As recently as 10 years ago one could plausibly talk about mtDNA Eve and Y chromosomal Adam. The “Human Story” might then be stylized into a rapid expansion from a small core East African population which flourished ~100,000 years ago, and engaged in a jailbreak sweep out of Africa and across the rest of the World Island, and beyond, to Oceania and the New World. In the process all other human lineages extirpated, marginalized, and eliminated, their culture and genes consigned to oblivion. No longer, the origin of our species may have been characterized by several admixture events with “other” lineages, both within, and outside of, Africa. Instead of a bifurcating tree, imagine a graph with reticulation. A phylogenetic tree with a light, but noticeable lattice scaffold, tying together disparate branches.
All this must be kept in mind when we see a paper such as An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree. The authors discovered a Y chromosomal lineage, A00, which diverges on the order of ~338,000 years before the present from other extant paternal lineages (the next oldest divergence is A0, ~200,000 years before the present. The 95% interval is 237 to 581 thousand years. Even taking the lower bound this implies that this Y chromosomal lineage diverged from the others before the emergence of anatomically modern humans in Africa ~200,000 years ago.
This sort of result is not about ingenious method or deep insight, but the reality that thick, dense, and expansive population coverage is going to uncover interesting and insightful detail. Though these basal Y (and mtDNA) lineages tend to be found in African hunter-gatherers, A00 is present among Bantu and West African populations. The simplest explanation is that A00 represents at case of genetic admixture between the dominant root lineage to our own species, as a collateral branch. In light of all that we know about genetics and paleontology now this is not entirely surprising. Rather, my question is simple: why is it that we have not found similar Y and mtDNA lineages in non-African populations?
Cite: Mendez et al., doi:10.1016/j.ajhg.2013.02.002