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Category Archives: Cameroon

Cameroonian Y-DNA lineage A00 is older than Homo sapiens

The news has been floating around in the anthropology and human population genetic circles for some time but it was not formally confirmed until now: a very ancient Y-DNA lineage appears to be so old that it can hardly be considered to be strictly Homo sapiens at its ultimate origin. The lineage is extremely rare however and has only been found so far in two men: an African-American (from the USA?) and eight Mbo individuals from Western Cameroon.

Fernando L. Méndez et al., An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree. AJHG 2013. Pay per view (free 6 months after publication) → LINK [doi:10.1016/j.ajhg.2013.02.002]

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.6

It could still be a very early diverging H. sapiens lineage, as is surely the case of the more recent and slightly more common A0 (former A1b, found in Cameroonian Western Pygmies, 8.3%, and among Algerian Mozabites, 1.5% – see here) but both are in the blurry zone of the time of birth of our species (judging from archaeological and paleoanthropological data) c. 200 Ka ago. The first documented “modern human” skull, Omo 2, is dated to 190 Ka ago and it shares locality with another one, Omo 1, which is rather H. rhodesiensis, so in that “dawn of modern humankind” there was surely not a very clearly drawn line between modern humans or Homo sapiens and archaic humans or Homo rhodesiensis (or whatever). Some of those proto-Sapiens lineages still remain among us at very low levels.

Their presence may also suggest minor admixture between the first migrant H. sapiens to arrive to Cameroon and their then still close relatives from previous flows, which we don’t consider H. sapiens because we have drawn a convenient, but as we see now somewhat blurry, anthropometric or paleoanthropological line at Omo 2 and later specimens close to us in skull shape. While there is some generic comparability, the fact of admixture between such closely related populations is much less impressive than the one of admixture with Neanderthals or, probably, Homo erectus (non-Neanderthal Denisovan relatives), more distant from us in the tree of Greater Humankind. 
As for the “molecular clock” estimate I suspect that this one is correct. I would have liked to explain it today but it will have to wait because it is a complex matter and I have been all day writing for this blog, so I am quite tired now.

Update (Mar 3): Kalupitero commented in another entry that this lineage has very distinctive STR markers and that he has spotted 9 Cameroonians and one French (probably of African ancestry) with it at the Sorenson Molecular Genealogy Foundation database.

Update (Mar 5): A reader directed me to a free copy of this paper, from where I selected fig. 1 (above) and fig. 3 (below). I realized that the number of sequences detected among the Mbo was not one as I originally said but eight. They also mention that the frequency of this lineage in Africa must be very low: c. 0.19% (CI: 0.11-0.35%).

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.



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