qpAdm thread

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Originally Posted by Zoro

I think the outgroup set EurasianDNA used is good because they are high quality and have high SNP overlap with your test subjects plus they can differentiate streams of ancestry well

For Serbs you can start out with higher quality neolithic farmer samples + Iron gates Whg + relevant MLBA steppe + Iron age steppe/turkic

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but is there anything obviously wrong with these outgroups? I used Afanasievo instead of Yamnaya because it's a larger and higher quality sample, and they seem to be of pure Yamnaya descent.

also Nganasan and Ami because admixture detects them as "pure" and important admixture sources, so they probably the purest descendants of some ancient populations we don't have samples of yet?

is it ok to do things like this?

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Originally Posted by vbnetkhio

but is there anything obviously wrong with these outgroups? I used Afanasievo instead of Yamnaya because it's a larger and higher quality sample, and they seem to be of pure Yamnaya descent.

also Nganasan and Ami because admixture detects them as "pure" and important admixture sources, so they probably the purest descendants of some ancient populations we don't have samples of yet?

is it ok to do things like this?

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Papuan, Nganassan, etc... are redundant since there will be no stream of ancestry from these pops to pleft.

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Originally Posted by Token

Papuan, Nganassan, etc... are redundant since there will be no stream of ancestry from these pops to pleft.

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would Tianyuan and Devil's Cave samples be a better choice?

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Originally Posted by vbnetkhio

a new version of ADMIXTOOLS is out:
https://uqrmaie1.github.io/admixtools/index.html

it's faster and more user friendly.

has anybody tried it out yet?

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I'll check it out. I'm updating my operating system to a newer version it could take hours. This new version looks interesting.

Is this different ? :

Full support for genotype data in PACKEDANCESTRYMAP/EIGENSTRAT format and PLINK format

So it will take just regular plink converted files now ? The documentation used to suck and especially for the Eigenstrat program or whatnot. That is where I got stuck If I remember correctly. I never got stuck with qpAdm I got stuck before that because the documentation sucked balls with converting files to Packagedancestrymap/Eigenstrat. However, if it just works with plink, at least with this new version, everything should be fine for me.

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Originally Posted by JamesBond007

I'll check it out. I'm updating my operating system to a newer version it could take hours. This new version looks interesting.

Is this different ? :

Full support for genotype data in PACKEDANCESTRYMAP/EIGENSTRAT format and PLINK format

So it will take just regular plink converted files now ?

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yep.

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Originally Posted by Token

Papuan, Nganassan, etc... are redundant since there will be no stream of ancestry from these pops to pleft.

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The opposite is true. In qpAdm you don’t want recent geneflow right to left

Quote:

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Originally Posted by vbnetkhio

but is there anything obviously wrong with these outgroups? I used Afanasievo instead of Yamnaya because it's a larger and higher quality sample, and they seem to be of pure Yamnaya descent.

also Nganasan and Ami because admixture detects them as "pure" and important admixture sources, so they probably the purest descendants of some ancient populations we don't have samples of yet?


is it ok to do things like this?

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We do actually have high quality WGS and diploid ancients. Yana ANS WGS and Kolyma-Mesol WGS and Devils-Gate-N Neo-Siberians such as Nganasan are descended from these. Ami have Devils-Gate

Anyways I would replace those ancient Africans with Mbuti because they have quality and SNP overlap issues

Also if you’re modelling Serbs with Neolithic and Chalcolithic keep your outgroups Neolithic and older

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Originally Posted by Zoro

The opposite is true. In qpAdm you don’t want recent geneflow right to left

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False. QpAdm assumes no streams from pleft into pright, so you choose 'deep' pops for pright to avoid violating this premise and not because you don't want recent geneflow from pright into pleft.

and how to intepret this?
the first 2 rows tell me that Estonia BA has WHG and EHG admixture, and the others just tell me that Estonia BA has steppe admixture.
how does this help me choose my outgroups?

-	pop1	pop2	pop3	pop4	est	se	z	p
	<chr>	<chr>	<chr>	<chr>	<dbl>	<dbl>	<dbl>	<dbl>
1	Greece_BA_Mycenaean	Estonia_BA.SG	Russia_Afanasievo	Luxembourg_Loschbour	0.00514	0.000811	6.35	2.22e-10
2	Greece_BA_Mycenaean	Estonia_BA.SG	Russia_Afanasievo	Russia_HG_Karelia	0.00316	0.000714	4.43	9.33e-6
3	Greece_BA_Mycenaean	Estonia_BA.SG	Russia_Afanasievo	Anatolia_N	-0.00744	0.000396	-18.8	1.63e-78
4	Greece_BA_Mycenaean	Estonia_BA.SG	Russia_Afanasievo	Poland_Globular_Amphora	-0.00546	0.000648	-8.43	3.60e-17
5	Greece_BA_Mycenaean	Estonia_BA.SG	Russia_Afanasievo	Iran_GanjDareh_N	-0.00437	0.000534	-8.17	3.08e-16
6	Greece_BA_Mycenaean	Estonia_BA.SG	Russia_Afanasievo	Kazakhstan_Eneolithic_Botai	0.00196	0.000605	3.24	1.20e-3
7	Greece_BA_Mycenaean	Estonia_BA.SG	Russia_Afanasievo	Georgia_Kotias.SG	-0.00388	0.000768	-5.05	4.48e-7
8	Greece_BA_Mycenaean	Estonia_BA.SG	Russia_Afanasievo	Morocco_Iberomaurusian	-0.00490	0.000579	-8.47	2.41e-17
9	Greece_BA_Mycenaean	Estonia_BA.SG	Russia_Afanasievo	Nganasan	-0.00152	0.000456	-3.32	8.85e-4
10	Greece_BA_Mycenaean	Estonia_BA.SG	Russia_Afanasievo	Papuan	-0.00257	0.000545	-4.72	2.30e-6
11	Greece_BA_Mycenaean	Estonia_BA.SG	Russia_Afanasievo	Ami	-0.00195	0.000484	-4.03	5.64e-5
12	Greece_BA_Mycenaean	Estonia_BA.SG	Russia_Afanasievo	ONG.SG	-0.00233	0.000579	-4.01	5.98e-5
13	Greece_BA_Mycenaean	Estonia_BA.SG	Russia_Afanasievo	South_Africa_400BP.SG	-0.00319	0.000623	-5.12	2.99e-7
14	Greece_BA_Mycenaean	Estonia_BA.SG	Russia_Afanasievo	Kenya_PastoralN	-0.00571	0.000513	-11.1	8.98e-29
15	Greece_BA_Mycenaean	Estonia_BA.SG	Russia_Afanasievo	Nepal_Samzdong_1500BP.SG	-0.00204	0.000686	-2.97	2.99e-3
16	Greece_BA_Mycenaean	Estonia_BA.SG	Russia_Afanasievo	Russia_OldBeringSea_Ekven	-0.00108	0.000469	-2.30	2.15e-2

Quote:

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Originally Posted by vbnetkhio

would Tianyuan and Devil's Cave samples be a better choice?

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Are these potential sources of ancestry for pleft pops? If no, the you don't need them. If Sunghir shows some Siberian admixture (which can be tested with G25), then it might be a good idea to include Devils Gate.