The avian world is packaged into genetic assemblages that we call species. Although ornithologists can, with a few important exceptions, agree on the boundaries among avian gene pools that delimit species, the evolutionary process that created this structured subdivision of Aves remains uncertain and contentious. Moreover, although avian species are recognizable and diagnosable, many bear signatures of recent, often substantial, exchange of nuclear (N) genetic material. As a result, there is debate regarding the process that gives rise to and maintains the genetic structure of avian populations. I propose that a key missing consideration in discussions of speciation is the necessity of coadaptation between N and mitochondrial (mt) genes to enable core energy production via oxidative phosphorylation. Because mt genomes are non-recombining and subject to high mutation rates, they evolve rapidly. Consequently, N and mt coadaptation persists only through perpetual coevolution between mt and N genes. Mitonuclear coevolution leads to rapid divergences in coadapted mitonuclear gene sets whenever there is a disruption in gene flow among populations. As a result, once populations diverge in coadapted mitonuclear genotypes, the reduced fitness of offspring due to mitonuclear incompatibilities prohibits exchange of mt and N-mt genes and effectively isolates individuals with shared coadapted N and mt genotypes. Given these considerations, I propose that avian species can be objectively diagnosed by uniquely coadapted mt and N genotypes that are incompatible with the coadapted mt and N genotype of any other population. According to this mitonuclear compatibility species concept, mitochondrial genotype is the best current method for diagnosing species.
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