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’).
I have put that in capslock because I’ve been emphasizing this problem for a long time, and yet many systematists and evolutionary geneticists still persist in using the DNA from mitochondria (the energy-producing organelles in cells that stem from ancient bacteria and have their own DNA) to make evolutionary trees of organisms and estimate their divergence times. They do this because 1) mtDNA is much easier to purify and sequence than is DNA from the nucleus (“nuclear DNA”, or nDNA), and 2) mtDNA usually evolves much faster than nDNA, supposedly making mtDNA a better indicator of species relationships, since it sorts out into definitive patterns more rapidly.
The problem is that, for reasons we don’t fully understand, mtDNA also moves between species during hybridization much more readily than does nDNA, and that can screw up species relationships. This is true for both animals and plants, and not just for mtDNA either: in plants, DNA from another organelle, the chloroplasts (site of photosynthesis, this DNA is called “cpDNA”) also moves between species more readily than nDNA.
Although the species definition used by most evolutionists, the “biological species concept” (BSC) uses the presence reproductive isolation between groups (mate discrimination, ecological preferences, hybrid sterility) as the criterion for their status as separate species, those reproductive barriers aren’t always complete, and sometimes genes can leak between species via hybridization. (The hybrids have to be partially fertile to transfer genes between species).
In the pair of Drosophila species I’ve worked on for 15 years, for example, the mitochondria from one species have completely replaced those of another species on the island of São Tomé. If you made a phylogeny of those species based entirely on mtDNA, you’d find that on the island they appear to have diverged only a short time ago, and that they did so on the island (“sympatrically”). But analysis of nuclear DNA shows that this is wrong: the two species are about 400,000 years old, and diverged when one ancestor invaded the island, formed a new species, and then a second wave of invasion from the second ancestral group re-invaded, yielding the two sister species on the same island.
We see this situation over and over again in biology. We don’t really know why mtDNA (and cpDNA) leak so readily between species, but we do know that this leakage makes it dicey to use only organelle’s DNA to make species trees. But the reason for this leakage compared to nDNA (so common to be almost a “rule of biology”) would make a useful paper topic for some enterprising graduate student.
But enough harangue. The misleading evolutionary conclusions one can draw from using mtDNA alone are well demonstrated in a new study of the phylogeny of polar bears and brown bears published by Miller et al. in Proc. Nat. Acad. Sci. (reference below; free access and download; see also J. D. Gorman’s summary in today’s New York Times).
The phylogenetic position and age of the polar bear (Ursus maritiumus) versus its closest relative, the brown bear (Ursus arctos), has for some reason become a lively topic of research. A while back I posted (here) that a population of brown bears on Alaska’s Alexander Archipelago (called “ABC brown bears”) might be more closely related to polar bears than to other brown bears. If that were true it would mean that the species “brown bear” was “paraphyletic,” i.e., some populations of brown bears are more closely related to another species than to other brown bears. For some biologists, that menas that brown bears wouldn’t be qualified as a “species” .
In a paper by Lindqvist et al. in 2010 (ref. below), the divergence time between polar and brown bears was estimated at about 150,000 years: a remarkably short time for a speciation event. A more recent study published this year in Science (reference also below) used nDNA to estimate a divergence time that is more reasonable: 600,000 years. But they used only a limited sample of nuclear DNA.
In my post on the Lindqvist study, I cautioned people about trying to reconstruct population history from mtDNA alone because its easy movement between species makes it a bad candidate for reconstructing the history of populations and species. That warning now appears reasonable based on a full-genome analysis of polar and brown bears (as well as black bears) reported in the PNAS paper noted above.
Now that we can sequence full genomes fairly rapidly and cheaply—this amazing advance has occurred in only the past 30 years—it’s possible to reconstruct evolutionary histories using nearly every gene in an animal or plant, and that’s as close as we can get to an accurate reconstruction without having been around when evolutionary lineages diverged. And that’s what Miller et al. did: they sequenced genomes of one polar bear, two ABC brown bears, a non-ABC brown bear, and a more distant relative, the American black bear (Ursus americanus). As they state in their paper, the goals were these:
We gathered extensive genome sequence data from modern polar, brown, and American black bear samples, plus a ∼120,000-y-old PB, to address the following questions. (i) What is the more precise association between the PB and its sister species, the brown bear; and do we find any signatures of past genetic interchange between the two species? (ii)Did the PB indeed evolve recently, as suggested by mitochondrial DNA and fossil evidence, or did it have an older origin, as demonstrated by nuclear DNA loci? (iii) Can we deduce any past responses in ancient bear population histories that may be connected with climatic changes?
Here are the results, summarized briefly:
- Polar bears diverged from brown bears about 4-5 million years ago, shortly after (i.e., within a million years) their common ancestor diverged from the ancestor of the black bear, the next most closely related species. Polar bears, then, are far older than previous studies suggested.
- The young age previously estimated from mitochondrial DNA suggests that that DNA was moved between polar and brown bear ancestors by hybridization after the lineages had been diverging. This is not unreasonable, since polar and brown bears are able to hybridize and produce fertile offspring in zoos, and appear to do so rarely in the wild. This suggests that the speciation event producing modern polar and brown bears was sporadically interrupted by hybridization and gene flow between them, probably because climate change forced them to encounter each other when their ranges moved.
The figure below shows the discordance between family trees based on mtDNA and nuclear DNA: the tree based on mtDNA is in orange, that based on many nuclear genes is given by the white bars outlined in black. Notice the deceptively recent divergence time between brown and polar bears indicated by mtDNA, and that suggestion that in one instance the polar bear was more closely related to a brown bear than the tw0 brown bears are to each other. This “paraphyly,” too, is an illusory result.
- As the authors note, “The clear discordance between mitochondrial and nuclear genomes in the phylogenetic placement of the ABC brown bears mirrors that found in the evolutionary histories of archaic and anatomically modern human lineages.” What they mean is that up to several percent of modern human DNA comes from Neanderthals, probably via ancient hybridization. If one looked only at that DNA, one would reach the false conclusion that some modern humans are more closely related to Neanderthals than to other modern humans. This is the danger of using only a limited amount of DNA to draw conclusions about evolutionary history. Some ABC brown bears share as much as 11% of their genes with polar bears!
- The 4-5 million-year-old split between black bears and the polar/brown bear lineage was also followed by hybridization lasting until about 100,000 years ago. In contrast, the near-simultaneous split between the sister species of brown and polar bears was followed by hybridization that can’t be said to have stopped even today. Genes are still, to our knowledge, occasionally exchanged between these species. In that sense we can’t say they are “complete” biological species, but are “nearly complete” biological species. Such is the case when there is sporadic gene exchange between groups whose reproductive isolation is nearly but not fully impeded by biological barriers.
- Based on genetic reconstructions, the polar bear population has declined drastically during the last half million years; the authors impute this to (nonanthropogenic) warming of the climate.
The overall lessons are these. First, use nuclear DNA to reconstruct evolution whenever you can, and always be suspicious of evolutionary trees based solely on mitochondial or chloroplast DNA. Second, polar bears and brown bears diverged a long time ago, not, as other studies suggested, quite recently. Third, the polar/brown bear divergence, as well as their joint divergence from black bears, involved occasional hybridization, so that speciation in these cases did not involve the classic scenario of complete geographic isolation up to the point where genomes diverged to the point of immiscibility. As Gorman says in his NYT piece: “The progress of species formation, at least in this case, is a bit like a long, ambivalent divorce in which the two parties separate but occasionally fall back into bed even after the official decree.”
Finally, polar bears are sensitive to climate, and as we continue to heat up our environment through shortsightedness, those bears are liable to extinction. They will either be unable to support themselves ecologically as the polar ice disappears, or they’ll hybridize themselves out of extinction by mating with brown bears. Either way, the fate of this lovely animal is precarious.
Humans poison everything, and I see no way, given our greed and dependence on fossil fuels, that we’ll be able to stop the trend of global warming.
Whatever, just remember to conserve energy and be wary of mitochondrial DNA.
Hailer, F. et al. 2012. Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage. Science 336:344-347.
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,
Miller, W. et al. 2012. Polar and brown bear genomes reveal ancient admiture and demographic footprints of past climate change. Proc. Nat. Acad. Sci. USA, Published online before print July 23, 2012, doi: 10.1073/pnas.1210506109