tag:blogger.com,1999:blog-4123559132014627431.post6935010412556743543..comments2024-03-28T23:10:39.906-07:00Comments on Eurogenes Blog: ADMIXTURE analysis of Allentoft et al. and Haak et al. ancient genomesDavidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.comBlogger31125tag:blogger.com,1999:blog-4123559132014627431.post-3236917886288177472015-07-04T20:43:31.965-07:002015-07-04T20:43:31.965-07:00What I've seen is that if you remove Native Am...What I've seen is that if you remove Native Americans, you have to take out EHG. That's the only way to get a Yamnaya cluster.Anonymoushttps://www.blogger.com/profile/13876988480444711159noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-57018232076089121262015-07-04T17:47:18.810-07:002015-07-04T17:47:18.810-07:00Nice
Very "South asian" and very little...Nice <br />Very "South asian" and very little Levantine stuff. Same as K14. <br />Makes one wonder what was happening in the Palaeolithic near East Anonymoushttps://www.blogger.com/profile/12259212254098264600noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-8257336604820041762015-07-04T17:06:26.559-07:002015-07-04T17:06:26.559-07:00Yes, leaving out the Amerindians and SHG might rev...Yes, leaving out the Amerindians and SHG might reveal some interesting things. I'll try a couple of runs without them later today.<br /><br />By the way, here's the K15 for Oase1.<br /><br />North_Sea 8.12<br />Atlantic 13.45<br />Baltic 9.65<br />Eastern_Euro 0<br />West_Med 4.51<br />West_Asian 0.4<br />East_Med 0<br />Red_Sea 0<br />South_Asian 26.1<br />Southeast_Asian 7.65<br />Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-38855744011295916272015-07-04T10:54:56.619-07:002015-07-04T10:54:56.619-07:00Euro_HG is the one that seems to have also Basal E...Euro_HG is the one that seems to have also Basal Eurasian (or Middle_Eastern), since Unetice, Lithuanians and others (BB, Sintashta) are scoring 80%. So all 3 components sharing BE and Euro_HG sharing some ANE with Hindu_Kush might explain why they are so related.Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-48387464129334533852015-07-04T09:18:52.154-07:002015-07-04T09:18:52.154-07:00@David
In these kind of unsupervised runs, wouldn...@David<br /><br />In these kind of unsupervised runs, wouldn't it help to be more selective with the samples used? For example, leaving Amerindians out would improve our understanding of the components, I think. Eurasians don't have any Amerindian admixture (it's the opposite), but they immediately create their own cluster that hides the origin of some components (EHG being 10-20% Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-31141606447509299092015-07-04T09:06:47.222-07:002015-07-04T09:06:47.222-07:00@Matt
Thank, very interesting. I think we still h...@Matt<br /><br />Thank, very interesting. I think we still have quite a bit to learn about Basal Eurasian, ANE and Near Eastern components.<br /><br />At K6 the Middle_Eastern looks like Basal Eurasian + ANE, being very high in modern Near Easterners, Iranians and S-C Asians. But rather low in EEF, that look very European.<br /><br />At K10, it seems that Hindu_Kush takes the ANE with it + Basal Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-11665305347207661672015-07-04T08:35:12.741-07:002015-07-04T08:35:12.741-07:00@Mike
Yes, pure speculation on my side based on t...@Mike<br /><br />Yes, pure speculation on my side based on the bits of information we have. It could all be random founder effects, sampling bias and what not. But I'm usually not very happy with those explanations and try to speculate to find some reason to it (a defect, certainly. It's wiser to just wait for more data that would allow us to really know).Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-14089305851461756652015-07-04T08:26:33.207-07:002015-07-04T08:26:33.207-07:00@Tobus
Yes, the result is very low compared to th...@Tobus<br /><br />Yes, the result is very low compared to the at least slightly significant Z-score. Here's the complete D stat:<br /><br />Yoruba baCw baAfan baYam -0.0069193453 0.0026427011 -2.6182852949 506941<br /><br />The quality of the genomes are certainly not the worst ones in the paper, but I guess none are really that great either. In any case there's probably not too much to Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-43015917459937769652015-07-04T08:07:46.596-07:002015-07-04T08:07:46.596-07:00Yep. That's certainly possible.Yep. That's certainly possible. Anonymoushttps://www.blogger.com/profile/12259212254098264600noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-67383022577968386682015-07-04T08:03:27.294-07:002015-07-04T08:03:27.294-07:00What about m73 Samara and m269 Sredni Stog, pushin...What about m73 Samara and m269 Sredni Stog, pushing m73 to Central Asia.Anonymoushttps://www.blogger.com/profile/13876988480444711159noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-71910222506361025732015-07-04T06:45:56.872-07:002015-07-04T06:45:56.872-07:00@ Alberto
"This leads me more to think that ...@ Alberto<br /><br />"This leads me more to think that R1b kind of "passed" through the steppe. The native people before and after look to be clearly R1a. R1b coincides with the southern impetus of Yamnaya"<br /><br />I really don't know and can only speculate without direct evidence. But its been long noticed that R1a is found extensively from Scandinavia to India, but Anonymoushttps://www.blogger.com/profile/12259212254098264600noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-36582737478049042502015-07-04T06:23:59.839-07:002015-07-04T06:23:59.839-07:00Alberto: What are the SNP counts for that D-stat.....Alberto: What are the SNP counts for that D-stat.. -0.006 is a very low result and not usually associated with such a high Z-score. I'm wondering if it's running on only a handful of sites and so throwing the Z-scores out somewhat.Tobushttps://www.blogger.com/profile/05529220083970625733noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-49764666157380372832015-07-04T04:33:57.500-07:002015-07-04T04:33:57.500-07:00Thanks Matt. Yeah, I think the Hindu Kush componen...Thanks Matt. Yeah, I think the Hindu Kush component is very mixed and basically represents the complex ancestry and isolation of the Kalash. <br /><br />At K6 and K7 the Kalash are mostly Middle Eastern and European with various Eastern Asian influences, and that's essentially what the Hindu Kush component is, making it look sort of Euro HG.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-6749891136469994842015-07-04T04:14:14.242-07:002015-07-04T04:14:14.242-07:00As expected, quick couple of PCAs on the K10 value...As expected, quick couple of PCAs on the K10 values -<br /><br />http://i.imgur.com/MMf1WaY.png - with lots of the samples from West Eurasia, setting a cutoff point that looked about where it normally goes on these PCA. Limited to 5 samples with the same population label (which did unintentionally end up with tons of Spanish, as they all have slightly different labels by default). You'll be Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-76797978615791571782015-07-04T03:10:01.540-07:002015-07-04T03:10:01.540-07:00Related to the above speculation about Afanasievo ...Related to the above speculation about Afanasievo possibly being R1a, I find this stat interesting:<br /><br />Yoruba baCw baAfan baYam -0.0069193453 -2.6182852949<br /><br />Why would CW be closer to Afanasievo than to Yamnaya?<br />Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-86915784368489312402015-07-04T02:42:32.767-07:002015-07-04T02:42:32.767-07:00@Mike
Yes, I think we're seeing that the step...@Mike<br /><br />Yes, I think we're seeing that the steppe was unstable, but at the same time a very effective transit zone that played a very important role in spreading populations, cultures and languages east-west (both directions). A different thing is if it was the origin of any of them or not.<br /><br />Now for some speculative thinking:<br /><br />This leads me more to think that R1b Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-59188071695445842792015-07-03T21:38:54.829-07:002015-07-03T21:38:54.829-07:00David,
Will do. Once I get it, I'll run them ...David,<br /><br />Will do. Once I get it, I'll run them again.Anonymoushttps://www.blogger.com/profile/13876988480444711159noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-85736322709061090792015-07-03T21:30:12.471-07:002015-07-03T21:30:12.471-07:00Chad,
You need to run these samples with the main...Chad,<br /><br />You need to run these samples with the main Human Origins file (not the Haak one), and only with transversion SNPs.<br /><br />I'll send you the SNP list in a few minutes. When you get it, merge the ancient samples from Haak and Allentoft with the Human Origins (but be careful not to duplicate some of the samples, like Stuttgart and Loschbour).Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-1146185210205248382015-07-03T21:30:01.515-07:002015-07-03T21:30:01.515-07:00Excuse me, one BaMon looks Basque, the other Scand...Excuse me, one BaMon looks Basque, the other Scandinavian. Two CW samples look like BaHun. Most BaHun samples look between BR1 and Brits. Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-42540524497810954772015-07-03T21:20:34.815-07:002015-07-03T21:20:34.815-07:00K10 output. Some look like garbage, fair warning. ...K10 output. Some look like garbage, fair warning. <br /><br />https://docs.google.com/spreadsheets/d/1HNlr9AeZSpNNnAI2SQ3czlNaz9GePuHoTcDCmtBAZlM/edit?usp=sharingChadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-77398505610022233902015-07-03T21:15:42.259-07:002015-07-03T21:15:42.259-07:00Rise 436 M R1a1a1
Looks SW European.
BA Monteneg...Rise 436 M R1a1a1<br /><br />Looks SW European.<br /><br />BA Montenegrans look Basque.Anonymoushttps://www.blogger.com/profile/13876988480444711159noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-17665575760147433112015-07-03T18:38:24.935-07:002015-07-03T18:38:24.935-07:00The similarity of Andronovo to east-central Europe...The similarity of Andronovo to east-central European groups - which we've all noted- is striking, esp given that it is found where we'd expect Yamnaya-like predecessors during the early Bronze Age. Im sure if we had Catacomb culture samples, they'd look more east-central ("Baltoid") European too (that's certainly what the mtDNA evidence suggests). <br /><br />To me this Anonymoushttps://www.blogger.com/profile/12259212254098264600noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-75638093034617613322015-07-03T18:25:52.703-07:002015-07-03T18:25:52.703-07:00There's significant shift to the northeast fro...There's significant shift to the northeast from MN to BB, because in reality Yamnaya are more eastern than Armenians.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-26319706877132125732015-07-03T18:20:43.484-07:002015-07-03T18:20:43.484-07:00I know its perhaps the way the plot is set, and on...I know its perhaps the way the plot is set, and one can't make too much from visual inspections of PCA, but the major shift of BBs compared to MN predecessors is a northward one, rather than east. (?)Anonymoushttps://www.blogger.com/profile/12259212254098264600noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-60926405553543509842015-07-03T10:17:30.385-07:002015-07-03T10:17:30.385-07:00All of the BA Hungarians show Yamnaya ancestry. I&...All of the BA Hungarians show Yamnaya ancestry. I'll put up a K10 later, but I can only add a couple Allentoft samples at a time. They tend to push the Yamnaya cluster to the east, where most Yamnaya samples come up 80-90% of that, plus 10-20% WHG.Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.com