Ancient Y chromosomes confirm origin of modern human paternal lineages in Asia rather than Africa

Analyses of Y chromosome variations of extant people have resulted in two models for the paternal phylogenetic tree of modern humans with roots either in Africa or East Asia. These two trees are differentiated mainly by when and where their mega-haplogroups branched apart. This paper examines previously published Y chromosome sequencing data of 17 ancient samples to compare these two competing models. As ancient samples have had less time to evolve, they are expected to have mutated in some, but not all, of the sites that define present day haplogroups to which they belong. Indeed, most of the ancient DNAs here showed that expected pattern for both the terminal and the basal haplogroups to which they belong, all of the ones which are non-controversial or considered real by both of the two competing models followed that pattern. However, for basal haplogroups not shared by the two models, such expected pattern could be observed only if the haplogroups specific to the Asia rather than the Africa model are real, including ABCDE, ABDE, AB, A00-A1b. Another important point is that, if the mega-haplogroups of the Africa model were real, including BT, CT, CF and F, it would mean that numerous alleles would be shared between these haplogroups and several ancient A1b1b2 samples, which is unexpected and unseen in present day samples. Sharing alleles like this would also violate the infinite site assumption that makes the Africa rooting possible in the first place. Therefore, the data from ancient Y chromosomes confirm the actual existence of the haplogroups specific to the Asia model.