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Thread: Waves of migration into South Asia

  1. #561
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    Quote Originally Posted by parasar View Post
    This one is from STRs - relatively useless. Actually the Z93 number is not worth the paper (or pixel) it is written on.
    The one I had posted is from SNPs as are YFull's.
    I think there are at least 4 acknowledged chromosome mutation rates:
    (And there is no widespread consensus because of the uncertainty concerning the mutation rates)


    1) 1x10-9 mutations/bp/year, based on a single deep-rooting pedigree (Xue et al. 2009);

    2) 0.82x10-9 mutations/bp/year, based on the divergence between two lineages belonging to
    haplogroup Q and calibrated with archaeological dates for the entry into the Americas (Poznik et al.
    2013);

    3) 0.74x10-9 mutations/bp/year, based on an internal calibration with two aDNA sequences
    (Karmin et al. 2015);

    4) 0.62x10-9 mutations/bp/year, based on a conversion from the autosomal rate
    (Mendez et al. 2013).

    The one you posted Poznik et al ones seems to be simply a median value of the 4.

    And the issue of consensus between the rates, (STR and SNP) is covered by the paper link I had posted,
    each rate would produce a different number which is self evident.

    https://link.springer.com/article/10...439-017-1805-8


    Regarding the STR rates used in the table I had posted, yes I understand that and I have seen many papers pre -2012 to have used STR rates with very inflated range. However the fact to be noted is the same rate has been applied to both sub-groups in that table. It is unlike Z280 used SNP rate and Z93 used STR rate, else such a glaring mistake would have been caught by the peer reviewed journal which published that study. So inflation/fudge/deflation is applied uni formally to the groups, which should not result in a 1:3 gap between the groups.

  2. #562
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    Quote Originally Posted by lgmayka View Post
    Quite hilarious! A 2015 paper that uses 12 Y-STRs and the infamous Zhivotovsky fudge factor. I didn't realize that the Paris Institute of Molecular Anthopology has an endowed chair for comedy.
    Yup I know it is hilarious. And the joke is on the journal which published the study.

  3. #563
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    Quote Originally Posted by homosapien View Post
    I think there are at least 4 acknowledged chromosome mutation rates:
    (And there is no widespread consensus because of the uncertainty concerning the mutation rates)


    1) 1x10-9 mutations/bp/year, based on a single deep-rooting pedigree (Xue et al. 2009);

    2) 0.82x10-9 mutations/bp/year, based on the divergence between two lineages belonging to
    haplogroup Q and calibrated with archaeological dates for the entry into the Americas (Poznik et al.
    2013);

    3) 0.74x10-9 mutations/bp/year, based on an internal calibration with two aDNA sequences
    (Karmin et al. 2015);

    4) 0.62x10-9 mutations/bp/year, based on a conversion from the autosomal rate
    (Mendez et al. 2013).

    The one you posted Poznik et al ones seems to be simply a median value of the 4.

    And the issue of consensus between the rates, (STR and SNP) is covered by the paper link I had posted,
    each rate would produce a different number which is self evident.

    https://link.springer.com/article/10...439-017-1805-8


    Regarding the STR rates used in the table I had posted, yes I understand that and I have seen many papers pre -2012 to have used STR rates with very inflated range. However the fact to be noted is the same rate has been applied to both sub-groups in that table. It is unlike Z280 used SNP rate and Z93 used STR rate, else such a glaring mistake would have been caught by the peer reviewed journal which published that study. So inflation/fudge/deflation is applied uni formally to the groups, which should not result in a 1:3 gap between the groups.
    There are problems with using pedigree rates.
    I would go with 3.
    I myself use two ancient specimens (Ust Ishim and Anzick1) that have good coverage, well dated, and with long enough spacing to give us a good average over many SNPs over a long period of time.
    Last edited by parasar; 05-10-2017 at 01:57 AM.

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  5. #564
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    Quote Originally Posted by parasar View Post
    There are problems with using pedigree rates.
    I would go with 3.
    I myself use two ancient specimens (Ust Ishim and Anzick1) that have good coverage, well dated, and with long enough spacing to give us a good average over many SNPs over a long period of time.
    I respect your opinion. And I am not doubting or alluding to how you calculate.

    I was merely point out the fact that there is no wide concensus on the mutation rate calculation.
    And trying to base analysis considering one fixed date as absolute date does not seem right.

    Even Underhill gave a envelope of STR mutation rate and a pedigree mutation rate for the subgroups. I am sure he must be aware and sharp enough to know how to calculate SNP mutation rate when his paper was released but used STR for the subclades.

    " Applying Y-SNP and Y-STR rates to the same haplogroups recently helped to clarify the issue. Genealogical and evolutionary STR rates typically provide lower and upper bounds of the “true” (SNP-based) age. The genealogical rate often—but not always—works well for haplogroups less than 7000 years old."

    And the YFULL dates for splits under R1a-M417, they clock like clockwork and have equi-time spaced splits at 5000 years, 4700 years 4300 years and so on which seems unfathomable to wrap your head around.

    Anyways it is an interesting conversation as always, through my questions to you over the past days I have come across many gaps in the mainstream theory of Yamna to Sintashta to BMAC and Ingress into India, which I am assuming the other side of the coin, aDNA from ISVC may fill.

  6. #565
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    Quote Originally Posted by homosapien View Post
    ...

    And the YFULL dates for splits under R1a-M417, they clock like clockwork and have equi-time spaced splits at 5000 years, 4700 years 4300 years and so on which seems unfathomable to wrap your head around.

    ...
    Of course the proof is in the pudding. If a 6000 year old Z94 turns up, then YFull's mutation rate is wrong.
    "1) the accumulation of BigY and FGC test data, and 2) the publication of Y-chromosome sequences for three ancient samples (Anzick-1, Ust-Ishim, and K14), have made it possible to estimate the average rate of base-substitutions (SNPs). The authors of this study have developed a new method of selecting true mutations in modern and ancient samples, and have defined with high accuracy the rate constant of SNP mutations: 0.82 • 10 per year per bp (95% CI: (0.70 − 0.94) • 10).
    Defining a New Rate Constant for Y-Chromosome SNPs based on Full Sequencing Data (PDF Download Available). Available from: https://www.researchgate.net/publica...equencing_Data [accessed May 9, 2017]."
    https://www.researchgate.net/publica...equencing_Data

    What we have seen so far has been reasonably consistent. My own calculations are on a slightly slower mutation rate giving about 10% higher ages.

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  8. #566
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    Quote Originally Posted by homosapien View Post
    Yup I know it is hilarious. And the joke is on the journal which published the study.
    Yes, I agree. It also shows the pathetic weakness of so-called peer review, which often forces writers to kowtow to the same "conventional wisdom" that their data debunks.

    Zhivotovsky's fudge factor was utterly illogical the very day it was published, as Ken Nordtvedt--the world's foremost expert in Y-STRs--made clear. For years, we all laughed at research papers which continued to apply Zhivotovsky's folly to haplogroup ages, with ridiculous results. Thankfully, those days are now mostly behind us.
    Last edited by lgmayka; 05-10-2017 at 09:47 AM.

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  10. #567
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    Posted by paoloferrari in the new papers thread.
    http://journals.plos.org/plosone/art...l.pone.0176985
    Vahia et al.
    A diffusion based study of population dynamics: Prehistoric migrations into South Asia
    "... AAA population enters the Deccan Plateau from Goa, it appears to merge with the ASI population in southern Karnataka. This merged group then goes on to meet the ANI population in central India. As a result one may not expect any population group in Eastern India with significant AAA and ANI genes (Fig 4C). This is not in agreement with observations that have been reported of significant AAA genes in Eastern India [12]. We, therefore, pursue an alternative scenario (Fig 4D) where the AAA population is assumed to have entered through northern Orissa ...

    The results of our simulations seem to suggest that the scenario that best fits the available genetic data involves entry of AAA into the subcontinent from the Easterly direction. This seems to agree with the fact that the Austro-Asiatic tribes (such as Ho, Santal, Korwa, Birhor) are largely seen in this region, extending to eastern Maharashtra. Our simulations indicate that the initial populations start to coalesce around 4,000 YBP before the commencement of a period of relative geographical isolation of each population group ...

    the exact location of the point of origin in south India does not appear to be critical to the profile of the spread of the ASI population in India. Similarly, the simulation seems to be not very sensitive to initial ANI population locations. However, the entry of the AAA into the subcontinent would be most efficient through the points of break in the Western Ghats and the Eastern Ghats. However, if we assume that the entry occurred from Goa (Fig 4A and 4C) the genetic profiles of the Central Indian tribes would be far different from what has hitherto been reported in the literature. The fit is seen to be much better with our simulation if we assume that the AAA entered through Northern Orissa, thus resolving a hitherto-contentious issue."


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    There was a theory that Austro-Asiatic ancestry came through Goa?

  12. #569
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    Quote Originally Posted by Megalophias View Post
    There was a theory that Austro-Asiatic ancestry came through Goa?
    Their simulation is showing that, but they are disregarding their own results and favoring an entry point in Orissa to accommodate relative ANI/ASI/AAA levels.

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    Title: E-P18.02 - Reconstructing the human population history of the Indian subcontinent using ancient population genomics.

    Keywords: Ancient DNA; population Genetics
    Authors: N. Rai1, K. Thangaraj1, V. Shinde2;

    1Centre for Cellular and Molecular Biology, Hyderabad, India, 2Deccan College Post-Graduate and Research Institute, Pune, India.

    Abstract: More than 1.3 billion people who live in Indian subcontinent correspond to several large ethnic groups who are highly diverse and complex. Importantly, India’s genetic past remains a subject a great debate due to numerous hypotheses surrounding population origins and migrations within and from outside India. In order to reconstruct and explain the patterns of genetic diversity evident in modern humans, an understanding of both past and present population dynamics is crucial. Several studies have shown that genetic data from ancient individuals are indispensable when reconstructing past population histories. We for the first time use the ancient genomics approach in South Asia to reconstruct the complex human population history of Indian Sub continent. We are exploring the recent technological advancement to directly test these hypotheses using ancient and modern human DNA in India. We have collected several ancient skeletal remains from different time scale of human civilization ranging from early Mesolithic, Neolithic, Harappan (Indus Valley civilization) and Megalithic culture. With the whole/partial genome NGS data, we are reconstructing the prehistoric peopling and migration of modern human in the Indian subcontinent. We are also testing the pervasive founder events and gradient of recessive genes accumulation by comparing the ancient genome with the modern human population of India.

    (Emphasis is mine)
    Last edited by homosapien; 05-12-2017 at 10:54 PM.

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