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Abstract
Within-species genetic diversity is thought to reflect population size, history, ecology, and ability to adapt. Using a comprehensive collection of polymorphism data sets covering ∼3000 animal species, we show that the widely used mitochondrial DNA (mtDNA) marker does not reflect species abundance or ecology: mtDNA diversity is not higher in invertebrates than in vertebrates, in marine than in terrestrial species, or in small than in large organisms. Nuclear loci, in contrast, fit these intuitive expectations. The unexpected mitochondrial diversity distribution is explained by recurrent adaptive evolution, challenging the neutral theory of molecular evolution and questioning the relevance of mtDNA in biodiversity and conservation studies.
