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Thread: Global25 automated nMonte for South/Central Asian members

  1. #3901
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    Code:
    Averages	850	Barcin_N +Dai +Ganj_Dareh_N +Han +Khvalynsk_Eneolithic +Levant_N +Simulated_AA_Basal_by_DMXX +Simulated_ASI_NW_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N +Yoruba	Pashtun:surbakhun_AGUser	2.7725	Pashtun	surbakhun_AGUser	19.17	0	47.5	4.17	19.17	0	0	7.5	0	2.5	0
    Individuals	850	Barcin_N +Dai +Ganj_Dareh_N +Han +Khvalynsk_Eneolithic +Levant_N +Simulated_AA_Basal_by_DMXX +Simulated_ASI_NW_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N +Yoruba	Pashtun:surbakhun_AGUser	2.0048	Pashtun	surbakhun_AGUser	23.33	0	41.67	3.33	12.5	0	0	9.17	0	10	0
    
    Averages	844	Barcin_N +Dai +Ganj_Dareh_N +Han +Khvalynsk_Eneolithic +Levant_N +Simulated_AA_Basal_by_DMXX +Simulated_ASI_NW_by_DMXX +Simulated_ASI_South_by_DMXX+West_Siberia_N +Yoruba	Pashtun:HGDP00259		2.1791	Pashtun	HGDP00259		15	0	45	3.33	25	0	0	11.67	0	0	0
    Individuals	844	Barcin_N +Dai +Ganj_Dareh_N +Han +Khvalynsk_Eneolithic +Levant_N +Simulated_AA_Basal_by_DMXX +Simulated_ASI_NW_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N +Yoruba	Pashtun:HGDP00259		1.5147	Pashtun	HGDP00259		17.5	0	41.67	3.33	22.5	0	0	12.5	0	2.5	0
    
    Averages	540	Barcin_N +Dai +Ganj_Dareh_N +Han +Khvalynsk_Eneolithic +Levant_N +Simulated_AA_Basal_by_DMXX +Simulated_ASI_NW_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N +Yoruba	Kalash:Average		        2.479	Kalash	Average		        11.67	0	46.67	1.67	23.33	0	0	11.67	0	5	0
    Individuals	540	Barcin_N +Dai +Ganj_Dareh_N +Han +Khvalynsk_Eneolithic +Levant_N +Simulated_AA_Basal_by_DMXX +Simulated_ASI_NW_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N +Yoruba	Kalash:Average		        1.5575	Kalash	Average		        15	0	42.5	1.67	18.33	0	0	12.5	0	10	0
    It seems the difference for the most part is higher Barcin and lower AASI. She doesn't even score Levant N. Difference in AASI is more apparent here(default pen):

    Code:
    1	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Naxi +Simulated_AA_Basal_by_DMXX +Simulated_ASI_NW_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Custom:AGUser_Kaido	        1.7808  Open Map	16.67	0	44.17	10	1.67	0	12.5	4.17	10.83
    2	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Naxi +Simulated_AA_Basal_by_DMXX +Simulated_ASI_NW_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Kalash:Average		        1.9565	Open Map	12.5	4.17	42.5	17.5	0.83	0.83	10.83	1.67	9.17
    3	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Naxi +Simulated_AA_Basal_by_DMXX +Simulated_ASI_NW_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Pashtun:HGDP00259		2.1689	Open Map	18.33	5.83	37.5	12.5	0.83	0.83	10.83	3.33	10
    4	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Naxi +Simulated_AA_Basal_by_DMXX +Simulated_ASI_NW_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Pashtun:surbakhun_AGUser	2.5251	Open Map	20	4.17	44.17	11.67	4.17	0.83	5.83	0.83	8.33
    Last edited by Censored; 01-17-2019 at 12:03 AM.

  2. #3902
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    Quote Originally Posted by Sapporo View Post
    The decrease isnít consistent across individuals. When you say ENA portion, are you referring to the WSHG in Iran N or the 6-8% AASI? The AASI % is too small for it to cause Ganj Dareh to decrease from like 42% to 35%. It could be the WSHG coming out though. Although, thatís not consistent either as poiís father in law is scoring 25% WSHG and 3% Khvalynsk, which is sort of ridiculous. Finally, I have no idea what the batch or cycle settings were either. If they were low, the run could have just been very noisy. Poi, do you mind including batch and cycle counts in future runs?
    If you score East Eurasian, WSHG /EHG scores will be lopsided more than often, because of the East Eurasian in WSHG. Ganj Dareh does not have WSHG, but some how all the Turan samples and IVCp samples harbor something similar to it. My guess its part of the genome of the hunter gatherer populations which lived in this area during the Younger Dryas . The splitting of the AASI seems to trigger a split up the Iran_N part of it goes into Barcin, this likely is the Basal Eurasian/ Dzu forager effect I feel.

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  4. #3903
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    Quote Originally Posted by pegasus View Post
    If you score East Eurasian, WSHG /EHG scores will be lopsided more than often, because of the East Eurasian in WSHG. Ganj Dareh does not have WSHG, but some how all the Turan samples and IVCp samples harbor something similar to it. My guess its part of the genome of the hunter gatherer populations which lived in this area during the Younger Dryas . The splitting of the AASI seems to trigger a split up the Iran_N part of it goes into Barcin, this likely is the Basal Eurasian/ Dzu forager effect I feel.
    That makes sense. Most NW South Asians in Punjab, Haryana and Sindh score negligible East Eurasian. However, those from Jammu, Himachal or AJK/Potohar along with Pashtuns, Burusho, Kho and Nepali Brahmins might be getting inflated WSHG/EHG scores in certain runs.
    pegasus modeling:
    sample": "Punjabi_Jat:Sapporo_AGUser",
    "fit": 1.1506,
    "IRN_Shahr_I_Sokhta_BA3": 43.33,
    "TKM_Gonur1_BA": 31.67,
    "RUS_Sintashta_MLBA": 25,
    "closestDistances": [

    avatar credit goes out to aaronbee2010

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  6. #3904
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    Quote Originally Posted by Sapporo View Post
    I still see that the biggest issue with these runs is that there is no significant preference for Simulated AASI NW vs. South between groups and individuals. Look at the Tarkalani for example. For 1000/120 cycles/batches and default pen, they're scoring 8.33% Simulated AASI South and 5.83% Simulated AASI NW and 2.5% Simulated AA Basal By DMXX. This is despite the huge difference in distance between AASI NW and AASI South as previously illustrated by DMXX. Even for groups with very low AASI such as Tajik_Ishkashim, it's a similar situation.

    I'll note that I'm specifically referencing 1000/120 cycles/batches and default pen as it should be the most reliable despite having the worst fits.
    You're right. Something seems amiss with those settings. I'm coming out as 4% Simulated AA, as is Kaido.

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  8. #3905
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    Quote Originally Posted by Sapporo View Post
    That makes sense. Most NW South Asians in Punjab, Haryana and Sindh score negligible East Eurasian. However, those from Jammu, Himachal or AJK/Potohar along with Pashtuns, Burusho, Kho and Nepali Brahmins might be getting inflated WSHG/EHG scores in certain runs.
    Yes, the same may be true for the people in G25 from around central Kerala. I'd be surprised if I have 13% WSHG but pretty much 0% Khlvanysk.

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  10. #3906
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    Quote Originally Posted by traject View Post
    Yes, the same may be true for the people in G25 from around central Kerala. I'd be surprised if I have 13% WSHG but pretty much 0% Khlvanysk.
    Do you score non negligible East Eurasian? WSHG is certainly going to be more common throughout South Asia than Khvalynsk, which we're using as a proxy for Pontic Steppe (+ some of Barcin N). Though, Khvalynsk itself is certainly part WSHG like with the rest being more WHG like. Someone correct me if I'm wrong but I believe EHG is an even more WSHG shifted version of Khvalynsk and also a much older sample.
    Last edited by Sapporo; 01-17-2019 at 07:25 PM.
    pegasus modeling:
    sample": "Punjabi_Jat:Sapporo_AGUser",
    "fit": 1.1506,
    "IRN_Shahr_I_Sokhta_BA3": 43.33,
    "TKM_Gonur1_BA": 31.67,
    "RUS_Sintashta_MLBA": 25,
    "closestDistances": [

    avatar credit goes out to aaronbee2010

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  12. #3907
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    Quote Originally Posted by Sapporo View Post
    Do you score non negligible East Eurasian? WSHG is certainly going to be more common throughout South Asia than Khvalynsk, which we're using as a proxy for Pontic Steppe (+ some of Barcin N). Though, Khvalynsk itself is certainly part WSHG like with the rest being more WHG like. Someone correct me if I'm wrong but I believe EHG is an even more WSHG shifted version of Khvalynsk and also a much older sample.
    Wel, partially the reason why I am skeptical is because the Khvalnysk sample is not particularly high-res (I would wait for G25 samples from Wang et al.) and secondly I am skeptical I have such a low percentage of Steppe associated EHG when historically it makes sense to have more of that than WSHG (the inconsistency of the results do not seem encouraging in that aspect). If the same patterns noticed now hold with the higher quality Wang samples, then I may have to reconsider my skepticism.

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  14. #3908
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    Quote Originally Posted by traject View Post
    Wel, partially the reason why I am skeptical is because the Khvalnysk sample is not particularly high-res (I would wait for G25 samples from Wang et al.) and secondly I am skeptical I have such a low percentage of Steppe associated EHG when historically it makes sense to have more of that than WSHG (the inconsistency of the results do not seem encouraging in that aspect). If the same patterns noticed now hold with the higher quality Wang samples, then I may have to reconsider my skepticism.
    Well, the easiest way to currently address your skepticism is to model yourself with higher res Steppe samples such as Sintashta, Srubnaya, Afanasievo, etc. alongside WSHG and see if your Khvalnysk + Barcin N score is roughly comparable. It's also possible that if your Barcin N score is high and you score low Khvalnysk but high WSHG, then your EHG like (WHG + WSHG) Steppe just might be quite low.
    Last edited by Sapporo; 01-17-2019 at 07:44 PM.
    pegasus modeling:
    sample": "Punjabi_Jat:Sapporo_AGUser",
    "fit": 1.1506,
    "IRN_Shahr_I_Sokhta_BA3": 43.33,
    "TKM_Gonur1_BA": 31.67,
    "RUS_Sintashta_MLBA": 25,
    "closestDistances": [

    avatar credit goes out to aaronbee2010

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  16. #3909
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    Quote Originally Posted by Sapporo View Post
    Do you score non negligible East Eurasian? WSHG is certainly going to be more common throughout South Asia than Khvalynsk, which we're using as a proxy for Pontic Steppe (+ some of Barcin N). Though, Khvalynsk itself is certainly part WSHG like with the rest being more WHG like.
    You've suddenly reminded me of the old discussions that were had many months ago about a pre-MBA steppe, WSHG-like ancestral layer in the Subcontinent. Well, this was before I created the phantom ASI coordinates.

    Let's see... (cyc=1k bat=0.5k pen=def):

    Code:
    	Model	Sample	Details	Fit	Map	Barcin N	CHG	Ganj Dareh N	Khvalynsk Eneolithic	Simulated AA Basal By DMXX	Simulated ASI South By DMXX	West Siberia N
    1	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Bonda:Average		3.6124	Open Map	0	0	0	0	58.6	41.4	0
    2	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:Average		3.3032	Open Map	1.6	0.8	8.6	2	0	82.8	4.2
    3	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Paniya:Average		2.6309	Open Map	1.2	0.4	4.2	2	0	90.2	2
    4	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Pulliyar:Average		3.5421	Open Map	3.6	0.6	6.4	2.6	0	84.4	2.4
    5	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Santhal:Average		3.011	Open Map	0	0	2.4	0.6	21.8	73.6	1.6
    Interestingly, the peripheral Dravidian tribal average score for WSHG (~3%) is more than Khvalynsk (~2.3%) - WSHG is double Khvalynsk in the Irula. That does seem to confirm the "early WSHG" idea for the Subcontinent.

    Checking the individual Irula samples:

    Code:
    	Model	Sample	Details	Fit	Map	Barcin N	CHG	Ganj Dareh N	Khvalynsk Eneolithic	Simulated AA Basal By DMXX	Simulated ASI South By DMXX	West Siberia N
    1	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:IL-1		3.3661	Open Map	2.4	1.2	7.6	1.8	0	83.4	3.6
    2	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:IL-10		3.3369	Open Map	2.4	1.4	8.6	2	0	82	3.6
    3	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:IL-12		3.3205	Open Map	2	1.2	8.8	2.4	0	81.8	3.8
    4	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:IL-16		3.6854	Open Map	1.4	1.4	6.6	1.4	0	84.8	4.4
    5	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:IL-18		4.7266	Open Map	4.2	2	9.4	3	0	77.4	4
    6	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:IL-22		3.606	Open Map	1.8	0.8	6.6	1.6	0	86.8	2.4
    7	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:IL-24		3.9081	Open Map	1.8	0.4	8.6	2.4	0	83.6	3.2
    8	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:IL-25		3.3501	Open Map	2	1.2	7.2	2	0	84.8	2.8
    9	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:IL-26		3.4611	Open Map	2.8	0.8	7	2.2	0	82.8	4.4
    10	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:IL-27		3.8878	Open Map	1.4	1.2	7.6	1.6	0	85.4	2.8
    11	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:IL-29		3.9534	Open Map	1.4	0.8	8.8	2.2	0	83.6	3.2
    12	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:IL-3		3.4047	Open Map	2.2	0.8	9.6	1.8	0	82.6	3
    13	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:IL-30		5.0169	Open Map	3	1.8	8.4	2	0	79.2	5.6
    14	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:IL-31		3.9712	Open Map	3.4	1	11.4	1.6	0	78.4	4.2
    15	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:IL-33		4.7136	Open Map	1.8	0.8	6.2	1.8	0	85.6	3.8
    16	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:IL-34		3.9023	Open Map	1.4	2	7.6	1.8	0	84	3.2
    17	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:IL-35		3.6811	Open Map	2.8	1.2	7.8	2.2	0	82	4
    18	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:IL-7		3.7554	Open Map	1.4	1.6	6.6	1.2	0	84.6	4.6
    19	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:IL-8		3.7349	Open Map	1.2	1	8.6	2	0	83.4	3.8
    20	Barcin_N +CHG +Ganj_Dareh_N +Khvalynsk_Eneolithic +Simulated_AA_Basal_by_DMXX +Simulated_ASI_South_by_DMXX +West_Siberia_N	Irula:IL-9		3.8867	Open Map	2.6	0.6	7	1.2	0	85.4	3.2
    IL-30 is 6% WSHG and only 2% Khvalynsk. Cool stuff.

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  18. #3910
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    Quote Originally Posted by Sapporo View Post
    Well, the easiest way to currently address your skepticism is to model yourself with higher res Steppe samples such as Sintashta, Srubnaya, Afanasievo, etc. alongside WSHG and see if your Khvalnysk + Barcin N score is roughly comparable. It's also possible that if your Barcin N score is high and you score low Khvalnysk but high WSHG, then your EHG like (WHG + WSHG) Steppe just might be quite low.
    At 500 batches/100 cycles/pen=0,
    Without Barcin:
    WithoutBarcin.png
    With Barcin (which may be warranted given extra West Asian affinities of my ethnic group even given the cost of perhaps overfitting with Sintashta):
    WithBarcin.png

    Adding or removing Barcin causes either WSHG or Sintashta to dominate but the results with Barcin added most closely echo the earlier Elemental SC/S Asia run percentage wise (Ganj Dareh scores and Naxi appear to increase substantially without Barcin). So there may be good merit to the explanation of a pre-existing WSHG layer in the subcontinent perhaps.

  19. The Following 2 Users Say Thank You to traject For This Useful Post:

     FrostAssassin0701 (01-17-2019),  poi (01-17-2019)

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