April 24, 2013

Criticism of Y-chromosome Adam old age

... has just appeared on the arXiv. This refers to the paper by Mendez et al. announcing the basal clade A00 of the phylogeny and estimating a TMRCA for Y-chromosome Adam of 237-581ka.

The author argues that such an old age is inconsistent with neutral theory, although that assumes no population structure in the origin of modern humans; it may very well be that A00 introgressed into the modern human gene pool via an admixture event from a different African population.

The best evidence for the authors' of the original paper choice of mutation rate is their estimate that the common ancestor of all Eurasians being ~63ky vs. ~39ky using the faster rate. While a date between these two can be probably accommodated, the ~39ky age seems difficult to accept, given that Homo sapiens had arrived in various parts of Eurasia by the mid-40ky's and had been admixing with Neandertals 47-65ky BP; a higher date would also be more in line with age estimates of Eurasian mtDNA macro-haplogroups M and N.

In any case, it's probably a good idea to get a better handle on the mutation rate: Mendez et al. rely on the autosomal rate, adjusting for the Y-chromosome; while the faster rate derives from a single Chinese deep pedigree study.

arXiv:1304.6098 [q-bio.PE]

Timing of ancient human Y lineage depends on the mutation rate: A comment on Mendez et al

Melissa A. Wilson Sayres (Submitted on 22 Apr 2013)

Mendez et al. recently report the identification of a Y chromosome lineage from an African American that is an outgroup to all other known Y haplotypes, and report a time to most recent common ancestor, TMRCA, for human Y lineages that is substantially longer than any previous estimate. The identification of a novel Y haplotype is always exciting, and this haplotype, in particular, is unique in its basal position on the Y haplotype tree. However, at 338 (237-581) thousand years ago, kya, the extremely ancient TMRCA reported by Mendez et al. is inconsistent with the known human fossil record (which estimate the age of anatomically modern humans at 195 +- 5 kya), with estimates from mtDNA (176.6 +- 11.3 kya, and 204.9 (116.8-295.7) kya) and with population genetic theory. The inflated TMRCA can quite easily be attributed to the extremely low Y chromosome mutation rate used by the authors.

Link

2 comments:

mathbionerd said...

I'm thinking of delving deeper into the aspect that really has me unsettled: I do not think it is appropriate to estimate the mutation rate on the Y chromosome using data from the autosomes. If there is a linear correlation between mutation rates on each sex chromosome and the autosomes, then the estimates of male mutation bias should be the same regardless of which pair (X/A, Y/A or X/Y) are used to estimate it, but they are actually quite different. The lack of high quality noncoding Y sequence data has been the biggest drawback in studying this, but I think there may be enough published now for a more comprehensive study.

(Also, thanks for sharing this!)

terryt said...

"However, at 338 (237-581) thousand years ago, kya, the extremely ancient TMRCA reported by Mendez et al. is inconsistent with the known human fossil record (which estimate the age of anatomically modern humans at 195 +- 5 kya)"

Why do the authors automatically assume that why Y-DNA 'Adam' was necessarily a 'modern' human being? Surely that is an unjustified assumption.

"The inflated TMRCA can quite easily be attributed to the extremely low Y chromosome mutation rate used by the authors".

Even using a more rapid mutation rate Y-DNA Adam is still very ancient. And looks to have a separate origin to mt-DNA Eve.

Here's what I think the African haplogroups tell us, although many will disagree. To me it seems obvious that Y-DNA Adam is West African, originally from somewhere between Lake Chad and Cameroon. In fact I'm reasonably sure that Y-DNA B originated in the same region. And possibly even E. On the other hand mt-DNA Eve is from further east, somewhere between Lake Tanganyika and the Ethiopian Highlands.

Two separate populations. By the time the two mixed two mixed Y-DNA DE was able to enter mt-DNA Eve's territory. As were A1b, B2b and CF. And mt-DNAs L1c and L2 were able to enter Y-DNA Adam's territory. From the headwaters of the Nile and the Congo members of the hybrid population were able to spread through much of Africa and even beyond. They spread past pockets of other human populations, including many who had left Africa long before. And mixed with them. Possibly resulting in increaed hybrid vigour. Many of these ancient populations have contributed to the modern human gene pool. One of these populations had become a remnant population in West Africa to the west of Cameroon (Nigeria?). Another remnant population was present in Europe, but its main contribution to the genetic makeup of the modern human gene pool was from further east. Some mystery population has contributed genes shared between Denisovans and Melanesians. Other pockets of remnant human populations have almost certainly made their separate contributions. For example the EDAR370A variant may have introgressed from an ancient East Asian population.