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Thread: Waves of migration into South Asia

  1. #931
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    Pretty doubtful that the ikshvakus have anything to do with the scythians. The chief eastern clans of kosala, vaishali and videha as well as minor kshatriya families allied to them all seem to have shared a common origin myth tracing their origin through ikshvaku and manu to the sun. The theory of scythian origins refers only to the shakyas of kapilavastu. Hindu and Buddhist traditions though place them as an offshoot of the ruling ikshvaku clan of kosala

  2. #932
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    Quote Originally Posted by bmoney View Post
    What is the pure MA-1 admixture component of EHG?

    EDIT: and what was the order of admixture ie who came first
    EHG is WHG with a dose of MA1. I donít exactly remember the percentages but maybe 60/40 WHG/MA1. MA1 1st because it is over 10000 years older than EHG. No idea when and where the 1st admixture events took place between MA1 and WHG

    Although my analysis shows that EHG is only about 3% modern W European DNA contaminated, MA1 maybe significantly more W European DNA contaminated, which would mean that EHG is significantly less MA1 and more WHG than current numbers indicate. I would have to 1st diploid genotype MA1, then attempt to figure out how much modern W European DNA contaminated it is. See my previous post a couple of pages back regarding this

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  4. #933
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    Quote Originally Posted by Kurd View Post
    EHG is WHG with a dose of MA1. I don’t exactly remember the percentages but maybe 60/40 WHG/MA1. MA1 1st because it is over 10000 years older than EHG. No idea when and where the 1st admixture events took place between MA1 and WHG

    Although my analysis shows that EHG is only about 3% modern W European DNA contaminated, MA1 maybe significantly more W European DNA contaminated, which would mean that EHG is significantly less MA1 and more WHG than current numbers indicate. I would have to 1st diploid genotype MA1, then attempt to figure out how much modern W European DNA contaminated it is. See my previous post a couple of pages back regarding this
    A good test would be 7000 years after MA1 - the AG samples. Do the AGs show any excess non-modern contaminated WHG compared to MA1?

    Another thing, despite the potential modern autosomal contamination, MA1's Y and mtDNA are in concordance with his 24000ybp time-frame.

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  6. #934
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    Quote Originally Posted by parasar View Post
    A good test would be 7000 years after MA1 - the AG samples. Do the AGs show any excess non-modern contaminated WHG compared to MA1?

    Another thing, despite the potential modern autosomal contamination, MA1's Y and mtDNA are in concordance with his 24000ybp time-frame.
    Afontova Gora are substantially worse than MA1 with regards to modern DNA contamination. Even the paper which published them is estimating 21-49% contamination. People really should not be using AG in any analysis

    Raghavan 2014, Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans
    [IMG][/IMG]

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    The above was estimated by the authors using the mt method. They also estimated contamination using the X chromosome method. Their results were:

    AG-2: 30%
    MA1: 1.5%

    Compared with the Mt method above:

    AG-2:35%
    MA1 1st extraction: 1%


    Thus there doesn’t seem to be much doubt that Afontova Gora is around 30-35% contaminated with modern European DNA and thus 30-35% artificially European shifted

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  10. #936
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    Quote Originally Posted by Kurd View Post
    A couple of words about MA1 since it is relevant here. MA1 was excavated by Russian archaeologists by 1958 and lay in a museum in St Petersburg for 50 years until DNA was extracted by a team of the University of Copenhagen, ample time for the remains to have been handled multiple times and DNA from Russians from the St Petersburg area to have been incorporated therein.

    Modern human DNA mixed with aDNA is the most challenging thing to overcome, and the practice to date has been to simply not use the sample for scientific work if estimates show modern human contamination is high. I have discussed the issue on my website at http://www.eurasiandna.com/2017/10/0...e-ancient-dna/


    I know of only a single technique to isolate aDNA from modern DNA, which is a technique discussed in Skoglund et al, 2014 "Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal" The technique uses post-mortem damage patterns to assign PMD scores to DNA segments. I implemented the technique on the steppe sequences that I genotyped, but found that I was left with a very small fraction of useable SNPs.


    With regards to estimating modern human contamination I use the program DICE, discussed in Racimo F, Renaud G, Slatkin M (2016), Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans. PLoS Genet 12(4): e1005972. doi:10.1371/journal, pgen.1005972.


    With regards to MA1, here is a table that includes MA1. This table is from the above paper:

    Attachment 19900

    Although the Western European modern human contamination of 43% is not reliable
    as indicated by the "F" in the convergence column (meaning the program did not converge. We consider various factors such as Tau being <1, cont rates being much lower than 100%, error rates), it is nonetheless thought provoking considering that the remains lay in a museum for 50 years before being sequenced.


    The implication in all of this is the REAL MA1 was likely less W European shifted (by whatever contamination %) and more S/E Eurasian shifted, meaning that it is likely more important to Asians than any analysis using the sample shows.


    Also, I believe that the Raghavan paper that published MA1 and Afontova Gora, gave an estimate of modern human contamination of Afontova Gora as 30% in the supp. Thus, Afontova Gora results should also be viewed in that context, namely 30% artificially Russian handler shifted.
    1) Any contamination involving modern Western Eurasian DNA would introduce basal Eurasian.
    2) MA1 does not demonstrate any signal of basal Eurasian.
    Conclusion: MA1 does not possess modern Western Eurasian contamination.

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  12. #937
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    Quote Originally Posted by Kale View Post
    1) Any contamination involving modern Western Eurasian DNA would introduce basal Eurasian.
    2) MA1 does not demonstrate any signal of basal Eurasian.
    Conclusion: MA1 does not possess modern Western Eurasian contamination.
    I’m not saying that MA1 is substantially contaminated by Russian DNA because I personally have not genotyped it yet or analyzed it for contamination.. In fact, the ones that published it estimated only 1-2% contamination for MA1 1st extraction and 10-20% for MA1 supernatant. I assume what they published is 1st extraction. What raised a little doubt for me was the analysis published by Renaud et al (attachment 19900 in my post you quoted). However, for the results showing contamination of MA1, the program did not converge, thus the results are not valid.

    I am curious though what test you are basing your basal eurasian statement on (please post), because that same test should show AG with basal eurasian since we know it is 30-35% contaminated as per the authors that published it.

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  14. #938
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    Quote Originally Posted by Kurd View Post
    The above was estimated by the authors using the mt method. They also estimated contamination using the X chromosome method. Their results were:

    AG-2: 30%
    MA1: 1.5%

    Compared with the Mt method above:

    AG-2:35%
    MA1 1st extraction: 1%


    Thus there doesnít seem to be much doubt that Afontova Gora is around 30-35% contaminated with modern European DNA and thus 30-35% artificially European shifted
    Jebus... should be dropping AG from any reference pop in calcs

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  16. #939
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    Quote Originally Posted by Kurd View Post
    I’m not saying that MA1 is substantially contaminated by Russian DNA because I personally have not genotyped it yet or analyzed it for contamination.. In fact, the ones that published it estimated only 1-2% contamination for MA1 1st extraction and 10-20% for MA1 supernatant. I assume what they published is 1st extraction. What raised a little doubt for me was the analysis published by Renaud et al (attachment 19900 in my post you quoted). However, for the results showing contamination of MA1, the program did not converge, thus the results are not valid.

    I am curious though what test you are basing your basal eurasian statement on (please post), because that same test should show AG with basal eurasian since we know it is 30-35% contaminated as per the authors that published it.
    Mbuti Ust_Ishim MA1 Han -0.0036 -0.699 38616 38893 683873
    Mbuti Ust_Ishim MA1 Karitiana -0.0031 -0.593 36390 36619 683873
    Mbuti Ust_Ishim Loschbour MA1 0.0064 1.122 37100 36627 677413
    Mbuti Ust_Ishim LaBrana1 MA1 0.0102 1.756 35061 34353 638962
    Mbuti Ust_Ishim Motala_HG MA1 0.0124 2.490 33656 32830 632149

    I don't have any equivalent stats for AG2 because frankly nobody tends to run it because of such low snp count; everybody uses AG3 instead.

  17. #940
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    Quote Originally Posted by Kale View Post
    Mbuti Ust_Ishim MA1 Han -0.0036 -0.699 38616 38893 683873
    Mbuti Ust_Ishim MA1 Karitiana -0.0031 -0.593 36390 36619 683873
    Mbuti Ust_Ishim Loschbour MA1 0.0064 1.122 37100 36627 677413
    Mbuti Ust_Ishim LaBrana1 MA1 0.0102 1.756 35061 34353 638962
    Mbuti Ust_Ishim Motala_HG MA1 0.0124 2.490 33656 32830 632149

    I don't have any equivalent stats for AG2 because frankly nobody tends to run it because of such low snp count; everybody uses AG3 instead.
    Dstats are very useful but clearly not for this purpose, because there is so many things besides basal Eurasian admixture that can affect the outcome. First, the MA1 split is closer to the Ust split than splits such as WHG are to Ust. Second, it is impossible to assess how "drifted" the various WHGs are in comparison to MA1, and one can go on. Each of these factors can act to increase or decrease shared alleles with Ust.

    If you want to use dstats, then it is best to compare members of the same clade (MA1, AG2, AG3) against various genomes to assess basaleness, Russian shift, W European shift, etc. I ran a few for you which you can archive for future use. You may be able to discern patterns although it is still impossible to quantify the amount of modern DNA contamination based on these, but you can certainly pick up oddities. To gauge basalness, I used the imputed Satsurbila, the high coverage (10X) Iran WC1, and Natufian. To assess Russian shift, I used Belarousans, and to assess W European shift I used French.

    One should also keep in mind that AG2 is only 0.071 average coverage, AG3 is 0.17 average coverage, and MA1 is quite a bit better at 1.17 coverage, although none are high coverage enough for me to diploid genotype.

    No POP1 POP2 TARGET OUTGROUP D Z SNPs
    1 AfontovaGora3_Damage_Fu AfontovaGora2_Fu Belarusian Mbuti -0.0403 -2.881 12771
    2 AfontovaGora2_Fu EHG Belarusian Mbuti -0.0231 -2.756 38621
    3 AfontovaGora3_Damage_Fu EHG Belarusian Mbuti -0.0318 -5.453 133025
    4 AfontovaGora2_Fu EHG_I0061_ATLAS_DP2 Belarusian Mbuti -0.0198 -2.587 29932
    5 AfontovaGora3_Damage_Fu EHG_I0061_ATLAS_DP2 Belarusian Mbuti -0.0279 -5.124 104838
    6 AfontovaGora2_Fu EHG_I0061_PMDS_DP2 Belarusian Mbuti -0.0349 -3.062 12081
    7 AfontovaGora3_Damage_Fu EHG_I0061_PMDS_DP2 Belarusian Mbuti -0.0488 -6.854 46020
    8 AfontovaGora2_Fu Malta1_Fu Belarusian Mbuti 0.0252 2.67 30593
    9 AfontovaGora3_Damage_Fu Malta1_Fu Belarusian Mbuti 0.0055 0.878 100007
    10 AfontovaGora3_Damage_Fu AfontovaGora2_Fu Iran_n_WC1 Mbuti -0.0011 -0.034 3432
    11 AfontovaGora2_Fu EHG Iran_n_WC1 Mbuti -0.0077 -0.398 9898
    12 AfontovaGora3_Damage_Fu EHG Iran_n_WC1 Mbuti -0.0184 -1.675 36514
    13 AfontovaGora2_Fu EHG_I0061_ATLAS_DP2 Iran_n_WC1 Mbuti 0.0043 0.247 8801
    14 AfontovaGora3_Damage_Fu EHG_I0061_ATLAS_DP2 Iran_n_WC1 Mbuti -0.0095 -0.958 33030
    15 AfontovaGora2_Fu EHG_I0061_PMDS_DP2 Iran_n_WC1 Mbuti -0.0955 -3.778 3764
    16 AfontovaGora3_Damage_Fu EHG_I0061_PMDS_DP2 Iran_n_WC1 Mbuti -0.0643 -4.655 15388
    17 AfontovaGora2_Fu Malta1_Fu Iran_n_WC1 Mbuti 0.0036 0.159 7680
    18 AfontovaGora3_Damage_Fu Malta1_Fu Iran_n_WC1 Mbuti -0.013 -1.072 27206
    19 AfontovaGora3_Damage_Fu AfontovaGora2_Fu Natufian Mbuti -0.0111 -0.391 7544
    20 AfontovaGora2_Fu EHG Natufian Mbuti -0.0049 -0.29 20211
    21 AfontovaGora3_Damage_Fu EHG Natufian Mbuti -0.0227 -2.177 74063
    22 AfontovaGora2_Fu EHG_I0061_ATLAS_DP2 Natufian Mbuti 0.0081 0.534 15852
    23 AfontovaGora3_Damage_Fu EHG_I0061_ATLAS_DP2 Natufian Mbuti -0.0247 -2.642 58714
    24 AfontovaGora2_Fu EHG_I0061_PMDS_DP2 Natufian Mbuti -0.0115 -0.495 6811
    25 AfontovaGora3_Damage_Fu EHG_I0061_PMDS_DP2 Natufian Mbuti -0.026 -2.007 27192
    26 AfontovaGora2_Fu Malta1_Fu Natufian Mbuti 0.0378 1.915 15856
    27 AfontovaGora3_Damage_Fu Malta1_Fu Natufian Mbuti -0.0181 -1.541 56040
    28 AfontovaGora3_Damage_Fu AfontovaGora2_Fu Satsurbila_Imputed Mbuti -0.0119 -0.423 4584
    29 AfontovaGora2_Fu EHG Satsurbila_Imputed Mbuti -0.0105 -0.622 13303
    30 AfontovaGora3_Damage_Fu EHG Satsurbila_Imputed Mbuti -0.0076 -0.743 50218
    31 AfontovaGora2_Fu EHG_I0061_ATLAS_DP2 Satsurbila_Imputed Mbuti -0.0089 -0.58 11823
    32 AfontovaGora3_Damage_Fu EHG_I0061_ATLAS_DP2 Satsurbila_Imputed Mbuti -0.0057 -0.609 45491
    33 AfontovaGora2_Fu EHG_I0061_PMDS_DP2 Satsurbila_Imputed Mbuti -0.0401 -1.72 5108
    34 AfontovaGora3_Damage_Fu EHG_I0061_PMDS_DP2 Satsurbila_Imputed Mbuti -0.0337 -2.7 21172
    35 AfontovaGora2_Fu Malta1_Fu Satsurbila_Imputed Mbuti 0.0003 0.014 10297
    36 AfontovaGora3_Damage_Fu Malta1_Fu Satsurbila_Imputed Mbuti 0.0001 0.013 37364


    To recap the authors estimated AG2 contamination with modern human DNA at 30-35%. You can get a hint of this in the no 2 & 3 stats where AG2 is quite a bit more Belarousan shifted than AG3. I'm sure you can pick up more such patterns. Nothing like that sticks out for MA1, you may want to check yourself though.

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