At first, I calculated the histogram of pairwise TMRCA between all these 109 Y-chromosomes:
It will appear therefore that the HG00640 Puerto Rican belongs to the R1b1-L278 clade, but not to the R1b1a-P297 subclade. He thus represents an earlier split from the tree than the R1b1a2-M269 (frequent in West Eurasia), as well as the R1b1a1-M73 (frequent in Central Asia). It seems that I have chanced upon a real relic Y-chromosome!
The estimate of the age difference between HG00640 and the remaining M343+ chromosomes that cluster on the right is: 15,426 years. We now have direct evidence that haplogroup R1b1 is quite old, and R1b-M343 itself must have emerged sometime between 23,657 years (the TMRCA of R1a vs. R1b) and 15,426 years.
This little exercise reinforces my belief, first expressed in the outliers article, that there are real relic Y chromosomes in the world today, and we neglect them at our own peril.
Most European and European-derived men from the 1000 Genomes Project who belong to the R1b-M343 clade share patrilineal descent within the last 7,000 years or so. But, not all of them do, and outliers like HG00640 can only be caught with very large worldwide sample sizes and full genome sequencing.
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Addendum: There appears to be a R1b1(xP297) DNA Project. There appear to be a quite rich collection of men with SNP results similar to HG00640, including R1b1c-V88+ (as suggested by Roy King in the comments), but also of V88- individuals. I see great utility in such projects, because if one can detect very aberrant Y-STR haplotypes (which can be done with a simple histrogram or MDS plot, as in this post), then one can identify candidate Y chromosomes for full sequencing.
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