December 03, 2012

'globe13anc' calculator with chimp outgroup

I was thinking a bit about my suggestion to use Palaeo_African as an outgroup for D-statistic calculations using my new admixtureDstat script, and it occurred to me that it would be fairly easy to modify one of my calculators to include a sample that is indeed symmetrically related to all modern human groups.

To do this, I created an individual possessing the ancestral allele using hgdpGeo as a reference. According to the reference for this table:

Samples collected by the HGDP-CEPH from 1,043 individuals from around the world were genotyped for 657,000 SNPs at Stanford. Ancestral states for all SNPs were estimated using whole genome human-chimpanzee alignments from the UCSC database. For each SNP in the human genome (NCBI Build 35, UCSC database hg17), the allele at the corresponding position in the chimp genome (Build 2 version 1, UCSC database pantro2) was used as ancestral.
My new globe13anc calculator is simply a version of the latest globe13 one, but with an extra "Ancestral" component, so it has 13+1 = 14 ancestral components in total.

You can of course use globe13anc as any other calculator designed for DIYDodecad, and hopefully no one will get anything other than 0% for the "Ancestral" component :)

But, the main point of building this is to help you infer D-statistics with no suspicion that gene flow within the human species may affect the results; while the Khoesan of South Africa (where the Palaeo_African component is modal) are an approximate outgroup to the rest of mankind, there is evidence that even their most isolated groups have some external gene flow. So, using this "Ancestral" outgroup instead of Palaeo_African ought to make things cleaner for everyone.

12 comments:

pconroy said...

Great work Dienekes!

Surprise, surprise - my father is 0.04% Ancestral!!!

0.24% Siberian
0.78% Amerindian
0.00% West_African
0.04% Palaeo_African
0.46% Southwest_Asian
0.00% East_Asian
33.57% Mediterranean
0.21% Australasian
0.00% Arctic
6.40% West_Asian
57.13% North_European
1.04% South_Asian
0.08% East_African
0.04% Ancestral

I guess it's random noise - or is it?

What Outgroup would I use to check this?

Ponto said...

My ancestral result for the calculator was 0.07% which is small but the South_Asian was 0.01%.

What intrigues me is the Australasian 0.56%. I find that rather strange considering the Asian admixture especially the South_Asian and East_Asian results are smaller in magnitude.

eurologist said...

"What intrigues me is the Australasian 0.56%"

Therrre be pirrrates in your closet!

shenandoah said...

Lol, I wish someone would run my data for me (I can't do it, and don't even know if I have the right data for it)... I'm itching to find out what it would say about me.

shenandoah said...

Ponto says: "What intrigues me is the Australasian 0.56%. I find that rather strange considering the Asian admixture especially the South_Asian and East_Asian results are smaller in magnitude."

Didn't you say you're from S. America? I have a theory, that many ancient SA aboriginals originated in the ~Southern Hemisphere in places like Australia, Indonesia and Africa. I also believe that probably a lot of N. American aboriginals originated in the ~Northern Hemisphere, from Europe and Northern Asia, etc. (Something to do with the tides and wind patterns, probably.)

George said...

I hope to see a spreadsheet for these results run on Dienekes' high-powered computer. He is able to eliminate some of the noise that you can't by DIY.

Dienekes said...

on Dienekes' high-powered computer

lol

idurar said...

I scored 0.14% Ancestral.

I guess it means nothing, knowing that I still have noisier results such as over 2.5% South Asian or nearly 1% Arctic, which is very unlikely for a Berber.

Dienekes said...

It is very likely that Berbers might have an ancestral North African component that is not well-represented with the available samples. The Northwest African component which appears at higher K may be one such proxy for that, but it is also influenced by one particular Berber population (Mozabites), since there are no other ones available.

I wonder, do your "South Asian"- and "Arctic"-type components disappear if you use a calculator that includes the Northwest_African component, such as K12b?

idurar said...

I still score 1.26% South Asian with K12b but naught % of the 3 main East Eurasian components.

However I also have 1.72% Gedrosia and 1.28% North European.

Charles said...

I have analyzed a couple of genomes using this program file on a couple of primarily West African origin. I have found them to have an ancestral component from .50 to .64%. It would be interesting to see if all those of Tropical African descent have this ancestral component.

Larry said...

DOD101 I scored a 0.00% as expected.