tag:blogger.com,1999:blog-4123559132014627431.post5410252455789266353..comments2024-03-28T16:06:27.256-07:00Comments on Eurogenes Blog: A homeland, but not the homeland #2Davidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.comBlogger106125tag:blogger.com,1999:blog-4123559132014627431.post-61809723682778805602017-08-27T20:15:33.407-07:002017-08-27T20:15:33.407-07:00@ Unknown
http://replicatedtypo.com/wp-content/upl...@ Unknown<br />http://replicatedtypo.com/wp-content/uploads/2012/05/Picture-72.png <br /><br /><br />Surely you don't publish your name for avoiding a mess of raspberries: Albanian Tosk not with IE but with Brahui!Gioiellohttps://www.blogger.com/profile/13578860964923773647noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-42117019372265365772017-08-27T17:21:40.238-07:002017-08-27T17:21:40.238-07:00>The problem here is also that EHG is significa...>The problem here is also that EHG is significantly further from Ust_Ishim than WHG, suggesting possible CHG>EHG flow confounding the stat. <br /><br />That's probably due to much higher Paleolithic European derived ancestry in WHG than in EHG.Unknownhttps://www.blogger.com/profile/10595025984675876037noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-25234493101131247912017-08-27T17:13:22.497-07:002017-08-27T17:13:22.497-07:00>A relation with Dravidian is also quite possib...<br /><br />>A relation with Dravidian is also quite possible . I am working on it , here is a draft:<br /><br />Basque may be related to Dravidian suggesting Neolithic Iranian origin.<br /><br />http://replicatedtypo.com/wp-content/uploads/2012/05/Picture-72.pngUnknownhttps://www.blogger.com/profile/10595025984675876037noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-54639966819234566922017-08-25T11:06:55.247-07:002017-08-25T11:06:55.247-07:00@Matt
High RoH affecting fst has been apparent for...@Matt<br />High RoH affecting fst has been apparent for a long time, hasn't it? Lower fst between English and Palestinians than between Chukchis and Eskimos, but IBS and shared drift will surely tell a different story. <br /><br />The fst stuff I did with Natufians was like this (using Lazaridis 2016 fst's):<br /><br />Fst(Natufian-Mbuti)/Fst(Natufian-Papuan) = 0.9522<br />Fst(Shaikorthhttps://www.blogger.com/profile/04468485423355664299noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-30746866199296868122017-08-22T14:59:07.640-07:002017-08-22T14:59:07.640-07:00I didn't ask any specifics about quantifying t...I didn't ask any specifics about quantifying the amount of effect. Although that is a good question. I'm not sure it really matters when it comes to modeling based on ancients, say MN as a mix of WHG and EEF, as they two should even out anyway and not effect modeling. That may be where using a non-anachronistic mix is best. As in not making older groups as admixed with younger groups and Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-48327308585447714622017-08-22T14:04:42.844-07:002017-08-22T14:04:42.844-07:00Chad: High ROH will affect (Fst).
That's conc...Chad: <i>High ROH will affect (Fst).</i><br /><br />That's concerning if so. Did he say if there is any way to quantify this? That is, does CHG have +0.010 Fst against Iran_N from this effect (so without RoH would be something like 0.044?) or +0.030 (so 0.024), etc.<br /><br />Pretty much all the ancients have higher ROH across all their runs than modern people. Less so the EEF, but even thenMatthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-84674796220145916362017-08-21T03:51:24.721-07:002017-08-21T03:51:24.721-07:00I can ask about this too.I can ask about this too.Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-58631583029363759782017-08-21T03:51:04.673-07:002017-08-21T03:51:04.673-07:00The African thing may also be Neandertal related. ...The African thing may also be Neandertal related. Iran is quite a bit lower than CHG, if I remember correctly.Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-44930896975681617522017-08-21T03:31:08.211-07:002017-08-21T03:31:08.211-07:00I've asked Nick about this since he obviously ...I've asked Nick about this since he obviously deals with this area. High ROH will affect it. Being inbred is no bueno. Boncuklu is highly inbred too. Not like Satsurblia, but pretty bad. He said it is best to check f4 (Outgroup, X; CHG, Iran) to find issues. Not only will inbreeding after separation create false distance, but relateds between two pops can create artificial closeness. Even Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-82441553731553260532017-08-21T01:14:59.032-07:002017-08-21T01:14:59.032-07:00Chad:
Wouldn't high inbreeding, such as Sats...Chad: <br /><br /><i>Wouldn't high inbreeding, such as Satsurblia be ruining the stats? Ex: Creating false extra drift.</i><br /><br />My understanding of the fst estimator is that it should not be accelerated by any drift that is private to one of the samples (e.g. anything in Satsurblia that's not been passed down by the population to Kotias). I could be wrong here, but that's as Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-46951441747062077302017-08-20T17:07:42.454-07:002017-08-20T17:07:42.454-07:00Not significant, but it's there. Couldn't ...Not significant, but it's there. Couldn't a small founder population for CHG create these false distances in fst?Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-49572828365677977722017-08-20T17:06:20.174-07:002017-08-20T17:06:20.174-07:00meaning dstats (Mbuti, EHG/Iran; Kotias, Satsurbli...meaning dstats (Mbuti, EHG/Iran; Kotias, Satsurblia.Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-11316991786647481992017-08-20T17:01:31.346-07:002017-08-20T17:01:31.346-07:00Wouldn't high inbreeding, such as Satsurblia b...Wouldn't high inbreeding, such as Satsurblia be ruining the stats? Ex: Creating false extra drift.. His parents were close relatives. Excluding him might change it. It certainly affects drift stats. Satsurblia is further from basically everything than Kotias.Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-52782955721081691472017-08-20T13:24:30.971-07:002017-08-20T13:24:30.971-07:00@Chad: "Zarzian is 18,000-8000BCE."
Su...@Chad: <i>"Zarzian is 18,000-8000BCE."</i> <br /><br />Sure, but that's the Upper Paleolithic / Mesolithic kind of dating period Piranha said he thought that they'd split?<br /><br /><i>Higher ROH in CHG, compared to Iran_N might be causing its isolation in that regard.</i><br /><br />I have not heard anything saying increased long ROH should have any major effect on Fst or showMatthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-86804138784416927232017-08-20T12:37:00.019-07:002017-08-20T12:37:00.019-07:00IMO, you guys are getting too hung up on this fst ...IMO, you guys are getting too hung up on this fst thing. Higher ROH in CHG, compared to Iran_N might be causing its isolation in that regard. Clearly, CHG is significantly closer to Iran N than any other population. Even significantly closer to Iran N than Steppe EMBA. They have EHG, maybe and likely more than 10%, but not 40%. Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-45807009466248448722017-08-20T12:23:40.922-07:002017-08-20T12:23:40.922-07:00Back to Anatolians, specifically Boncuklu.
My qpG...Back to Anatolians, specifically Boncuklu.<br /><br />My qpGraph model has them as <br /><br />27.52% Natufian-related<br />58.48% CHG-related<br />14% WHG-related<br /><br />Here is the worst f-stat:<br /><br />Chi Nea Bon Nat 0.000215 -0.002744 -0.002959 0.001336 -2.215<br /><br />Using qpAdm:<br /><br />Outgroups:<br />Mbuti<br />Ust_Ishim<br />LaBrana1<Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-23450795372149354362017-08-20T12:13:43.657-07:002017-08-20T12:13:43.657-07:00The non EHG-line side of CHG shares a good drift l...The non EHG-line side of CHG shares a good drift length with Iran N. The two cannot be separated. Zarzian is 18,000-8000BCE. The ones that moved into the Caucasus picked up EHG-like admixture. This isn't that complicated. They split just before Satsurblia, obviously. Not way before. The material culture shows that. Plus, qpGraph requires Iran to share drift with CHG after aquiring Basal Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-79930551831375302032017-08-20T10:31:48.376-07:002017-08-20T10:31:48.376-07:00@ Chad, just to clarify it from my perspective, ma...@ Chad, just to clarify it from my perspective, main points I took here in your conversation with P Piranha in order were:<br /><br />1. P Piranha: "Iran_Neolithic and CHG. From haplotype diversity in ADMIXTURE components the two are likely diverged since the Paleolithic or early Mesolithic"<br /> <br />Seemed probably correct to me.<br /><br />2. Chad: "Both are closely related Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-71071975431101009552017-08-20T09:54:24.922-07:002017-08-20T09:54:24.922-07:00I could be remembering Shaikorth in that area. How...I could be remembering Shaikorth in that area. However, simple Dstats are not informative as one might believe. <br /><br />I think we are splitting hairs here. CHG and Iran_N are, in-large, derived from the same population. The two form a cluster compared any ancient sample, except when EHG is involved, simply because of extra HG input to CHG, as I said. The problem here is also that EHG is Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-716039505088640332017-08-20T08:28:20.391-07:002017-08-20T08:28:20.391-07:00Simple Fst, IBS, f3 provide simple estimates of re...Simple Fst, IBS, f3 provide simple estimates of relatedness. qpAdm, qpGraph are doing something quite different. <br /><br />If you ask the people who are putting out papers for a simple measures that allow comparison of differentiation between pairs of populations, they will not tell you to go off, model them with qpAdm and if they can mostly be modeled as one another plus another population, Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-38417878180845107772017-08-20T07:53:19.896-07:002017-08-20T07:53:19.896-07:00Fst and Dstats are not useful compared to qpAdm an...Fst and Dstats are not useful compared to qpAdm and qpGraph. Way more power there. You have to remember the fact that Satsurblia is quite inbred, as well as the fact that Iran_N has more BEu, which will really mess with stats of relatedness. The fact is that the hunter ancestry of both is near identical, with both about equally related to WHG and MA1. Both being connected to the Zarzian, which Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-63214254427860340882017-08-20T04:43:55.051-07:002017-08-20T04:43:55.051-07:00@Chad and P Piranha's discussion, whether CHG ...@Chad and P Piranha's discussion, whether CHG and Iran_N plot together on PCA probably is not the best measure of how related they are.<br /> <br />Just use simple summary stats of relatedness between then, e.g.<br /><br />Fst: http://i.imgur.com/l9WuQXP.png<br />Fst: http://i.imgur.com/JdXtOKq.png<br />D-stat (outgroup): http://i.imgur.com/ubmNb2T.png<br /><br />CHG and IranN pretty Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-44805866710248141902017-08-20T01:19:02.979-07:002017-08-20T01:19:02.979-07:00George
I see. The sword is the last argument of I...George<br /><br />I see. The sword is the last argument of IE-s.:)<br /><br />But for some reasons it didn't worked in Levant despite the fact that it was ruled by IE-s (Persians,Greeks, Romans) for more than 1000 years. It didn't work for Ottomans also. No much Arabs dhifted to Turkish. But IE-s shifted to Turkish.<br /><br />How is that?<br /><br />PS btw the correct way to say would beAramhttps://www.blogger.com/profile/05717857095182763668noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-72865173384693998782017-08-19T20:55:13.512-07:002017-08-19T20:55:13.512-07:00Lastly, just for perspective, the WHG samples plot...Lastly, just for perspective, the WHG samples plot together while separated by 6000 years from oldest to youngest. More than the separation between the age of Iran and Satsurblia, and nearly twice the difference of Satsurblia and Kotias. It's pretty sound statistically and archaeologically.Chadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-81889826746450299072017-08-19T20:30:52.800-07:002017-08-19T20:30:52.800-07:00Not comparable.. periodNot comparable.. periodChadhttps://www.blogger.com/profile/10118937611048574688noreply@blogger.com