In the sake of fairness, it’s worth reporting that mitochondrial DNA (mtDNA) may not be as flawed as previously thought (see the original paper here). I spent a bit of time earlier this year barking about how mtDNA is a less than stellar marker for inferring demography because it’s subject to recurrent selective sweeps which wipe out all signatures of demographic history. Thanks to Dr. Rob, I revised my position to take into account the effects of population size on selection.
If mtDNA mutations are only weakly advantageous, then they should only be under selection in large populations (this is the essence of the nearly neutral theory). This was brought up by Adam Eyre-Walker in his review of the Bazin et al mtDNA/population size paper. Eyre-Walker pointed out that mtDNA-based estimates of the MRCA of humans agree with those based on nuclear markers. That’s because the human population size is too small for mtDNA mutations to be under adaptive evolution. No selective sweeps means mtDNA can be used to infer demographic history.
That brings us to this paper in which Mulligan et al examine the relationship between mtDNA polymorphism and allozyme diversity (an estimate of nuclear DNA polymorphism, which should be a good proxy for population size) in eutherian mammals. While mtDNA may be a poor estimate of population size in organisms with large populations (insects, for example), it appears to work quite well for small populations (I have reproduced their graph below the fold).
There must be some threshold of effective population size below which selective sweeps on mtDNA are near impossible. This result also implies that there are next to no highly advantageous mutations in mtDNA. But we must also take into account the fact that the effective population size of mtDNA will be 1/4 that of a nuclear gene (it’s a haploid genome and only transmitted maternally — I hope I didn’t screw this up, again). So, a mutation in an mtDNA gene will need confer a greater fitness benefit than the same mutation on an equivalent nuclear gene in order to be fixed by selection.
Also, I still maintain that one should use more than one marker to infer demographic history. Even though mtDNA correlates well with population size for small populations, one should sample a couple more loci before reaching any conclusions about demography.