An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree

Abstract

We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237-581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins.

Figure 1

Genealogy of A00, A0, and the Reference Sequence Lineages on which mutations were identified and lineages that were used for placing those mutations on the genealogy are indicated with thick and thin lines, respectively. The numbers of identified mutations on a branch are indicated in italics (four mutations in A00 were not genotyped but are indicated as shared by Mbo in this tree). The time estimates (and confidence intervals) are indicated kya for three nodes: the most recent common ancestor, the common ancestor between A0 and the reference (ref), and the common ancestor of A00 chromosomes from an African American individual and the Mbo. Two sets of ages are shown: on the left are estimates (numbers in black) obtained with the mutation rate based on recent whole-genome-sequencing results as described in the main text, and on the right are estimates (numbers in gray) based on the higher mutation rate used by Cruciani et al.

Figure 2

Map Showing Cameroon and the Approximate Location where Mbo Speakers Live

Figure 3

Median-Joining Network of A00 Haplotypes The network is based on haplotypes (constructed with 95 Y-STRs) of eight Mbo and an African American (AA) individual. All mutations are assumed to be single step and were given equal weight during the construction of the network. Marker names are indicated without “DYS” at the beginning.