Monday, September 14, 2020

A New Root For Y-DNA P

Y-DNA haplogroup P (a.k.a. K2b2) whose subclade P1 is the parent haplogroup of Y-DNA Q and Y-DNA R and a descendant of Y-DNA K2, has a new and older root. 

It probably emerged in Southeast Asia and then ends up in Northern Asia and Europe through a counter-clockwise across Asia during the Upper Paleolithic era (and hence, prior to the Holocene era).

Y-DNA Q is the predominant pre-Columbian male lineages in indigenous peoples of the Americas and is also found across Eurasia, with the highest frequencies in Northern and Central Asia. 

Y-DNA R is the most common Y-DNA haplogroup Europe and is also common in South Asia.
With almost 35,000 branches comprised of 316,000 SNPs, branches on the Y DNA tree are split every day. In fact, roughly 1000 branches are being added to the Y DNA tree of mankind at Family Tree DNA each month. I wrote about how to navigate their public tree, here, and you can view the tree, here. You can also read about Y DNA terminology, here.

Splitting a deep, very old branch into subclades is unusual – and exciting. Finding a new root, taking the entire haplogroup back another notch in time is even more amazing, especially when that root is 46,000 years old. . . .  
Recently, Goran Runfeldt who heads the R&D team at FamilyTreeDNA was reading the paper titled Ancient migrations in Southeast Asia and noticed that in the supplementary material, several genomic files from ancient samples were available to download. Of course, that was just the beginning, because the files had to be aligned and processed – then the accuracy verified – requiring input from other team members including Michael Sager who maintains the Y DNA haplotree.

Additionally, the paper’s authors sequenced the whole genomes of two present-day Jehai people from Northern Parak State, West Malaysia, a small group of traditional hunter-gatherers, many of whom still live in isolation. One of those samples was the individual whose Y DNA provided the new root SNP, P-PF5850, that is located above the previous root of haplogroup P, P-P295.

Until this sample was analyzed by Goran, Michael and team, three SNPs, PF5850, P295 and F115, were considered to be equivalent, because no tie-breaker had surfaced to indicate which SNPs occurred in what order. Now we know that PF5850 happened first and is the root of haplogroup P.

I asked Michael Sager, the phylogeneticist at FamilyTreeDNA, better-known as “Mr. Big Y,” due to his many-years-long Godfather relationship with the Y DNA tree, how he knew where to place PF5850, and how it became a new root.

Michael explained that we know that P-PF5850 is the new root because the three SNPs that indicated the previous root, P295, PF5850 and F115 are present in all previous samples, but mutations at both P295 and F115 are absent in the new sample, indicating that PF5850 preceded what is now the old P root.

The two SNPs, P295 and F115 occurred some time later.

This sample also included more than 300 additional unique mutations that may become branches in the future. As more people test and more ancient samples are found and sequenced, there’s lots of potential for further branching. Even with more than 50,000 NGS Big-Y DNA tests in the Family Tree DNA database, there’s still so much we don’t know, yet to be discovered. . . .  
Goran was kind enough to provide additional information as well, including the estimated “Time to Most Recent Common Ancestor,” or TMRCA, a feature currently in development for all haplogroups. You can see that P-PF5850 is estimated to be approximately 46,000 years old, “ca 46 kybp,” meaning “circa 46 thousand years before present.”
The founding ancestor of haplogroup Q lived approximately 31,000 years ago, and ancestral R lived about 28,000 years ago, someplace in Asia. Their common ancestor, P-P226, lived about 33,000 years ago.
From here.


Darayvus said...

"from here" link just goes to Blogger

DDeden said...

Northern Parak State


andrew said...

@Darayvus Thanks. Fixed.

andrew said...

Acknowledging the error, but won't change as it is in quoted material.