tag:blogger.com,1999:blog-64432681109287285332024-03-06T08:33:11.832+00:00ArtemisDiogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.comBlogger47125tag:blogger.com,1999:blog-6443268110928728533.post-76647685783739275352011-06-14T22:59:00.005+01:002011-06-15T19:41:12.632+01:00Panasian-Part IV: Malaysia and IndonesiaPart IV (and last) of the unsupervised Panasian set ADMIXTURE analysis.<br />
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Fst distances provided by ADMIXTURE:<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjjd9fj3ttjRsULK5rW66GLvevzeAP-S736RP3NQSPAKsGWK1ClKTWU_OqcSiAz2vebv4TnQX058a4K7FLDYzfe1fyKxcFPJpqGl-t_TEkmo7eml_e3PWuwnnsU2PD1m3J4hH4CPB5FmBA/s1600/Screenshot-2.png" imageanchor="1" style=""><img border="0" height="98" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjjd9fj3ttjRsULK5rW66GLvevzeAP-S736RP3NQSPAKsGWK1ClKTWU_OqcSiAz2vebv4TnQX058a4K7FLDYzfe1fyKxcFPJpqGl-t_TEkmo7eml_e3PWuwnnsU2PD1m3J4hH4CPB5FmBA/s400/Screenshot-2.png" /></a></div>About the populations in this part:<br />
The "Malay" population is comprised by Malaysian Malays; "SGMalay" individuals are from Singapore; while MalayIndonesia are equally Malay dialect-speaking, but from South Sumatra, Indonesia (the official languages of Malaysia and Indonesia, Bahasa Malaysia and Bahasa Indonesia, are different registers of a dialect continuum called <a href="http://en.wikipedia.org/wiki/Varieties_of_Malay">"Malay"</a> historically used as a lingua franca spanning both countries).<br />
Temuan speak a language from the "<a href="http://en.wikipedia.org/wiki/Aboriginal_Malay">Aboriginal Malay</a>" or "Proto-Malay" group. They are a small group nowadays, and still practice Animism and slash-and-burn agriculture.<br />
Sundanese and Javanese are the main Austronesian-speaking inhabitants of Java and represent together almost half of the Indonesian population (20M and 80M respectively), dominating its politics. <a href="http://en.wikipedia.org/wiki/Sundanese_language">Sundanese</a> and <a href="http://en.wikipedia.org/wiki/Javanese_language">Javanese</a> languages are distinct from official Malay-derived Bahasa Indonesia which most of them nowadays speak as well (some exclusively).<br />
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Mentawai are Animist/Christian <a href="http://go.galegroup.com/ps/infomark.do?action=interpret&u=wash_main&source=gale&eisbn=0-02-866087-0&prodId=GVRL&userGroupName=wash_main&tabID=T001&docId=CX3458100063&type=retrieve&contentSet=EBKS&version=1.0&authCount=2">slash-and-burn (swidden) farmers</a> planting sago, yams, taro and raising pigs and chickens much as the original Austronesians and as other modern-day isolated Austronesian peoples; supplemented by much hunting and fishing as well. They live in the Mentawai islands just off West Sumatra.<br />
Batak Karo and Batak Toba are also Austronesian speakers from inland Sumatra; they seem to be dry rice-agriculturalists, also cultivating paddies in some regions.<br />
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The "Dayak" sample is derived from an (Austronesian-speaking) Indonesian Dayak tribe from East Borneo, and are slash-and-burn agriculturalists. Biduyah are also Dayaks, but differ from the "Dayak" sample in that they are from Sarawak, Malaysia (Northwestern Borneo). They have presumably received more outside influence than the more Eastern Dayaks, and appear to be more involved in the current plantation economy. (The Iban, represented in a <a href="http://dioegenesartemis.blogspot.com/2011/04/unsupervised-northern-eurasianew.html">previous run</a> with the main set, are also Dayaks from Western Borneo).<br />
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Toraja are Austronesian speakers from Sulawesi's mountainous interior. They're farmers who remained Animist until recently (they are mostly Christian nowadays).<br />
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Kambera, Manggarai, Lamaholot, Lembata and Alorese live in the <a href="http://en.wikipedia.org/wiki/Lesser_Sundas">Lesser Sundas</a> in Southeastern Indonesia. They speak Austronesian languages, and are mostly Christian today. These groups present visible Melanesian admixture.<br />
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Naasioi are Melanesians, speaking a Papuan language. They share Bougainville island in Papua New Guinea with Austronesian-speaking groups, and are slash-and-burn farmers.<br />
Kensiu and Jehai are Malaysian Negrito peoples.<br />
<br />
Some candid observations (and shameless speculations):<br />
1) Austronesian tongues seem to correlate with the darkgreen component modal in Taiwanese Aborigines. Earlier there seemed to be a <a href="http://dioegenesartemis.blogspot.com/2011/06/panasian-part-ii-se-asia.html">weaker correlation with Tai-Kadai languages</a>.<br />
These linguistic families <a href="http://en.wikipedia.org/wiki/Austro-Tai_languages">have important similarities</a>, and it is controversial among linguists weather they are branches of a more ancient proto-language, or if both branches shared geographically close homelands- their present distribution suggests homeland(s) in Southern China, and populations analysed from China, including all Han groups, also have darkgreen elements.<br />
These are however largely lacking in represented <a href="http://dioegenesartemis.blogspot.com/2011/06/panasian-part-ii-se-asia.html">Austro-Asiatic speaking populations</a> (though I would be surprised if more Southern Chinese-influenced Vietnamese weren't the exception); <a href="http://dioegenesartemis.blogspot.com/2011/06/panasian-part-i-altaic-and-sino-tibetan.html">Burmese</a> Sino-Tibetan speakers; Uyghur; Okinawans; and are small in Koreans and Japanese mainlanders (perhaps due to an old Han admixture event/secondary wave?)- all these groups have important "red" elements however.<br />
This could be interpreted as suggesting an origin, or at least diffusion of Sino-Tibetan and Altaic with Neolithic Expansions directly from the Northern China/Yellow River region before the ethnogenesis of the Han (before admixture from populations from the Yangtze River valley?).<br />
(At this moment I would tend to interpret the Altaic element, even in Central Asians, as being derived early on from the East Eurasian Neolithic just as I previously interpreted their Western admixture as being <a href="http://dioegenesartemis.blogspot.com/2011/05/inland-ocean-restricted-pole-run-part.html">derived from the Fertile Crescent</a>).<br />
<br />
2) Austronesian-speaking groups closer to continental SE Asian influence tend to have smaller darkgreen and larger darkblue elements- such as Bidayuh (SW Borneo) and the populations from Java.<br />
The darkblue component is important in continental Southeast Asian populations and those from the Indonesian Archipelago with more historical SE Asian connections. It somewhat correlates with Austro-Asiatic languages, perhaps it indicates an early agricultural wave from China into SE Asia, before the Tai-Kadai-Austronesian one? Darkblue is a bit more distant in fst from the other East Asian Neolithic components, perhaps due to having a larger degree of stabilised ancient local variation included in it.<br />
Darkblue in Indonesians decreases with distance to SE Asia. It may have some association in this context with later expansion of populations- possibly associated with wet rice and other agricultural innovations from SE Asia- from <a href="http://en.wikipedia.org/wiki/Srivijaya">more</a> <a href="http://en.wikipedia.org/wiki/Majapahit">developed</a> and more densely populated Java, a development <a href="http://en.wikipedia.org/wiki/Irian_Jaya#Demographics">continuing to this day</a>.<br />
4) Groups further towards the East present an increasing burgundy element modal in Papuan-speaking Melanesian Naasioi. These groups are swidden agriculturalists. Their relative success in resisting the farmer waves versus distantly related Negrito groups from the Philippines and SE Asia may hint at some primitive agriculture in coastal Papuan-speaking peoples prior to the Austronesian expansion.<br />
Melanesians such as Naasioi probably have some Austronesian admixture, which may be invisible here due to lack of reference highland Papuan populations- the burgundy component may be a fusion of mostly "Papuan" with a little Austronesian- a possible reason why it may pull some of the Philippine Negrito variation in the more admixed tribes.<br />
Polynesians also seem to have <a href="http://dioegenesartemis.blogspot.com/2011/04/unsupervised-northern-eurasianew.html">important Melanesian admixture</a>.<br />
<br />
sorry I didn't include East Asian participants in this run but the ~50000 SNPs in this set do not overlap much with the 23andme ones, so including them would reduce the resolution too much.<br />
<br />
Many thanks to Zack from <a href="http://www.harappadna.org/">Harappa</a> for drawing my attention to this set -he also wrote and posted the conversion code to bed format.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com0tag:blogger.com,1999:blog-6443268110928728533.post-57178819548846952382011-06-11T16:17:00.013+01:002011-06-11T18:53:22.808+01:00Panasian-Part III: PhilippinesThird part of the Panasian run (excluding Yoruba, South Asians).<br />
This post is about populations from the Philippine Archipelago:<br />
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About the populations:<br />
Amis and Atayal are Taiwanese aborigines speaking Formosan Austronesian languages. It is generally believed the Austronesian language family derives from Taiwan, having spread into the Philippines, Indonesia and Polynesia as an agriculturally-driven expansion. Taiwanese "Aboriginals" are historically primitive farmers supplementing their diet with some hunting and fishing.<br />
Until recently they were the main inhabitants of Taiwan, having been swamped by Fujianese Han groups only in the last few centuries (Minnan and Hakka). There is some evidence they shared the island with a minority of Taiwanese Negritos- possibly the true Paleolithic forager native inhabitants- who <a href="http://en.wikipedia.org/wiki/Saisiyat_people#Negrito_connection">don't exist anymore</a> as a distinct group today.<br />
<br />
Filipino populations are farmers, speaking various Austronesian dialects. Tagalog is the dialect on which the National Language of the Philippines, "Filipino" is based. They live in Southern Luzon. Ilocano is spoken by related populations in more Northern regions of Luzon island. Visayan is a third Filipino group of dialects spoken in the Visayas (central group of Philippine islands) as well as in some parts of Mindanao. The sample represented here was from Visayan-speaking colonists from West Mindanao. These groups comprise the majority of the islands population, and are at the core of self-identification with the modern "Filipino" nationality.<br />
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Minanubu or Manobo; Iraya are incipient farmers using slash and burn methods in Mindanao and Mindoro respectively. They speak Austronesian languages. These peoples have been suffering pressure from neighbouring more agriculturally advanced and socially complex Filipino migrants (such as Visayans), and are <a href="http://en.wikipedia.org/wiki/Manobo#Social_issues">being pushed out</a> of the more fertile soil in their homelands.<br />
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Ayta, Agta, Ati and Mamanwa are Philippine Negritos, who are generally hunter-gatherers, at least until very recently. Ayta and Agta are from Luzon; Ati are from the Visayas; Mamanwa from Mindanao.<br />
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The diversity of populations in the Philippines seems to fit very well into the Neolithic expansion model I've been exploring. Three groups can be identified, with a degree of continuity between groups: advanced farmer "Filipinos"; slash-and-burn farmers such as Iraya and Minanubu; and forager Negritos.<br />
1) Negritos probably represent the ancient (forager) population of the Philippines. They present varying hybridization with farmers (as seen in farmer-associated components).<br />
The similar pattern of "forager-components" (Kensiu are SE Asian Negritos. Naasioi are Papuans) in Agta, Ati and Ayta may represent Philippine-Negrito unique genetic patterns that ADMIXTURE didn't pick out in this analysis (maybe due to a more inbred Mamanwa sample taking it's own component and non-represented variety in the other Negritos being allocated to related Naasioi and Kensiu-modal components- something similar often happens in Siberian peoples' ADMIXTURE runs).<br />
2) The earliest "First Wave" farmer intrusion in the Philippines is probably associated with Austronesian languages. Taiwanese Aboriginal groups speak the most divergent and diverse Austronesian tongues, and they are modal for the darkgreen component found in much larger amounts in Philippine farmers than in foragers (Negritos). Iraya and Minanubu have large such components but mostly lack the red, blue and lightgreen ones - they may represent a "First Wave" stage of Austronesian Expansion proper.<br />
3) Han Fujianese and Cantonese migration into the Philippines is historically documented even before the Spanish Conquest. A "Second Wave" process may be interpreted as being in full swing in the Philippines in recent centuries and up to today. Slash-and-burn agriculturalists such as Iraya and Minanubu seem to be in the process of assimilation or expulsion to more marginal lands. These more primitive agriculturalists also present larger forager-modal components than "Filipinos", though less than Negritos, just as expected.<br />
4) "Filipino" populations of advanced agriculturalists have more significative red and lightgreen elements, in which I tend to see absorption of much Han admixture in the last few centuries. Interestingly, <a href="http://en.wikipedia.org/wiki/Sangley">mestizos de Sangley</a> have been historically prominent as advanced farmers and plantation owners. Filipino ethnogenesis may derive from admixture between ancient slash-and-burn agriculturalists and migrants from China. Some admixture with Europeans (Spaniards, Americans) may also have occurred, to a smaller degree than with the Han, but a much higher degree than in other regional populations.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com0tag:blogger.com,1999:blog-6443268110928728533.post-28284148606265665492011-06-08T23:39:00.011+01:002011-06-09T00:53:34.596+01:00Panasian-Part II: SE AsiaThis part II is about continental SouthEast Asian populations from the Panasian dataset K=9 analysis I ran earlier. Some useful populations for comparison from <a href="http://dioegenesartemis.blogspot.com/2011/06/panasian-part-i-altaic-and-sino-tibetan.html">part I</a> are represented again- Their ADMXITURE component percentages are exactly the same since this is the very same run.<br />
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About the populations:<br />
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Hmong live in Southern China, particularly in more mountainous regions often separated by Han-inhabited areas, suggesting they were once more widespread in China, but were possibly swamped by an agriculturally more advanced wave of Han in the lowlands. They also live in South East Asian countries, such as Thailand. Yao people likewise live in Southern China and SouthEast Asia (the Yao sample in this set is from Thailand). Both Hmong and Yao speak <a href="http://en.wikipedia.org/wiki/Hmong-Mien_languages">Hmong-Mien languages.</a> These peoples in China are often lumped as "Miao" by the Han. Interestingly, Han Chinese foundational myths speak of the <a href="http://en.wikipedia.org/wiki/Miao_people">Miao</a> as a people originally from the Yellow River, forced to migrate south after conflict with the Huaxia, another Yellow River people, from whom the Han claim to descend. Such stories may be just folklore, but they do resonate somewhat with a Neolithic model of East Asian population expansion. Interestingly, the Hmong-modal component (light green) is larger in populations from the Yellow River southwards, while the closely related red component is more important in Han Chinese and northeastwards from the Yellow River in Koreans and Japanese.<br />
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Wa or Va, Lawa, Blang or Plang, Paluang, Mal and Mon speak Austro-Asiatic tongues and live in pockets dispersed between Southern China, Southeast Asia, and Burma. In this set, the Wa sample's from China, the remaining ones from Thailand.<br />
Vietnamese also belongs to the linguistic family. These languages are generally thought of as the original languages of SE Asia, being mostly replaced by Tai-Kadai and Austronesian languages today, but their geographical dispersion might also <a href="http://en.wikipedia.org/wiki/File:Se_asia_lang_map.png">suggest expansion from a Chinese homeland</a>, where they largely didn't survive.<br />
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Tai Yuan, Tai Khuen, Tai Lue, Tai Yong, Zhuang and Jiamao are Tai-Kadai speaking.<br />
Tai-Kadai languages have some similarities to Austronesian tongues, suggesting <a href="http://en.wikipedia.org/wiki/Austro-Tai_languages">possible common origin</a> in Southern China- with one expanding <a href="http://en.wikipedia.org/wiki/File:Taikadai-en.svg">West</a> into continental SE Asia, the other <a href="http://en.wikipedia.org/wiki/File:Austronesian_languages.PNG">East</a> into Taiwan and insular SE Asia. Both would be largely become <a href="http://en.wikipedia.org/wiki/Baiyue#Language">extinct in Southern China itself</a> after the "Second Wave"-like Han expansion from the North.<br />
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Malays and Temuan speak Austronesian languages, as do the aboriginal Taiwanese Amis. SG Malays are from Singapore.<br />
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Jehai and Kensiu are Malaysian Negritos. They speak Austronesian languages as well, very likely adopted from their agriculturalist neighbours. <br />
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Considerations/speculation:<br />
1) China Hmong appear to differ with Thailand Hmong only in some southern Han admixture in the former. This may also apply to Yao.<br />
2) Temuan speak an Austronesian dialect apparently somewhat mutually intelligible with Malay. They preserve many ancient traditions maybe lost among the Malay, such as religious Animist practices. They also have a larger "pink" element modal in local Negrito foragers. Their presumed greater isolation may help explain less dark green genetic admixture than in Malays.<br />
3) Jehai have substantial "dark blue" element absent in Kensiu. This may suggest an association of the dark blue element with agriculturalists (fst distances to other components are in agreement-see <a href="http://dioegenesartemis.blogspot.com/2011/06/panasian-part-i-altaic-and-sino-tibetan.html">part I</a>).<br />
4) Some "Burgundy" component starts to become visible in Malays, unlike in more Northern populations.<br />
5) The presence of an element clustering with West Eurasians in Mon and Malays is interesting. It's small, so it may be just noise. But since Indian populations weren't included and there's no "South Asian"-modal component, I wouldn't find it strange if this element would have a similar pattern to Fertile Crescent ones as found in South Asia- either from the time of the arrival of Neolithic West Asians to India, perhaps also <a href="http://en.wikipedia.org/wiki/Chola_empire">later</a>?<br />
6) ADMIXTURE patterns at this K and language families have some correlation. A common origin in an ancient Yellow River-Yangtze River Nelithic Core Area can also <a href="http://en.wikipedia.org/wiki/Austric_languages">be argued for linguistically</a>.<br />
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Next I'll post results from this run for Insular Southeast Asia (Philippines, then Indonesia).Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com0tag:blogger.com,1999:blog-6443268110928728533.post-41716435200372076042011-06-06T22:44:00.013+01:002011-06-07T20:40:24.945+01:00Panasian-Part I: Altaic and Sino-TibetanI've been away from ADMIXTURE for a couple of weeks, too busy with other stuff.<br />
This time I've decided to tackle East Asia. I got access to a new dataset from the <a href="http://www4a.biotec.or.th/PASNP">Pan Asian SNP Consortium</a>, with some 50.000 snps. Sadly few of them appear to overlap with my current dataset, so fusing them together means I'd have to work with just a few thousand. I may try anyway in the future, but decided to play with the Panasian set on it's own for the time being. I didn't use the South Asian or Yoruba samples in this series to simplify things, but I did include White Utahns to check for possible West Eurasian (Fertile Crescent) influence.<br />
I intend to apply some old tricks to get components to be more informative and less "isolated group"-tied, but firstly I wanted to see how this set would behave in an unsupervised ADMIXTURE analysis; namely I intend to check which unsupervised components are interesting and coherent with ethnographic/historical data so I can pick them for supervised analysis and hopefully gain some further insights.<br />
I'm presenting in the next few days a series of regionally-split results.<br />
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Unsupervised results are good for inter-population comparisons. Most components likely don't represent any particular ancient populations. A certain amount of small component noise is expected also.<br />
The following results are at K=9.<br />
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<br />
About the populations:<br />
JapaneseML are from the mainland, as presumably are most "Japanese" without the ML qualification. They were separated in the set and I didn't fuse them. JapaneseRyukyu are from Okinawa.<br />
SGChinese are Chinese from Singapore; BJG from Beijing.<br />
Taiwan <a href="http://en.wikipedia.org/wiki/Hakka_people">Hakka</a> and Taiwan <a href="http://en.wikipedia.org/wiki/Hoklo_people">Minnan or Hoklo</a> are Han Chinese, comprising the overwhelming majority of the island's current population. They represent the people generally meant when speaking of "Taiwanese" nowdays. They are however recent arrivals, presumably overwhelming the native <a href="http://en.wikipedia.org/wiki/Taiwanese_aboriginal">aboriginals</a> (Taiwan Ami and Atayal) with more efficient agricultural/social technologies only in the <a href="http://en.wikipedia.org/wiki/Taiwan#History">last 500 years or so</a>.<br />
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Taiwan<a href="http://en.wikipedia.org/wiki/Ami_people">Ami</a> and Taiwan<a href="http://en.wikipedia.org/wiki/Atayal_people">Atayal</a> are much older Taiwanese populations, but some discontinuity in the Paleolithic-Neolithic transition in Taiwan may imply an exogenous origin (possibly from early Neolithic China). They speak "proto-<a href="http://en.wikipedia.org/wiki/Austronesian_languages">Austronesian</a>" languages, and the Austronesian wave of language and agricultural lifestyle seems to have spread from there (or perhaps from Southeast mainland China, with a side branch going to Taiwan?).<br />
The Austronesian Expansion seems to have been sort of a "First Wave" of agriculturalists (maybe secondary in some regions). Much later, advanced agriculturalist "second wave" Han Chinese then had again a major demographic effect, going beyond to other Austronesian lands as well, and <a href="http://en.wikipedia.org/wiki/Sangley">apparent even in the Philippines today</a>, with some 20% of the population having <a href="http://en.wikipedia.org/wiki/Filipino_mestizo">recent Chinese ancestry</a>. Without Western interference, this possible Han "secondary wave" might have spread further still, given the large amounts of land then still occupied by foragers in insular South East Asia and Oceania. Indeed Negrito forager and semi-forager tribes are <a href="http://en.wikipedia.org/wiki/Aeta#History">still under pressure today</a> from their agricultural neighbours.<br />
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Jinuo and Karen are Burmese populations with <a href="http://en.wikipedia.org/wiki/Sino-Tibetan">Sino-Tibetan tongues</a> (same family as Chinese languages such as Mandarin and Cantonese and also Tibetan. Mon speak an AustroAsiatic tongue but also live in Burma.<br />
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Mlabri, Mamanwa and Kensiu are all forager/semi-forager tribes. Mlabri live in South East Asia; Mamanwa are Philippine Negritos, while Kensiu are SouthEast Asian Negritos. Naasioi are Papuans.<br />
<br />
Fst distances:<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjjd9fj3ttjRsULK5rW66GLvevzeAP-S736RP3NQSPAKsGWK1ClKTWU_OqcSiAz2vebv4TnQX058a4K7FLDYzfe1fyKxcFPJpqGl-t_TEkmo7eml_e3PWuwnnsU2PD1m3J4hH4CPB5FmBA/s1600/Screenshot-2.png" imageanchor="1" style=""><img border="0" height="98" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjjd9fj3ttjRsULK5rW66GLvevzeAP-S736RP3NQSPAKsGWK1ClKTWU_OqcSiAz2vebv4TnQX058a4K7FLDYzfe1fyKxcFPJpqGl-t_TEkmo7eml_e3PWuwnnsU2PD1m3J4hH4CPB5FmBA/s400/Screenshot-2.png" /></a></div>I'm not naming the components since I'm not sure they are historically informative.<br />
It's interesting "Red" is very close to "DarkGreen" and LightGreen". The genetic distance is similar to that between closely related components from other Neolithic centres I've run before.<br />
Some ancient stabilized admixture with very different local forager groups, present in these unsupervised components may even explain some of the distance, so the affinity may be higher than seen here.<br />
On the other hand, "Forager-components" are much less similar both to the presumed Neolithic ones and with other forager components. Actually, since I strongly suspect these modern day foragers are hybridized with their agriculturalist neighbours, the distance between different "Negrito"-modal components may be even larger.<br />
The distance between Westerner White Utahns and these groups seems to be roughly similar to the distance between foragers and agriculturalists, and different groups of foragers, but much larger than distance between agriculturalists. A possible explanation is multiple waves of forager-swamping agriculturalists from a single centre or group of related centres in the region.<br />
Some minor forager admixture in farmers and major farmer admixture in foragers, would both be invisible to unsupervised ADMIXTURE if ancient in the absence of "pure" control groups.<br />
<br />
I'll reserve more discussion for the supervised run, right now I'd venture to say the red, light green, dark green and blue components are all closely related, tend to exist in a gradient of admixture with one another in similar ethnic groups and may correspond to different but related Neolithic waves probably all from China. There is some interesting correlation with language groups.<br />
Ryukyu Japanese may lack some components more important in mainland Japanese and Koreans due to greater geographic insulation from Chinese secondary Waves. Perhaps like Sardinians and Basques in the West.<br />
Taiwanese Aborigines look promising as the representatives of a vast farmer demographic wave. Darkgreen presence in China may indicate it's origin there, since agriculture is older and was presumably more advanced in the continent.<br />
<br />
In the next days I will post results for other Austronesian and Southeast Asian peoples. Then I'll do a restricted pole-supervised run.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com4tag:blogger.com,1999:blog-6443268110928728533.post-65965989411625268482011-05-24T23:28:00.002+01:002011-05-24T23:32:18.905+01:00Back to Africa- individualsThese are some of the individuals from the run.<br />
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(There is likely a lot of small component noise here, and also between NMPC, WMPC, EMPC due to their high similarity and small number of European individuals included)<br />
Although African-Americans appear to present some variability in their African elements, their African ancestry can probably be best described as the product of a New World melting pot of originally Niger-Congo-speaking, West African ethnic groups. Affinity seems to be higher with ethnic groups from the Gulf of Guinea region, and the more Northern Bantu-speaking groups.<br />
Their non-SubSaharan African ancestry is mostly composed of elements found in Europe as expected. There is very little East African ("Nilo-Saharan").<br />
As for the Fulani it seems they have been somewhat isolated genetically from neighbouring populations, even though they live nearby non-Fulani peoples across a vast swath of the Sahel/West Africa region. Only a few individuals appear to be recently admixed to any degree. High levels of the Northwest African element, their general lack of any NCongo components except for NCongo1, together with NCongo1 being particularly high in presumably more isolated Sahel populations such as the Dogon all point to an ancient ethnogenesis for this group, perhaps in the (last) Green Sahara itself at the time of the West Asian Neolithic colonization of North Africa.<br />
<br />
Bear in mind this run attempted to distinguish very closely related components and a high amount of "noise" is likely at the individual level.<br />
Also Fertile Crescent components (FC) are being based in a small sample since this was about Africa. So NMPC here is different from my previous run, since it is based on the Lithuanians who have much more WMPC (Basques) than the Chuvash. EMPC was based on the Urkarah. So they don't have the same exact distributions as before.<br />
<br />
Niger-Congo components are also very close and shouldn't be taken as exact at the individual level. "Nilo-Saharan" is not very distant from the NCongo components either, some people postulate a common origin for the language families, and thus perhaps some genetic similarity is expected. Indeed if both Neolithic expansions are related and come from the "southern shore" of the Sahara, most modern African populations may have derived from demographic and linguistical expansion, from the whereabouts of the desert only a few thousand of years ago, probably in association with a Neolithic Revolution associated with the Green Sahara.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com0tag:blogger.com,1999:blog-6443268110928728533.post-23421172833190681542011-05-23T23:51:00.008+01:002011-05-24T11:22:00.683+01:00Back to Africa- populationsI've been busy with unrelated stuff lately so didn't find time to post last week.<br />
I've decided to take a new look into variation within African populations, using the restricted pole trick I <a href="http://dioegenesartemis.blogspot.com/2011/05/inland-ocean-restricted-pole-run-part.html">used before</a> in West Eurasian ones. I wanted to take a look at variation within the Niger-Congo or West African Neolithic Core variation in particular, by trying to split it up into 3 components.<br />
I should point out I'm doing these runs seeking support for a <a href="http://dioegenesartemis.blogspot.com/2011/03/clarifying-my-departing-point.html">theoretical model</a>. It's hard if not impossible to provide definitive evidence (if such a thing exists at all) through ADMIXTURE results. But models which provide unexpected results or predictions which can then be tested by other methods or analysis of future data not available right now, have value in my opinion.<br />
<br />
I've run a few unsupervised runs of the African samples available to me, compared with those in <a href="http://africanancestryproject.org/">other projects</a>, and used a few observations to guide me in pole choice. I was particularly interested in possible language-family-related components, since even though language groups don't always correlate exactly with genetics, there tends to be some relationship.<br />
Restricted poles comprising only a few individuals are a good way of establishing one or more "centres" for a cline in the data. They don't "stick" however if there is no such cline, or if the cline extremes are not represented. For instance, I chose a "Palestinian5" pole using 5 Palestinians, yet it was immediately stolen by the Saudis, who present a similar and otherwise unrepresented component to Palestinians yet at a higher level.<br />
However, for such clines as the Niger-Congo or "West African" cline, from Mandenka/Dogon to the South and East African Bantus, it is useful to establish some such "hand-picked centres" to differentiate subpopulations. The frontier between the 3 Niger-Congo components I've come up with is thus necessarily somewhat artificial. Choosing different "restricted poles" would result in different components to a much larger degree than in previous "Basque5" or "Lithuanian5" poles I've used, since these are much stabler.<br />
<br />
These were the poles chosen:<br />
1) Three Mandenka and two Dogon for a Northwestern Niger-Congo component. Dogon often appear as modal for the West-African component in unsupervised runs, indicating possible origin of the West African Neolithic in the Sahel. I named this component NCongo1 (Niger-Congo1)<br />
2) Five Yoruba: NCongo2<br />
3) One Pedi, two Fang, two Kongo and one Luhya to try to identify the Bantu component, which I named NCongo3 (Bantu)<br />
4) Three Bulala and two Masai. Masai often claim their own component and at higher Ks even multiple ones, due to close family links between some of them. I removed some of these individuals, but in order to avoid such artefacts, I used Bulala trying to make the Masai pole more independent from the Masai themselves. This component turned out to be important in all Nilo-Saharan speaking populations (plus the Sandawe, and even these can be split away into their own pole) so I took the liberty of naming it so, which shouldn't be taken too seriously.<br />
5) Five Biaka Pygmies (BPygmy)<br />
6) Five Mbuti Pygmies (MPygmy)<br />
7) Five Hadza<br />
8) Five Namibian San- Khoisan pole<br />
9) Five Palestinians. This pole was taken by the Saudi sample, as mentioned before. I named it FC(NEAfr). It seems to be important in Semitic language speaking populations, but it goes further into other populations as well. It roughly corresponds to the "second wave" or WMPC+NC component used in Fertile Crescent runs. <br />
10) Two Mozabite, two Tunisians and 1 N Moroccan. This pole peaks in the Tunisian sample and was named FC(NWAfr)<br />
11) Five Basques. Named FC(WMPC) - Fertile Crescent Western "Mesopotamian Core"<br />
12) Five Lithuanians, named FC(NMPC)<br />
13) Five individuals from Urkarah, Northern Caucasus. Named FC(EMPC)<br />
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<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgyfsz7Nx1T8VHxfmE5n38iT9xDU93znPwg-NaPxQKJ2kjc4zznIDQKZ6DK94dItYV1jMaTPXaXm1vGgAzyK6JvOV8qS0-z8NAST8dfnDMBg4TSebPS6tNeiivP22AGRQbLMjLBzVNVEWk/s1600/Screenshot-1.png" imageanchor="1" style=""><img border="0" height="100" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgyfsz7Nx1T8VHxfmE5n38iT9xDU93znPwg-NaPxQKJ2kjc4zznIDQKZ6DK94dItYV1jMaTPXaXm1vGgAzyK6JvOV8qS0-z8NAST8dfnDMBg4TSebPS6tNeiivP22AGRQbLMjLBzVNVEWk/s400/Screenshot-1.png" /></a></div>I'm sorry for some repeated colours, Google graphs made the choices.<br />
Populations are roughly distributed by language group in the graph.<br />
1) Hausa is Afro-Asiatic from the Chadic group<br />
2) Mandinka and Bambaran belong to the <a href="http://en.wikipedia.org/wiki/Mande_languages">Mande group</a> of Niger-Congo languages. <a href="http://en.wikipedia.org/wiki/Dogon_languages">Dogon languages</a> may be related early offshoots of proto-Niger-Congo.<br />
3) Brong, Yoruba and Igbo speak NC languages of the <a href="http://en.wikipedia.org/wiki/Atlantic-Congo_languages">Atlantic-Congo group</a>, the group which includes Bantu languages. Their languages are not Bantu though, and each belongs to a different subgroup distinct from the Bantoid one and from each other<br />
4) Bamoun or Bamum speak an Atlantic-Congo language of the <a href="http://en.wikipedia.org/wiki/Bantoid_languages">Bantoid subgroup</a> but their language though related is not considered part of the more narrow Bantu-proper group.<br />
5) Fang, Kongo, Luhya, Xhosa, Pedi, Nguni, Sotho, Tswana all speak Bantu-proper languages. These are a subgroup of Bantoid, itself a group within Atlantic-Congo, which is a major Niger Congo family.<br />
6) Bulala or Bilala, Masai, Alur, Hema and Kaba all speak languages of the <a href="http://en.wikipedia.org/wiki/Nilo-Saharan_languages">Nilo-Saharan family</a><br />
7) Mada seem related genetically but speak an Afro-Asiatic language of the <a href="http://en.wikipedia.org/wiki/Chadic_languages">Chadic group</a><br />
<br />
Considerations:<br />
-NCongo1, NCongo2 and NCongo3 seem to exhibit clines as expected since these are more or less spurious components dividing a continuous cline of West African-like peoples from the Sahel to South Africa. Judging by fst to neighbouring forager components, they seem to have absorbed a bit of these elements into the components (eg NCongo3 seems to have absorbed a bit of San).<br />
-There seems to be a remarkable concordance between component patterns and language families, including subgroups of such families. The model predicts such languages would expand in association with Neolithic peoples' colonization movements. Some discrepancies may be explained as later elite imposition of intrusive languages.<br />
-Dogon languages seem to be the outgroup in the Niger-Congo languages, and they are the most distant to the Bantu genetically within the Niger-Congo group. They may represent an early offshoot, perhaps isolated since, of the original Neolithic Core/Revolution. In unsupervised runs, Dogon are often the "most West-African" of all these population samples.<br />
-Nilo-Saharan-speaking populations share a common component, indicating spread of most Nilo-Saharan tongues not only by elites but more likely by another food-producing revolution. Bulala are from Chad, Masai live in Kenya. Both are pastoralist peoples.<br />
- Alur seem to have some small but significant Mbuti Pygmy ancestry. These peoples live not far from each other and both speak Nilo-Saharan languages, probably adopted by the Pygmies in the last few thousand years in contact (and marginalization) with Alur-related peoples from the North.<br />
-Similarly there are Biaka Pygmy segments in Bantus, and Biaka Pygmies today speak Bantu languages adopted from their agriculturalist Bantu neighbours.<br />
- Both Chadic-speaking groups (<a href="http://en.wikipedia.org/wiki/Hausa_people">Hausa</a> and Mada) seem to have some "Nilo-Saharan" component. Hausa's Niger-Congo-speaking neighbours mostly lack it. Hausa may be a West-African population subjected to elite language-shift towards Afro-Asiatic after intrusion from AA-speaking herders from the East.<br />
-It is possible the reverse may explain Luhya ethnogenesis, with an intrusion of Bantu agriculturalists into Nilo-Saharan pastoralist occupied land.<br />
-Fertile Crescent ancestry of Masai and Ethiopians is mostly FC(NEAfr), or most like that of Saudis, which seems to be in agreements with <a href="http://en.wikipedia.org/wiki/Ethiopian_Semitic_languages">linguistics</a>. However these populations also seem to have some Northwest African influence (FC(NWAFr), just as Egypt but unlike in Saudis (remember the pole were actually 5 Palestinians). I think it's possible that at the time of the Semitic speaking migrations from Arabia, possibly some 2000-3000 years ago, there was already an older Egypt-derived Fertile Crescent element in the region, whose languages do not survive.<br />
-Fertile Crescent elements <a href="http://dioegenesartemis.blogspot.com/2011/03/fertile-crescent-impact-in-africa-plus.html">found earlier</a> in the Fulani seem to be wholly derived from North West African populations. Fulani speak a Niger-Congo language and have much affinity to other West African populations as well, so I'd say this admixture event is more likely very ancient.<br />
-I don't know why FC(NMPC) elements appear in North African and Levantine populations here but not in my previous run. But I included very few European and Near Eastern populations in the analysis and these FC poles are very very close in comparison with the African ones, so it's possibly just due to noise and lack of definition due to few individuals with actual FC(NMPC) and WMPC. Also my last NMPC was based in the Chuvash (Lithuanians have much more affinity to Basques), but I didn't want to include Siberian poles in order to keep things simpler. This run is complicated enough as it is and small components may not represent anything much.<br />
-North African populations may have an aboriginal substrate more complicated than I thought earlier, with possibly aboriginal NorthWest African, Green-Saharan refugee African and possibly other elements in addition to the West-Asian (FC) dominant element, so small segments may be representing such hidden elements and not actual admixture here I think. I'm still convinced elements with SubSaharan African affinity mostly represent <a href="http://dioegenesartemis.blogspot.com/2011/04/not-quite-egyptians.html">aboriginal populations</a> and are not the result of the caravan slave trade. <br />
<br />
Tomorrow I'll present individual results.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com0tag:blogger.com,1999:blog-6443268110928728533.post-71335105473839191672011-05-14T15:46:00.016+01:002011-05-14T16:50:28.767+01:00Restricted Pole Run: Part IV- experiments, conjecturesDue to Blogger problems I had to delay this last post. <br />
<br />
This is a very experimental part of the run, not altering any other results. Also my interpretations here are quite speculative and I don't have very high confidence in them.<br />
<br />
I found out a while back, that when including many individuals of similar background between themselves, but very different from the remaining samples, in one run, ADMIXTURE will pull one of the restricted poles towards the group, irrespective of any relation between actual pole individuals and this different population.<br />
Thus if I had included all the South Asian data-set in my last run, one of the poles would simply become dominated by them, and would peak in the Irula. I didn't want to do that yet, since South Asia is a complex place genetically, and would only make results less clear. Still, I wanted some clues as to which Fertile Crescent elements made their way there.<br />
By including just a few individuals from the area in the run, the pole-pulling problem can be avoided, and ADMIXTURE will instead try to fit them into the non-South Asian-dominated poles.<br />
This means that some results are necessarily artificial for these samples. For instance no adequate pole for Ancestral South Indian (ASI) is present. Since ASI are somewhat "Asian" when compared to Fertile Crescent populations, I expected ASI elements to be mainly allocated to the Siberian poles.<br />
So bear in mind in this run, "Siberian" in South Asians is mostly not actual Siberian or Turkic admixture. It is simply the least inadequate pole for the ASI element. It doesn't matter anyway for this experiment since what I really wanted to check was which Fertile Crescent elements were present -that is, which patterns are present in ANI.<br />
<br />
So this part is highly experimental, but the additional individuals analysed here don't alter the remaining results appreciably (if removed, other individuals in the run still retain their admixture patterns).<br />
In addition you may have noticed I didn't include an Amerindian pole in this run. I didn't for two reasons, firstly "Amerindian"-components in Europeans tend to be absorbed by the NMPC since they exist in mostly NMPC populations (including Chuvash used as restricted pole). Siberian tends to detach because many NMPC-rich populations don't have much Siberian, but the same can't be said for the "Amerindian" I found earlier, so they tend to get mixed up (except if using a FC pole without any of it such as the <a href="http://dioegenesartemis.blogspot.com/2011/04/native-americans-native-europeans.html">Egyptians</a>).<br />
The other reason was I wanted to check which poles would ADMIXTURE allocate to Amerindians themselves, if denied an exclusive pole for them. Amerindians are quite distinctive in PCA/MDS and in unsupervised runs. They cluster far away from Western populations, further away even than Siberians.<br />
If "Amerindian"-like populations were present in Paleolithic Europe, we would expect them to be more "western" than their very "eastern" plotting position would imply -and namely more "westerly" than East Siberians.<br />
But what if Amerindians are plotting in the "far-east" because for some reason they had a few highly distinctive genetic variants, but were otherwise not so distinctive. When denied their own poles, these distinctive variants wouldn't be allowed to pull them away. ADMIXTURE would be forced to allocate the remaining more conventional variability to conventional poles.<br />
Two things might happen: <br />
1) Amerindians would be allocated 100% to some Far-Eastern Siberian pole- which would support their plotting position being derived from their assumed Far-Eastern departing position into the New World.<br />
2) Amerindians would be split into more conventional poles and their more "western" position, if abstracting from the few exotic elements, would be revealed. This would support <a href="http://en.wikipedia.org/wiki/Solutrean_theory">western routes</a> into the Americas, or perhaps a fast sprint after the end of the Ice Age, through recently ice-cleared far Northern Eurasia (mostly bypassing then more southeastern Siberian populations).<br />
<br />
I thus introduced 5 unadmixed (no significant Spanish or European elements) Totonac individuals. As expected just 5 individuals weren't enough to pull the remaining poles towards them too much- they didn't get any Amerindian pole.<br />
<br />
I actually expected Amerindians to come out as some Far-Eastern Siberian+Nganasan pole pattern. But this is what I actually got:<br />
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Siberian1 peaks in the Nganasan. Siberian2 (blue) in Yakuts and Mongolians. Siberian3 peaks in Far-East Siberians (Chukchis and Koryaks). Siberian3 is actually based on "Mongolian5", but "ran away" from them.<br />
<br />
EBengal1 is Razib Khan from Gene Expression.<br />
UKIND is British (explaining high WMPC) with some Indian.<br />
I picked also 3 random Kalash, who I'm not sure are distinctive mostly because of <a href="http://bga101.blogspot.com/2011/05/french-basques-and-sardinians-are.html">inbreeding or long term isolation</a>.<br />
Naturally for these populations part of the admixture components is artificial. There is no high "Siberian" in Indians, but it is the "least inadequate" pole to represent ASI in this run.<br />
As for the Totonac neither of the 3 poles is actually adequate since Amerindians are a highly distinctive population. I should point out that the NMPC in Totonac does not correspond to European elements, the Totonac sample is quite homogeneous, with very little such admixture.<br />
<br />
EMPC is the predominant Fertile Crescent element in India. There is no other likely reason for ADMIXTURE not to pick the most adequate FC element from all such poles it had to choose. There is some NMPC as well. The lack of WMPC+NC in these populations, which is present in the steppe pastoralists (even in the Kyrgyzstani) points IMO to distinct migrations from similar origins. The colonization of the Steppe with the development of advanced pastoralist lifestyles seems to have occurred <b>after</b> the Second, Out-of-Egypt, wave. The colonization of India, departing from the same region (Iranian plateau, Caucausus, South Mesopotamia?) seems to have happened <b>before</b> the Egyptian wave, but possibly <b>after</b> the EMPC one. The earliest Northwest Indian Neolithic settlements are dated approximately about 6000BC which is in accordance with this possibility.<br />
The representation of ASI-like segments variously by Siberian3, Siberian1 and Siberian1+ WMPC+NWAf may be related to ASI diversity among these populations. If South India was mostly settled, and even then with a high aboriginal persistence, only after the secondary EMPC wave developed (as opposed to a possible Northwestern settlement by a "primary" NMPC wave) this could point to a native incipient Neolithic, at least in South India.<br />
<br />
One conjectural model:<br />
1) An earlier less advanced expansion by a high NMPC containing population influencing only "easy" Fertile Crescent toolkit niches in the Northwest<br />
2) Later an advanced secondary Neolithic expansion containing high EMPC from a developed Near Eastern Neolithic Centre, with much improved seeds and techniques finally making some way into Southern and Eastern India, while mostly replacing the earlier wave in the Northwest? <br />
3) Maybe followed by a small reexpansion of the Northern element from the periphery (now mostly EMPC but still with more NMPC than Southerners?)<br />
I'm not sure why ADMIXTURE didn't find WMPC+NC small elements apparently typical of Central Asian populations here. But a possibility is that Central Asian demographic influence in India is overestimated in other models.<br />
<br />
About the Totonac results. Indians had an "Eastern element" (ASI) that had to be assigned to an Eastern pole (Siberian poles). South Indians seem to have a more "Southerly" ASI variant which was perhaps artificially allocated to the MPC+NWAf pole. This can be seen in PCA plots.<br />
Amerindians on the other hand are "far eastern" even relative to Siberians. There could be a number of explanations for this, but I think it's interesting ADMIXTURE chose to represent them with Siberian3+NMPC+Siberian2. These don't correspond to actual admixture events (much like <a href="http://dioegenesartemis.blogspot.com/2011/04/searching-for-native-north-africans.html">"Chinese Mexicans"</a>). They could be partly due to much "Amerindian"-like admixture in North Europeans being allocated to the NMPC pole (since I didn't include an Amerindian pole and high NMPC populations all have residual "Amerindian"-like elements)-making it slightly more "Amerindian"-like than some other poles available.<br />
<br />
This is pure speculation but it's as if ADMIXTURE, when forced to ignore some possible Amerindian exotic elements (due to having to pick exclusively from among pole populations without as much of them), is telling us that Amerindians are otherwise "more Western" than they seem to be in the PCA plots.<br />
It was already strange that "Chinese Mexicans" had a smaller "Chinese" component than a Totonac one. Greater proximity between Chinese and Europeans in PCA plots would imply that a Chinese pole would tend to overestimate the Amerindian element not the reverse. East African <a href="http://dioegenesartemis.blogspot.com/2011/04/searching-for-native-north-africans_28.html">overestimated</a> the African component in African-Americans as predicted.<br />
<br />
So summarily: Totonac obviously don't have <b>any</b> <i>real</i> NMPC. Possibly neither much of the Siberian admixture they seem to have. ADMIXTURE component patterns simply "plot" the Totonac's position relative to the poles available while excluding elements not present in any of the respective aggregated components.<br />
They have some affinity to NMPC only because they're denied their proper poles in this run. This is I think because NMPC has some slight affinity (having "absorbed" them in this run) to possible "Amerindian"-like variants in North Europeans. +Totonac being more "Western" than they seem as long as a few conjectural exotic small elements are forcefully ignored by the run set-up.<br />
<br />
Here is the <a href="https://spreadsheets.google.com/ccc?key=0AtQ1KMSaWd3kdGxfaVRuMm1hOEVzQ1MwcWE1SnBuT3c&hl=en&authkey=CNPgj6gL">participant's spreadsheet</a>. Full run <a href="https://spreadsheets.google.com/ccc?key=0AtQ1KMSaWd3kdDJPYzhRNkZYeWVyNlMwUVVXTEVpU1E&hl=en&authkey=CKeLwJAF">spreadsheet</a>.<br />
You may also be interested in checking out an interesting 3D PCA model at <a href="http://www.harappadna.org/2011/05/more-reference-3-pca-3d-plots/">Harappa</a>.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com1tag:blogger.com,1999:blog-6443268110928728533.post-26904391237521451112011-05-14T15:27:00.000+01:002011-05-14T15:27:49.898+01:00Inland Ocean. Restricted Pole Run: Part IIIThis is the third part of the restricted pole run of Western Eurasia. All results are from the same set-up and analysis. This part concerns Central Asian and Siberian populations. Central Asia is a sparsely populated Steppe expanse connecting all major Eurasian population centres: West Eurasia, East Eurasia, and South Eurasia, and these with remaining Siberian populations to the North (today mostly replaced by Russians).<br />
Like finding ancient bones is tropical areas, finding ancient population genetic fossils in Steppe populations is probably more difficult. Unlike settled agriculturalist populations, who I think present much more continuity since the Neolithic Revolutions, there have likely been major changes in the sparsely populated, pastoralist inhabited, sand and grass oceans of the Eurasian interior.<br />
For instance historically it can be presumed that such populations were more "West Eurasian" thousands of years ago than they are now, since a North or East Asian component has become important or even predominant. Still, looking at the Fertile Crescent-related components across the populations, we can perhaps get hints about early Western Neolithic influence. Component proportions preserved across all groups likely were derived from founding populations. Those exhibiting clines, maybe more likely introduced more recently.<br />
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<div><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3TrJ2makTx9M108M8FW7osh-dZ3IKzmEniOE5zb_GO064nKFFBwUy3SpMweZ5ekUTgKFwC5hkRcoL6WnuDOFI_TGxe98m2Pcuk6Bz2aOTflj9InWLrslfrrOspONirAzFQdPTO2cxN6Y/s1600/Screenshot.png" imageanchor="1" style=""><img border="0" height="111" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3TrJ2makTx9M108M8FW7osh-dZ3IKzmEniOE5zb_GO064nKFFBwUy3SpMweZ5ekUTgKFwC5hkRcoL6WnuDOFI_TGxe98m2Pcuk6Bz2aOTflj9InWLrslfrrOspONirAzFQdPTO2cxN6Y/s400/Screenshot.png" /></a></div><br />
<br />
For more extended interpretations of the components please read my previous two posts.<br />
In retrospect, I think using the "Chuvash5" as the NMPC pole may have underestimated it and overestimated a bit the "Basque5" one. Next time I may use a combination of Chuvash and Lithuanians and see what happens.<br />
<br />
Regarding the above results, some considerations:<br />
1) Uzbekistan Jews seem to have, like most Jewish populations, a predominant Levantine element. They give better contrast to patterns consistent between the other Central Asian populations.<br />
2) All Central Asian populations have large Yakut and Mongolian-like components corresponding to a likely Turkic and Mongolic element.<br />
3) All Central Asian populations also have a "Fertile-Crescent" element composed of EMPC+NMPC+2nd Wave in that order of importance. This element is quite similar to that of the Caucasus populations. These last don't have much Turkic/Mongolic. A good model explaining these patterns is that the Central Asia steppe (as opposed to the river valleys of the Ukraine and South Russia) was initially populated by a Fertile Crescent element coming from the Caucasus/Iranian plateau at a relatively later date.<br />
4) The Turkic/Mongolic component varies widely in a cline between them. Removing it, allows for a much better view of Fertile Crescent element patterns:<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEidSzb9lk_sTqmh3eRAIEp-L6CcDdWz3ut2zz0pFSZflb5S7X9TajibiNCS2r-WR41KTE0sCAD2MH6M7mspidnCfgbmxJVGE7rWrMD4ICxOXqzsR32ncAn668Qjy3NT4a-bnywbGrb1CgA/s1600/casia.png" imageanchor="1" style=""><img border="0" height="277" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEidSzb9lk_sTqmh3eRAIEp-L6CcDdWz3ut2zz0pFSZflb5S7X9TajibiNCS2r-WR41KTE0sCAD2MH6M7mspidnCfgbmxJVGE7rWrMD4ICxOXqzsR32ncAn668Qjy3NT4a-bnywbGrb1CgA/s400/casia.png" /></a></div>CAsia is a participant, mostly Kazakh in origin I believe. Hazara may have more EMPC due to admixture with Iranian plateau populations. PonticCaspian, a participant represented in the main graph above, with Moldavian Gagauz and some Ossetian ancestry presents much the same pattern except with higher WMPC (possibly due to proximity to Balkan/West Caucasus populations). Much of the same pattern can be observed in Altaians and Buryats, in a much smaller FC element.<br />
I really don't see population changes after the initial invention/introduction of advanced pastoralism producing such an homogeneous pattern (bear in mind some of these are small components, indeed all of these in the Mongolian case are small, since they're mostly an Eastern population and can be overinflated by the exclusion of major "Siberian" ancestry). Certainly not from Mongolia to the far west. These patterns I think most likely roughly correspond to the <b>original</b> <a href="http://en.wikipedia.org/wiki/Kurgan">Kurgan </a>pastoralist people, and possibly also to the ancient <a href="http://en.wikipedia.org/wiki/Tocharians">Tocharian</a> peoples.<br />
5) Northeast Europeans have much NMPC but little EMPC. This "Chuvash5" element could have come from the same region at an earlier time, before or in the beginning of the EMPC expansion/ intrusion. Some small EMPC elements in Northeast European populations may indicate that the expansion Northwards into more marginal lands of NMPC was driven by competition/conflicts with the EMPC intruders.<br />
6) Another explanation for EMPC in Northeast Europeans is a secondary expansion of Steppe peoples into the region, <b>after</b> the NMPC primary expansion.<br />
- WMPC+NMPC in Koryaks, Chukchis and other Siberians should correspond to recent Russian admixture. WMPC may be overestimated in this run, but proportions appear similar in Russians in my previous post.<br />
7) Caucasus mountain valley populations appear to have preserved various demographic "pictures" of past admixture patterns (much like Basques and Sardinians), pointing to demographic changes in the Caucasus-North Fertile Crescent region: firstly mostly NMPC agriculturalists expanding into the rivers of the Ukraine and South Russia, as seen in Lithuanians (and Chuvash); then affected by the EMPC expansion as seen in the Urkarah; later affected by the "2nd wave" (WMPC+NC) as seen in Lezgins and Stalskoe. It seems it was at this last stage that pastoralist populations emerged into the steppes, otherwise it is difficult to explain the remarkable consistency in EMPC vs NMPC proportions <b>in all pastoralist populations sampled</b>.<br />
<br />
So the current model I think most likely:<br />
-NMPC was primarily an early (pre-EMPC expansion or simultaneous to it) agriculturalist expansion into the river valleys of South Russia and the Ukraine, likely not affecting the remaining marginal steppe to a large extent.<br />
-Populations from the Caucasus and Iranian plateau were then heavily affected first by the EMPC and then to a smaller extent by the subsequent 2nd wave (WMPC+NC) secondary expansions. These had "higher drag" and didn't affect more northern NMPC populations much (possibly also due to much colder climate rendering secondary wave innovations less applicable).<br />
-At some point not long after the WMPC+Nile Core expansion (so around 3000BC or so), people from the Caucasus and/or Iranian plateau expand into the Steppe with developed pastoralist lifestyles, probably identifiable archaeologically with the Kurgan culture.<br />
-All these steppe populations are subsequently affected, in a more clinal thus more recent way, by Siberian/East Asian elements, corresponding to Turkic/Mongolic expansions.<br />
<br />
I thought this would be the last post from this run, but I've decided to leave some South Asian and other individuals I included in the run (just a few samples, results without them aren't appreciably different) for later, since otherwise it's too much for just one post. I'll present the spreadsheet and individual participants then, possibly today if I can find the time.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com0tag:blogger.com,1999:blog-6443268110928728533.post-17856967508494847672011-05-11T01:46:00.007+01:002011-05-14T15:26:50.080+01:00Old New World. Restricted pole run: Part IIThe European results of my "restricted pole" supervised run of the Fertile Crescent area follow. This is the exact same run as this <a href="http://dioegenesartemis.blogspot.com/2011/05/western-eastern-northern-southern.html">one</a>.<br />
I didn't include most individual participants results here (only regional averages and a few isolated representatives of populations not otherwise sampled) since they're too many to post with every run. I'll post the spreadsheet with Part III (Central Asia, Siberians and a few others), including all participant's results.<br />
<br />
I have a few warnings to readers not familiar with the variability of ADMIXTURE results:<br />
1) ADMIXTURE is a bit stretched figuring out patterns representing components as close as these, particularly over 30.000 or so SNPs. So small components aren't very reliable.<br />
2) This run includes lots of extra populations and extra poles to my last "Basque5" vs "Chuvash5" one, so components, though related to those and named similarly, aren't the same <b>and will differ</b>.<br />
3) In particular, the WMPC, WMPC+NC and WMPC+NWAf seem to vary at each other's expense a bit. WMPC+NC ended up being too much drawn to the Druze, and WMPC+NWAf too much to Tunisians. These samples may have multiple distant family links within them. I decided to keep these populations for the time being, but may remove them in a future run. So for some small elements in some populations, one of these components may be standing up for another one.<br />
4) Any ancestry from regions not represented in the poles will tend to be pulled towards the "least inappropriate" pole. For example if some individuals have some East Asian ancestry it may appear as a Siberian segment.<br />
5) My interpretations are obviously just conjecture, sometimes better argued than others.<br />
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<div><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3TrJ2makTx9M108M8FW7osh-dZ3IKzmEniOE5zb_GO064nKFFBwUy3SpMweZ5ekUTgKFwC5hkRcoL6WnuDOFI_TGxe98m2Pcuk6Bz2aOTflj9InWLrslfrrOspONirAzFQdPTO2cxN6Y/s1600/Screenshot.png" imageanchor="1" style=""><img border="0" height="111" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3TrJ2makTx9M108M8FW7osh-dZ3IKzmEniOE5zb_GO064nKFFBwUy3SpMweZ5ekUTgKFwC5hkRcoL6WnuDOFI_TGxe98m2Pcuk6Bz2aOTflj9InWLrslfrrOspONirAzFQdPTO2cxN6Y/s400/Screenshot.png" /></a></div><br />
You can read more extended interpretations of components in my previous post.<br />
Summarily:<br />
-WMPC: "West Mesopotamian Core", referred to before as "Western Wave". First wheat planting Neolithic colonization of the Mediterranean and Western Europe. I think they came from the Levant and Anatolia. I think it may correspond to Megalithic and Danubian archaeological horizons. In colder climes, this wave probably only occupied wheat-congenial regions, leaving less adequate ones to foragers. They're best represented today in Basques, Sardinians, and also at a lower lever in Western Europeans in general. Possibly with high R1b (and I?) Y-haplogroups<br />
-NMPC: referred to before as the "eastern wave". Cold, poor-soil-adapted first Neolithic wave, maybe due to innovations such as winter-rye. Expanded North into the Steppe rivers from a homeland possibly in the Eastern Iranian Plateau, Caucasus range or Northern Mesopotamia. Later, after adaptation, it would have spread throughout cold and sandy soils in all of Europe, especially in the North, bypassing rich agricultural areas already inhabited at high densities by WMPC people. Possibly with high R1a Y-haplogroup levels. mit-haplogroups introduced by this wave into WMPC areas might explain why there's a "mit-DNA gap" between Danubian remains and modern Central Europeans. I would tend to identify the beginnings of NMPC expansion into Central and Western Europe with the Corded Ware culture. This may have been also the "melting pot" from where East Slavs began their long expansion towards the Pacific.<br />
-WMPC+NC: synthesis of WMPC early intruders into Egypt and local Nile Core elements. Referred before as "Second Wave".<br />
-WMPC+NWAfr: synthesis of Green-Sahara derived native North West Africans and WMPC. I think the expansion of this element into Iberia and beyond may have happen very early on (much earlier than the second wave in the East), at the time of initial WMPC colonization of the region via the Northern Mediterranean route.<br />
-EMPC: East Mesopotamian Core. Patterns of NMPC and WMPC suggest to me this is a local, more eastern element that underwent expansion into the NMPC and WMPC homelands in ancient times, before the second wave from Egypt. I think a model of Neolithic developments generating higher surpluses and elites/specialists generally should coincide with a demographic expansion from the same region. That is any ancient people developing agricultural productivity high enough to enable them to live at much higher densities, and thus partially swamp out neighbouring related already agricultural peoples, must have produced enough food surpluses to allow relatively much larger elites/specialists and better social organization. Such secondary wave origin points should thus be identifiable archaeologically. The "Second Wave" I have identified with <a href="http://en.wikipedia.org/wiki/Ancient_egypt">Egyptian Civilization</a> (which begins at around 6000-5000 years ago, at the same time according to some studies as the early proto-Semitic expansion). Based also on ADMIXTURE patterns, I would tentatively relate the EMPC expansion with a <a href="http://en.wikipedia.org/wiki/Sumer">Southern Mesopotamian</a> homeland.<br />
-All these components, except for the Siberian ones, derive I think from the ancient Near East. The Siberian ones correspond to perhaps ancient traces of European hunter-gatherers. I didn't include an Amerindian pole this time, since with multiple MPC components they tend to be identified and subsumed into the NMPC I think (since NMPC and forager residual segments tend to exist in the same populations-possibly due to NMPC late occupation of much of the colder, less fertile soil niche). More on that later.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com0tag:blogger.com,1999:blog-6443268110928728533.post-88020958071809067772011-05-09T18:10:00.012+01:002011-05-10T13:45:40.894+01:00Western, Eastern, Northern, Southern: Motherland?In this post I'll tackle the last unsupervised component: the West Asian-modal component, which peaks in Georgians and exists in high amounts in all West Asians. This component appears much throughout Europe, and strangely, in unsupervised runs it is a bit closer by Fst distances to the Lithuanian-modal component than it is to the Sardinian or Basque-modal ones. What is going on here?<br />
<br />
To recapitulate my previous results/interpretations:<br />
1. Basque and Sardinian-modal. In MDS and PCA plots, Sardinians and Basques plot not far from each other, but in distinct clusters out of the European "mainstream". Sardinians further towards modern Near Eastern populations, Basques more towards modern North European populations. In supervised admixture runs, both populations seem to be dominated by the same element, with Sardinians having a smaller element with North African/Near Eastern affinities, and Basques mostly without this element but with another element predominant in Northeastern Europe. I interpreted these results as indicating "2nd wave" influence on Sardinians, and "Eastern Wave" influence on Basques, exclusively superimposed on a common "Western Wave" element. This element, also found in large percentages in Southern, Northwestern and Central Europeans, but lacking in Northeastern ones, would correspond to the first Wheat-planting Neolithic expansion into Europe. Less fertile/colder areas not congenial to Wheat would have been moslty left to remaining forager populations providing meat and fish in exchange for wheat. Indeed such an arrangement is documented in several places in the World, and is still found in some Southeast Asian regions, where demographically dominant agriculturalists in more fertile/rice adapted soils exchange agricultural products with protein from foragers in marginal lands.<br />
2. Lithuanian-modal, also present mixed with Siberian elements in the Chuvash, seems to be prevalent in cold/poorer soil areas of Europe. I think it may correspond to an Eastern Neolithic Wave from the Northern Near East through the Caucasus and Steppe into Eastern Europe. After adoption of cold-adapted agricultural techs, such as winter-rye, it expanded into the vast niches left mostly unoccupied by the earlier Western Mediterranean-Atlantic and Danubian waves. It replaced the forager populations still present in those marginal lands. An analogy is to the settlement of Japan by the <a href="http://en.wikipedia.org/wiki/Yayoi_people">Yayoi people</a>. Only after developing cold-adapted rice varieties and techniques were they able to perhaps migrate and completely replace the Ainu-like foragers in rich coastal foraging environments less suited to earlier Neolithic lifestyles.<br />
3. Mozabite/Tunisian and Bedouin/Saudi/Egyptian components are mostly about peaks of NW African and NE African ("NileCore") components. The Green Sahara may have had semi or full pastoralist developments explaining the presence of such components, admixed with "Mesopotamian Core" ones in such a high degree in some nomadic populations.<br />
4. "Siberian" and "Amerindian"-like small elements in Finns, Russians, Scandinavians, Balts and Irish, British are I think not derived from any undocumented migration of ancient Siberian peoples but genetic traces of Native European populations. I've tentatively interpreted "Amerindian"-like segments in North Europeans and people from the Caucasus Mountains (which <a href="http://dioegenesartemis.blogspot.com/2011/04/unsupervised-northern-eurasianew_19.html">also appear</a> in <a href="http://dioegenesartemis.blogspot.com/2011/04/unsupervised-northern-eurasianew_20.html">unsupervised runs</a>) as survivals of an old "Amerindian"-like aboriginal population, making it's <a href="http://en.wikipedia.org/wiki/Solutrean_theory">way to the Americas</a> through the Ice Age ice cap with a lifestyle similar to that of Inuit/Eskimos today.<br />
<br />
So the last component still eluding explanation is the "West Asian" one. Why is this closer to North European than to any other unsupervised mode component?<br />
I've stated before, I think this component is a Mesopotamian Inner Core element, very similar to the European Western and Eastern Wave ones. Indeed these last may be "frontier" elements with less diversity, subsets of the Inner Core one. This would explain why Near Easterner and Southeast European populations tend to have large balanced "Basque5" and "Chuvash5" elements in previous runs. So the Inner Core element may be the "Mother" of these less diverse frontier elements that expanded into Europe. Later, the Inner Core populations, perhaps in Mesopotamia, would achieve more evolved Neolithic capabilities and expand into the Western and Eastern Wave settled regions.<br />
<br />
So "West Asian" peaks in Northern Near East populations, such as Armenians, Iranians, Georgians, however using these populations as the pole is problematic since these same populations have signatures of "Nile Core" influence. It however also appear in high levels in Northern Caucasus populations such as Lezgins, Adyghei, and in the samples from the Mountain Dagestan towns of Urkarah and Stalskoe.<br />
Using my "restricted pole" supervised run trick, I used first Georgians as the pole. As expected this erased much "2nd Wave" influence from European populations, since the "Georgian5" pole attracted many such segments together with the North African one. Using "Urkarah5" I got higher percentages in Northern Europe than seemed reasonable and since in previous unsupervised runs, Lezgins, Urkarah and Stalskoe seem to have some "Northern European" in addition to predominant "West Asian" I thought it would be best to combine some Georgian, Iranian and Urkarah individuals to allow the pole better to "focus" on the element I was searching for.<br />
Naturally this is discussible, but results using any of the poles are not very different.<br />
I also decided to ditch Mozabites and Egyptians and replace them by Tunisians and Palestinians as NW African and NE African (Nile Core) poles respectively. Mozabites and Egyptians are more southern populations and any influence from North Africa in European populations is already represented in Tunisians and Palestinians. I excluded all other North African populations in order not to complicate things further, except for predominantly agricultural Northern Moroccans, which I wanted to use to pull the "Tunisian5" pole into the region (in order to find influences in South Western Europe).<br />
<br />
I'm dividing this run into three parts: Near East; Europe; and Siberia+Central Asia. They are all part of the same run. First I'll present results for the Near East. I included some populations in Near East and European posts to link them, since it's all from the same analysis.<br />
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<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj2RxupxZlqnXHkSMwJ1c40GITfkVvzls68wTvm-feCGlPAdkD9YGXULuTM2UfkfrSS9rKIvtLJqu4ZKBM_UVCk4OmM0HtYdnouAU0zsm-8xefYJOG-xT9PWhyphenhyphenIMpREp49LNVvzllLk1J4/s1600/Screenshot.png" imageanchor="1" style=""><img border="0" height="111" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj2RxupxZlqnXHkSMwJ1c40GITfkVvzls68wTvm-feCGlPAdkD9YGXULuTM2UfkfrSS9rKIvtLJqu4ZKBM_UVCk4OmM0HtYdnouAU0zsm-8xefYJOG-xT9PWhyphenhyphenIMpREp49LNVvzllLk1J4/s400/Screenshot.png" /></a></div><br />
Poles used:<br />
1. Siberian1: 5 random Yakut individuals "Yakut5" restricted pole. This captured most of the Siberian Turkic and Mongolic elements. It peaks in Buryats, with Yakuts and Mongols not far behind.<br />
2. WMPC: "Basque5". This pole captured an element which peaks in Basques and Sardinians, but is also present in Southern and Northwestern Europe in important amounts. Somewhat surprisingly, it is also important in the Levant (unlike the other element present in Northwest Europe, "Chuvash5"). This is the Neolithic first Western Wave, perhaps associated with a Mediterranean-Atlantic migration route and its Megalithic monuments, depending on river-valley wheat agriculture. It also presumably represents here the probably very closely related Danubian wave.<br />
3. NMPC: "Chuvash5". I renamed it Northern MPC since it seems to be Northern relative to the Fertile Crescent area. It peaks in Europe in the North East, and I've called it "Eastern Wave" before. Maybe a cold and poor soil-adapted Neolithic Wave, and rye agriculture (also perhaps occupying much of the "wheat niche" in some parts of Eastern Europe).<br />
4. WMPC+NC. West MPC with some Nile Core, also referred before as "2nd Wave", or out-of-Egypt. Perhaps associated with proto-Semitic (and Exodus tales). A late expansion from <a href="http://rspb.royalsocietypublishing.org/content/276/1668/2703.abstract">perhaps 6000-5000 years ago</a>. It was based on "Palestinian5" however it came to be dominated by the Druze, perhaps due to multiple family connections in this somewhat isolated population. It doesn't matter though, since the Druze are still adequate representatives even as a modal population. The Palestinians, Jordanians and others had their higher Nile Core component taken over by the Tunisian pole. I could remove the Druze, but things wouldn't change much and I prefer to keep all populations at this point. French Basques also seemed "inbred" before, but I'm now convinced their "isolated population pole-pulling" tendency is mostly due to their unique Neolithic wave mix.<br />
The second wave element is closer to the "Basque5" element than to any other MPC element. I think the native element of the Levant may be closely related to the "Basque5" element, and this would be the subset expanding into less advanced incipiently Neolithic, Nile Core dominated Egypt, synthesize with it, and reexpand into its homeland and beyond as the "2nd Wave". This would be a more advanced Wheat-planting expansion, and the probably much larger food surpluses making it possible also allowed higher organization levels, specialization, and elite forming in Egypt itself- a process leading to ancient Egyptian Civilization.<br />
I seem to recall a R1b Y-haplogroup found in ancient Egyptian remains-perhaps it was native after all since ancient Egyptians might have been a synthesis of WMPC and NC? <br />
5. EMPC: based on two Urkarah individuals+1 Iranian+2 Georgians. If based on "Urkarah5" or "Gorgian5" it has a greater tendency to draw too many non-pole individuals of said population and any 2nd Wave or NMPC elements also present there. By combining the restricted pole, this problem can be reduced. I think EMPC is an inner-core MPC element perhaps present in Mesopotamia itself. It seems to have expanded against the WMPC and NMPC within the Near East after these lasts' expansion outside of it, but likely well before the second wave. Also seems to be the subset corresponding to Ancestral North Indians.<br />
6. WMPC+NWAf: based on "Tunisia5". This component likely consists of mostly WMPCA+some Green Saharan derived NWAfrican I found before. Tunisians were drawn at almost 100% into the pole, unlike Northern Moroccans, probably due to multiple distant family relations within the Tunisian sample. Still matters little, since it is representative of Western North Africans. Since I believe Tunisians are still representative of ancient Berber-speaking Neolithic populations I removed Mozabites. Using Tunisians may allow more sensitivity, since Mozabites are more distant.<br />
7. Siberian1. "Nganasan5" using only unadmixed Nganasan. Representing a Western Siberian element.<br />
8. Siberian3. "Mongolian5". Strangely this pole didn't pick up much in other Mongolians, but instead focused on Chukchis and Koryaks from the Far East. Mongolians turned out mostly "Siberian2". This happened presumably due to closeness of "Yakut5" and "Mongolian5" (just as before I used "Dogon5" to capture NWAfrican with the help of another West African pole). This happens frequently in "restricted pole" supervised runs, for instance in Northern Europe runs even a "Orcadian5" versus "Hungarian5" pole analysis reproduces imperfectly the "Basque5" vs "Chuvash5" scenario, since "Orcadian5" and "Hungarian5" shift away from their individuals' populations and peak in Basques/Sardinians and Lithuanians/Chuvash instead. So restricted pole runs in my opinion tend to shift towards real patterns in the data.<br />
<br />
This is still an imperfect run, don't read too much from smaller components. Still results are similar using various different set-ups (and not too different from unsupervised ones).<br />
<br />
Some speculative considerations:<br />
-WMPC is present in the Levant and North Africa, whereas NMPC is not. It is also dominant over it in Turks, Armenians, different Jewish groups. This suggests that WMPC ("Basque5") has its ultimate origin here, in the Levant and Anatolia. It seems to have expanded not only into the Mediterranean and Balkans, but also into North Africa. I think the 2nd Wave likely is just WMPC admixed with some North Eastern African ("Nile Core").<br />
-NMPC is dominant over WMPC in Iranians, Kurds, North Caucasus and Eastern Caucasus. I tend to think it derives from an ancient population living in the Northern Mesopotamian/Caucasus range/Western Iranian plateau region.<br />
-EMPC may correspond from an expansion into both the WMPC homeland (Levant/Anatolia) and NMPC homeland (Northern Mesopotamia?/Eastern Anatolia?/Western Iran?) from an inner area, perhaps Southern Mesopotamia.<br />
<br />
I'll present European results later.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com0tag:blogger.com,1999:blog-6443268110928728533.post-86922784608855647752011-05-05T00:59:00.010+01:002011-05-05T02:07:31.153+01:00Individual Results for "Basque5"I've decided to post the "Basque5" individual data after all. I think it's a good departing point and it helps to understand why "Chuvash5" (I'm interpreting it as the cold adapted "Rye"-farmer wave component) or "Basque5" (the warmer river valley dweller, earlier "Wheat"-farmer wave) percentages in one individual may vary quite a bit between runs. ADMIXTURE can give quite different results under different set-ups. This is not a reason for ignoring them, but in my opinion another source of very valuable information. If you keep in mind the framework, some result variability is sometimes enlightening.<br />
"Mesopotamian Core" elements in particular tend to grow and decrease a bit at each other's expense in different runs. This happens due to their great similarity, sharing a common source (possibly in ancient Anatolia).<br />
I want to reiterate that this is a first experimental run, and smaller percentages in an individual have high likelihood of being just noise, and even small percentages in populations are merely indicative.<br />
Also forager elements may be eaten up by other components, or may be representing more exotic admixture in some cases as well (South Asian, East Asian may appear as "Siberian in a few cases).<br />
In addition, I included participants with only European/ME ancestry, but 2nd wave may be eating up any very small non Nile Core African elements in some New World, and perhaps other, individuals, for instance.<br />
Particularly in the "Sardinian5" run, the "Chuvash5" element was I think overestimated in several populations, due to a little deviation of this component towards the what I've been calling the "2nd Wave" element, which Sardinians have in significant amounts. <br />
So this is a very imperfect run. It is self-admittedly very chunky and will be improved in the future. Please don't assume for now any 1-2% of anything is actually something.<br />
<br />
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<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgy2xOzjs-f46zfc9z5ilp9Vu0JWa7PAnZ6Jap4G0QeGKwbjUip46YH-phsh_Y4ICYGcwdz8SYyN8hVsweisiKpuxgQqtpVhbSTko5gL3TYJ3zv-7jj4aXBbOBTP5wWyUav7pvkuT68yQw/s1600/NECHUBA1.png" imageanchor="1" style=""><img border="0" height="394" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgy2xOzjs-f46zfc9z5ilp9Vu0JWa7PAnZ6Jap4G0QeGKwbjUip46YH-phsh_Y4ICYGcwdz8SYyN8hVsweisiKpuxgQqtpVhbSTko5gL3TYJ3zv-7jj4aXBbOBTP5wWyUav7pvkuT68yQw/s400/NECHUBA1.png" /></a></div>AJ2 is Dan Vorhaus from Genomes Unzipped.<br />
Some considerations:<br />
SWFrance is from Gascony and shows large "Basque5" as expected.<br />
Germany1 has much Rhineland ancestry, and also has much "Basque5".<br />
Southern Germany, Switzerland, Slovenia and Hungary appear to have more significative "2nd Wave" than more northern populations, which I assume would be present in neighbouring populations as well. <a href="http://en.wikipedia.org/wiki/Raetic_language">Raetic</a>, a relative of Etruscan, was spoken in the region in pre-Roman times.<br />
PonticCaspian has mostly southern steppe and whereabouts origins. He has very high levels of "Chuvash5" relative to "Basque5".<br />
Some Americans have Southern European ancestry.<br />
Balanced "Chuvash5"+"Basque5" elements in Southeasterner populations closer to the Fertile Crescent may correspond to an "Inner-Core" component including diversity present in both "outer-core" components and thus not the product of West Wave/East Wave admixture.<br />
<br />
I'll post more, better results in the near future.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com0tag:blogger.com,1999:blog-6443268110928728533.post-90738853276900075352011-05-03T23:47:00.013+01:002011-05-04T01:08:56.141+01:00Irula and Basques, Sardinians, Lithuanians?I have stated before that I think unsupervised results of European populations are based on modal populations that are admixed themselves.<br />
<br />
Just as the "Irula" component tends to pick up most of South Asian diversity in an artificial manner contradicting<br />
some recent research (<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842210/">Reich et al</a> -see also <a href="http://dodecad.blogspot.com/2011/03/ancestral-north-indian-ancestral-south.html">Dienekes</a>); and different supervised methods seem to confirm it, so I believe the same can be done to European populations.<br />
<br />
The Irula are modal for the South Asian component for a simple reason. All Indian populations are a mix of Fertile Crescent incomers (Ancestral North Indian-ANI) and older established populations (Ancestral South Indian-ASI). Yet even though we have extant relatively unadmixed Fertile Crescent populations (ANI), we do not have any extant ASI populations. So Irula, in whom ASI peaks among public genotyped populations appear as if almost 100% "South Asian", even though they are really roughly 1/2 ANI- 1/2 ASI. Most Indian populations tend to be dominated by this element as well, the remaining part being more conventional Fertile Crescent components. So the "South Asian" component is really ASI+ANI and doesn't correspond to either of them in any "unadmixed" form.<br />
<br />
Zack has done <a href="http://www.harappadna.org/?s=reich">interesting work</a> using the Onge of the Andamans as a proxy for them, and I have run <a href="http://dioegenesartemis.blogspot.com/2011/03/third-eurasian-neolithic-revolution.html">a simple analysis</a> using Papuans. Neither really correspond to the actual ASI.<br />
<br />
In Europe and nearby regions thus we similarly get Lithuanian-modal, Sardinian-modal, Basque-modal, and West-Asian-modal components. Mozabite modal and Southwest Asian-modal populations I've <a href="http://dioegenesartemis.blogspot.com/2011/04/not-quite-egyptians.html">previously analysed</a> in a way that suggests they derive from peaks in Mozabites and Bedouin of "NW African" and "Nile Core" respectively.<br />
<br />
So I'll be trying to do the same to European populations in the next few days, and reveal unsupervised results for what they probably mostly are: clines, in which ADMIXTURE picks the peak population as the modal one. Naturally revealing intra-"Mesopotamian Core" clines is much harder and inexact than clines between less closely related populations.<br />
<br />
Here are the first runs. I've used my trick of using "restricted" poles in order to get more accurate estimates, but these are experimental runs, and the thing to note is what remains similar in either. I plan to develop better ways to fish out these components soon, so don't take these first results too literally. I've used European populations, excluding most Middle Easterners since I think "inner-Core" Mesopotamian subsets different from the "frontier" ones may be hidding there and don't want to make the run more complex than it already is. For the same reason I excluded Cypriots. I did include a handful of participant samples from the ME and Southeast Europe: being few, they won't "demand" their own component and confuse results, yet can give me some clues as to how to proceed when expanding the set. <br />
<br />
Firstly "Basque5" versus "Chuvash5" versus 5 Egyptians+ 5 Mozabites. Bear in mind having an element doesn't mean ancestry from one of these modern groups, only that portions of DNA tend to cluster together with these available poles.<br />
Admixture proportions for Chuvash and Basque obviously exclude the 5 pole individuals in each.<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgy2xOzjs-f46zfc9z5ilp9Vu0JWa7PAnZ6Jap4G0QeGKwbjUip46YH-phsh_Y4ICYGcwdz8SYyN8hVsweisiKpuxgQqtpVhbSTko5gL3TYJ3zv-7jj4aXBbOBTP5wWyUav7pvkuT68yQw/s1600/NECHUBA1.png" imageanchor="1" style=""><img border="0" height="394" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgy2xOzjs-f46zfc9z5ilp9Vu0JWa7PAnZ6Jap4G0QeGKwbjUip46YH-phsh_Y4ICYGcwdz8SYyN8hVsweisiKpuxgQqtpVhbSTko5gL3TYJ3zv-7jj4aXBbOBTP5wWyUav7pvkuT68yQw/s400/NECHUBA1.png" /></a></div>FST genetic distance estimates by ADMIXTURE<br />
"Basque5" to "Chuvash5" 0.035<br />
"2nd Wave" to "Basque5": 0.048<br />
"2nd Wave to "Chuvash5": 0.040<br />
Siberian to "Basque5": 0.133<br />
Siberian to "Chuvash5": 0.104<br />
Siberian to 2nd Wave: 0.120<br />
Amerindian to "Basque5" 0.231<br />
Amerindian to "Chuvash5" 0.194<br />
Amerindian to 2nd Wave: 0.216<br />
Amerindian to Siberian: 0.164<br />
<br />
As fst shows, "2nd wave" is much more of a "Mesopotamian Core" element than a Northeast African element here. It contains a measure of the Nile Core-admixture found in Europeans though. Since the Egyptian expansion itself I think had more Mesopotamian than Nile Core, this is not surprising. The smaller presumably forager components are merely indicative since this run is too rough and they might be partially subsumed or be subsumed by bits of other elements.<br />
<br />
Now with "Basque5" substituted for "Sardinian5", remaining poles being the same. Sardinian population averages presented exclude the 5 Sardinian samples used as pole.<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgAsDa1egG4xbFb8rjsB4U5AQHYwwcV-o_BlBmmsA8ThMSasR2kKDtcO7RFIHqvXkymhyphenhyphen5Ih2DyNLFJRUTVMEGRWQHSZrffJTg-6blzaGD42LGrFdERRHehNYF9Po3yZNrqy_l_2xX4M-I/s1600/NECHUBA2.png" imageanchor="1" style=""><img border="0" height="396" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgAsDa1egG4xbFb8rjsB4U5AQHYwwcV-o_BlBmmsA8ThMSasR2kKDtcO7RFIHqvXkymhyphenhyphen5Ih2DyNLFJRUTVMEGRWQHSZrffJTg-6blzaGD42LGrFdERRHehNYF9Po3yZNrqy_l_2xX4M-I/s400/NECHUBA2.png" /></a></div>FST<br />
"Sardinian5" to "Chuvash5" 0.035<br />
"2nd Wave" to "Sardinian5": 0.049<br />
"2nd Wave to "Chuvash5": 0.045<br />
Siberian to "Sardinian5": 0.128<br />
Siberian to "Chuvash5": 0.111<br />
Siberian to 2nd Wave: 0.122<br />
Amerindian to "Sardinian5" 0.225<br />
Amerindian to "Chuvash5" 0.203<br />
Amerindian to 2nd Wave: 0.218<br />
Amerindian to Siberian: 0.163<br />
Notice that the largest distances are not similar so the smaller ones can't be exactly compared between different runs. I think "2nd wave" is slightly more concentrated in this last run, but still mostly Mesopotamian.<br />
<br />
Balanced "Chuvash5" + "Basque5" in more "inner-core" influenced populations such as Assyrians and South Italians simply means that their "Mesopotamian" is simply the more diverse parent of both "outer-core" "Basque5" and "Chuvash5", who are perhaps West-Anatolian and NorthEast Anatolian particular subsets of it. I now see some evidence for a secondary "inner-core" expansion before the second wave. More on that later.<br />
I think these results are a bit inexact, but general components seem to hold in runs with other quite different European poles (tomorrow I may present some of these). They also appear in a very confused and mixed way in unsupervised results. So they very likely represent something real. Yet these are obviously preliminary results. I'm not sure if Lithuanians are so much Eastern Wave-derived as these particular results seem to imply, although I now think my early estimate of "Basque Admixture" using the full-set supervised Basque and Chuvash poles <a href="http://dioegenesartemis.blogspot.com/2011/03/estimating-basque-admixture-in-balts.html">overstimated</a> the "Basque" or Western Wave element there (Basques seem to have quite a bit of the Eastern element themselves!). Still <a href="http://dioegenesartemis.blogspot.com/2011/04/searching-for-native-north-africans_28.html">"restricted poles"</a> seem to estimate actual components better.<br />
<br />
So firstly it is interesting that Sardinians <b>do not</b> have the Eastern Wave element in either run. This is as expected, if "Chuvash5" came from the Northeast (perhaps more remotely from the Steppe, Caucasus and originally Northeastern Anatolia in that order).<br />
Sardinians do have, however a large Second Wave element mostly <b>absent</b> in Basques. And Basques, even in the "Basque5" run, seem to have <b>quite a bit</b> of this "Chuvash5" component.<br />
<br />
Northern Europeans seem to have more "Chuvash5" than the Basque, particularly towards the East; and some small Second Wave element in some regions.<br />
<br />
This seems an adequate explanation for unsupervised ADMIXTURE runs' results. Sardinians are modal for their "Sardinian" component since they lack the "Chuvash5" and Basques because they lack "Second Wave" yet have much more West Wave than most. Lithuanians are modal also for their component since they have both little Second Wave and "Basque5". And West Asians like the Assyrian Christians appear to have some "Chuvash5" (more on this latter) but much more Second Wave. All other European peoples are intermediate between these 4 "extreme" extant populations. Thus they can be adequately reconstructed by unsupervised ADMIXTURE using components modal to the Basques, Sardinians, Lithuanians and West Asians. Unsupervised ADMIXTURE has no way to know if actual Sardinians, Basques, Lithuanians, West Asians actually settled Europe. It assumes it was so since it was meant, I think, to determine admixture proportions for populations whose parent populations still exist (like Mexicans and African-Americans).<br />
<br />
Faced with such a scenario in which unadmixed parent populations are mostly not there anymore, it picks the most extreme populations and uses these admixed populations as if they were the parent ones, generating historically illogical results.<br />
<br />
Looking back to the results. Why do Basques have this Eastern element at the 10-20% range? Why did it spread to Spain if it arrived AFTER the "Basque" or western element (archaeology strongly supports a model of agricultural spread from the South towards the Northeast)? And why do Middle Easterners and Southeast Europeans have both even though they're likely source? A few points:<br />
<br />
From it's smallish presence in Basques, I think it's clear this is an later intrusive element to an already agricultural population. I don't think these farmers were the carriers of Indo-European languages. Maybe they spoke distantly related languages. One argument concerns Y-haplogroups. R1a is prevalent, R1b mostly absent, in populations with very high "Chuvash5" in the run. R1b is dominant in Basques, but also common in Sardinians, but R1a absent. Languages spread with elites, but these people weren't passing much of their Y-Chromossomes to their children, at least West of Central Europe, and yet West Europeans appear to have plenty of their genes. Some discrepancies between mit-DNA Danubian Neolithic remains' and modern Europeans suggests to me that they perhaps did contribute plenty of mit-DNA together with autossomes. Language imposing elites behave in exactly the opposite way, with high Y, low mit transmission.<br />
<br />
"Chuvash5" people likely had high levels of R1a, "Basque5" people high levels of R1b. R1b is well characterized as originating from Western Anatolia and is present in high levels in Southern Europe. Another argument as to why it must have arrived first, is that Sardinians are 20-30% R1b and have no "Chuvash5" (yet plenty of "Basque5"). So "Chuvash5" likely entered the "Basque5" dominated Basque country, Spain, France, Ireland, the British Isles and the Central European river valleys, and had major impact in autossomes and probably also in mitochondrial haplogroups yet very little Y-chromossome haplogroup impact.<br />
<br />
How can this pattern be explained? I have been thinking about a speculative model and now it's taking shape.<br />
Northwestern Europeans (France and British isles in this context) have generally >60% R1b, but in these runs ~50% "Chuvash5". If "Chuvash5" were intruders specializing in cold environment, poor soil, agriculture (with <a href="http://en.wikipedia.org/wiki/Rye">Rye</a> and other innovations/developments), they would find the most fertile soils in the region already inhabited by the "Basque5" people and their wheat agriculture. So in a simple scenario, villages would form in a checkered-board pattern. "Basque5" villages would be already established near rivers and the best soils at very high densities, and thus impossible to remove or substitute. However there may have been plenty of other areas to which primitive wheat agriculture was not congenial, and these would still be inhabited by foragers at much lower densities. Most of these areas would however allow for productive rye agriculture, at much higher densities than foraging. "Chuvash5" migrants could very well have used such niches. They would not be able to settle in the "Basque5" areas, but they would have major advantages versus foragers in their mountain, inter-fluvial and sandy soil regions. So "Chuvash5" villages would maybe become established not far from "Basque5" villages downhill. "Chuvash5" is really about a Mesopotamian subset-derived, cold-adapted Neolithic wave I believe.<br />
<br />
In such a scenario, good years would lead to large surpluses in "Basque5" villages, but smaller ones in "Chuvash5 ones. Densities in the former's areas would be quite higher than in the last's too. Lowland elites would form much more easily in "Basque5" villages, but "Chuvash5" ones would remain more egalitarian.<br />
<br />
In good years, high levels of surplus would allow men in "Basque5" villages to find other occupations, war, trade for less basic resources for instance. With time social structure would make such arrangements permanent at the expense of peasants. Militarized and commercial elites from rich "Basque5" villages would come to dominate less wealthy "Chuvash5" ones. The result over thousands of years and multiple elite forays from the wheat agriculturally rich areas into rye less productive ones would be exactly what you see: elite Y-DNA spreading while autossomes and mit-DNA remain balanced.<br />
<br />
In even colder areas such as Scandinavia and Northeastern Europe, colonization by R1a agriculturalists had much greater advantages. Fewer wheat-adequate environments exist there, vast Rye-congenial ones predominate, and Y-DNA would be more balanced or even the reverse.<br />
<br />
So "Chuvash5" is I think really about a new subset of Fertile Crescenters, one adapted to marginal lands and cold-environment agriculture during their passage and evolution in the steppe. The spread of some more admixed people from the <a href="http://en.wikipedia.org/wiki/Corded_ware">Corded Ware region</a> and their explosion into the Eastern expanses of Eurasia suggests to me the final "critical point" may have been reached in this region and time. <br />
<br />
Later on, perhaps related pastoralists came again out of the Steppe, not as farmers, but as horse-mounted warriors and conquerors. These maybe were the source of some small Y-DNA contribution. But without major food producing improvements, I very much doubt they had a significative autossomal contribution. They may have had a major linguistic impact, as such horse-mounted militarized elites often have. Or maybe such tongues are a different story entirely.<br />
<br />
Tomorrow I'll run a better version of the runs posted above, and will post individual participants results. I decided not to post spreadsheets for this one since people would be reading too much into individual results. Tomorrow's run will be very similar but more solid and valid I think.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com1tag:blogger.com,1999:blog-6443268110928728533.post-28143990662237792442011-05-02T23:12:00.007+01:002011-05-03T11:15:13.035+01:00Hammering the ironTrying to extend my last analysis Northwards I was faced with a few difficulties.<br />
Finding 2nd ("African"-like) wave elements; or Aboriginal ("East Asian"-like -or perhaps Amerindian-like) in Europeans is easy, since contributor populations were quite different.<br />
The problem lies, I think, with different subsets and possibly pre-2nd wave expansions, within what I've been calling the Mesopotamian Core. This is much harder to detect and differentiate reliably, since I don't have many if any still "unadmixed" populations from that time.<br />
So I'll kind of have to find the unknown "metals" through comparisons of how differently mixed "alloys" relate to each other.<br />
<br />
In supervised ADMIXTURE terms this means I generally get series of tightly related components coming from the Mesopotamian region but probably also from Eastern Anatolia and the Levant. ADMIXTURE seems to be picking a series of distinct but very close clusters in the MPC. When considering only North Africans, Basque poles stretched to become the local variety of MPC. <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. Thus in many runs "Basque" becomes dominant in Europeans, erasing most of Siberian, "Sandawe" expands to the point of having Mesopotamian Core-like fsts incompatible with North East African origins, and ends up including most Middle Easterner diversity. South Europeans end a mix of mostly "Basque" with some "Sandawe5". The "Sandawe5" in a few cases swaps places with the "Dogon5" pole everything else similar, proving IMO that these components are real and not directly related (although perhaps somewhat distantly akin) to actual Dogon or Sandawe. And the whole thing is often very "chunky".<br />
Unsupervised ADMIXTURE on the other hand always picks out supposedly but in my opinion not generally "unadmixed" group of individuals (see Irula in the "Indian cline"). It kind of makes it's own poles up. If original populations are not present in the data, results are not reliable (in terms of actual progenitor populations, they're reliable for relationships if properly interpreted).<br />
<br />
Neolithic Revolutions are quite uncompromising after a "critical point" in their maturation. Before they reach this point however, they consist of distinct if related populations or subsets competing with each other, and perhaps mixing and differentiating constantly via short breath regional expansions.<br />
<br />
The MPC seems to be composed of such a group of subsets. Here are some I think may be hidding in the data:<br />
1) A "Basque centred" Med-Atlantic Wave subset important from Italy to the British Isles and beyond, but also present in Central Europe. Probably from Western Anatolia via a maritime coastal village-to-village route. Very similar to another Western Anatolian wave via the river valleys of central Europe.<br />
2) A "Chuvash centred" East wave subset predominant in the Northeast but present in much of Europe. Probably from the Caucasus and Northeast Anatolia via the Steppe river valleys. It may have later spread with new agricultural developments for colder environments or poorer soils (Rye).<br />
3) A Levant-East Anatolian element, now centred in Armenians, Druze, Georgians. I'm not sure if this isn't the parent component to the Basque and Chuvash ones, thus being distinct due to greater diversity. Meaning it could be a first level MPC population and the Basque and Chuvash ones being peripheral subsets of this subset. It could be also, or simultaneously, an "inner-core" MPC element that superseded the others in a posterior expansion. Y-haplogroup markers seem to support this possibility. This subset seems to be the one which made it all the way into India. It was probably present in Mesopotamia as well.<br />
<br />
As I said all these components are very closely related. That's why in unsupervised ADMIXTURE you get apparently surprising results, such as the Northeast Europe-modal component being closest to the Anatolian/Levantine one (makes sense if you realise one is a subset of the other). <br />
<br />
I increasingly think it's likely none of the above subsets emerged in an unadmixed form, in any population, from the settling of the Neolithic Revolution. Some seem to have admixed with elements from other non-MPC cores. Others mixed with other subsets of the same MPC core (for instance in the Corded Ware area). Still others with possible forager elements. Middle Eastern populations all have this presumably Northeast African element I've named the Nile Core. From preliminary runs, I feel that some European populations are less admixed than others, but all seem to have significant admixture from other elements. Which creates a problem concerning appropriate pole populations.<br />
<br />
I will dedicate the next few days to search for different "Mesopotamian Core"-only subsets and expansions. For lack of suitable public sets, I will include participants data, but please don't read too much into the first experimental provisional results. When I have a model that makes more sense, it will be apparent I think.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com3tag:blogger.com,1999:blog-6443268110928728533.post-5945849502979653842011-04-29T01:59:00.008+01:002011-04-29T14:49:42.012+01:00Not quite Egyptians?So continuing my search for Native North African components, I use the <a href="http://en.wikipedia.org/wiki/Dogon_people">Dogon</a> as the West African pole. The Dogon are a people of <a href="http://en.wikipedia.org/wiki/Mali">Mali</a>, living in the Sahel region not far from the southern "shore" of the Sahara. They speak the Dogon language, presumed but not universally accepted as, a Niger-Congo language. So they are likely related, perhaps central to, the West African Neolithic Revolution Core.<br />
Any source for slaves carried by caravans to the North must have come from here.<br />
For the first run I used 24 Dogon as the pole, all Masai and all Basques:<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjeg3Mo_5CuBmspj-MDZmPv2qXuIznsITglqG3NADxsv8wi0XXSqTCYbEDYRIQWq2HbRM6Ptz_f-xa7GTuy97_MUq8eXCZRGkz5YmSpDVX8D585Gjki_jsxLdl2cldOBBye0mEE1vpKM6Y/s1600/dogon1.png" imageanchor="1" style=""><img border="0" height="247" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjeg3Mo_5CuBmspj-MDZmPv2qXuIznsITglqG3NADxsv8wi0XXSqTCYbEDYRIQWq2HbRM6Ptz_f-xa7GTuy97_MUq8eXCZRGkz5YmSpDVX8D585Gjki_jsxLdl2cldOBBye0mEE1vpKM6Y/s400/dogon1.png" /></a></div>Fst:<br />
"Dogon24" to Basque 168 (to "Yoruba24" <a href="http://dioegenesartemis.blogspot.com/2011/04/searching-for-native-north-africans.html">previously</a> 166)<br />
Basque to Masai 97 (98 in "Yoruba24" run)<br />
Masai to "Dogon24" 42 (to "Yoruba24" 35)<br />
So results are very similar to the "Yoruba24" run using an otherwise identical set-up. Suggestive of great similarity of the Dogon and Yoruba, due to common West African Neolithic descent. Interestingly, "Dogon24" seems more distant to Masai and Basques than <a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEioJKr2-BH5eDNqYSJx4EwpigFsHhUfAPf4c1SU_-MyqETbKButEFXGXv7s_efFPGPwDNYwijdICn0GlYw_cTjXtc2shvrACdAbch6KPnrUAHwQ2_8Oe0d5gKWXjbYCHJfcgMUV9oLBj8I/s1600/Yoruba24.png"><b>"Yoruba24"</b></a>.<br />
<br />
Now using only 5 Dogon individuals:<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiYMI5zUCSB7w-GpNoqnG7HoXe5CFllxLiPjg_xP4QKgQlSjj2cwVpP_VldYVLPQkxWlV82vsJ3TxGZRdca93uKxgBmgKMZEMQB8TAd5CBBG3f1XwVV3I8eOsdA6IbVdSWG5P9Tocws2YY/s1600/dogon5.png" imageanchor="1" style=""><img border="0" height="247" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiYMI5zUCSB7w-GpNoqnG7HoXe5CFllxLiPjg_xP4QKgQlSjj2cwVpP_VldYVLPQkxWlV82vsJ3TxGZRdca93uKxgBmgKMZEMQB8TAd5CBBG3f1XwVV3I8eOsdA6IbVdSWG5P9Tocws2YY/s400/dogon5.png" /></a></div>Fst<br />
"Dogon5" to Basque 179 (to <a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1lT-eo4gbikm6YC-yKd4ZpM2MRkYtyw3JJ15DIbUcGGCKq5K49SQjGYvpG7sU37IKcYJB8CsUM0DSaA-6kayIpcEG0XBL9JuUUNHSuMkS6jx9gNkyys2VbkHp6INAl8Mw8VGoULi4IN4/s1600/Yoruba5.png">"Yoruba5"</a> 180)<br />
Basque to Masai 113 (112 in "Yoruba5" run)<br />
Masai to "Dogon5" 55 (to "Yoruba5" 53)<br />
Results are somewhat similar as well. Dogon and Yoruba are interchangeable as poles. Reducing individual numbers in either pole leads to major changes in components. I don't think the "West-African" in North Africans is derived from West African Neolithic populations. It must be native to North Africa.<br />
<br />
So how can more be found about it?<br />
<a href="http://dioegenesartemis.blogspot.com/2011/03/fertile-crescent-impact-in-africa-plus.html">Previously</a> I used population isolates, with little or no relation to populations analysed, as "childless" poles to "fish out" <a href="http://dioegenesartemis.blogspot.com/2011/03/twisting-admixtures-arm-ancient.html">unknown components</a>.<br />
Now I'm going to be more straightforward. I'll use restricted poles, each comprised of only 5 individuals, from perhaps slightly more related populations, together with full-set ones just a bit more distant. Here are the poles used:<br />
1) "Dogon5" Five random Dogon individuals - I named the component "Nortwest Africans". Dogon are West Africans, but I believe the restricted pole captured instead such a hidden component<br />
2) All 150 or so Yoruba - "West African". Yoruba serve to "focus" the "Dogon5" pole into capturing the hidden element since the 150+ Yoruba will pull the actual West African I think.<br />
3) "Sandawe5" similarly to "Dogon5" - named "Nile Core Component" or NC. I don't know what's the relation of Sandawe to possible Green Saharan populations, but it doesn't matter since it's intended as a pole for NC anyway. They seem to be just a Masai-like East African population, but I want them to pick something else here, since the much more numerous Masai pole is meant to pull the East African elementf<br />
4) All 100+ Masai - named "East African". They serve the same function vs "Sandawe5" as Yoruba vs "Dogon5": focusing the lens into the desired independent component if it exists (some of the poles in previous blindly supervised runs got nothing)<br />
5) All Basques plus all Lithuanians: named "Mesopotamian Core" or MPC. They are meant to be representative of Anatolian/Mesopotamian/Levantine Core expansion into the region.<br />
6) All San-Namibia: to pick out Subsaharan African Forager elements.<br />
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I included some control pops and individuals. FRNA has French and North African ancestry. Tigrinya is ancestraly from Eritrea. Assyria1 and 2 are Assyrian Christians.<br />
Results are <b>very similar</b> to <a href="http://dioegenesartemis.blogspot.com/2011/03/twisting-admixtures-arm-ancient.html">previous</a> <a href="http://dioegenesartemis.blogspot.com/2011/03/fertile-crescent-impact-in-africa-plus.html">blindly </a>supervised runs with different set-ups.<br />
Unsupervised runs tend to pick more composed components centred in Bedouin/Saudis and Mozabite/Tunisians instead, but with lots of MPC as well.<br />
Bedouin and Palestinians may have high NC elements due to early spread of NE Green Saharan incipient pastoralists into the Arabian Peninsula. Pastoralist lifestyles seem to have been important in the evolution of the Green Saharan Neolithic cores from a much earlier stage compared to the MPC Neolithic perhaps giving them from an early stage more of a comparative advantage for marginal soils.<br />
I suspect all four populations derive at least partially from the Green Sahara incipient Neolithic. <br />
1) The Nile Core matured earlier and fused with Neolithic intruders from the North, and would later expand into the same region.<br />
2) Native Northwest Africans lived in a Mediterranean climate but held the Fertile Crescent onslaught well and thus may not have been much behind. They fused with the MPC element and possibly then had a minor expansion into Iberia. I suspect from some recent runs that these are really a Western wing of the Northern Green Sahara pastoralists/incipient Neolithics. There may be an exotic forager element here too, early divergent but sufficiently distinct from the Pygmies and San (whose pole seems to have picked up Pygmy elements quite well). Both elements may be lumped together here.<br />
3) West Africans were protected by a difficult tropical climate from Fertile Crescenters whose crops weren't adapted. They took a longer time to reach a Neolithic critical expansion point maybe for the same reason.<br />
4) East Africans saw some small Fertile Crescent intrusion and admixture, but were also somewhat protected by envirnmental factors<br />
These groups may also have unseen important Forager admixture. This would explain why Pygmies cluster so tightly in PCA and yet have a homogeneous large "West African" element.<br />
<br />
FST <br />
E African to W African 28<br />
E African to NC 57<br />
E African to NW African 50<br />
W African to NW African 64<br />
W African to NC 93<br />
NW African to NC 81<br />
E African to MPC <b>123</b><br />
W African to MPC 187<br />
NW African to MPC <b>150</b><br />
NC to MPC 125<br />
African F to MPC 280<br />
African F to NC 179<br />
African F to E African <b>116</b><br />
African F to NW African <b>168</b><br />
African F to W African 116 (same as for E African)<br />
<br />
Fst is somewhat distorted by seeding individuals, but since they're only 5, it should have some vague validity. It's interesting NW Africans are seemingly both considerably less like the San/Pygmies and the MPC than E Africans. <br />
Note that E African's fst values are being affected by the very many (100+) Masai who seeded the pole, and thus the smallish Northern element in the Masai is pushing fst closer to MPC and away from African F, so that it seems to be closer to MPC than the NC. The high number of individuals shouldn't be a problem for the Yoruba pole since it is more representative of the actual corresponding core population.<br />
NC is considerably closer to MPC than W African, and fst is including some "East Asian" in the MPC pole populations used, as well as NC being based on the Sandawe pole. If corrected for genetic distance "Subsaharan African" contributions to Middle Easterners are not that dissimilar to those reported by various papers.<br />
<br />
A thought: Why do Druze and Assyrians have less of this NC component? Is it because they have been more recently isolated due to their different culture and religion? Or have they from ancient times been more isolated from outside influences due to environmental (eg mountains) or cultural idiosyncrasies and thus have kept distinctive cultures/religions?<br />
<br />
<a href="https://spreadsheets.google.com/ccc?key=0AtQ1KMSaWd3kdEt0Z2VzWUZCd3RsXzUwNEhRYmpSZFE&hl=en&authkey=CLXEzZgN">spreadsheet</a><br />
<br />
Next I'll expand this into Europe and rest of ME to see if it holds together.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com5tag:blogger.com,1999:blog-6443268110928728533.post-57480118885661028782011-04-28T11:42:00.000+01:002011-04-28T11:42:06.118+01:00Sahara: Pump and Valve of Africa (and Eurasia)?The title is provocative, but I just want to draw attention to Razib's <a href="http://blogs.discovermagazine.com/gnxp/2011/04/the-continuing-tangling-of-the-human-tree/">comment</a> on the new paper.<br />
In addition I want to clarify I intend to go further on why there are so many discrepancies in the Masai vs Yoruba North African runs soon. This may be confusing to many, but I believe results are telling us something.<br />
One reason is due to different pole sizes. I have very many Yoruba in my database (some 150) and in some runs I used only 5 in others 24 of them, creating quite different results versus the full set in supervised mode. ADMIXTURE stretches small poles a lot more than large ones, sometimes making them about something different from the pole individual's population.<br />
<br />
This indicates there may have been a Northwest African aboriginal population quite distinct from modern West and East Africans, but related to them. This component even sometimes appears as if more distant from Eurasians than West Africans themselves...<br />
<br />
Also high absorption levels in a Mediterranean climate environment IMO indicates some incipient level of Neolithic adaptation in this people before partial replacement by Mesopotamian/Anatolian/Levant and Northeast African Neolithics.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com0tag:blogger.com,1999:blog-6443268110928728533.post-30385328598102317242011-04-28T02:12:00.001+01:002011-04-28T02:19:59.356+01:00Searching for Native North Africans, Part II: EastAfrican-AmericansI'm short on time, so I'm only presenting for now the Masai restricted-pole results and some experiments with 53 African-American samples.<br />
<br />
I used either the full set or just five individuals as poles in each run. I didn't use 24 vs 5 since I assure you for the following analysis the behaviour of poles comprising all individuals vs 24 is basically the same.<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhIT4s3attxzN8wzIr92Hwc1LZ-TEqh0ZJw7HUtZOZAFKnA14_XdHvmFrA2_gaXQ3d1KG7CMKaaJoDkHUsUja4xCaGW0gUZruy-qzQ-hykRvUe2oASSIe2mnfGaVf1weLoiDj2R3H3AAE/s1600/AF3.png" imageanchor="1" style=""><img border="0" height="63" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhIT4s3attxzN8wzIr92Hwc1LZ-TEqh0ZJw7HUtZOZAFKnA14_XdHvmFrA2_gaXQ3d1KG7CMKaaJoDkHUsUja4xCaGW0gUZruy-qzQ-hykRvUe2oASSIe2mnfGaVf1weLoiDj2R3H3AAE/s400/AF3.png" /></a></div>Fst: 164<br />
This is the straightforward result against which all other runs should be compared. Yoruba are historically a good proxy for the West-African parent population of African-Americans. White-Utahns are obviously a near perfect proxy for the other ancestor population. There is also a little bit of Amerindian but I decided to ignore it since it's so small, and after realising in the Mexican run that small component poles can act quite strangely in such experimental set-ups.<br />
<br />
Here's what happens when the Yoruba pole is reduced to just five individuals:<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjFp49j-v_U_1Eih_QE3fSN89aG0muT8y7WVoJ7MxFveheIYg1-woDmoA0D3MXuu6z1VC2Hg_7YJYu2yM0DWGHKpIVipAOqNs96DN59TJQBXAhvYX8UDh0nAwcr7maFdIix_PxtaR4tWJk/s1600/AF4.png" imageanchor="1" style=""><img border="0" height="63" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjFp49j-v_U_1Eih_QE3fSN89aG0muT8y7WVoJ7MxFveheIYg1-woDmoA0D3MXuu6z1VC2Hg_7YJYu2yM0DWGHKpIVipAOqNs96DN59TJQBXAhvYX8UDh0nAwcr7maFdIix_PxtaR4tWJk/s400/AF4.png" /></a></div>Fst:167<br />
Not much change. Yoruba here are representative of West African ancestors and a valid full-set pole.<br />
<br />
Now all Masai as the pole.<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjp-lGluvTnWascaUmNScyvKB6QoSIY47k5CfAedRfUXrNaM2kukcKEDCxJKKvKwjuqzu08vLM0XsP0VnhipSfZlSOM13snpwD5OOh5Oe_pM8mbQ27aLEOhG2UT7qmaRBV8Up-U0xR9ggk/s1600/AFAM1.png" imageanchor="1" style=""><img border="0" height="63" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjp-lGluvTnWascaUmNScyvKB6QoSIY47k5CfAedRfUXrNaM2kukcKEDCxJKKvKwjuqzu08vLM0XsP0VnhipSfZlSOM13snpwD5OOh5Oe_pM8mbQ27aLEOhG2UT7qmaRBV8Up-U0xR9ggk/s400/AFAM1.png" /></a></div>Fst: 108<br />
Such discrepancies suggest what's already well known. The Masai are not good proxies for the parent population of African-Americans.<br />
<br />
Using five Masai as the African pole:<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8vUSLD6Zkz7qqzP79PUkrkeGVWUzHYGXfckvnUJArzHQKbpP6hxV4I2HjG89uhbRE98yKnP3W7FVT8zb7S8Ub_TPpGRecLyfjs7E59PM6GETcDOcsEooXyqoCbry_F8Kj1Mw2cheffRA/s1600/AFAM2.png" imageanchor="1" style=""><img border="0" height="63" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8vUSLD6Zkz7qqzP79PUkrkeGVWUzHYGXfckvnUJArzHQKbpP6hxV4I2HjG89uhbRE98yKnP3W7FVT8zb7S8Ub_TPpGRecLyfjs7E59PM6GETcDOcsEooXyqoCbry_F8Kj1Mw2cheffRA/s400/AFAM2.png" /></a></div>Fst: 123<br />
<br />
Genetic distance between components is now considerably closer to the actual one, and much of the divergence is due to unavoidable weighting in of the 5 Masai used. Admixture proportions are now basically the same. The pole was stretched and here it appears to be almost wholly dominated by the hidden West-African component.<br />
<br />
In my previous "Chinese Mexican" experiment the "Chinese24" pole underestimated the actual admixture proportions and "Chinese5" grew correcting it. Here the larger Masai pole overestimates it, and "Masai5" shrinks to correct it.<br />
Naturally this is easier with just two populations, since there's no extra-component to be "eaten-up".<br />
<br />
Now back to North Africa<br />
.<br />
All Masai, all Yoruba and all Basque as 3 poles:<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgDG-pGrDvSLv4fPKcj3K4sBPjtqMPCg3yd8B4Y-EIN6b2Eihx6oGMrnHueQfsU5EgWeM8w6lIEYQu7DtuY9kfbiy6xMq8zsSkXQdvuxwbxrcCLqy2mH3y81w0iW_gPA8CX-4lzJ97NUoc/s1600/NA1.png" imageanchor="1" style=""><img border="0" height="250" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgDG-pGrDvSLv4fPKcj3K4sBPjtqMPCg3yd8B4Y-EIN6b2Eihx6oGMrnHueQfsU5EgWeM8w6lIEYQu7DtuY9kfbiy6xMq8zsSkXQdvuxwbxrcCLqy2mH3y81w0iW_gPA8CX-4lzJ97NUoc/s400/NA1.png" /></a></div>Fst:<br />
"Masai" to "Yoruba": 38<br />
"Masai" to "Basque": 117<br />
"Yoruba" to "Basque": 163<br />
(distances are slightly different to those of "Yoruba24" since I used all Yoruba here and Yoruba are a poor substitute in this case I believe)<br />
<br />
Only 5 Masai as the "Masai5" pole, remaining poles full-set:<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj2YKasleTZc0iQ6tWR92Srm31enU6zClfaMhBekaVEmmBVAW12BrXeAXGDQ3oMDQ35lvzMQAMpY2R03yyAvvZKsJLJSOQ4eh9xs_gBCsvO-Rue9Zj8rmTwgjm1cu67UbveSqv5vsvmTk4/s1600/NA2.png" imageanchor="1" style=""><img border="0" height="247" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj2YKasleTZc0iQ6tWR92Srm31enU6zClfaMhBekaVEmmBVAW12BrXeAXGDQ3oMDQ35lvzMQAMpY2R03yyAvvZKsJLJSOQ4eh9xs_gBCsvO-Rue9Zj8rmTwgjm1cu67UbveSqv5vsvmTk4/s400/NA2.png" /></a></div>Fst:<br />
"Masai" to "Yoruba": 82<br />
"Masai" to "Basque": 99<br />
"Yoruba" to "Basque": 182<br />
Tunisians are similar to Northern Moroccans. These are the two large fertile areas and mostly agricultural; while other sampled populations live in regions with some fertile but other less fertile areas more suited to pastoralism. <br />
Moroccan-Jews mostly lose their "Yoruba"-like component.<br />
So Masai are likely not a good proxy for the component it's picking up here...<br />
That's all I'll imply by now. Don't pay too close attention to fst since it's possible the pole's inadequacy made them eat up quite a bit of the other components. Masai have some Northern admixture making this more likely.<br />
<br />
I don't have more time right now, so tomorrow I'll try to go further...<br />
I should warn you I think in a very probability-based manner and all I need to jump is to feel a significantly higher probability in the validity of a trick/interpretation. I don't play the "wrong"/"certain" game. Good bets are valid even if sometimes "erroneous", because they can add up (as long as they don't bankrupt you). I won't tie my hands up for fear of being wrong.<br />
<br />
I soon may have to review my early replacement from Egypt model for North Africa. Native Northwest Africans may also have had incipient Neolithic capabilities just as Northeast Africans... Maybe other Green Saharan melting pot populations shared them too. The Green Sahara may well have been an incipient Neolithic Eden. West Africans, East Africans, the Nile Core, and aboriginal Northwest Africans may all be the sons of another Neolithic Eve.<br />
<br />
Also <a href="http://dienekes.blogspot.com/2011/04/single-out-of-africa-origin-of-humans.html">Dienekes comments on a new paper</a> possibly relevant.<br />
<br />
So take these experiments with a pinch of salt right now. It's only food for thought...Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com2tag:blogger.com,1999:blog-6443268110928728533.post-17822016899410405142011-04-27T01:08:00.002+01:002011-04-27T01:13:01.417+01:00Searching for Native North Africans, Part I: Chinese MexicansBeing a skeptic of the "Slave theory" of demographic change in established peasant populations at the Malthusian limit (that is excluding frontier situations with a land surplus like those in the New World) I've long suspected that West and East-African-like admixture in North Africans was really about a substrate (semi-)forager/pastoralist Western Green Saharan population and a Neolithic expansion from Egypt. Indeed I think the Tuareg may very well be at least a population with a large component corresponding to this ancient no longer extant in an unadmixed form group of people.<br />
<br />
Seeking evidence about Native North Africans I've been thinking about ways to uncover evidence about them indirectly using some supervised mode tricks I've been developing.<br />
<br />
First I ran a supervised analysis of Mexicans. I used historically appropriate pole populations: all my 12 Spaniard samples, all 24 Totonac representing Mesoamerican Amerindians, and 68 Yoruba representing the bit of West African present in this population. The Mexican samples were 58. I didn't use recent individual samples in any of the runs since results are highly experimental:<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg20Y0R2QXCwpTgjTkjqvdjkPEvk8hol9MbVchrKj-5kxt7l4lCdBVjP_858K8TV4_GQ7wLmhLFQMS9fohUQC90tOSwNG8CAoFtBTN72eOvjfJiw36yLTahhiwIiyJUYfZI6Zhm5qgQLlA/s1600/totonac24.png" imageanchor="1" style=""><img border="0" height="63" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg20Y0R2QXCwpTgjTkjqvdjkPEvk8hol9MbVchrKj-5kxt7l4lCdBVjP_858K8TV4_GQ7wLmhLFQMS9fohUQC90tOSwNG8CAoFtBTN72eOvjfJiw36yLTahhiwIiyJUYfZI6Zhm5qgQLlA/s400/totonac24.png" /></a></div>ADMIXTURE's own Fst estimates:<br />
"Spanish" to "Yoruba": 164<br />
"Spanish" to "Totonac24": 170 <br />
"Yoruba" to "Totonac24": 258<br />
ADMIXTURE always mixes some bits of components up, it's a statistical tool, so it doesn't matter for this purpose if these are exactly correct or not.<br />
Results are in line with other studies.<br />
<br />
It also doesn't matter much how many Totonac samples are used as a pole, since these are close to the actual parent population(s). Here is the same run using only 5 Totonac:<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhQu0FobAzQEdE-DHqQlsEGLKsws0eMJwN7TUY9UV5g2uPJEsD86n10Ffsah5__5eyuJWyEPAhxpJ9R4m2huKLRfO5TQYfb2y2P-xCXYlekq3g1_uhU1RXgf6WScPnTf3f3IjLQxVfF99Y/s1600/totonac5.png" imageanchor="1" style=""><img border="0" height="78" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhQu0FobAzQEdE-DHqQlsEGLKsws0eMJwN7TUY9UV5g2uPJEsD86n10Ffsah5__5eyuJWyEPAhxpJ9R4m2huKLRfO5TQYfb2y2P-xCXYlekq3g1_uhU1RXgf6WScPnTf3f3IjLQxVfF99Y/s400/totonac5.png" /></a></div>"Spanish" to "Yoruba": 168 <br />
"Spanish" to "Totonac5": 182<br />
"Yoruba" to "Totonac5": 255 <br />
Results and fst distances aren't very different. I actually believe these restricted pole results may be closer to the truth since the Amerindian pole is less dominated by the Totonac and more by the Mexican samples' actual Amerindian ancestors.<br />
<br />
Now imagine Amerindians were no longer present as unadmixed populations to sample directly. We might know or discover however that this parent population of Mexicans was somewhat similar to the East Asians. So we might try to use say, Beijing-Chinese samples as the proxy for the actual parent population (I used only 24 BJG-Chinese just as Totonac):<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjma-aup5RVRXjqGXXjeIZsk21VfpIPuw7XqU2b3NlqynFvxdttT8F0sXgsCX5xhuIBltpZ4oIYlCJmWTyZLUoCh4akund4K8HiGifns5cOko_mYL5FSnPwQXD1OSzfexhgtzS-TmOjJ2g/s1600/bjg24.png" imageanchor="1" style=""><img border="0" height="75" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjma-aup5RVRXjqGXXjeIZsk21VfpIPuw7XqU2b3NlqynFvxdttT8F0sXgsCX5xhuIBltpZ4oIYlCJmWTyZLUoCh4akund4K8HiGifns5cOko_mYL5FSnPwQXD1OSzfexhgtzS-TmOjJ2g/s400/bjg24.png" /></a></div>"Spanish" to "Yoruba": 160 <br />
"Spanish" to "BJG-Chinese24": 117<br />
"Yoruba" to "BJGChinese24": 210 <br />
So, genetic distances and admixture proportions change quite a bit, suggesting as known that BJG-Chinese are not the parent population. The pole was stretched by the 24 Chinese seeding it.<br />
<br />
So what would happen by doing the same as in the Totonac runs, restricting the Chinese samples to five?<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEic885ZqjWxg4c5lmrpFpsaERqilH5PAYCxVl13UDLYtg5vZ0PVO3tDm4VoNl99gaClyPysCN1iN251d5l9Eh18PEQSQLORm_aLlRiV-OCO1vJxVp6W3Le-II23pUZMBOXBhhwFcTQBql0/s1600/BJG5.png" imageanchor="1" style=""><img border="0" height="63" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEic885ZqjWxg4c5lmrpFpsaERqilH5PAYCxVl13UDLYtg5vZ0PVO3tDm4VoNl99gaClyPysCN1iN251d5l9Eh18PEQSQLORm_aLlRiV-OCO1vJxVp6W3Le-II23pUZMBOXBhhwFcTQBql0/s400/BJG5.png" /></a></div>"Spanish" to "Yoruba": 181<br />
"Spanish" to "BJG-Chinese5": 113 <br />
"Yoruba" to "BJGChinese5": 188 <br />
As sometimes happens with inadequate poles, the poles ate up some unrelated segments in this run. But results suddenly became more in line with the Totonac ones. The pole isn't as distorted with 5 as it is with 24 Chinese and it becomes more dominated by the Mexicans East Asian-like ancestors.<br />
<br />
Note how genetic distances don't change much with Totonac24 vs Totonac5. They do change a lot with the restriction of the inadequate BJG-Chinese pole. ADMIXTURE is trying to tell us Mexicans aren't really descended from the Chinese.<br />
<br />
Now applying these techniques to North African populations. I used all my Basque samples (24), 61 Masai and 24 Yoruba as poles:<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEioJKr2-BH5eDNqYSJx4EwpigFsHhUfAPf4c1SU_-MyqETbKButEFXGXv7s_efFPGPwDNYwijdICn0GlYw_cTjXtc2shvrACdAbch6KPnrUAHwQ2_8Oe0d5gKWXjbYCHJfcgMUV9oLBj8I/s1600/Yoruba24.png" imageanchor="1" style=""><img border="0" height="247" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEioJKr2-BH5eDNqYSJx4EwpigFsHhUfAPf4c1SU_-MyqETbKButEFXGXv7s_efFPGPwDNYwijdICn0GlYw_cTjXtc2shvrACdAbch6KPnrUAHwQ2_8Oe0d5gKWXjbYCHJfcgMUV9oLBj8I/s400/Yoruba24.png" /></a></div>Fst:<br />
Basque to "Yoruba24": 166 <br />
Basque to Masai: 98 <br />
Masai to "Yoruba24": 35 <br />
<br />
With only five Yoruba as pole:<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1lT-eo4gbikm6YC-yKd4ZpM2MRkYtyw3JJ15DIbUcGGCKq5K49SQjGYvpG7sU37IKcYJB8CsUM0DSaA-6kayIpcEG0XBL9JuUUNHSuMkS6jx9gNkyys2VbkHp6INAl8Mw8VGoULi4IN4/s1600/Yoruba5.png" imageanchor="1" style=""><img border="0" height="247" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1lT-eo4gbikm6YC-yKd4ZpM2MRkYtyw3JJ15DIbUcGGCKq5K49SQjGYvpG7sU37IKcYJB8CsUM0DSaA-6kayIpcEG0XBL9JuUUNHSuMkS6jx9gNkyys2VbkHp6INAl8Mw8VGoULi4IN4/s400/Yoruba5.png" /></a></div>Fst<br />
Basque to "Yoruba5": 180<br />
Basque to Masai: 112 <br />
Masai to "Yoruba5": 53 <br />
There is change. The situation is a bit more like Mexicans with BJG-Chinese than with Totonac I think. Basque is now closer to "Yoruba5" just as Masai is more distant. This could be absorption due to the inadequate pole just as in the Chinese5 pole experiment.<br />
<br />
So Yoruba are clearly somewhat related but I think also distinct from the Northwest African substract. Perhaps West Africans, East Africans and ancient North Africans are all populations born of a Green Sahara melting pot.<br />
Tomorrow I'll run a control, and do the same using Niger-Congo-speaking Sahel populations. And the same for the Maasai pole. And then it gets even more complicated but hopefully revealing.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com0tag:blogger.com,1999:blog-6443268110928728533.post-69894438105059760512011-04-23T22:44:00.007+01:002011-04-23T22:57:23.946+01:00More Egyptian than the Egyptians themselvesNext I ran a supervised run of North Africans. The poles were:<br />
<br />
1) Masai<br />
2) Yoruba<br />
3) Basque<br />
4) Egyptian<br />
<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhtjQuLGCDxjbDGVqSIm8C152LI0QYytd4G8lHWDPHQMyNTPvIEYfcn3UfMy6dT_6M184ldJcMnXiRHysBYJ3yS_ehiPQatm34HVtVAFqck3ON4b1-eV8LnUAjviGXvkLRzVSh6lV34jHw/s1600/tunis2.png" imageanchor="1" style=""><img border="0" height="200" width="310" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhtjQuLGCDxjbDGVqSIm8C152LI0QYytd4G8lHWDPHQMyNTPvIEYfcn3UfMy6dT_6M184ldJcMnXiRHysBYJ3yS_ehiPQatm34HVtVAFqck3ON4b1-eV8LnUAjviGXvkLRzVSh6lV34jHw/s400/tunis2.png" /></a></div>The population with about 50/50% Basque-Egyptian are Moroccan Jews.<br />
<br />
Again populations from more agriculturally productive regions (Tunisia and N Morocco) lack significant Subsaharan segments as expected. Desert regions tend to present them in a chunky way which I ascribe not to slavery but to recent movement of desert tribe members anciently less affected by Neolithic migrations (Tuareg and others) into the coast and cities.<br />
<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEil0i3qVxQjCnCPJkkow7c-YDZKaccQmB9VnXerot5roxfQDtLmzSeGEMbWy1YdRc9FLFf_W13h_HHLFDq29r4aZZDO9TenSPKxPk6aHgbOI4kDfkfjow8LEbht4nD3o74bZFpQyFNvvMw/s1600/tunis2b.png" imageanchor="1" style=""><img border="0" height="400" width="95" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEil0i3qVxQjCnCPJkkow7c-YDZKaccQmB9VnXerot5roxfQDtLmzSeGEMbWy1YdRc9FLFf_W13h_HHLFDq29r4aZZDO9TenSPKxPk6aHgbOI4kDfkfjow8LEbht4nD3o74bZFpQyFNvvMw/s400/tunis2b.png" /></a></div>It's noteworthy how Tunisians have all 100% affinity to Egyptians versus other pole populations. If affected by Subsaharan Caravan Slave trade, we would expect to see West African segments. As it is, segments apparently Subsaharan African in some other runs are all attracted to the Egyptian pole.<br />
As for North Moroccans, much of the same applies, except that here some Northern influence is visible as well.<br />
South Moroccan heterogeneity may be regional, due to fertile versus more desertic areas.<br />
W Saharan's low homogeneous West-African-like elements may be aboriginal or otherwise ancient.<br />
<br />
Together with my <a href="http://dioegenesartemis.blogspot.com/2011/04/debunking-mozabites-and-company-again.html">previous run</a>, it appears to me that an Early Neolithic wave from the Nile spread West even as Egypt itself continued to receive Northeastern influences. This wave would maybe carry Berber languages. Later a second Nile wave would spread not only West but all over the Near East and Mediterranean.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com2tag:blogger.com,1999:blog-6443268110928728533.post-79452267311596337322011-04-23T21:48:00.004+01:002011-04-23T22:14:21.357+01:00Debunking Mozabites and Company - againAs a first step towards uncovering structure in Fertile Crescent populations, I have run a few unsupervised runs of the region's populations. In these you generally get Mozabite, Saudi or Bedouin, and Druze or Armenian modal components. Egypt generally comes out as a population combining all elements available in largish amounts. This could have two explanations. Either Egypt is where Mozabites, Saudis and Druze all arranged to have a party by the Nile, or Egypt is actually the Mother of them all (there's likely a Father as well) and ADMIXTURE is simply rendering different levels of parental admixture into distinct components. This would happen because Egypt itself has a dominant non-African component mixed with an important African one. Since this component doesn't exist unadmixed anymore, at K=2 with Yoruba and say Basques, you do get an African vs non-African division in the populations, but it's lost at higher Ks, suggesting Yoruba or Masai are not good proxies for it.<br />
In a previous run, I found <a href="http://dioegenesartemis.blogspot.com/2011/04/adam-and-eve.html">evidence</a> of a native NorthEast African element in the region.<br />
<br />
So I've decided to study North Africa alone for a start. I'll study the Saudi and Druze dominant components later.<br />
<br />
Firstly unsupervised run of North Africans with Masai, Yoruba and Basques. I've removed a few problematic Masai and Tunisian individuals, who form their own component:<br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjuoP_iWZrH92l2HrWVwffUUeWjlBzsLBLhVzVCW2CtGATI_Os9G2Z-DmkizmbzIlfwm-T2Uin2YsgZEzy3vDXjoxJCDfo5biWd7ZW4HqWn76IPQyjkazy2c-OarDGDSaad_RYDp7h3oDI/s1600/TUNIS1.png" imageanchor="1" style=""><img border="0" height="269" width="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjuoP_iWZrH92l2HrWVwffUUeWjlBzsLBLhVzVCW2CtGATI_Os9G2Z-DmkizmbzIlfwm-T2Uin2YsgZEzy3vDXjoxJCDfo5biWd7ZW4HqWn76IPQyjkazy2c-OarDGDSaad_RYDp7h3oDI/s400/TUNIS1.png" /></a></div><br />
Notice how regions with especially fertile soils (Tunisia and North Morocco) have little "West African" whereas more desert areas have larger such components. Many such segments are confined to a few individuals, indicating admixture possibly with desert tribes such as Tuareg. I believe such West African segments are actually aboriginal western Green Sahara foragers and semiforagers, largely replaced by the Nile Wave.<br />
Notice also how even in Morocco you get a lot of East African, just like in Egypt, even though southern populations are exclusively West African.<br />
<br />
Genetic Distance estimates (Fst):<br />
Nile 1st Wave to East African <b>84</b><br />
Nile 1st Wave to Basque <b>51</b><br />
Nile 1st Wave to West African <b>124</b><br />
Basque to East African 127<br />
Basque to West African 177<br />
East African to West African <b>44</b><br />
<br />
<br />
So what's happening here? The Nile component, higher in Tunisians and many Moroccans than in Egyptians themselves, has actually more affinity to East African than to geographically closer West Africans. It also may have a lot of Basque-like (Mesopotamian Core) admixture.<br />
<br />
My point is: Mozabites and other North Africans plot in MDS distantly to Subsaharan Africans but much closer than their low affinity to West Africans would predict, as shown in this run. I think this is due to a Neolithic North Eastern African migration. In other words, for North Africa it's maybe more due to a more recent "Out of Egypt" than due to an ancient "Out of Africa" event.<br />
<br />
Next I'll look into North Africans in supervised mode.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com0tag:blogger.com,1999:blog-6443268110928728533.post-23992854944004364052011-04-23T16:40:00.002+01:002011-04-23T16:44:37.628+01:00The Fertile Crescent variation: a modelUp to this point, I've been concentrating on "macroscopic" ADMIXTURE runs defining the affinity of populations in the Fertile Crescent zone, from Scandinavia to North Africa to West Asia.<br />
I've presented runs proposing a <a href="http://dioegenesartemis.blogspot.com/2011/04/dual-core-neolithic-revolution.html">two core</a> Neolithic Replacement model, with a Northern "Mesopotamian" Core best preserved today in <a href="http://dioegenesartemis.blogspot.com/2011/04/new-world.html">North Europeans</a>; and a Northeast African Southern "Nile" Core today inexistent as the predominant component in any population, but <a href="http://dioegenesartemis.blogspot.com/2011/04/adam-and-eve.html">important in North Africa, also in the Near East</a> and to a lesser extent, in Southern Europe. These runs, as a bonus, also revealed a <a href="http://dioegenesartemis.blogspot.com/2011/04/native-americans-native-europeans.html">"Siberian"-like</a> small component in peripheral and mountain populations, very suggestive of aboriginal DNA absorption.<br />
I still think this model is a very coherent first approach to intra-Fertile Crescent variation. However as always, the picture becomes more complex as one digs further, in a more "microscopic" way.<br />
<br />
So I'm restating my model in a more detailed manner. My confidence is not extremely high, but I think this is the simpler model to explain patterns.<br />
1) The first Neolithic people in the World are born in the Mesopotamia/Levant/Anatolia around 10.000BC<br />
2) Europe like all of Northern Eurasia (and the Americas) is inhabited by Siberian/Amerindian-akin foragers<br />
3) Most of Africa is inhabited by San/Pygmy-akin foragers<br />
4) Climate change leads to the Green Sahara, a savanna-like environment with very large lakes and river valleys, inhabited by peoples existing in a gradient of DNA variation, much as Siberians/Amerindians. To the west, these people are more West-African-like, to the East more East-African-like. In the Northeast and Nile valley a related people, similar but distinct to both modern West and East Africans, develops incipient Neolithic capabilities.<br />
5) Mesopotamians reach a critical point in their Neolithic evolution. They then expand in all directions namely: Western Anatolia and Europe; Caucasus and Steppe river valleys; Iran plateau and India; and also Southwest Asia and into the Nile itself. Due to prolonged genetic and environmental contact with neighbouring peoples, replacement is incomplete, especially in the more developed Nile valley. Replacement is largely complete in Europe and the Northwest of the Subcontinent though.<br />
6) Thus a western subset of the Mesopotamian/Anatolian/Levantine core expands into the Med and Atlantic regions; and up the Balkans into the fertile Central European river valleys. A Northeastern subset into the Caucasus and Steppe. And a related Eastern subset into Iran and India.<br />
7) The Nile populations are absorbed by invading Southwestern subset Mesopotamian populations. This new hybrid population reaches a balance around 6000BC and then expands into the <a href="http://en.wikipedia.org/wiki/Green_Sahara">Green Sahara</a> absorbing West and East-African-like foragers and semi-foragers in the process. Berber languages are born in the area.<br />
8)The Sahara dries up and refugees with variable Neolithic capabilities flee to North Africa, the Sahel region, East Africa and back to the Nile valley.<br />
9) All the environmental stress and ensuing selection of organizational and food producing strategies leads to the evolution of a more advanced Neolithic lifestyle in Egypt. Food surpluses become more abundant. A new more efficient critical point is reached and a new Neolithic wave is born, carrying Afro-Asiatic tongues. It expands from Egypt in all directions. Egyptian Civilization is born.<br />
10) Afro-Asiatic speakers migrate into Mesopotamia itself, as well as Anatolia and all over the Mediterranean following the routes of earlier Anatolian migrations. Sumerian becomes extinct and is replaced by Akkadian.<br />
10) At some point (first or second Nile wave) North Africans spill into Iberia, blending with majority Anatolian elements mostly into fertile coastal regions in the West and South of the peninsula. <br />
12) The West and East Anatolian (Mesopotamian) waves clash in the Northern European plains. The resulting melting pot of seeds, ideas and genes is archaelogically known as the Corded Ware culture. A new Neolithic lifestyle adapted to cold and sandy soils is born, depending on Rye monoculture and other innovations. This people then expand into Scandinavia, British Isles, and to a smaller degree into Western France and Iberia, blending with Wheat-planting West Wave Basque-like peoples but bypassing the modern Basque country. Militarized elites bring the horse from the steppe simultaneously or following later. In the opposite direction, movements into Siberia, and directly from the Steppe into India begin.<br />
<br />
<a href="http://dienekes.blogspot.com/2011/04/genetic-structure-of-west-eurasians.html">Dienekes has new unsupervised results.</a> Bear in mind that unsupervised mode fails to detect components corresponding to ancient but currently inexistent populations (such as ancient Northeast and Northwest Africans) and that it tends to represent admixed clines containing the majority component and such unrecognized minority components as a series of closely related spuriously independent components.<br />
My above model is quite in accordance with his results. I will be exploring FC structure further with supervised runs.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com1tag:blogger.com,1999:blog-6443268110928728533.post-17215710536941873222011-04-21T00:36:00.000+01:002011-04-21T00:36:28.452+01:00"Rapid, global demographic expansions after the origins of agriculture"<a href="http://dienekes.blogspot.com/2011/04/global-demographic-expansions-followed.html">Dienekes</a> and <a href="http://blogs.discovermagazine.com/gnxp/2011/04/modern-europeans-modeled-as-middle-eastern-farmers/">Razib</a> comment on a new paper.<br />
"Who are we? Where do we come from?" -a <a href="http://en.wikipedia.org/wiki/Paradigm_shift">Paradigm Shift</a> shapes upDiogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com0tag:blogger.com,1999:blog-6443268110928728533.post-67617853432178766232011-04-20T00:05:00.010+01:002011-04-20T01:06:21.382+01:00Unsupervised Northern Eurasia+new samples part 3In this last part of the unsupervised run I'll present results of New World populations and participants, and some South Asians I introduced into the run without South Asian populations (to avoid the artificial Irula modal component).<br />
<br />
<br />
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<br />
Mexico1 and Mexico2 are demonstrative of the high variability still found in Mexicans, a young population in terms of ethnogenesis from mostly Spaniards and Neolithic Amerindians, with a little West African as well. Unlike ancient admixture events in the Old World which are mostly stabilized with little variation between components in different individuals. Same can be said of Dominican Republic samples (Hispaniola1 and 2) even though here the West African component is larger and the Amerindian smaller. EUDR has major ancestry directly from Europe. You can also see likely continuing admixture in populations with exclusively aboriginal self-identification.<br />
<br />
GeUSA has half German ancestry. Some of the USAs are mostly colonial but colonialUSA1 will remain the only one with such a tag since its hard to find Americans without either some colonial or non-colonial ancestry. USA6 is African-American, another very young New World population drawing from diverse Neolithic Core Areas, still with very different admixture levels between individuals.<br />
Afrikaner1 is a White South African sample of Afrikaner ancestry. The Cape has a Mediterranean climate little suited for Bantu crops, but ideal for Fertile Crescent ones. This may explain why Dutch farmers managed to settle and flourish in the forager/pastoralist (San and Khoikhoi)) inhabited area unlike Europeans in other regions of Africa, who had few food producing advantages and local disease resistance over the West African Neolithics.<br />
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As for the South Asian samples. I welcome samples from the area, was a little surprised to get 3 Tamil Brahmins. SIndia1 is mostly Tamil from Sri Lanka. UKIND is British with some Indian ancestry.<br />
Interestingly the Fertile Crescent element in the Tamil samples isn't very different <a href="http://dioegenesartemis.blogspot.com/2011/03/third-eurasian-neolithic-revolution.html">here</a>.<br />
The remaining components I tend to believe are artificial. Ancient South Indians (ASI) were likely a Coastal Migration derived population. Yet Papuans are separated by seas, thousands of kilometres and tens of thousands of years and the genetic affinity may not be close enough, so this ASI component is IMO being split artificially between the remaining poles. This shouldn't be considered evidence of admixture with the pole modal populations though. It possibly simply means that ASI is somewhat distantly intermediate between them. I'll look closer to South Asian populations later.<br />
But before I want to search for finer <a href="http://dioegenesartemis.blogspot.com/2011/03/estimating-basque-admixture-in-balts.html">structure</a> in the Fertile Crescent Cores.<br />
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Here's the <a href="https://spreadsheets.google.com/ccc?key=0AtQ1KMSaWd3kdHpiNGlNaUZueXFMRk0xN25EMWhrMEE&hl=en&authkey=CISC8lA">spreadsheet</a>. Don't take small components literally, especially in an unsupervised run. They may be real, but also noise or may be replacing something different not represented in the other 6 components.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com4tag:blogger.com,1999:blog-6443268110928728533.post-50503640012950194612011-04-19T00:11:00.002+01:002011-04-19T00:25:21.486+01:00Unsupervised Northern Eurasia+new samples part 2This is part 2 of the unsupervised North Eurasian Run. Just as any unsupervised run including such diverse populations, you can expect a lot of noise, <b>especially when evaluating single individuals versus large n populations</b>.<br />
So don't see meaning in every single small component you may find in one or two individuals. It is most likely just noise. Still you can see some patterns, and I'd like to call attention to the dark blue (peaks in Amerindians) and pink (Nganasan) elements. This is an unsupervised run, all I did was decide on the populations and individuals to be analysed and how many components I wanted to ADMIXTURE to figure out. In an unsupervised run I can't tell ADMIXTURE "find this versus that" as in supervised. It finds what it does on its own. And yet results are globally pretty similar to <a href="http://dioegenesartemis.blogspot.com/2011/04/first-results.html">these</a>.<br />
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<br />
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FRNA has French and North African ancestry.<br />
FRMA French and Madagascar/South Asian<br />
Tigrinya is from Eritrea.<br />
<br />
Some considerations<br />
Unsupervised mode in my opinion tends to overestimate/make up smaller components which is why I don't like it much. It clusters segments without an historically informed departing point and tends to amalgamate more exotic variation with some of the dominant component. It is also more chunky and less reliable IMO than some of my <a href="http://dioegenesartemis.blogspot.com/2011/04/new-world.html">blindly supervised results</a>.<br />
Green in Med populations I think corresponds to the Nile Core Element (ancient Northeast African, which doesn't exist "unadmixed" anymore) which is likely intermediate between the Mesopotamian Core and very anciently related also to West and East African maybe through the Green Sahara of thousands of years ago. In the Tigrinya sample the Yoruba modal component is likewise drawing on East not West African elements.<br />
Red and light blue elements in more Eastern populations are likely representative of assimilated Coastal Migration elements. In Europeans they are most likely noise, even though at least in some Romanians they might indicate Roma admixture.<br />
Yellow segments could be interpreted as Central Asian elements but their unevenness and presence in unlikely places (Spain) may mean its just noise.<br />
<br />
My point in presenting this unsupervised run is to prove ADMIXTURE does find what can be interpreted as both Fertile Crescent replacement and Amerindian-like residual segments in Northern Europe and the Caucasus on its own at the adequate K.<br />
One very interesting new indication of the new samples is the near complete absence of Siberian/Amerindian-like segments in Germany. Germany was an <a href="http://en.wikipedia.org/wiki/LBK">entry point</a> for early Neolithic colonization of much of Northern Europe, the Danubian Wing of the 1st Wave up the Balkans, Danube and Rhein valleys from Western Anatolia -other sources were likely the Med-Atlantic Wave via Iberia and British Isles also from Western Anatolia and the Wave from Eastern Anatolia via the Caucasus and the Ukranian/South Russian river valleys.<br />
This region has (in West/South Germany) excedingly fertile river valleys, congenial to wheat/barley agriculture. Residual forager elements are expected to reach a nadir here. And the results speak for themselves.<br />
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Tomorrow I'll present New World data, and also the results of a few South Asian samples I threw in the analysis without my South Asian populations to keep them company. Their results are a bit artificial I think, but still revealing.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com0tag:blogger.com,1999:blog-6443268110928728533.post-69091883240539178872011-04-17T23:21:00.009+01:002011-04-18T00:30:56.296+01:00Unsupervised Northern Eurasia+new samples part 1I've rerun my <a href="http://dioegenesartemis.blogspot.com/2011/04/unsupervised-north-eurasia-run-part-ii.html">previous unsupervised analysis</a> of Northern Eurasia at K=7 with the new data. First part is about East Asia. I have a new Korean sample and two Philippine ones both from the Visayas.<br />
Results are basically identical, I'm only providing the new ones and a few reference populations. The colours are different and the bars have components in different positions.<br />
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The spreadsheet will follow at the end of both parts.<br />
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Korea1 is from Southeast South Korea.<br />
Both Philippines samples are from the Visayas.<br />
Philippines2 has some known minor Spanish ancestry.<br />
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The purple component peaks in Fertile Crescent populations. Red in Papuans. Pink in Siberians and dark blue in Amerindians. I believe as I said previously that yellow and light blue are somehow related to the two cores of the Chinese Neolithic (Yellow and Yangtze Rivers), a "Siberian" related expansion, explaining the presence of these elements in the populations analysed. <br />
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Part II of the same run will present the new data for the West.<br />
Yesterday's <a href="https://spreadsheets.google.com/ccc?key=0AtQ1KMSaWd3kdFV2LWpCQUNDY3p6NUdlSXQtSGdHUVE&hl=en&authkey=CMDI_4AD">spreadsheet</a>.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com0tag:blogger.com,1999:blog-6443268110928728533.post-91792655734460216842011-04-16T21:18:00.003+01:002011-04-16T23:25:47.117+01:00First ResultsI've done a supervised run on some of the samples I've been receiving. The set up was identical to a previous <a href="http://dioegenesartemis.blogspot.com/2011/04/native-americans-native-europeans.html">one</a>, with three poles, Amerindian (unadmixed Totonac+Surui+Karitiana); Siberian (Unadmixed Nganasan); and Fertile Crescent (Egyptians). Results are basically identical, so I'm only publishing the new data:<br />
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<br />
I've named individuals with ancestry from one region of a country with a regional tag (N North, C Central, NW Nortwest etc). Individuals with mixed ancestry from a single country were given IDs with that country's name.<br />
Some ancestry info:<br />
CAsia is from Central Asia<br />
Russian1 comes from North/Central Russia, Urals.<br />
SEFI is a Swedish-speaking Finn<br />
SwedenNorway has about 50/50 ancestry from either country<br />
UKDK likewise UK and Denmark<br />
CEuro has mostly German with some Polish and Ukrainian<br />
SWFrance1 and CPortugal1 come from mountainous regions of their countries<br />
PonticCaspian is mostly Gagauz with some North Ossetian<br />
USA2 has major Amerindian ancestry<br />
FRCA1 is French Canadian with colonial ancestry and also Faroe Islander<br />
Brazil1 is a White Brazilian of colonial ancestry. No known recent Amerindian ancestors.<br />
<br />
Considerations. <br />
For some reason, just as in previous runs, if Fertile Crescent-like segments are pulled away by a suitable pole, Europeans with ancestry from the North or from mountainous regions have a small but detectable amount of DNA segments clustering with those of Amerindians. Other segments cluster with those of nearby Siberians. Samples from more Central/Southern or presumably fertile regions show such segments to a much smaller degree, being almost completely attracted to the Fertile Crescent pole.<br />
I'm sorry for anyone not included this time, I didn't want to include too many recently mixed samples and also couldn't include individuals with major ancestry not covered by the poles. I'll run a more inclusive analysis soon.<br />
<br />
Still accepting all non-recently admixed samples from the same country, even non-European ones. I have two Philippine samples already and would welcome more East, Southeast Asian ones.<br />
I'm now considering more mixed samples as well as long as ancestry is well defined.Diogeneshttp://www.blogger.com/profile/00827839380414245914noreply@blogger.com7