qpAdm thread

[JamesBond007]

nice! are those reference populations from the Reich lab dataset? I can send you Danish, Irish, Welsh etc. if you are interested

Yes, please, that would be great thanks ! Those reference populations are from a combination of HGDP and the 1,0000 genome project I merged them so it is likely they come from both projects but maybe most of them from one I'd have to double check if you want details.

P.S. it is shame this thread is so dead but other stupid threads here are more popular !

[vbnetkhio]

Yes, please, that would be great thanks ! Those reference populations are from a combination of HGDP and the 1,0000 genome project I merged them so it is likely they come from both projects but maybe most of them from one I'd have to double check if you want details.

P.S. it is shame this thread is so dead but other stupid threads here are more popular !

this dataset has Welsh samples:
https://evolbio.ut.ee/Ongaro_2019/

German:
https://evolbio.ut.ee/turkic/

Swedish:
https://evolbio.ut.ee/khazar/

i'll send you the rest later

[JamesBond007]

this dataset has Welsh samples:
https://evolbio.ut.ee/Ongaro_2019/

German:
https://evolbio.ut.ee/turkic/

Swedish:
https://evolbio.ut.ee/khazar/

i'll send you the rest later

Ok, thanks a lot man.

[Lucas]

I want to know if playing in qpadm only with modern samples is "valid" methodology. Outside TA all people discussing qpadm use only ancient samples.
But honestly I am much more interested in modern admixtures.

[vbnetkhio]

I want to know if playing in qpadm only with modern samples is "valid" methodology. Outside TA all people discussing qpadm use only ancient samples.
But honestly I am much more interested in modern admixtures.

it 's valid

here on page 91 onwards they start modelling with moderns:
https://www.ncbi.nlm.nih.gov/pmc/art...Supplement.pdf

they also use moderns as outgroups:

From Imperial period onward
To further increase the power to find best fit models for samples in Imperial era and later in qpAdm
analysis, we defined an additional “right” (outgroup) population set consisting of 18 diverse modern
populations (MOD18) (with the sample size indicated by the number in the parentheses):
Ami (10), Basque (29), BedouinB (19), Biaka (20), Bougainville (2), Chukchi (20), Eskimo_Naukan (12),
Han (43), Iranian (38), Ju-hoan_North (5), Karitiana (12), Mbuti (10), Papuan (14), Russian (22),
Sardinian (27), She (10), Ulchi (25), Yoruba (30).
As for earlier time periods, we performed qpAdm admixture modeling for Italian individuals sampled in
Imperial era and later in a stepwise fashion. Having observed the high inter-individual ancestry diversity
in Iron Age and after, we did not test one-way models, as a positive result (p>0.05) would only indicate
that the average ancestries of the sampled individuals from the two populations happened to be similar.
Instead, we tested two-way models for individual in each time period, proposing the two sources to be
preceding Italian samples in last period and another ancient population (Iron Age onward) or a modern
population. We considered a model to be acceptable if it has p>0.05 with both ANC17 and MOD18 as the
right set, and reported the results under MOD18, unless otherwise noted.

[JamesBond007]

I want to know if playing in qpadm only with modern samples is "valid" methodology. Outside TA all people discussing qpadm use only ancient samples.
But honestly I am much more interested in modern admixtures.

It is a matter of statistics I'd venture to guess maybe some statistical methods are valid or 'more valid' than others when dealing with modern populations. It is really a math issue here not the tool itself IMHO but I'm not a mathematician.

[Zoro]

well that's unfortunate, I wanted to hear both sides and try out both yours and his advice.

Ok I’ll give a 2nd chance but any wise guy comments from him or anyone else who thinks they know better and I’m out for good.

[Zoro]

I want to know if playing in qpadm only with modern samples is "valid" methodology. Outside TA all people discussing qpadm use only ancient samples.
But honestly I am much more interested in modern admixtures.

Yes

[Zoro]

It is a matter of statistics I'd venture to guess maybe some statistical methods are valid or 'more valid' than others when dealing with modern populations. It is really a math issue here not the tool itself IMHO but I'm not a mathematician.

QpAdm is a powerful tool in modelling present-day pops as admixtures of other present-day pops except perhaps in situations of continuous geneflow over an extended period of time

[Zoro]

P.S. it is shame this thread is so dead but other stupid threads here are more popular !

Nothing more than a reflection of the type of audience here. Looks like just a handful of people interested in more serious analysis, or are able to understand serious analysis in the first place