"False signature" of past population expansions in North Atlantic minke whales mitochondrial control region sequences

The most common approach used to assess the demographic history during
evolutionary time is by analysis of DNA sequences, typically mitochondrial
(mt) DNA. The shape of the genealogy estimated all sampled mt control
region sequences in a population differs between expanding, stable and
declining populations. The mt control region genealogies estimated from
population samples in several North Atlantic cetaceans (e.g., minke whale,
fin whale, beluga and narwhal) are highly consistent with exponential
population expansions during recent evolutionary time. These results agree
well with the distribution of the ice coverage during the last glaciations. We
sequenced additional mt genes (cytochrome b and cytochrome oxidase I) in
addition to the entire control region in samples from North Atlantic minke
whales. While the mt control region showed the previously reported
expansion signature, the distribution of genetic variation at the other two
genes was as expected for a population of constant population size. As all
three genes are fully linked the effects of selection and/or demographic
changes is expected to be observed at all three genes, contrary to our
observation. The cause for the discrepancy appears to be due to the extreme
site-heterogeneity in substitution rates at the mt control region. Our results
have implications for the many studies in cetaceans, and other species which
have inferred demographic history from sequence variation in the mt control
region.