tag:blogger.com,1999:blog-4123559132014627431.post7113625180657296149..comments2024-03-18T18:30:48.719-07:00Comments on Eurogenes Blog: On the enigmatic early Neolithic farmers from IranDavidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.comBlogger204125tag:blogger.com,1999:blog-4123559132014627431.post-79145773527495464582016-08-14T19:25:02.112-07:002016-08-14T19:25:02.112-07:00There is some CHG in the Anatolians, and there'...There is some CHG in the Anatolians, and there's more of it in the Central Anatolians than the Western Anatolians.<br /><br />But CHG has a lot of ANE and a very strong eastern pull. The Anatolians lack these features for the most part.<br /><br />qpAdm can show a lot of interesting and useful things, like Mota standing in for Basal Eurasian, more or less. So it's possible to get good Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-34305562195119547362016-08-14T19:06:03.816-07:002016-08-14T19:06:03.816-07:00Some CHG in early Anatolian shouldn't be surpr...Some CHG in early Anatolian shouldn't be surprising. Some "bullet core" substratum is seen in Anatolia, Caucasus and northern levant, but not south levant or Greece. Robhttps://www.blogger.com/profile/07166839601638241857noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-18541862858594752152016-08-14T17:50:30.227-07:002016-08-14T17:50:30.227-07:00Nah, I just can't see any major EHG, CHG or Ir...Nah, I just can't see any major EHG, CHG or Iran_N in the Anatolians, not even the Central ones.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-78595964750125917902016-08-14T15:57:49.331-07:002016-08-14T15:57:49.331-07:00Natufians, sorry.Natufians, sorry.Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-59614676730313117432016-08-14T15:57:36.026-07:002016-08-14T15:57:36.026-07:00Oh, the other thing is that Levant is supposed to ...Oh, the other thing is that Levant is supposed to be a mix of Natifians and a group from near the Boncuklu group. So, that might be another reason for errors. Use the 9 and Iran in the outgroups, with Narufians in the pleft.Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-28479998827435277882016-08-14T15:55:15.097-07:002016-08-14T15:55:15.097-07:00David,
What are errors like with Natufians and Ir...David,<br /><br />What are errors like with Natufians and Iran in the outgroups?Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-41197889598738692202016-08-14T14:49:08.805-07:002016-08-14T14:49:08.805-07:00Thanks for giving it a shot.
Yeah, the Basal_Rich...Thanks for giving it a shot.<br /><br />Yeah, the Basal_Rich in that model averages at around 85% of the same named in K7. Though depends on population - most proportionately reduced is Steppe and populations from recent Iran / South Central Asia / Caucasus, while populations that increase or stay constant are European, and the very early-mod Neolithic populations (Iran Neolithic, Israel Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-68773391208144938592016-08-14T14:04:21.460-07:002016-08-14T14:04:21.460-07:00Matt,
Can't get any good models with AG3 or I...Matt,<br /><br />Can't get any good models with AG3 or Iran_Hotu, at least not with those outgroups. It seems that CHG is the best proxy for the eastern influence in the Anatolians.<br /><br />But the standard errors always approach the actual CHG mixture coefficient, which makes me think that we don't yet have any good reference pops for the CHG-related admix in the Anatolians.<br /><br Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-88127822276134066872016-08-14T09:24:32.409-07:002016-08-14T09:24:32.409-07:00I'm going to merge and make my Geno files, but...I'm going to merge and make my Geno files, but this would be consistent with Barcin being about 90% Boncuklu, 10% Levant. That would make my exact output on qpAdm with 71% Levant, 14% CHG, 15% WHG.Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-32123524635087204332016-08-14T08:58:12.872-07:002016-08-14T08:58:12.872-07:00Do any models like; Levant_N, Villabruna, AG3 or L...Do any models like; Levant_N, Villabruna, AG3 or Levant_N, Villabruna, Iran_Hotu, AG3 work for Boncuklu / Barcin? With outgroups as the O9 (Ust_Ishim, Kostenki14, MA1, Han, Papuan, Onge, Chukchi, Karitiana, Mbuti). <br /><br />(Or using any other European UP in place of Kostenki14).Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-84325520521331731552016-08-14T07:09:10.491-07:002016-08-14T07:09:10.491-07:00@ Davidski, I've been trying to come back with...@ Davidski, I've been trying to come back with thoughts about those stats and correlations. Nothing clear at the moment. If I come up with something that adds rather than reduces confusion, I'll post it.<br /><br />If you or @ Alberto were interested, I did try another experiment to estimate proportions from the stats. I wasn't quite happy with the model of using a regression on the Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-77629236906455955462016-08-14T06:57:50.642-07:002016-08-14T06:57:50.642-07:00No idea how Basal Eurasian fits into this and when...No idea how Basal Eurasian fits into this and when it split.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-36705092639362631842016-08-14T06:55:55.672-07:002016-08-14T06:55:55.672-07:00This looks plausible for Boncuklu (although the hi...This looks plausible for Boncuklu (although the high CHG is probably not crucial, judging by the rest of the output that I'm seeing here).<br /><br />left pops:<br />Boncuklu_Neolithic<br />Levant_Neolithic<br />Caucasus_HG<br />Villabruna<br /><br />best coefficients: 0.619 0.241 0.139 <br />std. errors: 0.229 0.237 0.115 <br /><br />And then the Barcin Anatolians areDavidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-27023861044086034292016-08-14T05:18:20.200-07:002016-08-14T05:18:20.200-07:00Dave
Boncukulu is right on the line where we migh...Dave<br /><br />Boncukulu is right on the line where we might expect Epipalaeolithic Anatolia to be split, into west & east regions. This sample is actually pre-ceramic Neolithic, not Epipalaeo, but i suspect it would be representative of the eastern Anatolian Epipalaeolithic, which is concentrated to the southeast, toward Syria. <br /><br />On the west side, the Marmara shows closest Robhttps://www.blogger.com/profile/07166839601638241857noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-40001054222792494052016-08-14T03:44:52.557-07:002016-08-14T03:44:52.557-07:00Alright, I managed to almost get a signal of admix...Alright, I managed to almost get a signal of admixture for the Barcin Anatolians using Levant_Neolithic. Guess what the other mixture reference is?<br /><br />Levant_Neolithic Boncuklu_Neolithic Barcin_Neolithic -0.005525 0.002109 -2.62<br /><br />So Barcin looks like a mix of Boncuklu and something from the Levant. Thus, the question becomes, what is Boncuklu exactly? It does show some eastern Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-18189825502266334402016-08-14T00:52:01.716-07:002016-08-14T00:52:01.716-07:00Not even broadly speaking. The southern Levant far...Not even broadly speaking. The southern Levant farmers just don't appear to be relevant to the Anatolian farmers as a mixture source.<br /><br />If they're forced to be a mixture source, then strange things are likely to happen.<br /><br />Definitely, we need samples from the Northern Levant, but I'm getting the feeling that this WHG-like and Basal combo was a feature of Near Eastern Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-26219743776271442122016-08-14T00:39:52.821-07:002016-08-14T00:39:52.821-07:00^^^
Broadly, the 'Levant Neolithic' sample...^^^<br />Broadly, the 'Levant Neolithic' samples from Lazarides were all from Israel, and hg E. We'd need more samples from pre-Neolithic central-eastern Anatolia & northern Syria.Robhttps://www.blogger.com/profile/07166839601638241857noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-5272958474291978942016-08-14T00:31:31.169-07:002016-08-14T00:31:31.169-07:00Chad,
Here are some f3 mixture stats for a few av...Chad,<br /><br />Here are some f3 mixture stats for a few average Barcin Anatolian farmers modeled as mixtures of various foragers and the most basal Barcin Anatolian farmers.<br /><br />Hungary_HG Barcin_Neolithic1 Barcin_Neolithic2 -0.002799 -2.101<br />Bichon Barcin_Neolithic1 Barcin_Neolithic2 -0.001471 -1.185<br />Karelia_HG Barcin_Neolithic1 Barcin_Neolithic2 -0.001006 -0.77<br />Motala_HGDavidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-88857535509252428722016-08-13T23:40:03.623-07:002016-08-13T23:40:03.623-07:00But if all these groups are just your Basal rich a...But if all these groups are just your Basal rich and WHG, why is WHG significantly positive here, unlike EHG? There is a lot more going on than BE, plus WHG and minor CHG. I just don't think 14% CHG and 10% EHG is unreasonable. Stats are pointing to a more complex mix.Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-14947151023474993542016-08-13T23:31:20.011-07:002016-08-13T23:31:20.011-07:00These people are morons.These people are morons.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-68387438640456488752016-08-13T23:16:34.957-07:002016-08-13T23:16:34.957-07:00Hot off the presses!
"genome sequencing that...Hot off the presses!<br /><br />"genome sequencing that revealed that farmers from India moved to Iran 7,000-8,000 years ago"<br /><br />http://swarajyamag.com/magazine/we-were-always-thereKarl_Khttps://www.blogger.com/profile/10388217053237956318noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-33796963560685099752016-08-13T21:23:21.230-07:002016-08-13T21:23:21.230-07:00I reckon the Anatolians have minor CHG admixture a...I reckon the Anatolians have minor CHG admixture and also ANE via their Villabruna-related ancestry.<br /><br />None of the stats you posted contradict this. Sorry.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-37938049008731858452016-08-13T21:18:25.672-07:002016-08-13T21:18:25.672-07:00It's not significant, but it is the only thing...It's not significant, but it is the only thing that doesn't fail. I think you need Levant. Neolithic Anatolians are more Levantine-like and more BE than the HG's of Turkey from the new paper. Remember, Anatolians are significantly closer to Iran than Levant. Even though Levant is closer to Iran in BE. WHG is also significantly closer to Levant than Iran, so it isn't WHG into Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-37835476755202661562016-08-13T21:05:02.397-07:002016-08-13T21:05:02.397-07:00Chad,
This is a neutral Z score. Come on, you nee...Chad,<br /><br />This is a neutral Z score. Come on, you need something around Z -2 at least.<br /><br />Levant_EN1 Karelia_HG Anatolia_EN1 -0.000190 0.001686 -0.113 342440<br /><br />Try Karitiana instead of Karelia_HG. It might improve the Z score. But it won't prove anything, because all you're doing is matching up some allele frequencies that kind of match the ancestral populations Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-33156767717422549892016-08-13T20:36:00.088-07:002016-08-13T20:36:00.088-07:00F3s are lining up with that qpAdm which showed muc...F3s are lining up with that qpAdm which showed much more CHG and EHG admixture going from Levant to Anatolia, vs WHG.Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.com