October 31, 2008

60,000-year-old Y-chromosome haplogroup D? Not really

I am probably sounding like a broken record, but here comes another study which uses the wholly inappropriate "evolutionary" mutation rate of 0.00069/locus/generation. This rate is suitable for a haplogroup that grows due to drift alone and which is expected in 60,000 years (or 2,400 generations) to have grown to the grand number of ~1,200 men.

Not only is this the case, but the authors give "confidence intervals" on their age estimates of 61-71kya which is almost certainly an underestimate of the truth based on an incomplete assessment of the factors affecting uncertainty about the haplogroup's age. This nice and tight estimate is accomplished using the grand total of eight STRs!

Based on using the wrong mutation rate, and artificially narrow confidence intervals, the authors joyously proclaim:
The estimated ages of the D-M174 lineages are older than those previously reported
based on both Y chromosome and mtDNA variations in East Asia [8, 9, 21]. To see
whether it is over-estimated, using the same method, we calculated the divergence
time between DE* and E-M40. The estimated age is 27,176 years, which is much younger than the D-M174 lineage, but consistent with the previous estimation (27,800-37,000 years ago) [3]. Hence, the antiquity of D-M174 likely reflects the true prehistory of human populations in East Asia. The age estimation model developed by Zhivotovsky (2001) is not sensitive to effective population size and recent population expansion though the effect of population substructure cannot be totally ruled out. The antiquity of D-M174 was also supported by a previous study in which the origin of D-M174 was estimated more than 50,000 years ago [5].
Study [5] by Underhill et al., which supposedly supports the origin of haplogroup D 50,000 years ago, actually doesn't derive this estimate on the basis of any genetic data, but rather from theory about the "Southern Coastal Route":
The early human groups that used this route around 50000 years ago (taking the earliest occupation of Australia as the endpoint of this dispersal) were not restricted to coastal areas, and must have successfully colonized the Asian mainland, as shown by the distribution of surviving Group IV and V lineages.
I am constantly amazed by how the tremendous amount of effort required to identify, sample, catalogue, process, and genotype great numbers of people from around the world is accompanied by an apparently complete lack of interest in checking the basic premises on which interpretation of this data is based.

This paper and its supplementary data is a wonderful resource for Y-chromosome haplogroup D, but if you want to know more about the origins of this haplogroup, the sister clade of the common haplogroup E, you'll have to look elsewhere.

BMC Biology doi: 10.1186/1741-7007-6-45

Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations

Hong Shi et al.



The phylogeography of the Y chromosome in Asia previously suggested that modern humans of African origin initially settled in mainland southern East Asia, and about 25,000-30,000 years ago, migrated northward, spreading throughout East Asia. However, the fragmented distribution of one East Asian specific Y chromosome lineage (D-M174), which is found at high frequencies only in Tibet, Japan and the Andaman Islands, is inconsistent with this scenario.


In this study, we collected more than 5,000 male samples from 73 East Asian populations and reconstructed the phylogeography of the D-M174 lineage. Our results suggest that D-M174 represents an extremely ancient lineage of modern humans in East Asia, and a deep divergence was observed between northern and southern populations.


We proposed that D-M174 has a southern origin and its northward expansion occurred about 60,000 years ago, predating the northward migration of other major East Asian lineages. The Neolithic expansion of Han culture and the last glacial maximum are likely the key factors leading to the current relic distribution of D-M174 in East Asia. The Tibetan and Japanese populations are the admixture of two ancient populations represented by two major East Asian specific Y chromosome lineages, the O and D haplogroups.



McG said...

This article added to the subsequent one are very interesting. I am an advocate of Zhivs rates, as you know. I also believe germline rates and Zhivs rates should be the same. So whats the problem. The problem is that Chandlers rates are contaminated. I would argue that the equivalence only makes sense for the same HG!! If germline rates are estimated from one one haplogroup they are very close to the evolutionary. Look carefully at Chambers data for 426 and 388. From Zhiv and using 30 year per gen I get the same number for Zhiv and germline(chambers). This if possibly fortuitous but 426's rate for I1a and R1b is the same. However, depending on if you count using ASD or simple, 388 is 3X to 10X faster for I1a (3X to 10X the number of mutations)compared to R1b. Chambers used a mixed set of HG's, without paying attention to STR mutation rate variability across HG) and it is reflected in his results. Note the overall average mutation rate is the same for the two HG's. It is just that several different STR's differ from group to group and will give false estimates if they are used.

In conclusion, I think the second paper has it right - they give the same answer if the dys loci you use have the same rate across HG's, or if you stay within a haplogroup.

McG said...

To be fully clear about 426 and 388 above, I use the same mutation rate as Chambers does for this dys loci. My data is derived from the Zhiv evolutionary average. The 388 is 3X slower because I only use R1b for mys set of mutation rates.