Thursday, November 13, 2014
TreeMix graphs with Kostenki14 and Ust'-Ishim
First of all, here's a map with some basic info about these two Upper Paleolithic North Eurasian genomes. They're separated by less than 10,000 years and a couple thousand kilometers, so in theory they shouldn't be all that different.
Let's see what TreeMix has to say on the matter. Note that the graphs also include five other ancient genomes: Denisova, Altai Neanderthal, Loschbour, Stuttgart and BR2 (LBA_Hungary).
Admittedly, I'm still learning to use TreeMix. But with that in mind, I'd say the graphs above appear very reasonable, and show outcomes that generally fit with what I've seen elsewhere.
For instance, Denisova harbors something chimp-like that isn't shared with the Altai Neanderthal. This might be a signal of the introgression from an unidentified archaic hominin that has already been reported in scientific literature.
In regards to Kostenki14, the graphs back one of the main conclusions of Seguin-Orlando et al. (ie. the people who first analyzed and published this genome), in that it appears basal to later Europeans. However, the last two graphs suggest that this basal ancestry is not the same thing as the Stuttgart-related Basal Eurasian component described in Lazaridis et al., which, if I understand correctly, is what Seguin-Orlando et al. were saying.
In fact, the basal stuff carried by Kostenki14 seems to be related to the greater part of Ust'-Ishim's genetic makeup. I say the greater part, because Ust'-Ishim also appears to harbor Papuan-like ancestry not shared with Kostenki14.
Is there anything I can do to make these graphs more informative? Perhaps add or take away some samples? Feel free to let me know in the comments below.
By the way, I downloaded the Kostenki14, LBA_Hungary and Ust'-Ishim genomes from Genetic Genealogy Tools. The rest of the samples came from the Reich Lab's Human Origins dataset, available here.
Update 14/11/2014: After looking over the results above and reading the comments below, I made a few changes to the dataset and came up with a couple more graphs that I think are worth sharing. I'm quite certain now that the so called Basal Eurasian ancestry carried by Stuttgart and Kostenki14 can't be lumped into a single component.
Kostenki14: first genome of an Upper Paleolithic European
Ust'-Ishim belongs to K-M526