Summary and Conclusion
Science greedily seizes simplicity among complexities. Speciation occurs via alter- native pathways distinct in terms of the number of genes involved and the abruptness of transitions [148]. Nuclear variance in modern humans varies by loci in part due to unequal selection [149] and the linkage of neutral sites to those that undergo differential selection. Complexity is the norm when dealing with variance of the nuclear ensemble [150-154]. It is remarkable that despite the diversity of speciation mechanisms and path- ways the mitochondrial sequence variance in almost all extant animal species should be constrained within narrow parameters.
Mostly synonymous and apparently neutral variation in mitochondria within spe- cies shows a similar quantitative pattern across the entire animal kingdom. The pattern is that that most—over 90% in the best characterized groups—of the approximately five million barcode sequences cluster into groups with between 0.0% and 0.5% variance as measured by APD, with an average APD of 0.2%.
Modern humans are a low-average animal species in terms of the APD. The molecu- lar clock as a heuristic marks 1% sequence divergence per million years which is consis- tent with evidence for a clonal stage of human mitochondria between 100,000- 200,000 years ago and the 0.1% APD found in the modern human population [34, 155, 156]. A conjunction of factors could bring about the same result. However, one should not as a first impulse seek a complex and multifaceted explanation for one of the clearest, most data rich and general facts in all of evolution. The simple hypothesis is that the same explanation offered for the sequence variation found among modern humans applies equally to the modern populations of essentially all other animal species. Namely that the extant population, no matter what its current size or similarity to fossils of any age, has expanded from mitochondrial uniformity within the past 200,000 years.
Nonhuman animals, as well as bacteria and yeast, are often considered “model sys- tems” whose results can be extrapolated to humans. The direction of inference is re- versible. Fossil evidence for mammalian evolution in Africa implies that most species started with small founding populations and later expanded [157] and sequence analysis has been interpreted to suggest that the last ice age created widespread conditions for a subsequent expansion [158]. The characteristics of contemporary mitochondrial vari- ance may represent a rare snapshot of animal life evolving during a special period. Al- ternatively, the similarity in variance within species could be a sign or a consequence of coevolution [159].
Mitochondria drive many important processes of life [160-162]. There is irony but also grandeur in this view that, precisely because they have no phenotype, synonymous codon variations in mitochondria reveal the structure of species and the mechanism of speciation. This vista of evolution is best seen from the passenger seat.