Waves of migration into South Asia

[Vaishvamitra]

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

[Kurd]

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 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

[parasar]

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.

[Kurd]

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]

[Kurd]

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

[Kale]

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.

[Kurd]

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.

[bmoney]

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

Jebus... should be dropping AG from any reference pop in calcs

[Kale]

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.

[Kurd]

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.