tag:blogger.com,1999:blog-6191565439230824899.post3295065193417920163..comments2023-04-24T10:31:12.136-07:00Comments on Polishgenes Blog: Around 65% LN/EBA European ancestry in the Hindu Kush (?)Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.comBlogger53125tag:blogger.com,1999:blog-6191565439230824899.post-28621701094317690272015-08-04T00:00:16.294-07:002015-08-04T00:00:16.294-07:00I guess it depends on the samples. For example, he...I guess it depends on the samples. For example, here are RISE505's genotypes at some skin pigmentation-implicated SNPs:<br /><br />ASIP, rs2424984: TC (if I'm not wrong, northern Europeans are always homozygous for the derived allele T)<br /><br />ASIP, rs6058017: AG (same here, if I'm not wrong, northern Europeans are always homozygous for the derived allele A)<br /><br />SLC45A2, Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-7744336027466909792015-08-03T15:48:43.335-07:002015-08-03T15:48:43.335-07:00The Andronovo and Sintashta samples we have show n...The Andronovo and Sintashta samples we have show normal Northern/Eastern European pigmentation traits, and were probably lighter in real life than Southern Euros.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-65775826404981649292015-08-03T12:43:38.204-07:002015-08-03T12:43:38.204-07:00@Sein,
If you're from South/Central Asia you ...@Sein,<br /><br />If you're from South/Central Asia you would know. I trust actual DNA more than anything and expect other things to make sense later. Anyways, facial-features is probably the place to look because they change less quickly.<br /><br />There are many undiscovered mutations that cause Pale-features in Europeans. And they're all probably recessive. What I mean is both parentsKrefterhttps://www.blogger.com/profile/01055804913528477710noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-34211537374330908692015-07-26T17:30:06.391-07:002015-07-26T17:30:06.391-07:00South Asians aren't up to 65% modern European,...South Asians aren't up to 65% modern European, they're up to 65% EBA steppe, most of which lies in Central Asia.<br /><br />I have no idea what a 65% EBA steppe/23% Southwest Asian Neolithic farmer/12% South Asian hunter-gatherer is supposed to look like, but probably not like a modern Lithuanian, Norwegian or Ukrainian.<br /><br />Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-4024274966668825582015-07-26T16:22:59.789-07:002015-07-26T16:22:59.789-07:00If South/Central Asians were 65% European, wouldn&...If South/Central Asians were 65% European, wouldn't we be able to tell by their physical appearance? This should at least lead to suspicion of these numbers. <br /><br />I guess it's possible. I've seen a few Indian and half European people, and they could pass as Afghan or whatever. But, if an entire population was that way, I'm not sure if almost 100% of them would.Krefterhttps://www.blogger.com/profile/01055804913528477710noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-45349897827397420002015-07-20T01:29:02.474-07:002015-07-20T01:29:02.474-07:00@Sein
The Singapore Malay probably do have very m...@Sein<br /><br /><em>The Singapore Malay probably do have very minor West Eurasian admixture from India and the Near East.</em><br /><br />For what I've seen they seem to have less than Dai, who have less than Kharia. So it's very minor indeed. Do you think they have more than any of them?Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-10062624125649307102015-07-19T20:53:06.797-07:002015-07-19T20:53:06.797-07:00David,
A very interesting tree. So overall, the K...David,<br /><br />A very interesting tree. So overall, the Kalash are placed quite close to Georgians. But as you note about digging deeper, they clearly come out as predominantly LN/EBA European, but with very heavy Georgian-like admixture.<br /><br />Alberto,<br /><br />The Singapore Malay probably do have very minor West Eurasian admixture from India and the Near East.<br /><br />Matt,<br /><Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-1337646907470148112015-07-19T17:48:32.744-07:002015-07-19T17:48:32.744-07:00You can see on this tree why Georgians are such a ...You can see on this tree why Georgians are such a good proxy for ANI.<br /><br />https://drive.google.com/file/d/0B9o3EYTdM8lQd3kwN0k1Mk13NWs/view?usp=sharing<br /><br />But ANI wasn't a single population. It's a composite to describe the West Eurasian ancestry in South Asia. So when we dig a little deeper, we see this...<br /><br />https://drive.google.com/file/d/Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-88423753994474140682015-07-19T12:02:08.002-07:002015-07-19T12:02:08.002-07:00I think the only population with no West Eurasian ...I think the only population with no West Eurasian at all and more ASI than Dai might be Malay. They still have a lot of East Asian, but less than Dai.<br /><br />Re: the ANI-ASI study, they used Onge for the ASI, so I don't think it's likely that it confused ASI with steppe ancestry. But I do think that 29% ASI for Pathans is too high. The problem is probably that neither Onge nor Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-79669741964904927902015-07-19T11:47:37.546-07:002015-07-19T11:47:37.546-07:00The general population in Pakistan is put in the s...The general population in Pakistan is put in the sample of 638 here at around 37.1% - https://en.wikipedia.org/wiki/List_of_R1a_frequency_by_population.<br /><br />Doesn't seem like there's *too* much consistency. Sindhis of Pakistani, R1a in Underhill et al 2009 - 49%, Qamar et al 2002 - 12.3%. Same sample size (>100), same country. Pashtuns of Pakistan, Firasat 2007 - 44.8%, Qamar Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-29091094246775109422015-07-19T10:38:36.968-07:002015-07-19T10:38:36.968-07:00I should have posted this before, here are some Pa...I should have posted this before, here are some Pashtun y-DNA frequencies from a few papers:<br /><br />R1a1a=65.8%<br />G2c=6.2%<br />H1a=4.1%<br />L3=4.1%<br />J2b2=2.7%<br />J2a=2.1%<br />C3=2.1%<br />R2a=2.1%<br />Q1a3=1.4%<br />G2a=1.4%<br />G=0.7%<br />G2a1=0.7%<br />C5=0.7%<br />C5a=0.7%<br />J1=0.7%<br />J2a5=0.7%<br />J2b1=0.7%<br />L1=0.7%<br />Q1=0.7%<br />Q1a=0.7%<br />R1b1a2a=0.7%<brSeinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-81021772897821953902015-07-19T09:57:43.762-07:002015-07-19T09:57:43.762-07:00Matt,
Depending on the paper, Pashtuns range from...Matt,<br /><br />Depending on the paper, Pashtuns range from 50% R1a1a to 70% R1a1a (although two Ghilji groups in one paper are 80% R1a1a, and the sample size is very large). The people of the Punjab are around 50% R1a1a. After R1a1a, the next largest haplogroups for Pashtuns are usually either some subclade of Q or L, followed by G (not to mention H. Although, sometimes, some subclade of G Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-63786313849182997302015-07-19T07:14:07.375-07:002015-07-19T07:14:07.375-07:00Kharias may be a little more Atayal, but the Paniy...Kharias may be a little more Atayal, but the Paniya have more of the Onge/Papuan stuff.Anonymoushttps://www.blogger.com/profile/13876988480444711159noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-27000957204801884062015-07-19T07:04:54.239-07:002015-07-19T07:04:54.239-07:00David,
I only have the bed, bim, and fam files. I...David, <br />I only have the bed, bim, and fam files. I don't have the plink ones for the SA samples.Anonymoushttps://www.blogger.com/profile/13876988480444711159noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-34251374507013414212015-07-19T06:54:48.888-07:002015-07-19T06:54:48.888-07:00Sein,
//Also, David Anthony draws a somewhat diffe...Sein,<br />//Also, David Anthony draws a somewhat different picture in "The Horse, the Wheel and Language". Based on that text (my main introduction to the subject, at this point), BMAC settlements decreased radically in size, and in the later period we see a very strong intensification of contact and interaction with southernly extensions of the Andronovo culture (a melding of materialNirjhar007https://www.blogger.com/profile/12880827026479135118noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-60098270708568930992015-07-19T04:44:02.399-07:002015-07-19T04:44:02.399-07:00Davidski: I think what might have happened with on...Davidski: <i>I think what might have happened with one of those old ASI/ANI models is that they confused some of the steppe ancestry for ASI.</i><br /><br />I do think that has some plausibility - the ENA like affinity in WHG / EHG / ANE teaming up with real ENA affinity via ASI. But I don't know. It seemsmostly plausible when you're *just* thinking about Pathans and Kalash and other Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-58470978959612433272015-07-19T04:17:37.714-07:002015-07-19T04:17:37.714-07:00Sein
Your right about the timing. sorry. For some...Sein<br /><br />Your right about the timing. sorry. For some reason I thought the IVC ended much earlier (2500 BC instead of c. 1800). Nevertheless, my overall comment remains: <br /><br />* the BMAC appears to have been a native development from Chalcolithic villages in the foothills. <br /><br />* the forts must have been defensive at least in part, but also organization, storage. If anything, Anonymoushttps://www.blogger.com/profile/12259212254098264600noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-66413738199179778302015-07-19T03:26:59.836-07:002015-07-19T03:26:59.836-07:00Balaji, check this out...
https://drive.google.co...Balaji, check this out...<br /><br />https://drive.google.com/file/d/0B9o3EYTdM8lQN0dnUHppbWc4QUE/view?usp=sharingDavidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-49206104138096602552015-07-19T03:08:27.327-07:002015-07-19T03:08:27.327-07:00Davidski,
Thank you very much for your interestin...Davidski,<br /><br />Thank you very much for your interesting work. I am glad that you put in a “?” in the title of your post. You have recapitulated in a different format what the Reich Labs found. That is, that Pathans and Kalash have about 70% West-Eurasian-like ancestry (ANI) and about 30% of another kind of ancestry (ASI). Your tree mix results do not prove that the 70% ANI originated in Balajihttps://www.blogger.com/profile/09561110603904765636noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-74408593713137324102015-07-19T02:56:05.743-07:002015-07-19T02:56:05.743-07:00@ Chad, what kind of pright outgroups are you usin...@ Chad, what kind of pright outgroups are you using in those models? I'm interested in what is splitting apart the Onge, Papuan and Atayal like ancestry in Kharia?Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-5058187509376865222015-07-19T02:07:01.290-07:002015-07-19T02:07:01.290-07:00Sorry for multiple consecutive postings (this is t...Sorry for multiple consecutive postings (this is the final one), but the models you are trying might benefit from the addition of ancient samples.Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-45078920785667900862015-07-19T02:03:58.698-07:002015-07-19T02:03:58.698-07:00Also, HarappaWorld has the "South-Indian"...Also, HarappaWorld has the "South-Indian" component peak in Paniya at 84%, while the HGDP Pashtuns and Kalash average out to only 21%-23%. Same with Dodecad K12b. So, the 84% to 33% pattern you are seeing isn't some sort of necessary outcome.<br /><br />In addition, Everest tried the whole "zombie" approach with the component that peaks at 84% in Paniya (in HarappaWorld). Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-82026496838398656172015-07-19T01:57:25.910-07:002015-07-19T01:57:25.910-07:00The Kharia aren't carbon copies of the Paniya ...The Kharia aren't carbon copies of the Paniya on any ADMIXTURE run that I've seen. Quite the contrary, they have much more of a Southeast Asian affinity on HarappaWorld (the Paniya don't come even close to that much "SE-Asian" on that ADMIXTURE run), they have a lot of extra ENA that isn't ASI. <br /><br />Basically, the Paniya are more West Eurasian-admixed than the Seinundzeithttps://www.blogger.com/profile/14194936397714207913noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-80443745112176405092015-07-19T01:51:19.985-07:002015-07-19T01:51:19.985-07:00I've sent you the Paniya. But the files I sent...I've sent you the Paniya. But the files I sent you only have ~110K SNPs, because that's how many overlap between the usual Illumina chip and the Haak 2015 dataset.Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-6191565439230824899.post-63129569679949499802015-07-19T01:47:52.464-07:002015-07-19T01:47:52.464-07:00David,
If you have the Paniya in plink, I'll ...David, <br />If you have the Paniya in plink, I'll run it as the same mix.Anonymoushttps://www.blogger.com/profile/13876988480444711159noreply@blogger.com