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Thread: East Asians, Southeast Asians, and Pacific Islanders and etc' Genetic Discussion

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    Default East Asians, Southeast Asians, and Pacific Islanders and etc' Genetic Discussion

    There was not a lot of discussion about Asians' genetic studies going here. I will post various charts and link them to articles.



    http://www.nature.com/articles/srep14375





    http://www.nature.com/articles/srep26066#f5

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    According to the study the pink bar is "Proto-Malay". Proto-Malays are a hybrid of mainland-Negrito + East Asian component right? What's the difference from 'Austro-Asiatic' if any?

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    quite interesting that chinese have finnish

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    Quote Originally Posted by shazou View Post
    According to the study the pink bar is "Proto-Malay". Proto-Malays are a hybrid of mainland-Negrito + East Asian component right? What's the difference from 'Austro-Asiatic' if any?
    Malaysians and Javanese are the hybrid of Austronesian and AustroAsiatic with a minor S. Indian or Negrito admixture. Viets, Thais, and Cambodians are mostly AustroAsiatic, I think.

    Can you understand the PCA plot?

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    Quote Originally Posted by PinayWoman View Post
    Malaysians and Javanese are the hybrid of Austronesian and AustroAsiatic with a minor S. Indian or Negrito admixture. Viets, Thais, and Cambodians are mostly AustroAsiatic, I think.

    Can you understand the PCA plot?
    To understand it we'll have to know exactly how PCA plots work!..Dr McDonald also does PCA plot analysis. He mentions it in this guide:
    Interpreting the Results of the BGA Analysis

    In this analysis of BGA (biogeographical ancestry) people get, as a minimum, four types of data, the first in text, and the other three presented as visual representations that you click on to display.
    1) Quantitative Results: A list, shown in the body of the e-mail, of possible sets,
    one set per line, of possible ancestry. Some people don't get this list if they test
    as, within an error tolerance, 100% a certain ancestry. Each line represents
    the computer algorithm’s guess as to the test person’s makeup. The most likely sets in a statistical sense are at the top. However, this does not take into account what is called “prior knowledge”. The classic example of this is with Afro-(Euro)Americans: the computer quite frequently places Hungary or Romania at the top of the list, and England and Ireland below these, sometimes even too low to appear on the list it automatically send to people. But we know that most such people have European ancestors from Western Europe, which is “prior knowledge”. This means that in reality, all things considered (and you really need to consider all the info you have) , Hungarian is less likely than English unless you suspect Hungarian. There are other such cases, especially relating to Jewish versus Italian or Mediterranean ancestry. I provide written comments in these cases. Note especially that we lack specific comparisons for Native American ancestry from the USA and Canada east of the Rocky Mountains; people with such ancestry, as well as people from the Caribbean and central Mexico (Aztec, etc.), come out as “Maya”.
    2) Plot or Plots with Dots (“Scatter Plots”): These plots are labeled with comparison populations and a crosshair icon representing the testee. This is called the PCA (Principal Component Analysis) "scatter" plot. See below for how to read these. The computer generates several dozen of these, and I send only ones of interest for whatever makeup the test person is. There are a couple of special ones that test for specific ethnic ancestry. The most common of these is for Jewish, but others exist for such ethnicities as Sardinian, Kalash, Pygmy, and certain Native American tribes. None exist, unfortunately, for East Asian ethnic people.
    3) Chromosome Segment Painting: This feature gives a “painting” of the testee’s
    22 autosomes and (unless your data is from FTDNA and you
    did not send the X-specific file) the X chromosome which are "color coded"
    to show the "continental" ancestry found at places along them. This test is very important for people with small amounts of ancestry from a “continent” differing from their major ones. It can detect, just for example, as small as 0.4% Native American in a pure European or a mixed Afro-(Euro)American person even if the test described in #1 above cannot. Such results will be mentioned in the text. In the specific case mentioned above the American comes out of the European part.
    4) "Spot on the Map Plot": Here the data (as computed from number one above) is plotted as a summary. The green spot represent the average location of all ancestry except Native American and Oceanic. Note that for people with significant sub-Saharan African ancestry this green spot is essentially meaningless. But for people with just European, Mideast, and sometimes South Asian ancestry it is usually quite accurate as far as their average ancestry goes. The geographic map plot shows each continent’s average location, as well as
    an overall average (green) excluding the American and Oceanic ancestry.
    The “chromosomes” plot just shows which geographic region each part of each chromosome is most likely to have come from. Since everyone has two copies of each chromosome (except males for the X), they may be split in half. But note that while distant regions such as Europe and Africa split cleanly, nearby ones like Europe and the Mideast don’t. As a result often southern Europeans will show some Mideastern spots without having recent ancestry from the Mideast. Mideasteners, especially from North Africa often have sub-Saharan African regions, as do Mediterranean Europeans. Small regions (< 2 Mb) are often just “noise. I have special tests that can sometimes tell whether they are or not, and that will reported in the text if significant. Small regions may not show on the “quantitative” lists and will also be discussed if significant. It is important to remember that this plot cannot tell father from mother in any way.
    The PCA “scatter” plots are the result of a calculation across the whole genome (all the chromosomes except the X) and report the average ancestry. If a person’s ancestry is from one place that will be reflected on them directly. There exist dozens of possible plots but only the most informative ones are sent. In Europe and the Mideast the position on the main scatter plot directly indicates geography. Otherwise, it is indirect. This is taken into account when the spot(s) on the geographic map plot are calculated. The test person (you) is marked with a white circle with either a crosshairs or a white dot at the center. The other colored dots are “comparison” people from various populations.
    Mixed Ancestry and Related Details
    Now if someone is of mixed ancestry, as said earlier, the spot(s) on the map, as well as PCA plots indicate the average. The quantitative lists (which sometimes are not sent if it is just one line like the common “English 100%”) represent possible combinations which average to the correct spot on all the PCA plots. Each line in the list is one set of possible combinations. We fit to 9 of the PCA plots, including ones sent and unsent. This is a “least squares fit”. A person, to fit, has to have the same weighted average position on all 9. Thus, say somebody lies in Romania on a Euro and Mideast only “main” one. They might actually be Romanian, or could be 60% Hungarian and 40% Jewish, or 75% French and 25% Iranian, or something more complicated. On other of the plots (not usually sent) however, Romania does not lie directly between Hungary and the Jews or between France and Iran, so the program (or an experienced person simply looking at a pile of plots) can tell what is correct. Well, most of the time it can but not always. For these cases, especially Jewish ancestry, I sometimes have separate special tests, whose results are reported in words.
    People may wish to know “how far back in time do my tests go?” The answer is “forever”, in the sense that my tests all discuss single or mixed modern populations. For example modern populations such as North African ones can be mixtures several older ones (such as middle eastern and sub-Saharan African). This ancient mixture will appear on the chromosome plots. A similar situation exists with the Jews who are, on a long time scale, mixed Euro-Mideast. They will usually show spots of both Euro and Mideast on the chromosomes, even though we classify Jews as Mideastern.
    If your parents are a typical English person and a typical Jew, that mix likely will appear on the list. But a mix of Irish, British, Romanian, and Palestinian could also appear, since these two possibilities share the same ancient roots. The spot on the map would be similar.
    Small or modest amounts of, for example, Mideast or Eastern European in a basically English person can appear in the list to simply indicate that the person is from a point on the map east of England, such as Normandy, Germany, or Poland. Similar things happen on and across all continents, even Euro-East Asian. For example 97% European and 3% Han Chinese might simply be indicating a small eastward displacement on the map of the European component. If such a mix is truly recent, it almost always appears as such on the chromosomes. If ancient, it may or may not appear there. This fact is always very important to remember when interpreting the “quantitative” data listing.
    Technical notes
    The PCA plots use about 300,000 SNPs to create a (real symmetric) distance matrix which has dimension 200-1200 depending on how many populations are used. This is diagonalized, and the eigenvectors are what are plotted on the PCA graphs. The quantitative results are a fit to the first 9 "dimensions" of the full 1200x1200 matrix. The best few least squares fits to these
    are reported as the “quantitative”, with the proviso that the least number of continental groups needed to "adequately" fit you is used. "Adequate" means that, averaged over the 9 dimensions, you fit within the area (actually 9-D volume) of a "typical" comparison population. The "continental" spots on the map are the average of the quantitative list, but more may be averaged than are sent in some cases. The green spot on the map is the average of the best 4-continental group fits and is usually (slightly) more accurate. This 4-population fit is seldom reported because it usually contains several populations with really tiny amounts.
    The chromosome plots are an entirely separate calculation. They are a "maximum likelihood" estimate of the best two-continent fit over a sliding window using (for the autosomes) a Viterbi algorithm decision process. The "emission probabilities" of this are the probabilities of fitting 12-marker haplotypes. The block size for the "cut points" is 4 markers even though the average is over dozens of markers. The X is painted using fixed 12 marker blocks using a simple sliding window average, not Viterbi, and is less accurate. The computer program used is written by me and is not any of the “standard” ones such as “Structure”.
    It should be emphasized that the accuracy of the results depends significantly on how representative the reference samples are in relation to the testee’s ancestry. We use some 90 groups of reference samples, all from academic studies. Not all available groups are used because for some of the analysis methods using too many groups can cause mathematical problems, and in a few cases the results appear simply silly when certain pairs are used.
    Doug McDonald
    I am a former professor at the University of Illinois at Urbana-Champaign. This work is neither supported nor endorsed by the University.
    The list of populations we use as comparisons is
    English
    Irish
    Russian
    Basque
    French
    Italian
    Sardinian
    Tuscan
    Spain
    Romania
    Chuvash
    Belorus
    Hungary
    Lithuania
    Finland
    Adygei
    Jewish
    Mozabite
    Bedouin
    Bedouin South
    Druze
    Palestinian
    Iranian
    Egyptian
    Moroccan
    Turkish
    Georgian
    Cypriot
    Armenian
    Balochi
    Brahui
    Burusho
    Hazara
    Kalash
    Makrani
    Pathan
    Sindhi
    N_India
    S_India
    Uygur
    Melanesian
    Papuan
    Columbian
    Karitiana
    Surui
    Maya
    Pima
    Na-Dene
    Eskimo
    Bantu South Africa
    Bantu Kenya
    Mandenka
    Yoruba
    Biaka Pygmy
    Mbuti Pygmy
    San
    Maasai
    EthiopianOromo
    EthiopianTigray
    EthiopianAmhara
    Han
    Northern Han
    Dai
    Daur
    Hezhen
    Lahu
    Miao
    Oroqen
    She
    Tujia
    Tu
    Xibo
    Yi
    Mongolian
    Naxi
    Cambodian
    Malaysian
    Japanese
    Yakut
    Chukchi
    Altai
    Buryat
    Dolgan
    Evenk
    Ket
    Koryak
    MongolianChinese
    Nganassan
    Selkup
    Tuva

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    Quote Originally Posted by shazou View Post
    To understand it we'll have to know exactly how PCA plots work!..Dr McDonald also does PCA plot analysis. He mentions it in this guide:
    Thanks for the guide. I'm trying to understand how it works.

    Can you tell me which groups are Filipinos mostly closer to?


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    quite interesting that chinese have finnish
    What the Finns and Chinese have in common is Y-DNA haplogroup N. 15.0% of Guangdong Han and 6.8% of Shaanxi Han belong to this haplogroup (Hammer 2005). Haplogroup N1c entered Europe about 12,00014,000 years ago from Asia and the initial prehistoric migration of haplogroup N began in southern China. Haplogroup N is extremely rare in Southeast Asian populations (<1.5%).


    The Y-chromosome haplogroup N-M231 (Hg N) is distributed widely in eastern and central Asia, Siberia, as well as in eastern and northern Europe. Previous studies suggested a counterclockwise prehistoric migration of Hg N from eastern Asia to eastern and northern Europe. However, the root of this Y chromosome lineage and its detailed dispersal pattern across eastern Asia are still unclear. We analyzed haplogroup profiles and phylogeographic patterns of 1,570 Hg N individuals from 20,826 males in 359 populations across Eurasia. We first genotyped 6,371 males from 169 populations in China and Cambodia, and generated data of 360 Hg N individuals, and then combined published data on 1,210 Hg N individuals from Japanese, Southeast Asian, Siberian, European and Central Asian populations. The results showed that the sub-haplogroups of Hg N have a distinct geographical distribution. The highest Y-STR diversity of the ancestral Hg N sub-haplogroups was observed in the southern part of mainland East Asia, and further phylogeographic analyses supports an origin of Hg N in southern China. Combined with previous data, we propose that the early northward dispersal of Hg N started from southern China about 21 thousand years ago (kya), expanding into northern China 1218 kya, and reaching further north to Siberia about 1214 kya before a population expansion and westward migration into Central Asia and eastern/northern Europe around 8.010.0 kya. This northward migration of Hg N likewise coincides with retreating ice sheets after the Last Glacial Maximum (2218 kya) in mainland East Asia.
    http://journals.plos.org/plosone/art...l.pone.0066102

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    Quote Originally Posted by PinayWoman View Post
    Thanks for the guide. I'm trying to understand how it works.

    Can you tell me which groups are Filipinos mostly closer to?

    How about we dont group up racially different people and question which group that hodgepodge is most closer to

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    Quote Originally Posted by PinayWoman View Post
    Thanks for the guide. I'm trying to understand how it works.

    Can you tell me which groups are Filipinos mostly closer to?

    I think Filipinos form their own cluster to be honest. We have some South Asian and Papuan admixture that pulls us a little closer to Eastern Indonesians than the Dais. Some Filipinos will also be a little closer to Han because of Northeast Asian admixture.

    To me the plot looks at the overall average genetic distance of each individual sample like McDonald said, but I can't really say for sure; I could be wrong.

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