tag:blogger.com,1999:blog-4123559132014627431.post816846603267239970..comments2024-03-18T18:30:48.719-07:00Comments on Eurogenes Blog: Yamnaya = Khvalynsk + extra CHG + maybe something elseDavidskihttp://www.blogger.com/profile/04637918905430604850noreply@blogger.comBlogger77125tag:blogger.com,1999:blog-4123559132014627431.post-1171270447420337042016-06-22T08:53:12.439-07:002016-06-22T08:53:12.439-07:00@Davidski wrote :
" [1] "distance%=1.5...@Davidski wrote : <br /><br />" [1] "distance%=1.5072 / distance=0.015072"<br /><br />Spanish_Extremadura<br />"Bell_Beaker_Germany" 61.2<br />"Iberia_MN" 30.5<br />"Mozabite" 8.3<br />"Esan_Nigeria" 0" "<br /><br /><br />David, Which datasheet did you use ? I tought it was CHG_K10 but couldn't find north-africans in it...anthrospainhttps://www.blogger.com/profile/12619826700444535050noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-49911524548050788552016-05-22T08:05:36.594-07:002016-05-22T08:05:36.594-07:00In my previous comment I claimed that PCA may not ...In my previous comment I claimed that PCA may not be the perfect instrument to illustrate the relations of genomes.<br />As an alternative I want to take a look at hierarchical clustering.<br />A priori it can be expected that problems arise when populations get admixed, but lets see far how we can get.<br /><br />I used the last set of Dstats from Davidsky; but I removed the row Neadertal_Altai huijbregtshttps://www.blogger.com/profile/15146303681173955347noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-66222537380505597362016-05-22T06:13:11.345-07:002016-05-22T06:13:11.345-07:00While exploring these data, I learned a few things...While exploring these data, I learned a few things about the PCA methodology. Maybe some of them are useful for others too.<br /><br />To recapitulate the theory:<br />A PCA has optimal results when all the data belong to a single multivariate normal distribution.<br />Random processes in finite samples are responsible for the phenomenon of outliers. Due to the sum-of-squares calculations these huijbregtshttps://www.blogger.com/profile/15146303681173955347noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-38774943642427947582016-05-21T07:24:22.663-07:002016-05-21T07:24:22.663-07:00That's good, so no big problem in using double...That's good, so no big problem in using double outgroup stats as the input.<br /><br />BTW, I tested removing ancient samples from the columns and it's definitely a bad idea. We need those ancient samples as references in the columns.Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-53705237419571317302016-05-21T04:16:47.438-07:002016-05-21T04:16:47.438-07:00Btw, comparing the D(Mbuti,Outgroup)(Chimp,X) with...Btw, comparing the D(Mbuti,Outgroup)(Chimp,X) with the f3 stats from the Ice Age Europe f3 stats:<br /><br />http://i.imgur.com/3s4s9qb.png / http://i.imgur.com/mxy6aYm.png (without Dai)<br /><br />Dendrograms - http://i.imgur.com/kv6rNoC.png<br /><br />Pretty minor differences. Might be more serious for the ancient Europeans, but I think that Davidski said the marker differences would prevent Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-9951863562935161002016-05-21T02:16:24.890-07:002016-05-21T02:16:24.890-07:00David, thanks for the stats, and others (FrankN, H...David, thanks for the stats, and others (FrankN, Hujbregts, Matt...) thanks for the input.<br /><br />The results don't give a definitive answer (as it usually happens). More are in agreement with the original D(Chimp,X)(Mbuti,Outgroup) than with the alternative (14 vs. 6 if I'm forced to draw a line, but the magnitude varies).<br /><br />The other observations by looking at the Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-4035583202400712502016-05-21T01:45:45.050-07:002016-05-21T01:45:45.050-07:00@ Davidsky
My idea was that more Africans in ROWS...@ Davidsky<br /><br />My idea was that more Africans in ROWS will make the African column less attractive for non-African outliers.huijbregtshttps://www.blogger.com/profile/15146303681173955347noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-20765873104361428972016-05-21T01:19:33.807-07:002016-05-21T01:19:33.807-07:00@ Ryu, I think these were what you were looking fo...@ Ryu, I think these were what you were looking for, calculated using the same multiple regression method based on PC1 and PC2 of those stats plus the new Ust Ishim column:<br /><br /> Anatolia_Neolithic2 BedouinB2 Cypriot2 Dai2 Denisovan Druze2 Han2 Iberia_Chalcolithic Iranian_Jew2 Karitiana2 LaBrana1 Mansi2 Motala_HG2 Munda2 Papuan2 Samara_HG Satsurblia South_Indian2 Ust_Ishim Yoruba<br />Matthttps://www.blogger.com/profile/04517454865405705885noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-85926550896906892182016-05-21T00:46:32.664-07:002016-05-21T00:46:32.664-07:00The reason GujaratiA eats up the CHG in Kalash is ...The reason GujaratiA eats up the CHG in Kalash is because GujaratiA is mostly CHG.<br /><br />But GujaratiA is a modern population that in all likelihood did not contribute ancestry to the Kalash, so taking away CHG from the Kalash by using GujaratiA as a reference isn't informative when studying Kalash origins.<br /><br />So this comes back to what I said before; since we're humans, we Davidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-76972156804962567692016-05-21T00:28:13.069-07:002016-05-21T00:28:13.069-07:00@ Frank
Thank you for your survey of the vulnerab...@ Frank<br /><br />Thank you for your survey of the vulnerabilities of explorative methods. <br />I want to add some details about problems of nMonte, especially in combination with Dstat spreadsheets.<br />You mention that: <br />1. Monte-Carlo based clustering may converge on several quite different solutions. That is especially true if the the iteration is stopped before converge is completed.huijbregtshttps://www.blogger.com/profile/15146303681173955347noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-3594428344241981982016-05-20T22:31:17.620-07:002016-05-20T22:31:17.620-07:00@Krefter: You are right. According to that new Pes...@Krefter: You are right. According to that new Pesteri-Muierii paper, the W Eurasian sister clade to Papuan P is R0/HV. Sloppy reading on my behalf.FrankNhttps://www.blogger.com/profile/01292462554916779884noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-58533702535819427322016-05-20T22:05:20.822-07:002016-05-20T22:05:20.822-07:00@FrankN,
mtDNA P and U are not sister clades. The...@FrankN,<br /><br />mtDNA P and U are not sister clades. They descend from R but that's it. They don't have a relationship besides being descended of R. Krefterhttps://www.blogger.com/profile/01055804913528477710noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-8532737179142823232016-05-20T21:01:05.082-07:002016-05-20T21:01:05.082-07:00rk & Alberto,
https://drive.google.com/file/d...rk & Alberto,<br /><br />https://drive.google.com/file/d/0B9o3EYTdM8lQcld1dnRPRzloeFE/view?usp=sharing<br /><br />https://drive.google.com/file/d/0B9o3EYTdM8lQNWRIS0VIN0tOc28/view?usp=sharingDavidskihttps://www.blogger.com/profile/04637918905430604850noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-74615935344958430602016-05-20T20:08:49.194-07:002016-05-20T20:08:49.194-07:00@Dave: "TreeMix is a software for simple mode...@Dave: <i>"TreeMix is a software for simple models and exploring more complex models for further analysis. Its output should not be taken too literarily."</i><br />I feel this this applies to all the methods we have available. Monte-Carlo based clustering may converge on several, quite different solutions, depending on the starting point of the iteration. See <br />https://FrankNhttps://www.blogger.com/profile/01292462554916779884noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-80081317155831981292016-05-20T10:52:52.029-07:002016-05-20T10:52:52.029-07:00I went through the values in both datasheets looki...I went through the values in both datasheets looking for specific differences that could help in determining if one agrees more with non-double outgroup D-stats. If anyone (David? Chad?) has the chance to run them:<br /><br />Mbuti Dai Turkmen Papuan<br />Mbuti Han Turkmen Papuan<br />Mbuti Druze Germany_MN Anatolia_Neolithic<br />Mbuti Iberia_Chalcolithic ElMiron<br />Mbuti Iranian_Jew Greek2 Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-53255493403431123612016-05-20T05:26:00.879-07:002016-05-20T05:26:00.879-07:00This comment has been removed by the author.Ryukendo Khttps://www.blogger.com/profile/11588546655427153692noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-9645619023719020652016-05-20T05:20:31.962-07:002016-05-20T05:20:31.962-07:00This comment has been removed by the author.Ryukendo Khttps://www.blogger.com/profile/11588546655427153692noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-27439889819743892422016-05-20T05:14:41.752-07:002016-05-20T05:14:41.752-07:00FrankN
"At several occasions, a strange sign...FrankN<br /><br />"At several occasions, a strange signal of West African admix into East/South Asians popped up. The TreeMix diagrams in Raghavan 2015 "Peopling of the Americas" show a Yoruba->Han migration edge."<br /><br />I found a paper once during random googling showing that iodine in the oceans decreases away from the equator and as iodine mostly comes from the Greyhttps://www.blogger.com/profile/13398462488549380796noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-57105152599582005822016-05-20T04:24:54.509-07:002016-05-20T04:24:54.509-07:00@Frank, "mtDNA P9/P10 virtually exclusively o...@Frank, "mtDNA P9/P10 virtually exclusively occurring with Philippine negritos, there accounting for 28% of all mtDNA. P, otherwise primarily found with Papuans and Australian Aborigines, is a sister to West Eurasian U and Near Eastern R0, as well as Far Eastern B and F (Aeta: 39% B, 23% F1a3a), all derived from R (UI, AG3, KO1)."<br /><br />I noticed that in this new paper on Peştera Kristiinahttps://www.blogger.com/profile/02994105875605082112noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-65292544606626188352016-05-20T03:36:17.564-07:002016-05-20T03:36:17.564-07:00@ryuk,
"During the modelling in nMonte did yo...@ryuk,<br />"During the modelling in nMonte did you guys drop any columns?"<br /><br />Hells yeah. We be dropping those &*()^^%%$$^ columns. <br /><br />Seriously though yes I do. You have to sometimes. For example you can't estimate Basal Eurasian ancestry if Anatolia_Neolithic is in the columns. If you want to estimate WHG ancestry, you need WHG in the columns because they areKrefterhttps://www.blogger.com/profile/01055804913528477710noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-58479490295056902552016-05-20T02:41:08.053-07:002016-05-20T02:41:08.053-07:00This comment has been removed by the author.Ryukendo Khttps://www.blogger.com/profile/11588546655427153692noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-79692311237840520802016-05-20T02:36:16.599-07:002016-05-20T02:36:16.599-07:00@ Matt
Matt, do you kind providing us with the re...@ Matt<br /><br />Matt, do you kind providing us with the regression equation-derived ghost basal Eurasians 1, 2, and 3 to fit into the following datasheet? :<br /><br />https://drive.google.com/file/d/0B9o3EYTdM8lQak1CRW5jLWZLMTA/view<br /><br />With the following columns:<br />,Anatolia_Neolithic2,BedouinB2,Cypriot2,Dai2,Druze2,Han2,Iberia_Chalcolithic,Iraqi_Jew2,Karitiana2,Ket2,LaBrana1,Ryukendo Khttps://www.blogger.com/profile/11588546655427153692noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-31931811104660889912016-05-20T02:23:20.674-07:002016-05-20T02:23:20.674-07:00@ Alberto @ Krefter @ Chad
During the modelling i...@ Alberto @ Krefter @ Chad<br /><br />During the modelling in nMonte did you guys drop any columns?<br />Ryukendo Khttps://www.blogger.com/profile/11588546655427153692noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-60854756640694408552016-05-20T02:07:55.775-07:002016-05-20T02:07:55.775-07:00Frank, TreeMix trees were posted by Matt. I still ...Frank, TreeMix trees were posted by Matt. I still have them on my computer. In the first set, Mota receives gene flow from ENA base. In the tree with Papuan, Mota receives gene flow from Eurasian base. In the tree with Near Easterners, Mota branch splits in two: in Atayal/ENA branch and in Western Eurasian branch.<br /><br />If I remember correctly, in the paper on Native Americans (published in Kristiinahttps://www.blogger.com/profile/02994105875605082112noreply@blogger.comtag:blogger.com,1999:blog-4123559132014627431.post-34749746693079971122016-05-20T01:15:01.627-07:002016-05-20T01:15:01.627-07:00@Davidski
Yes, I see. Well, I understand that the...@Davidski<br /><br />Yes, I see. Well, I understand that there are limitations, and that the easier the problem the least differences there will be by using different methods. But in this specific case it seems that we've introduced a limitation that didn't exist before (the PCA based datasheet had no problems with Anatolia_Neolithic as a source either), so that looks like a regression.<Albertohttps://www.blogger.com/profile/10924243765876609481noreply@blogger.com