FTDNA draft Y-chromosome phylogeny

A draft of the Y-chromosome phylogeny, including the newly discovered basal A00 clade has been posted by FTDNA. Hopefully some progress can be made in the F portion of the tree, where currently there are subclades F1,F2,F3,G,H, and IJK. Determination of the bifurcation structure within F will doubtlessly be instrumental in informing our understanding of the dispersal of F descendants, which, according to the age of this major Eurasian haplogroup, are closely linked to the Upper Paleolithic event in Eurasia.

Investing in whole-genome sequencing of one individual from each of these clades would be very helpful in determining this structure. Of course, there are already the Complete Genomics data which include haplogroup G and various IJK descendants, so we now need to identify some F1,F2,F3, and H samples and give them the WGS treatment.

A00 at FTDNA2012: history in the making?

I've been following the #FTDNA2012 tag on twitter where Dr. Mike Hammer has been  talking about A00, the new most basal clade of the human Y-chromosome phylogeny. Apparently, 338ky old Y-chromosome ancestor for modern humans, at 98% confidence, with most basal clade found in western Cameroon and in African Americans separated by ~500 years from Cameroonian chromosome.

Root of human Y-chromosome phylogeny is now much older than both mtDNA Eve and first modern human fossils.

Conference attendees feel free to correct/supplement my understanding of what was said.

UPDATE: With respect to the confidence interval, Bonnie Schrack says:

The 338,000 years ago figure was the median (middle) of the confidence interval, which I believe was 95%, and not 98%. The lower limit of the confidence interval was still a bit over 200,000, I think -- that is, still before the time when fossils have been found showing fully anatomically modern features. Mike specifically said that even if the true age of A00 varied by 10 or 20% from the estimate, it would still be before the time when anatomically modern humans are thought to have appeared. I don't remember the upper limit too clearly, but as I recall, it was over 500,000 ybp.

UPDATE II: There is some uncertainty about the level of significance, with different people remembering anything from 90-98%. Some newer information from Tim Janzen:

Michael gave a TMRCA estimate of 338,000 years with a confidence interval range of 246,000 and 563,000 years for the A00/A0 node. He gave a TMRCA estimate of 202,000 years with a confidence interval range of 133,000 to 366,000 years for the A0/R-M269 node.

I guess we will have to wait for the publication to see the exact numbers, but it certainly appears that A00 branched off from the rest of mankind at an age that is much earlier than the next most basal clade (A0).

R1b1a2 variants in 1000G data

It's nice to see a group of independent researchers documenting their work using 1000 Genomes data. I've been following on-and-off developments in this field, and I have to say that it requires deep commitment from the persons involved to keep a mental picture of the ever-deepening phylogeny.

But, in a sense, that is what's great about the efforts of citizen scientists tackling a scientific problem: they are deeply invested in understanding their little part of the human Y-chromosome phylogeny, because it's their part and every SNP discovery in it represents a small victory. Thus, they can expend the time and effort to push the discovery process to its technological limits.

It's only too sad that this can at present be done only using 1000 Genomes data, a.k.a. the global collection of full genome data that completely ignores the part of the world between  Italy and China/India. Hopefully, sometime in the future, the ever-better-understood twig of R1b1a2 will be placed within its wider Eurasian context.

PLoS ONE 7(7): e41634. doi:10.1371/journal.pone.0041634


Discovery of Western European  R1b1a2 Y Chromosome Variants in 1000 Genomes Project Data: An Online Community Approach

Richard A. Rocca1*, Gregory Magoon2, David F. Reynolds3, Thomas Krahn4, Vincent O. Tilroe5, Peter M. Op den Velde Boots6, Andrew J. Grierson7

The authors have used an online community approach, and tools that were readily available via the Internet, to discover genealogically and therefore phylogenetically relevant Y-chromosome polymorphisms within core haplogroup R1b1a2-L11/S127 (rs9786076). Presented here is the analysis of 135 unrelated L11 derived samples from the 1000 Genomes Project. We were able to discover new variants and build a much more complex phylogenetic relationship for L11 sub-clades. Many of the variants were further validated using PCR amplification and Sanger sequencing. The identification of these new variants will help further the understanding of population history including patrilineal migrations in Western and Central Europe where R1b1a2 is the most frequent haplogroup. The fine-grained phylogenetic tree we present here will also help to refine historical genetic dating studies. Our findings demonstrate the power of citizen science for analysis of whole genome sequence data.

Link