tag:blogger.com,1999:blog-4123559132014627431.post7647418937383663833..comments2024-03-28T17:16:03.042-07:00Comments on Eurogenes Blog: Another look at the ancient mtDNA from Xiaohe, Tarim BasinDavidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.comBlogger125125tag:blogger.com,1999:blog-4123559132014627431.post-17428390990106119722015-07-16T14:30:44.578-07:002015-07-16T14:30:44.578-07:00@ Balaji, I kind of find that wierd to totally thi...@ Balaji, I kind of find that wierd to totally think of that as a European index as e.g. Surui>Lebanese and Karitiana>Syrian, but yeah, I really do think the relatedness to WHG and EEF, as you've shown by that stat for WHG, is important info to look at what the ancestral population of different West Eurasians is, not just the relatedness to the outgroups. (That's kind of really Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-64490970817714963962015-07-16T13:27:54.694-07:002015-07-16T13:27:54.694-07:00Matt,
You wrote, “So a population richer in WHG/A...Matt,<br /><br />You wrote, “So a population richer in WHG/ANE/EHG might have less disproportionate relatedness to an Indian one relative to Onge simply because of higher relatedness to ENA generally”<br /><br />You are right. And this does weaken my case for the lack of significant European ancestry in Pathans.<br /><br />ADMIXTURE analysis generally show a close relationship between the Balajihttps://www.blogger.com/profile/09561110603904765636noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-69802953991052764212015-07-15T13:10:43.024-07:002015-07-15T13:10:43.024-07:00Matt,
Your'e comparing a model for Pashtun ge...Matt,<br /><br />Your'e comparing a model for Pashtun genetic ancestry produced via a direct comparison of genomes to what Pashtuns get on a PCA that is itself based on a supervised ADMIXTURE test. Surely that isn't a reasonable comparison (and I'm sure we know which analysis carries more weight).<br /><br />This is a better model though (although the Yamnaya model can be seen as moreSeinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-7919351397106685852015-07-15T11:50:43.129-07:002015-07-15T11:50:43.129-07:00S: 47% Yamnaya + 43.2% Starcevo_EN + 9.8% Dai
Hmm...S: <i>47% Yamnaya + 43.2% Starcevo_EN + 9.8% Dai</i><br /><br />Hmmm. That case should have a bit more ENF and less WHG, but its still fairly similar. Hard to see why that should be unless the ASI ancestry actually does form a clade with Dai to the exclusion of Papuan (i.e. Papuan is the outgroup) though, rather than ASI as outgroup to Oceanian and East Asian. Which I guess is possible given the Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-78315208426339877242015-07-15T03:10:00.530-07:002015-07-15T03:10:00.530-07:00Balaji,
The fact remains that qpAdm has been deve...Balaji,<br /><br />The fact remains that qpAdm has been developed by the same people who worked on Reich et al. and Moorjani et al., and has been designed as a replacement for the much coarser methods utilized in those papers (but still using f-4 ratios). Basically, it would be quite strange to stand by those results, which preceded all the aDNA samples that are now at our disposal, and which Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-8430559657753237732015-07-15T01:18:32.919-07:002015-07-15T01:18:32.919-07:00Matt,
Thanks for your analysis suggesting the imp...Matt,<br /><br />Thanks for your analysis suggesting the importance of the choice of outgroups. Even with an ideal set of outgroups, sometimes there is no unique solution. Haak found that they could use qpAdm to model Yamnaya as EHG + Bedouin or EHG + Armenian or EHG + Lezgin. Davidski found that he could model Yamnaya as EHG + Georgian or EHG + Iranian. Some other extra information has to be Balajihttps://www.blogger.com/profile/09561110603904765636noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-88264814043618965262015-07-14T13:11:13.577-07:002015-07-14T13:11:13.577-07:00Matt,
Your observations concerning outgroups are ...Matt,<br /><br />Your observations concerning outgroups are quite pertinent, so I'd just like to add an empirical note. David has used a larger set of outgroups before, to model the HGDP Pashtuns (this set included Oceanians). The best fit he found for Pashtuns:<br /><br />47% Yamnaya + 43.2% Starcevo_EN + 9.8% Dai<br /><br />He didn't mention the chisq and tail probability, but did say:<Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-59806007165921995012015-07-14T12:02:12.057-07:002015-07-14T12:02:12.057-07:00Balaji: I agree with it and it illustrates again ...Balaji: <i> I agree with it and it illustrates again that qpAdm does not give unique and always correct solutions. Haak were able to model Corded Ware as 35% Karelia_HG + 65% Eperstedt_MN or as 72% Yamnaya + 28% Eperstedy_MN. These are two quite different things. It was only by adding European_EN samples as outgroups that they could figure that modeling with Yamnaya was better.<br /><br />Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-88478804316357904052015-07-14T01:29:06.852-07:002015-07-14T01:29:06.852-07:00Balaji,
Yet, in their first paper, they found tha...Balaji,<br /><br />Yet, in their first paper, they found that the closest West Eurasian population to Pashtuns were CEU (Americans of northern/northwestern European descent, from Utah). So it isn't really so clear cut. And with these new stats, we can't ignore the fact that Corded Ware are a better proxy than Georgians, and that this shows that Sintashta and Andronovo will be an even Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-21162213094634406722015-07-14T00:29:36.126-07:002015-07-14T00:29:36.126-07:00Seinundzeit,
Thanks for the interesting informati...Seinundzeit,<br /><br />Thanks for the interesting information. It does suggest some WHG-like ancestry in Pathans.<br /><br />However, we cannot ignore the Reich lab work. According to them, the West Eurasian populations most similar to Pathans are in decreasing order, Georgian, Armenian and Abhkasian. Also the qpAdm method seems to be a generalization of their f4 ratio method of estimating ANI. Balajihttps://www.blogger.com/profile/09561110603904765636noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-68709444426188729492015-07-13T04:21:38.757-07:002015-07-13T04:21:38.757-07:00Balaji,
This isn't correct. Chad ran a few st...Balaji,<br /><br />This isn't correct. Chad ran a few stats with the Onge included, at Anthrogenica.<br /><br />Source 1 Source 2 Target f_3 std. err Z SNPs<br /><br />Onge Corded_Ware_LN Pathan -0.008277 0.000954 -8.677 143113<br /><br />Onge Georgian Pathan -0.008108 0.000568 -14.267 144570<br /><br />Onge Yamnaya Pathan -0.006741 0.000765 -8.810 142987<br /><br />Onge Iranian Pathan Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-46750314695767043302015-07-13T00:34:31.657-07:002015-07-13T00:34:31.657-07:00Matt,
Thanks for your analysis. I agree with it a...Matt,<br /><br />Thanks for your analysis. I agree with it and it illustrates again that apAdm does not give unique and always correct solutions. Haak were able to model Corded Ware as 35% Karelia_HG + 65% Eperstedt_MN or as 72% Yamnaya + 28% Eperstedy_MN. These are two quite different things. It was only by adding European_EN samples as outgroups that they could figure that modeling with Balajihttps://www.blogger.com/profile/09561110603904765636noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-76406531583900913672015-07-12T18:06:21.436-07:002015-07-12T18:06:21.436-07:00Just for fun, here's a run with all of the UP ...Just for fun, here's a run with all of the UP samples.<br /><br />https://docs.google.com/spreadsheets/d/1DgmCJVtxI6BpAZyDbxm8TfIlJxFFRh9Esk5dEO1jESA/edit?usp=sharingDavidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-3677430771675621812015-07-12T05:50:47.097-07:002015-07-12T05:50:47.097-07:00Balaji, yeah, a population that is more or less eq...Balaji, yeah, a population that is more or less equivalent to some combination of other populations could get different ADMIX components.<br /><br />I don't think you're totally barking up the wrong tree though. One way that you could look at this might be to look at the FST from the components that would be predicted based on the Andronovo+Georgian+Dai model vs the actual Steppe K9, as Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-2333472511125735102015-07-12T04:33:27.105-07:002015-07-12T04:33:27.105-07:00The South Central Asian component is a mixture of ...The South Central Asian component is a mixture of Near Eastern, steppe and native South Asian elements.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-9894896478782619922015-07-12T01:20:09.891-07:002015-07-12T01:20:09.891-07:00Davidski,
I have compared your qpAdm modeling of ...Davidski,<br /><br />I have compared your qpAdm modeling of Pathans with your Stepppe_K9 modeing. <br /><br />https://docs.google.com/spreadsheets/d/1_JwkRSG7VrBPHi0-LG-wEhCxFWCq0vyI5y5gJu8haAw/edit?pli=1#gid=650646573<br /><br />In Steppe_K9, Pathan = 0.03 SE_Asian + 0.02 Siberian + 0.54 South_Central_Asian + 0.2 Steppe + 0.18 Middle_Eastern + 0.03 MN_European<br /><br />According to your apAdm Balajihttps://www.blogger.com/profile/09561110603904765636noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-10246398847718850672015-07-11T04:15:09.839-07:002015-07-11T04:15:09.839-07:00Alberto: Or alternatively, CW formed without Yamna...Alberto: <i>Or alternatively, CW formed without Yamnaya-like population, directly from EHG and MN, though I'm not sure if this model works.</i><br /><br />The simplest models of Corded Ware are as either 66% MN_Euro, 33% EHG or 20% MN_Euro, 80% Yamnaya. Split the difference and that's 43% MN_Euro, 17% EHG, 40% Yamnaya.<br /><br />p.96 Haak et al <i>"For none of the LN/BA populations Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-64700674122732922522015-07-11T01:25:05.954-07:002015-07-11T01:25:05.954-07:00David, yes, I tend to use South Asian and ASI with...David, yes, I tend to use South Asian and ASI without much care of their specific difference. Now I see that Seinundzeit also meant more specifically ASI, which does seem to be completely absent in Yamnaya.<br /><br />As for CW, the question of the origin of R1a there is still not clear. Yamnaya as far as we know (and we more more than anecdotal data already) was R1b (either because the HGs from Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-59939852836121768032015-07-10T20:34:50.949-07:002015-07-10T20:34:50.949-07:00Krefter,
I will rely mostly on Ancient SNP's :...Krefter,<br />I will rely mostly on Ancient SNP's :).Nirjhar007https://www.blogger.com/profile/12880827026479135118noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-26339879620188920572015-07-10T19:52:38.851-07:002015-07-10T19:52:38.851-07:00We need Ancient DNA ranging from Iran-Bangladesh. ...We need Ancient DNA ranging from Iran-Bangladesh. Ancient DNA from Europe revealed a lot modern DNA couldn't, especially about percentages of ancestry. Krefterhttps://www.blogger.com/profile/01055804913528477710noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-53935217382131436602015-07-10T18:07:12.368-07:002015-07-10T18:07:12.368-07:00I have no idea when EHG and R1a (or maybe rather R...I have no idea when EHG and R1a (or maybe rather R1) arrived in western Russia.<br /><br />It might have been just after the LGM from the Altai-Sayan refugium, or during the Mesolithic from western Siberia.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-70833914489857288362015-07-10T17:53:11.189-07:002015-07-10T17:53:11.189-07:00*as in**as in*Anonymoushttps://www.blogger.com/profile/12259212254098264600noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-9647307537610683272015-07-10T17:52:55.442-07:002015-07-10T17:52:55.442-07:00OK Dave I take your point, but the corollary of yo...OK Dave I take your point, but the corollary of your statement is that R1a must have arrived even to western Russia relatively recently, is in the late Mesolithic, just prior the Karelia sample. Anonymoushttps://www.blogger.com/profile/12259212254098264600noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-20095375205025174022015-07-10T17:41:31.888-07:002015-07-10T17:41:31.888-07:00Alberto,
The East Eurasian clusters in the K6 and...Alberto,<br /><br />The East Eurasian clusters in the K6 and K7 also represent native South Asian ancestry, which was Dai/Onge-like and part of the ENA node in the Eurasian phylogenetic tree.<br /><br />Some Yamnaya do show small amounts of the East Eurasian at K6, but when this cluster is broken up into Siberian and a more specific East Eurasian at K7, Yamnaya only show the Siberian, which is Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-85557835639580454782015-07-10T17:41:16.750-07:002015-07-10T17:41:16.750-07:00Maybe Im being stubborn, but I have difficulty acc...Maybe Im being stubborn, but I have difficulty accepting that model. Apart from the obvious issue that Yamnaya R1b separated from CWC R1a 16 k years ago, it has not considered that the "Teal" component entered CWC territory directly via the Dniester-Bug-Visla highway, and not from a peripheral SamaraAnonymoushttps://www.blogger.com/profile/12259212254098264600noreply@blogger.com