tag:blogger.com,1999:blog-6443268110928728533.comments2024-01-11T02:42:22.101+00:00ArtemisDiogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.comBlogger79125tag:blogger.com,1999:blog-6443268110928728533.post-44007847692550758562011-06-10T15:52:44.987+01:002011-06-10T15:52:44.987+01:00Those are small elements, may be just noise...
The...Those are small elements, may be just noise...<br />The sample is from the PR of China, comprising more southern Mandarin-speaking individuals than the ChineseBJG sample. In the panasian site map it's pinpointed to Shanghai.<br />http://www4a.biotec.or.th/PASNP/PASNP_MapDiogeneshttps://www.blogger.com/profile/00827839380414245914noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-73838117575277294052011-06-10T12:44:18.474+01:002011-06-10T12:44:18.474+01:00Where is HanMandarin from, geographically? The pr...Where is HanMandarin from, geographically? The prominence of the Ph-Mamanwa- and WhiteUtahns-modal components here as compared to the other Chinese samples is interesting.Ortu Kanhttps://www.blogger.com/profile/15835792445084398302noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-4750615456065744002011-06-09T18:39:14.785+01:002011-06-09T18:39:14.785+01:00I ran this unsupervised analysis to get hints for ...I ran this unsupervised analysis to get hints for a future supervised run using "restricted poles" which I think give more informative components than supervised ones.<br />I will name those supervised components, since I'll make significant set-up choices about them; but I don't want to name these unsupervised ones.<br /><br />With supervised runs I can create models through reasoned set-ups and then check for coherence and predictions. You make some interesting points. I hope the supervised run will give some clues.Diogeneshttps://www.blogger.com/profile/00827839380414245914noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-55679467829551332462011-06-08T02:59:34.892+01:002011-06-08T02:59:34.892+01:00After plotting the different "colours" a...After plotting the different "colours" as an MDS, I get the following impressions:<br /><br />-light green seems to close to an unadulterated neolithic core. Most likely somewhere between the Yangtze.<br />-dark green is a mix of mostly light green neolithic and some purple foragers. <br />-dark blue seems to be a mix between a bit of light blue forager and an already mixed neolithic populatins of light green neolithic core and pink foragers (probably similar to contemporary Jinuo and Karen). <br />-dark blue seems to be a mix between a very archaic forager population more related to both Burgundy and Yellow (Joumon like people?) and an already mixed neolithic populatins of light green neolithic core and pink foragers (probably similar to contemporary Jinuo and Karen).<br /><br />It would be interesting if we could see a split in red/blue between a Jinuo like population and their associated foragers (burgundy/pink), to confirm whether this seemingadmixture just an impression or not.<br />Also, I think if we had some Siberian people like the Yakut in the run, we might have been able to see a split within the current red component, between a component with greater melanesian affinities and one with greater Siberian affinities (Altaic?).<br /><br />To propose names for components:<br />light green : Yangtze core<br />dark green : proto-austronesian or southeastern Yangtze expension<br />dark blue : Mekong core or southern Yangtze expension<br />red : northeastern Yangtze extension?<br />light blue : SEAsian forager 1 (golden triangle centered)<br />pink : proto-Mon-Khmer or SEAsian forager 2<br />purple : SEAsian forager 3 (Southeastern China and Philippines centered)<br />burgundy : Melanesian forager (possibly originally spread north of SEAsian forager 2 in continental Asia too, with greater paleo-caucasian affinities there?)Gui Shttps://www.blogger.com/profile/10460980441040040539noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-71884548395963058462011-05-26T01:15:19.619+01:002011-05-26T01:15:19.619+01:00Do you accept Family Finder from FTDNA results?Do you accept Family Finder from FTDNA results?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-90456501045293871712011-05-16T13:27:09.812+01:002011-05-16T13:27:09.812+01:00Briefly examining my results, it seems that the EM...Briefly examining my results, it seems that the EMPC component largely corresponds with the Ancestral North Indian component, although it seems that a part of the Ancestral South Indian also seems to have been picked up as EMPC as the ASI is only marginally more related to East-Eurasian populations. Hence, given that the West Eurasian element in South Asians is largely derived from West Asia, the EMPC component being the dominant element is but natural. The Siberian2 component seems to be picking up the rest of the ASI, along with a bit of the Siberian3. I reckon that the Siberian2 component will be closer to the ASI and/or Onge component seen in other admixture runs. Diogenes mentions that the Siberian3 component peaks in far-eastern Siberians like the Chuckchis and the Koryaks. If we assume geographic proximity as the sole factor for closeness, the generic Siberian2 component should be closer to ASI than the far-eastern one as ASI is closer to SEA and East Asian populations in general. My Siberian3 score is consistent with the bits of East Asian I get on admixture runs all over the genome blogging projects. Incidentally, my N. Asian + Siberian + SEA score over at HAP was 3%. As for the NMPC, once again rather consistent with the 4 -5% Northern/North East European scores I usually get. In this regard however, TamilBrahmins2's scores seem especially elevated as compared to the other two Tamil Brahmins. The WMPC + NWAf might well be some sort of Neolithic signal from the Indus valley civilization?Vasishtahttps://www.blogger.com/profile/16475698920004634252noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-50653107360464225682011-05-05T04:45:27.458+01:002011-05-05T04:45:27.458+01:00Truly a very interesting possible scenario here!Truly a very interesting possible scenario here!jackson_montgomery_devonihttps://www.blogger.com/profile/17553257488930856466noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-45330773960379137562011-05-04T15:54:27.830+01:002011-05-04T15:54:27.830+01:00Ahhhh alright I understand now. This actually make...Ahhhh alright I understand now. This actually makes sense and thank you for clearing this up and answering my questions.jackson_montgomery_devonihttps://www.blogger.com/profile/17553257488930856466noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-80142000582113649712011-05-03T09:44:06.860+01:002011-05-03T09:44:06.860+01:00I'm very confident they're real, although ...I'm very confident they're real, although absolute percentages may not be exact to the decimal digit. I'm not questioning previous results just pointing out that the situation becomes more complex the more closely I look.<br />"Macroscopically", if you run Europeans as Fertile Crescent versus Amerindian/Siberian there is little complication and results are straightforward I think.<br />The problems start when you want to differentiate between different "Mesopotamian" waves. And see the North African components, the Amerindian ones, and "Mesopotamian" ones all at once.<br />Different "Mesopotamian" subsets are admixed with each of these more exotic elements, and when they split, they tend to take some of it with them, or to become subsumed into them.<br />In order to differentiate more precisely different "Mesopotamian" and other elements in Europeans I would ideally use unadmixed modern populations corresponding to the ancient subsets. But these mostly don't exist anymore. For instance French Basques are almost fully "Mesopotamian core". But I now am seeing results suggesting even they have are composed of one dominant and another smaller "Mesopotamian" subset.<br />Things will become clearer with the next few posts.Diogeneshttps://www.blogger.com/profile/00827839380414245914noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-41335678116247957412011-05-03T03:42:29.935+01:002011-05-03T03:42:29.935+01:00I do not fully understand what you mean by this.
...I do not fully understand what you mean by this.<br /><br />''With more populations, there are sufficient differences that ADMIXTURE tends to fall into lumping them with aboriginal/2nd wave smaller elements into artificial components. For instance the Siberian/Amerindian-like element of some North Europeans often disappears into the local MPC; the Nile Core of Southerners and especially Middle Easterners into their local varieties''<br /><br />Do you mean that the Siberian and Amerindian like components in some Europeans are subsumed or ''swallowed up'' by the larger MPC components?<br /><br />Are the Siberian and Amerindian components that have been shown in previous runs in many Europeans still real then?jackson_montgomery_devonihttps://www.blogger.com/profile/17553257488930856466noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-46345659971341268002011-05-02T01:10:23.308+01:002011-05-02T01:10:23.308+01:00It is nice to see someone taking a deeper look at ...It is nice to see someone taking a deeper look at the components that make up Africans both North and Sub-Saharan.jackson_montgomery_devonihttps://www.blogger.com/profile/17553257488930856466noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-22811935848603705882011-05-01T20:56:30.227+01:002011-05-01T20:56:30.227+01:00All this is highly experimental, but I wouldn'...All this is highly experimental, but I wouldn't be surprised if "NW African" turned out to be itself composed of an ancient forager substrate and a Green Saharan melting pot population. This would later suffer major superimposition by "MPC" elements.<br />Surprisingly, the fst distances provided by ADMIXTURE for NW African ("Dogon5" but clearly dominated by sequences in North Africans) are quite large versus MPC, NC and E African...<br />Don't know if this is real, or why it's so large.<br />Amerindian large fst distances, if they are related to "Native Europeans" are suggestive however...Diogeneshttps://www.blogger.com/profile/00827839380414245914noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-17739364702685716302011-05-01T16:54:38.956+01:002011-05-01T16:54:38.956+01:00ok I see and the results looks plausible. Have you...ok I see and the results looks plausible. Have you read these sudies about North Africa:<br /><br />1) Ancient Local Evolution of African mtDNA Haplogroups in Tunisian Berber Populations<br /><br />2)Biocultural Emergence of the Amazigh (Berbers) in Africa: Comment on Frigi et al. (2010)<br /><br /><br />http://muse.jhu.edu/subject_browse?subtopic=Berbers%20--%20Tunisia%20--%20Origin.Maurihttps://www.blogger.com/profile/12466415546180699759noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-2404149954582817132011-05-01T16:36:45.523+01:002011-05-01T16:36:45.523+01:00"Dogon5" is not representative of NW Afr..."Dogon5" is not representative of NW Africa, the Dogon are West Africans just as the Yoruba. But just as in previous runs Beijing-Chinese might be picking Amerindian in Mexicans; and Maasai West African in African-Americans, if the pole is sufficiently small; so does "Dogon5" capture what may be a distinctive component here, not directly related to them.Diogeneshttps://www.blogger.com/profile/00827839380414245914noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-52421263613208740402011-05-01T09:38:30.246+01:002011-05-01T09:38:30.246+01:00It is interesting but I dont understand very well ...It is interesting but I dont understand very well why dogon5 is representative of NW Africa.Maurihttps://www.blogger.com/profile/12466415546180699759noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-22490786417809133952011-04-29T00:13:38.798+01:002011-04-29T00:13:38.798+01:00Yes, but I've seen ADMIXTURE stretch totally u...Yes, but I've seen ADMIXTURE stretch totally unrelated poles as well to include hidden components such as Chukchi fishing out the West Eurasian and !kung the African elements in Middle Easterners. I've actually seen it do that repeatedly. I think some flexibility concerning possible variability in a postulated parent population, but not represented in pole individuals available, was written into the supervised mode's algorithm. I think it can be exploited to find hidden elements by using less individuals or totally unreasonable poles.Diogeneshttps://www.blogger.com/profile/00827839380414245914noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-87315562898912829522011-04-28T18:06:13.355+01:002011-04-28T18:06:13.355+01:00When you use only the 5 Maasai, many of the low-fr...When you use only the 5 Maasai, many of the low-frequency West Eurasian alleles that exist in the Maasai population become "fixed", and the Maasai appear more African than they are; correspondingly they appear more like Yoruba, and hence the African Americans' admixture proportions become more like those you get when you use Yoruba.Dienekeshttps://www.blogger.com/profile/02082684850093948970noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-7353922368340580192011-04-27T18:53:19.219+01:002011-04-27T18:53:19.219+01:00The Libyans are from the Henn et all public datase...The Libyans are from the Henn et all public dataset. I don't believe there are major separated groups of Arab/Berber Libyans. There are Arabised Libyans and Libyans still speaking Berber tongues. The former may have some small amount of Arab ancestry, which may rise to a substantial amount in a minority, maybe some traditional elite groups. But in general Libyans are just Libyans and have been so (I'd risk saying >80% in total genomic content) since the Neolithic Revolutions. I have not seen convincing evidence pointing otherwise yet.Diogeneshttps://www.blogger.com/profile/00827839380414245914noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-56891950990657831982011-04-27T01:22:09.449+01:002011-04-27T01:22:09.449+01:00Hello and thanks
may I ask you, the source of your...Hello and thanks<br />may I ask you, the source of your Libyan samples and the easterner/westerner and arab/berber grouping of them.<br />Also do you know the amount (mean) of southwest asian component on those libyans?<br />thanks for the attentionpiertrinkhttps://www.blogger.com/profile/08397246383625658816noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-44065983627800634422011-04-24T22:37:55.330+01:002011-04-24T22:37:55.330+01:00An interesting scenario again Diogenes. I am quite...An interesting scenario again Diogenes. I am quite interested to see the variations within Europeans of the different ''Fertile Crescent'' components in project participants. Also I am still very interested in the small ''Forager'' or Siberian/Amerindian like components that also show up in many Europeans.jackson_montgomery_devonihttps://www.blogger.com/profile/17553257488930856466noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-79314092558625531892011-04-20T01:47:04.582+01:002011-04-20T01:47:04.582+01:00Cool work again Diogenes!Cool work again Diogenes!jackson_montgomery_devonihttps://www.blogger.com/profile/17553257488930856466noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-38379443576160172752011-04-20T01:15:16.511+01:002011-04-20T01:15:16.511+01:00All 3 posts are from the very same run.All 3 posts are from the very same run.Diogeneshttps://www.blogger.com/profile/00827839380414245914noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-834532921158500572011-04-20T01:08:38.010+01:002011-04-20T01:08:38.010+01:00I'm not naming them since ADMIXTURE picked the...I'm not naming them since ADMIXTURE picked them up not me. This is unsupervised. You can check previous posts to see which population has the largest amount.Diogeneshttps://www.blogger.com/profile/00827839380414245914noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-31615933516594945072011-04-20T01:05:40.269+01:002011-04-20T01:05:40.269+01:00Can you please mention the reference populations/K...Can you please mention the reference populations/K's against the colored squares? I know that some components are likely noise, but it'd be nice to know them anyway. It's sort of tedious trying to find out where each component is modal via the spreadsheet.Vasishtahttps://www.blogger.com/profile/16475698920004634252noreply@blogger.comtag:blogger.com,1999:blog-6443268110928728533.post-66053558278915866512011-04-19T19:34:35.393+01:002011-04-19T19:34:35.393+01:00Ahhhh yes now I see what you mean. I just finished...Ahhhh yes now I see what you mean. I just finished reading through all of the posts from the first one's back in March until now. <br /><br />Both the Amerindian and Siberian poles are part of ''Forager A'' when seen in Europeans. They are both subsets of ''Forager A''.jackson_montgomery_devonihttps://www.blogger.com/profile/17553257488930856466noreply@blogger.com