Bayesian coalescent inference of major human mtDNA haplogroup expansions in Africa

Summary: Past population size can be estimated from modern genetic diversity using coalescent theory. Estimates of ancestral human population dynamics in Africa can tell us about the timing and nature of our first steps towards colonizing the globe. Here we combine Bayesian coalescent inference with a dataset of 224 complete human mtDNA sequences to establish effective population size through time for each of the four major African mtDNA haplogroups (L0-L3). We find evidence of three distinct demographic histories underlying the four haplogroups. Haplogroups L0 and L1 both show slow, steady exponential growth from 156-213 kya. In contrast, haplogroups L2 and L3 show evidence of substantial growth beginning 12-20 kya and 61-86 kya respectively. These later expansions may be associated with contemporaneous environmental and/or cultural changes. The timing of the L3 expansion - 8-12 ky prior to the emergence of the first non-African mtDNA lineages - together with high L3 diversity in east Africa, strongly supports the proposal that the human exodus from Africa and subsequent colonization of the globe was prefaced by a major expansion within Africa, perhaps driven by some form of cultural innovation