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Tuesday, July 24, 2012

Speciation in Bears

I read an interesting article a few months ago. It was a study of the phylogeny of bears with an emphasis of the origin of polar bears. In theory, it should be possible to put a date on the speciation event and to identify the probably ancestor of the modern polar bear.

The first thing you have to know is that polar bears and brown bears are not distinct species as defined by the biological species concept. This definition of "species" requires that there be no interbreeding with other populations, otherwise it's not a true species. (See Jerry Coyne's analysis of the problem with respect to humans.)

Polar bears and brown bears can mate to form hybrids, although this doesn't happen very often in the wild because the two "species" are geographically separated. The interesting question is when did these two populations diverge.

Many people thought the question had been answered a few years ago when Lindqvist et al. (2010) published the sequence of polar bear mitochondrial DNA ad compared it to that of other bears.

The result is shown here on the left in a figure taken from the recent paper in Science (Hailer et al, 2012). The Lindvist et al. paper showed conclusively that polar bears are relatively young as a "species" (about 150,000 years) and that they clearly arose from within the brown bear clade.

This result was somewhat surprising but not revolutionary. However, there were some experts on speciation who, questioned the conclusion; notably, Jerry Coyne [Do “polar bears” exist?]. They cautioned that using mitochondrial DNA could be misleading.

The latest study in Science shows that their concerns were justified. Hailer et al. (2012) lookd at 14 nuclear genes and constructed the tree shown shown below on the right.

This study indicates that polar bears diverged from brown bears about 800,000 years ago. Furthermore, the two populations of bear (brown and polar) form distinct clades.

What does this mean? It probably means that about 150,000 years ago there was a brief fling between a male polar bear and a female brown bear. The female offspring, carrying brown bear mitochondria, mated with male polar bears and all of their progeny contained brown bear mitochondria with mixtures of brown and polar bear alleles in their nuclei. Over time, the brown bear mitochondria became fixed by random genetic drift in the polar bear population.

This explains why the two trees differ and why you have to be cautious about using mitochondrial DNA in constructing phylogenies.

The story doesn't end there.

Just this week, a new paper appeared in PNAS confirming this result (Miller et al., 2012). Many of the authors are the same ones on the Lindqvist et al. (2012) paper. They are refuting the conclusions of their earlier paper by now showing that the sequence of nuclear genes indicate an earlier divergence of brown bears and polar bears.

I put off blogging about the Science paper because there were more important things to do and because it would have been difficult to explain the problem and the explanation. Fortunately, Jerry Coyne has now taken up the task of explaining the result at: A new study of polar bears underlines the dangers of reconstructing evolution using mitochondrial DNA. Please read his explanation of gene flow in bears based on his extensive knowledge of speciation.

The only issue I have with Coyne's explanation is that I don't think he gives enough emphasis to the idea that fixation of brown bear mitochondria in polar bears could be a genetic accident.

UPDATE: Ed Yong of Not Exactly Rocket Science already wrote about this three months ago [Polar bear origins revised – they’re older and more distinct than we thought]. John Hawks emphasizes Jerry Coyne's warning about using mitochondrial DNA and discuss the implications for hominid evolution [Polar bear mtDNA replacement].

Hailer F, Kutschera VE, Hallström BM, Klassert D, Fain SR, Leonard JA, Arnason U, Janke A. (2012) Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage. Science 336:344-347. [Abstract] [DOI: 10.1126/science.1216424]

Lindqvist, C., Schuster, S.C., Sun, Y., Talbot, S.L., Qi, J., Ratan, A., Tomsho, L.P., Kasson, L., Zeyl, E., Aars, J., Miller, W., Ingólfsson, O., Bachmann, L., and Wiig, O. (2010) Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proc. Natl. Acad. Sci. (USA) 107:5053-5057. [doi:10.1073/pnas.0914266107]

Millera, W., Schuster, S.C., Welch, A.J., Ratan, A., Bedoya-Reina, O.C., et al, (2012) Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. Proc. Natl. Acad. Sci. (USA) Published online before print July 23, 2012. [doi: 10.1073/pnas.1210506109]


Greg Laden said...

Those unsanctioned love affairs ALWAYS lead to trouble of one kind or another!

DK said...

I never really believed this "polar bear is a brown bear that went to live in Arctic only 150,000 years ago". The differences between brown and polar bear are simply too extensive for this short time to be enough (compare, for example, to humans over 150K). Of course, it is also completely crazy to claim that polar bears and brown bears are not distinct species.

anthrosciguy said...

Radical environments might well be expected to select for radical physical differences. Esp. in things like hair and head shape that seem (judging from our own recent prehistory as well as that of other animals) to be rather easy and quick changes, with minimal genetic tweaking.

DK said...

In theory. That theory didn't work for wolves or humans, though. In practice, I suspect that there are no examples of almost everything being so significantly different (including number of chromosomes) over just 150 KYA.

john harshman said...

I think you're taking the wrong lesson from this. It isn't mtDNA that's the problem, it's any single locus (or multiple tightly linked loci). mtDNA actually has the advantage of much faster coalescence than any single autosomal locus. And introgression can happen with any locus.

Chas Peterson said...

Can somebody who's read the two 2012 papers address an apparent discrepancy? AFAICT from second-hand sources like this and Coyne's, one puts the polar/brown bear split at 600,000 ya (don't know where Dr. Moran gets the 800,000) and the other one at 4-5 million ya.

DK said...

Same thing as before: one (the 600 KYA) is based on just 14 genes while another (the 4.5 MYA) is based on whole genome analysis. The latter estimates that 5-10% of the genome can be attributed to the admixture between two species, so there is plenty of room for error in the analysis of just a few sequences.

Anonymous said...

The Science paper says 600,000 (338,000 to 934,000) years ago. The PNAS paper is a little less straight-forward, but is basically saying 4-5 mya with a black bear - sister-group split and a split of this sister group to the polar and brown bears at an approximately similar time, but with more recent admixture events.

The major differences are due to the models used to infer the split, IMHO.