Outgroups Mota GoyetQ116-1 Kostenki14 Levant_Neolithic MA1 Ust_Ishim Vestonice16 Villabruna Steppe_EMBA X CHG 0.617±0.178 EHG 0.383±0.178 chisq 1.868 taildiff 0.93139015 allsnps: YES Steppe_EMBA Anatolia_ChL 0.139±0.050 CHG 0.356±0.063 EHG 0.505±0.025 chisq 5.084 taildiff 0.405658017In my opinion, despite the relatively low resolution of the X chromosome analysis, the Steppe_EMBA X chromosomes show a strong southern, in particular CHG, character, which suggests that CHG admixture into Steppe_EMBA was mediated largely via female gene flow. Interestingly, in one of the models, the Steppe_EMBA X chromosomes are fitted successfully as a two-way mixture of CHG and Iran_ChL (see here). It's impossible to model Steppe_EMBA in such a way with genome-wide data (for instance, see here and here).
Friday, March 17, 2017
Yamnaya X chromosomes
In this analysis I'm using the same qpAdm method and almost the same reference samples as Lazaridis & Reich 2017. However, to improve the resolution, in the right pops (or outgroups) I added European Late Upper Paleolithic forager Villabruna, and dropped the low quality Siberian Late Upper Paleolithic forager AfontovaGora3. Also, I ran tests with and without the allsnps: YES flag. In the left pops, apart from test group Steppe_EMBA (Early Middle Bronze Age steppe conglomerate made up of closely related Afanasievo, Poltavka and Yamnaya samples), we have the putative ancestral populations: Eastern European Hunter-Gatherers (EHG), Caucasus Hunter-Gatherers (CHG), Kura-Araxes (Armenia_EBA), a Chalcolithic Anatolian (Anatolia_ChL), Chalcolithic Armenians (Armenia_ChL), and/or Chalcolithic farmers from Iran (Iran_ChL). As far as I can tell, these are the best statistical fits with the X chromosome and genome-wide data, respectively. Feel free to set me straight; the full output is in a zip file here.