Jerry Coyne uses the occasion of polar bear genetics to give a biology lesson I've been trying to teach for 15 years: "A new study of polar bears underlines the dangers of reconstructing evolution using mitochondrial DNA".
Biology Lesson: DO NOT MAKE EVOLUTIONARY TREES OF ANIMALS AND PLANTS BASED ENTIRELY ON MITOCHONDRIAL DNA (mtDNA): PLEASE USE NUCLEAR DNA WHENEVER YOU CAN. THIS IS BECAUSE mtDNA APPEARS TO MOVE MORE READILY BETWEEN SPECIES THAN DOES NUCLEAR DNA (nDNA), CAUSING A DISCORDANCE BETWEEN EVOLUTIONARY TREES BASED ON MITOCHONDRIAL GENES (‘GENE TREES’) AND THOSE BASED ON POPULATION AND SPECIES HISTORY THAT ARE DISCERNED FROM ANALYSES OF MANY NUCLEAR GENES (‘SPECIES TREES’).
Could we put that somewhere in the preface of some genetics books?
I would add two things. The problem is just as pronounced within species (when examining the history of populations) as between them (when reconstructing phylogenies), and the idea that mtDNA "moves more readily between species" is an oversimplification.
In any single population, the behavior of mtDNA is rarely outside the very wide range of dynamics that happen by genetic drift alone, but that's more a sign of the extremely wide range of possibilities that drift allows. (This is why it took so long to demonstrate a problem with mtDNA in phylogenetic reconstruction). Now we know of many instances like polar bears, where the mtDNA genealogy has a different topology than that typical of nuclear genes. Moreover, we know that across many populations of different species, mtDNA is systematically less variable than the expected ratio from the nuclear genome. So it seems that once it enters a population, mitochondrial DNA sometimes spreads more rapidly and broadly than the typical gene. This dynamic sometimes may reflect extreme population histories, such as population bottlenecks and large-scale migrations. But in many cases it probably reflects selection on the mitochondrial genome.
I recommend Coyne's discussion of the polar bear phylogeny and the history of work on the subject. As I understand it, more research on the phylogenetic history of polar bears and brown bears is forthcoming.
One of my correspondents pointed out today that the case of polar bears and brown bears is an interesting analogy for the case of Neandertals and modern humans. According to current work, these bear species have been established for millions of years, but have continued to hybridize with widespread introgression of genes, including the complete mtDNA genome from brown bears into polar bears. We have much to learn still in this case about how much continued gene flow (or intermittent gene flow) must have existed between these large bear populations. Climate oscillations brought polar bears into more widespread contact with brown bears recurrently during the Pleistocene, but even today the populations of brown bears carry different proportions of genes derived from polar bears.
The bears serve as a useful reminder of just how little many anthropologists read biology. When Coyne writes that the previous (mtDNA-based) estimate for the divergence of polar bears and brown bears, at 150,000 years, would be "a remarkably short time for a speciation event", he is absolutely correct for medium- to large-sized mammals (as well he should be, having written the book on speciation). Yet anthropologists still blithely talk about Neandertals and other archaic human groups speciating over similar timescales.