The significant heterogeneity in substitution rates observed in avian mtDNA from different species means that there is scope for variation in mutation rate to also explain variations in within-species mtDNA diversity. Indeed, Nabholz et al
] find that substitution rate and level of polymorphism are positively related. However, two proxys for Ne
(body size and current population census size) are not. These observations support the idea that avian mtDNA diversity is primarily due to the extent of mutational input, not to the effective population size, corroborating the previous claim based on data from other organisms [1
Previously, the same authors had analyzed mammalian mtDNA for a correlation between the amount of adaptive evolution and Ne
but no correlation was found [9
], which is at odds with the general idea that the efficiency of selection relates to life history. It may be that the relatively small populations typical of mammals mean that genetic drift plays a big role in producing mtDNA diversity but, nonetheless, Ne
does not seem to correlate with mtDNA diversity in mammals [9
]. Perhaps past demographic changes or the influence of mutation rate variation mask a signal from present-day Ne
. In their new study, Nabholz et al
] do not find a strong footprint of selection in avian mtDNA, similar to the situation in mammals [7
]. Mutation rate variation therefore remains a vital explanation for variation in mtDNA diversity of birds.
Does this mean that it is time to rewrite those parts of population genetics textbooks that deal with predictions of polymorphism levels? Clearly, as far as mtDNA is concerned, there does seem to be a need for revision. However, a cautionary note should be sounded to acknowledge the difficulties in properly estimating Ne by proxys such as body size or longevity. At present, it would be premature to state that the role of selection in shaping levels of mtDNA diversity is more pronounced in birds or other female heterogametic taxa than in male heterogametic systems, such as mammals.
Even if levels of diversity in mtDNA do not give us an unbiased picture of the effective size of avian populations, the use of mtDNA as a genetic marker is still warranted for other purposes, such as studies of phylogenetics and phylogeography. New high-throughput sequencing technologies might, however, lead to a shift in focus from population genetic studies based on mtDNA to population genomic approaches based on nuclear DNA, to estimate effective population size. Large-scale analyses of nuclear DNA can provide better and more direct estimates of Ne, thereby allowing more careful tests of the relationship between life history and population genetic and molecular evolutionary parameters.