | Permalink

    Why didn’t they look at nucleus genes? Too many of them? Budget constraints?

    • PaulM
      Posted March 17, 2010 at 9:28 pm | Permalink

      Presumably for the reason that mtDNA, being present in many more copies per cell, is much more easily sequenced in such old samples. It’s fantastic that a 100,000+ year old sample can be sequenced at all!

      Secondarily, there are many existing mt sequences for the species, meaning the researchers didn’t then have to go and sequence a whole lot of extra nuclear genes, which would get expensive.

  2. Posted March 17, 2010 at 2:01 pm | Permalink

    Nice article explaining the concepts fundamental to tree-thinking, monophyly and paraphyly, with an example from animals we are all familiar with. However, you failed to include an alternative to lumping polar and brown bears and that is splitting lineages within the brown bears. We can salvage the polar bear as a separate species, even given the brown bear paraphyly, if we were to recognize all those separate lineages of brown bears as different species. Presumably to do this a taxonomist would require some morphological characteristic(s) unique to each and I no idea if such exist.

    But I, too, am dismayed that these authors could not work up a few nuclear loci to properly address the question of brown bear monophyly (or that they were not asked to by reviewers and editor, one might have expected better from PNAS!).

    • BaldApe
      Posted March 17, 2010 at 3:42 pm | Permalink

      What I’m disappointed about is the fact that the brown bears sampled were (if I am reading the abstract correctly) all Alaskan. I’d like to see a comparison with Eurasian brown bears, especially since the Poolepyenten specimen is from Europe.

      Given what I see, maybe separating European brown bears from a North American bears clade which would include polar bears and American brown bears would fit the data.

      But I agree that mitochondrial DNA evidence needs to be supplemented with nuclear DNA evidence.

  3. Insightful Ape
    Posted March 17, 2010 at 2:11 pm | Permalink

    Rush Limbaugh has been telling us all along we should worry about them polar bears going extinct. Now we know why.
    They don’t exist to begin with.

    • Posted March 17, 2010 at 2:53 pm | Permalink

      As the pack ice diminishes and seal hunting becomes increasingly difficult, we can always resort to feeding the bears Rush Limbaugh.

      • newenglandbob
        Posted March 17, 2010 at 3:01 pm | Permalink

        Are you trying to poison the bears? I know I come close to vomiting when I listen to Limbaugh for as little as ten seconds. Eating some would never work.

      • Insightful Ape
        Posted March 17, 2010 at 5:01 pm | Permalink

        I am not familiar with any reported examples of cannibalism among bears.

  4. Posted March 17, 2010 at 2:26 pm | Permalink

    My admittedly limited insight into phylogeny and paraphyletic groups made me think the same as expressed above – the question isn’t whether the polar bears excist, but whether the brown bears do…

    If they had been measly periwinkles, nobody would have hesitated to conclude they were probably cryptic species…

    BTW, don’t polar bears and brown bears occasionally interbreed, anyway?

    • blue
      Posted March 17, 2010 at 7:05 pm | Permalink

      Yup, they do, as Jerry mentions:

      If the ABC populations of brown bears exchanged, some time in the past, mitochondria with polar bears, though rare hybridization (and this is known to occur between the species), then sequencing mtDNA might tell us, erroneously, that for all genes, ABC populations are more closely related to polar bears than to other brown bears.

  5. Thanny
    Posted March 17, 2010 at 2:42 pm | Permalink

    I’m puzzled by your chosen dichotomy, between a paraphyletic species or lumping polar bears in with brown bears.

    It seems obvious that the error is claiming that all brown bears are the same species.

    So the correct conclusion is that there are several species of brown bears, or at least two (with subspecies), and polar bears.

    I think that’s likely even if the mtDNA tree doesn’t quite match the tree a nuclear DNA analysis would suggest.

    Looking at all the “subspecies” of brown bears, I have to wonder what possessed anyone to consider them the same species at all, given their wide range and reproductive isolation (Ursus arctos isabellinus is certainly not interbreeding with Ursus arctos horribilis).

    • whyevolutionistrue
      Posted March 17, 2010 at 2:59 pm | Permalink

      Yes, of course. Certainly they could designate all lineages of brown bears as different species. But that would only be valid if every lineage were monophyletic AND this were determined by looking at several genes rather than one.

  6. Posted March 17, 2010 at 3:17 pm | Permalink

    Fig 1a is one of the nicest species graphs that I’ve seen, especially the time line on top with the labels. And the red lines for the common ancestor. Now if you could just ‘zoom in’ the graph to see the action in the last half million years I’d be impressed.

    Good explanation of mtDNA as acting like a single gene. Are there cases where nuclear DNA introgresses while the mtDNA doesn’t?

  7. KP
    Posted March 17, 2010 at 4:00 pm | Permalink

    “(Ursus arctos isabellinus is certainly not interbreeding with Ursus arctos horribilis).”

    How much gene flow is there between other “subspecies” of brown bear? Are reproductive isolating mechanisms increasing or decreasing in these other examples?

    • KP
      Posted March 17, 2010 at 4:02 pm | Permalink

      Sorry that was meant to be a reply in the thread by Thanny (#5)

  8. Occam
    Posted March 17, 2010 at 6:00 pm | Permalink

    Will the pre-announced sequencing of nuclear DNA (ref. 34 in Lindqvist et al.; http://www.genomeweb.com/sequencing/bgi-plans-sequence-polar-bears-penguins-tibetan-antelope) help settle the phylogeny?

  9. Charles Evo
    Posted March 17, 2010 at 6:13 pm | Permalink

    There are some interesting behavioral differences between Polar and Brown (Grizzly) bears.

    Polar bears are exclusively carnivorous, whereas Grizzlies are not.

    And, from what I’ve heard, Polar bears are the only bears that will track humans in an attempt to eat them.

    • Thanny
      Posted March 17, 2010 at 11:20 pm | Permalink

      Polar bears are omnivorous. They simply don’t have anything but meat available (not a lot of vegetation on the polar ice caps, eh?).

      You go haul a 50lb bag of sunflower seed to a polar bear, and I guarantee you it will be quickly consumed. Don’t hang around too long, though, because you’re next on the menu.

      • Charles Evo
        Posted March 18, 2010 at 12:13 am | Permalink

        Well, that’s how species change over time.

        But do you think a Polar bear would enjoy Blueberries? Maybe.

        Hell, a snake would eat sunflower seeds if it were hungry.

        • Sven DIMilo
          Posted March 18, 2010 at 10:51 am | Permalink

          a snake would eat sunflower seeds if it were hungry

          nah

  10. stvs
    Posted March 17, 2010 at 8:46 pm | Permalink

    Cool polar bear facts: polar bears are really black skinned, and their hair is really clear and acts like fiber optics to transmit warm sunlight to the optically absorptive skin. But just like a bunch of fiber optic cables, the fur appears white. Which blends in with snow.

    And Iorek Byrnison.

    • Posted March 18, 2010 at 7:03 am | Permalink

      Another cool fact about polar bears, their hair is hollow.

      Cheers,
      Norm.

      • Sven DIMilo
        Posted March 18, 2010 at 10:57 am | Permalink

        that much is true, though not particularly unusual

        • Posted March 18, 2010 at 3:11 pm | Permalink

          I only knew about polar bears. A quick Google shows me that dogs too *might* have hollow hair.

          Can you please tell me of any others that do, I’m interested.

          Cheers,
          Norm.

          • Posted March 18, 2010 at 3:13 pm | Permalink

            Answering myself, how sad! 😉

            Reindeer too it seems.

            Cheers,
            Norm.

    • Sven DIMilo
      Posted March 18, 2010 at 10:57 am | Permalink

      sadly, no
      http://www.azadocents.org/conferences/2004/polarbear.pdf

    • Ted Powell
      Posted March 21, 2010 at 8:12 pm | Permalink

      Cool polar bear fact: A polar bear is actually a rectangular bear after a coordinate transformation.

  11. PaulM
    Posted March 17, 2010 at 9:50 pm | Permalink

    “And, for reasons we don’t understand, mitochondrial DNA (or chloroplast DNA) seems to move between species more easily than does nuclear DNA.”

    As the mitochondrial genome is not subject to recombination its transmission under hybridisation is going to be all-or-nothing. The same is true of chloroplasts.

    Hence I would not say it is a matter of more easy movement between species but more complete and easily detectible movement when it does occur.

    I too would be interested in a nuclear analysis of the two species, as this will inform much more of the interactions between the two.

  12. Posted March 17, 2010 at 11:23 pm | Permalink

    On top of the danger of hybrydization affecting the mtDNA phylogeny, perhaps it would matter if bear mtDNA varies within individuals as much as they do in humans:

    Although the mtDNA of human cells is considered to be homogeneous, we found widespread heterogeneity (heteroplasmy) in the mtDNA of normal human cells.

    From He et al., Nature, March 3, 2010.

  13. Jean Peccoud
    Posted March 18, 2010 at 2:27 pm | Permalink

    For the reason why mtDNA may introgress more readily than nDNA (though I am not sure if this really true), this paper is of interest: Petit RJ & Excoffier L.
    Gene flow and species delimitation, TRENDS IN ECOLOGY & EVOLUTION Volume: 24 Issue: 7 Pages: 386-393 Published: JUL 2009

    I am king of surprised that now one bothered to do population genetics of polar/brown bears based on nuclear markers.
    Whatever the results, I would be against considering brown bear populations as distinct species if populations only differ geographically. If we do, we would have to consider some human populations as species too (combining thousands of SNPs, human populations can constitute distinct and robust genetic clusters, but not in sympatry).
    I am certainly against considering particular gene clades as species. Many factors (and past history) can cause deep and ancient polymorphism as some loci. As you stress, people need to look at many independent loci to infer a general pattern of divergence and be able to assign individuals into distinct genetic clusters.

    Jean

  14. eptesicus
    Posted February 25, 2012 at 1:34 am | Permalink

    maybe – someone should dare to say that – something is wrong with orthodox cladistics. Long before era of cladistic’s domination in taxonomy, people accept the obvious fact, that one species could originate from another species – not only the two species could originate from one common ancestor. The first concept is much closer to real life, especially in allopatric speciation – that small portion of individuals restrict themselves from contacts with their relatives (e.g. by colonisation of island), and live in isolation (forming a NEW species), paralelly to that much more numerous relatives (still belonging to an OLD species). So paraphylly should not be always rejected in taxonomy – what is good in cladistics is rejection of polyphyletic taxa, but rejection of paraphyletic ones in unreasonable orthodoxy. Maybe the same is with higher taxa and macroevolution – that old, ‘outdated’ concepts (‘fish are ancestors of amphibians’, ‘reptiles are ancestors of birds and mammals’, when there is nothing like ‘fish’ and ‘reptiles’) should be restored.


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