tag:blogger.com,1999:blog-4123559132014627431.post4095295807019695686..comments2024-03-18T22:01:02.498-07:00Comments on Eurogenes Blog: Genetics of an early Neolithic pastoralist from western Iran (Gallego Llorente et al. preprint)Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.comBlogger145125tag:blogger.com,1999:blog-4123559132014627431.post-600788429677281022016-11-20T16:35:49.182-08:002016-11-20T16:35:49.182-08:00That PCA is garbage because it suffers from projec...That PCA is garbage because it suffers from projection bias. It's a common problem in ancient DNA studies.<br /><br />And Central Anatolian farmers didn't have Neolithic Iranian ancestry, they had Caucasus Hunter-Gatherer-like ancestry, which was probably native to eastern Anatolia.<br /><br />Not sure how else to communicate this, but at some point you people will have to grasp the data Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-73403175428656378292016-11-20T14:48:24.568-08:002016-11-20T14:48:24.568-08:00Indeed, judging from that PCA (in the new study BE...Indeed, judging from that PCA (in the new study BELOW), the Tepecik samples from South Central Turkey, do appear to be more leaning toward the Caucauses and Iran, which is still in line with the idea that there was reciprocal gene flow between Anatolian and Iranian Neolithics. And keep in mind, there is still plenty of ancient DNA geographically East, which which has not yet been sampled. Also Tminushttps://www.blogger.com/profile/14670330637347557641noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-2629934901145418972016-11-20T07:37:35.361-08:002016-11-20T07:37:35.361-08:00"Neolithic Anatolians don't have any admi..."Neolithic Anatolians don't have any admixture from Neolithic Iran. What you're seeing there is an abstract model of reality that just happens to fit the data."<br /><br />It's the simplest possible scenario, and it goes well with data. However, I myself don't agree with estimates as high as 40%, as was suggested by Lazaridis, but the estimate of ~15% Iran_N + WHG + biaystiorhttps://www.blogger.com/profile/05157451250973378990noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-55979089670047416602016-11-16T21:03:28.058-08:002016-11-16T21:03:28.058-08:00Neolithic Anatolians don't have any admixture ...Neolithic Anatolians don't have any admixture from Neolithic Iran. What you're seeing there is an abstract model of reality that just happens to fit the data.<br /><br />There weren't any migrations from Neolithic Iran to the west or north, so Europeans and West Asians don't have any Neolithic Iranian ancestry. This is a fact.<br /><br />What they do have is Caucasus Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-21674863946885458152016-11-16T19:59:10.658-08:002016-11-16T19:59:10.658-08:00Actually on that plot you posted, (https://lh5.goo...Actually on that plot you posted, (https://lh5.googleusercontent.com/WuAbiNcCcBkA3-9uLQmAneQppwsGwOFlpyEK_O95iTWyQTKQIwVRv0UWWVaMkXpMC9-ELkcE-R68MtM=w1920-h1070-rw), Neolithic Iranians along with GD13a look about as far from modern S. Asians, as it is to other Near Easterners and Caucaus groups (and remember True South Asian is defined by an indigenous ASI component, of which we have no example, biaystiorhttps://www.blogger.com/profile/05157451250973378990noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-73578641552876531652016-11-16T15:56:49.471-08:002016-11-16T15:56:49.471-08:00GD13a is the Iran_Neolithic individual sitting fur...GD13a is the Iran_Neolithic individual sitting furthest to the right on the plot here.<br /><br />http://eurogenes.blogspot.com.au/2016/06/a-moment-of-clarity.html<br /><br />The Iran_Neolithic cluster is actually pretty close to South Central Asians (SC_Asia) on my plot as well.<br /><br />Neolithic Iranians will always cluster close to modern-day individuals from the Indus Valley region, Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-64851083056345113912016-11-16T08:10:23.657-08:002016-11-16T08:10:23.657-08:00Very interesting. I agree the plot seemed odd to...Very interesting. I agree the plot seemed odd to me, as I thought GD13a as well as other Iranian Neoliths would be farther away from modern South Asians. Would you guess that GD13a would be more distinct from modern South Asians on your PCA, then the PCA generated in the study? Thanks.Finitowilliamshttps://www.blogger.com/profile/03877607152308845575noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-36708739032404516562016-11-09T12:36:04.482-08:002016-11-09T12:36:04.482-08:00Wishful thinking on your part.
There are a number...Wishful thinking on your part.<br /><br />There are a number of ancient Iranian samples available now, and it's clear that ancient populations from Iran did not contribute to the modern European gene pool.<br /><br />The reason modern Europeans are shifted east relative to some ancient Europeans, is because of the expansion of Bronze Age steppe pastoralists deep into Europe from the Eastern Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-71094887041544019592016-11-09T07:19:08.114-08:002016-11-09T07:19:08.114-08:00A proper interpretation of the data, is that Neoli...A proper interpretation of the data, is that Neolithic Iranians (or possibly only those restricted to Ganj Derah), only AS EARLY AS 10kybp, did not contribute European gene pool. This does not rule out the likely possibility that later Iranian Neoliths, and Iranian populations onward, did not. Just based on the significantly more eastern position of Modern European samples (relative to older biaystiorhttps://www.blogger.com/profile/05157451250973378990noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-8949377549801802016-06-23T01:24:34.839-07:002016-06-23T01:24:34.839-07:00@Seinundzeit
Thanks for sharing that! Yes, it'...@Seinundzeit<br /><br />Thanks for sharing that! Yes, it's interesting that Iran_N has stronger affinity to South Asians, though I think quite expected. We have to see better what Iran_N really is (does it have any ASI? Is it Basal Eurasian + EHG?), but its connection to South Asia is undeniable.<br /><br />The subject of the IVC is complicated to argue, because we're pretty much in the Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-77490080909468875922016-06-23T00:24:35.643-07:002016-06-23T00:24:35.643-07:00@Open Genomes
"5. The definitive proof of an...@Open Genomes<br /><br />"5. The definitive proof of an African origin of the "Basal Afro-Asiatics" is the fact that this group has no Neanderthal admixture. This would make sense only if they originated in the Afro-Asiatic Urheimat of the Red Sea Coast of Sudan (or an adjacent region)."<br /><br />You may be correct, but the lack of Neanderthal admixture is not in any way Karl_Khttps://www.blogger.com/profile/10388217053237956318noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-8887172689888066642016-06-22T15:13:41.327-07:002016-06-22T15:13:41.327-07:00@Nick Patterson (Broad) (continued):
Archaeologic...@Nick Patterson (Broad) (continued):<br /><br />Archaeologically, are the "Basal Eurasians" who are actually the "Basal Afro-Asiatics" in fact the Ramonian/Mushabian culture, which appears to enter the Southern Levant from East Africa around 16,000 BCE (18,000 ybp), at the end of the LGM, which also happens to be the tMRCA of Y-DNA E-M123 found among the Natufians of Rakefet Open Genomeshttps://www.blogger.com/profile/11207443325849433636noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-67566940808168484972016-06-22T15:00:27.939-07:002016-06-22T15:00:27.939-07:00@Nick Patterson (Broad) (continued):
Another sour...@Nick Patterson (Broad) (continued):<br /><br />Another source of much later back-migration to Africa from the Levant is R1b1c-V88. While R-V88 split from R1b1-M415* just after the LGM at 17,200 ybp, the expansion of R-V88 is 10,200 ybp, too late for the Natufians, but during the PPNA-PPNB transition.<br /><br /><a href="https://www.yfull.com/tree/R-V88/" rel="nofollow">R-V88 YFull tree tMRCA Open Genomeshttps://www.blogger.com/profile/11207443325849433636noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-89569825214799985972016-06-22T14:41:38.823-07:002016-06-22T14:41:38.823-07:00@Nick Patterson (Broad) (continued):
We know that...@Nick Patterson (Broad) (continued):<br /><br />We know that there was an influx of Levantines into East Africa around 1,000 BCE. T-M184 was found among the Levantine PPNB farmers and significantly, in the LBK. (The LBK sample does in fact have about 10% "Southwest Asian" while the Starcevo-Koros samples from Hungary do not.)<br /><br />T-M184 has a African distribution that extends toOpen Genomeshttps://www.blogger.com/profile/11207443325849433636noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-5486000955113370292016-06-22T14:37:09.170-07:002016-06-22T14:37:09.170-07:00@Nick Patterson (Broad) (continued):
The question ...@Nick Patterson (Broad) (continued):<br />The question is, is E-V1700 under E-V1515 a later arrival from East Africa to the Levant, or is a "back-migration" from the Levant?<br /><br />A map from <a href="http://gbe.oxfordjournals.org/content/7/7/1940.full" rel="nofollow">Trombetta (2015), Phylogeographic Refinement and Large Scale Genotyping of Human Y Chromosome Haplogroup E Provide Open Genomeshttps://www.blogger.com/profile/11207443325849433636noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-79922549440942631202016-06-22T14:30:55.037-07:002016-06-22T14:30:55.037-07:00@Nick Patterson (Broad):
In the paper you coauthor...@Nick Patterson (Broad):<br />In the paper you coauthored, <a href="http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003316" rel="nofollow">Haber (2013), Genome-Wide Diversity in the Levant Reveals Recent Structuring by Culture</a> we have two components from a K=10 ADMIXTURE analysis, also (roughly) plotted on a world map:<br /><br /><a href="http://www.open-genomes.org/Open Genomeshttps://www.blogger.com/profile/11207443325849433636noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-66271398601380007432016-06-22T10:55:52.150-07:002016-06-22T10:55:52.150-07:00Alberto,
This is an IBS list for Iran_Chalcolithi...Alberto,<br /><br />This is an IBS list for Iran_Chalcolithic:<br /><br />Assyrian 65.946% <br />Georgian 65.937% <br />Abkhasian 65.887% <br />Lebanese_Christian 65.859% <br />Iranian 65.844% <br />Chechen 65.830% <br />Cypriot 65.829% <br />Adygei 65.772% <br />Azeri 65.734% <br />Makrani 65.676% <br />Lebanese_Muslim 65.654% <br />Brahui 65.654% <br />Lebanese 65.644% <br />Balochi 65.641% <brSeinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-49742443176033257052016-06-22T07:15:15.362-07:002016-06-22T07:15:15.362-07:00This comment has been removed by the author.Ryukendo Khttps://www.blogger.com/profile/11588546655427153692noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-32210350724543638412016-06-22T05:31:00.582-07:002016-06-22T05:31:00.582-07:00Because I think that if Basal Eurasian is signific...Because I think that if Basal Eurasian is significantly closer to Iran_N than to Levant_N, then Levant_N (not to mention Natufian) will off the cline between Basal Eurasian and WHG. So this UHG will have to be quite divergent. Or do you see it possible to fit this UHG within West Eurasian variation?Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-89792905984701477802016-06-22T02:41:01.485-07:002016-06-22T02:41:01.485-07:00This comment has been removed by the author.Ryukendo Khttps://www.blogger.com/profile/11588546655427153692noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-57578460154859377162016-06-22T02:35:08.317-07:002016-06-22T02:35:08.317-07:00@RK
Thanks for all the insightful comments. I bas...@RK<br /><br />Thanks for all the insightful comments. I basically agree with you in all, especially about ANE. So just minor comments:<br /><br />- About Basal Eurasian, one problem I see with the estimates placing Iran_N as quite higher than Levant_N is that it pushes Basal Eurasian quite to the "East". So it becomes quite difficult to find a population that could be the "Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-52477061901724282942016-06-22T02:27:07.156-07:002016-06-22T02:27:07.156-07:00@vvv666
The physical appearance of the residents o...@vvv666<br />The physical appearance of the residents of the IVC is an interesting question.<br />Ruchika sharma is an idiot though. Look how she throws around terms like proto-australoid. She probably bases her ideas on colonial ideas of 'bull liped' 'noseless' and 'black' enemies of the Aryans based on mistranslations of the veda no longer accepted by mainstream scholars Jijnasuhttps://www.blogger.com/profile/14851649346012458747noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-30948083942706007292016-06-22T01:01:48.002-07:002016-06-22T01:01:48.002-07:00Hugely interested in pigmentation related SNPs for...Hugely interested in pigmentation related SNPs for the Iranian neolithic samples. There is a vibrant debate on whether it is historically accurate to depict Indus Valley inhabitants with light skin in a commercial fantasy movie:<br /><br />http://thereel.scroll.in/810387/from-horses-to-headgear-everything-that-is-wrong-about-the-mohenjo-daro-trailervvv666https://www.blogger.com/profile/05232051233080015896noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-60163456204272319652016-06-21T23:29:06.984-07:002016-06-21T23:29:06.984-07:00As we wait/look forward to David's analyses, K...As we wait/look forward to David's analyses, Kurd at Anthrogenica produced an IBS list for Iran_N. If we remove ancient populations/samples, and if we remove the 23andMe raw-data files he ran (to make things more reliable), this is the list:<br /><br />Makrani 65.732% <br />Brahui 65.714% <br />Iranian 65.697% <br />Balochi 65.696% <br />Abkhasian 65.596% <br />Georgian 65.568% <br />Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-84645490222892155442016-06-21T22:02:11.904-07:002016-06-21T22:02:11.904-07:00Yeah fair enough, I'm not an expert on Bedouin...Yeah fair enough, I'm not an expert on Bedouin genetics but I was under the assumption that BedouinB were basically Southwest_Asians with little other admixture. I got this assumption from Gedmatch calculators which put BedouinB as having little to no SSA ancestry.<br /><br />Anonymoushttps://www.blogger.com/profile/01646439425801110303noreply@blogger.com