New paper on Y chromosome haplogroup T

There are some haplogroups (like R1b) that garner lots of attention and public interest; then, there are others, like haplogroup T that most people don't even know about. This haplogroup's fame was largely due to the fact that Thomas Jefferson belonged to it, but, since at that time T was called K2, most people have probably forgotten about that too.

A new paper studies this mysterious haplogroup and uncovers some structure in it. Moreover, interestingly, it joins T with the somewhat less mysterious haplogroup L that is quite common from the Caucasus through Iran to South Asia. The internal structure of the Y-chromosome phylogeny is getting resolved.

The Lemba evidence is also interesting: this population was theorized to have a Jewish origin on the basis of its possessing the 6-marker Cohen Modal Haplotype within haplogroup J. When it was later recognized that this was insufficient as a Jewish marker because (a) it could be found on very different lineages (J1 and J2, even non-J), and (b) it could be found at how frequencies in non-Jewish Near Eastern populations, the case for the Jewish origin of the Lemba largely crumbled.

This is probably another blow to that theory, as T1b* does link the Lemba to the Near East but not particularly to Jews. Alternatively, modern Jews are a very restricted subset of ancient Jews, a possibility that probably needs to be entertained although it would be difficult to test.

Hum Biol. 2011 Feb;83(1):39-53.

Increased Resolution of Y Chromosome Haplogroup T Defines Relationships among Populations of the Near East, Europe, and Africa.

Mendez FL, Karafet TM, Krahn T, Ostrer H, Soodyall H, Hammer MF.

Abstract

Increasing phylogenetic resolution of the Y chromosome haplogroup tree has led to finer temporal and spatial resolution for studies of human migration. Haplogroup T, initially known as K2 and defined by mutation M70, is found at variable frequencies across West Asia, Africa, and Europe. While several SNPs were recently discovered that extended the length of the branch leading to haplogroup T, only two SNPs are known to mark internal branches of haplogroup T. This low level of phylogenetic resolution has hindered studies of the origin and dispersal of this interesting haplogroup, which is found in Near Eastern non-Jewish populations, Jewish populations from several communities, and in the patrilineage of President Thomas Jefferson. Here we map 10 new SNPs that, together with the previously known SNPs, mark 11 lineages and two large subclades (T1a and T1b) of haplogroup T. We also report a new SNP that links haplogroups T and L within the major framework of Y chromosome evolution. Estimates of the timing of the branching events within haplogroup T, along with a comprehensive geographic survey of the major T subclades, suggest that this haplogroup began to diversify in the Near East ∼25 kya. Our survey also points to a complex history of dispersal of this rare and informative haplogroup within the Near East and from the Near East to Europe and sub-Saharan Africa. The presence of T1a2 chromosomes in Near Eastern Jewish and non-Jewish populations may reflect early exiles between the ancient lands of Israel and Babylon. The presence of different subclades of T chromosomes in Europe may be explained by both the spread of Neolithic farmers and the later dispersal of Jews from the Near East. Finally, the moderately high frequency (∼18%) of T1b* chromosomes in the Lemba of southern Africa supports the hypothesis of a Near Eastern, but not necessarily a Jewish, origin for their paternal line.

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