"As part of our genetic analyses for the film SEARCH FOR ADAM, we analyzed additional markers on Jefferson's Y-chromosome in an effort to determine why it is so unusual. If you recall the original Hemmings paper in Nature by Foster et al., the haplotype was 'rare', which is what enabled them to implicate Jefferson as the source rather than another European. At the time there were no matches among the 607 European men (Jefferson's father claimed Welsh ancestry) who had been genotyped for the same 11 microsatellites. Recent searches of more comprehensive databases have turned up related haplotypes belonging to haplogroups O, K and Q. We investigated the 12 microsatellites routinely typed by FTDNA, which did not add to the haplogroup resolution. SNP testing, however, revealed that Jefferson's Y is positive for M70, which places him in haplogroup K2. K2 is rare in northern Europe (only one K was found among 1772 British men surveyed by Capelli et al., but it wasn't typed for M70) but quite common in the Middle East and northeast Africa, where it reaches frequencies of 10% or more. Interestingly, another person typed in the film, the Ethiopian prince, is also K2, but many mutational steps removed from Jefferson. We are currently looking at potential source populations for Jefferson's K2 as part of a broader survey of Y-chromosome variation in the Middle East and North Africa, and expect to submit a publication by the end of the year. I'm sure that all of you will appreciate the amount of effort that has gone into launching The Genographic Project, and hope that you will understand that our publication schedule has been somewhat delayed as a result.Some information on Y-haplogroup K2 and its presence in human populations: one two three.
National Geographic Society"
According to this paper (pdf), K2 is found at substantial frequencies in various Spanish populations. The simplest explanation for its presence in Thomas Jefferson might be that he was the descendant of a Spaniard.