I've written about the study of selection on human mtDNA many times, and discussed the signs that Neandertal mtDNA may have disappeared because of selection.
I love how larger samples are starting to get zoologists to test the neutral hypothesis much more widely. This week, a new paper in Biology Letters by Andrew Foote and colleagues  shows that different populations of killer whales. They find possible evidence for positive selection on amino acid-coding variants in cytochrome b in two Antarctic populations.
Here's the last paragraph of the paper. This isn't totally clear without the context (describing the whale populations) but it gives the best short summary of the complexity that was found.
Based on morphological differences  and reciprocal monophyly of the mitogenome sequences , it has been suggested that type B and type C are distinct species. Positive selection on the cytochrome b could therefore be caused by adaptive divergence relating to a combination of variables that influence metabolic requirements, such as body size or diet; type C is a fish-eating dwarf form of killer whale, whereas type B is one of the largest forms of killer whale and primarily feeds upon seals [21,22] (J. W. Durban & R. L. Pitman 2010, unpublished data). However, the amino acid changes in both ecotypes could be the result of parallel evolution owing to environmental conditions such as oxygen concentration or sea temperature. Both type B and type C at least seasonally inhabit Antarctic pack ice, and both have been sighted over-wintering in the pack ice . The third Antarctic ecotype, for which we found no evidence of positive selection, inhabits the offshore ice-free waters during the austral summer and over-winters at lower latitudes . However, the mutations are in the opposite direction for each ecotype, suggesting that divergent evolution may be more likely. The two changes were private alleles within type B and type C, respectively, and neither substitution was found in the reconstructed ancestral sequence (electronic supplementary material), suggesting that each mutation has occurred and become fixed and almost fixed, respectively, since type B and type C diverged from their most recent common ancestor, approximately 0.15 Ma . Therefore, the ancestral form may not have been subject to the same selective pressures.
1. We know how well "reciprocal monophyly" has turned out for human and Neandertal mtDNA genomes...
2. It's interesting how much play there seems to be in the mitochondrial genome. Lots of ways to change and have small phenotypic effects that may be adaptive in one or another ecology. The system as a whole is relatively robust to many mtDNA changes.
3. Many years ago, whale mtDNA was being explained in very similar ways to humans -- a matter of small effective size, in this case exacerbated by matrilineal pod structure. Might well be for many kinds of whales, but selection makes the story more complex.