It took me a while. Had so many organic errors; you know that life form between the chair and the keyboard J. Part of the reason why I wrote a little procedure here.
CAVEAT: Only was able to merge 22k SNPs. So this ratio is representative of only ~20% of my known SNPs from 23nMe. But I think the proportion is good enough to make some inferences.
Because of the caveat, it’s difficult to determine some of the populations. The Nusantao (Malay speakers), Ryuku and Hmong-Mien speakers (at the least) may have absorbed the Tai-Kadai, Mhon-Khmer, & Han genes because (as I described in this blog), the close genetic distance of these groups are small. It’s also possible these genes were eliminated from the limited SNP used in admixture analysis.
I’m Filipino (Both parents are Ilokano). Ilokanos are from Luson (Northern Philippines).
I initially tried to use what the cross-validation results showed as best from the complete 55K PASNP data but, because of the caveat, K=16 was makes more sense with the population assignment.
The biggest surprise was my Ita genes! Never expected it. Looking at the complete PASNP data, Filipinos have on average ~8% Ita genes which is similar to my results but if I include the Papuans (which I also consider Itas) my Ita gene would be ~11%. After looking into the PASNP data, I believe most/majority of Filipinos has Ita genes and this has been due to a symbiotic relationship that happened way before the Southeast Asian Maritime Trading Network began.
My admixture with Philippine Itas (Ati, Ayta, Agta, Iraya and Mamanwa) is basically due to the proximity. Now, for the Malaysia Ita and Papuan gene, my ancestors probably picked this up from admixture with Philippine Itas; the Philippine Itas themselves has a significant Malaysia Ita and Papuan gene.
The Dayak people are probably one of the first waves of Deutero-Malays in ISEA. One of the ways scientists stratify social evolutions is with food gathering
1. Hunter-gatherer
2. Slash and burn Agriculture (Neolithic)
3. Advance Agriculture
The Dayak peoples agricultural methods (slash-burn) may be clue to them being first wave. The Malay speakers are probably the later waves.
I’m not sure how I got the Ryukyu except that our Malay ancestors have been trading with them during the great Southeast Asian Maritime Trading Network (Solheim 2006). The Ryukyu samples in the PASNP data do have 0.3% admixture with the Malay speakers and out of the 49 samples one has 6.6%.
The European gene is likely because of the Spanish occupation of the Philippines.
REFERENCES
1. Yang X, Xu S, The HUGO Pan-Asian SNP Consortium (2011) Identification of Close Relatives in the HUGO Pan-Asian SNP Database. PLoS ONE 6(12): e29502. doi:10.1371/journal.pone.0029502
2. D.H. Alexander, J. Novembre, and K. Lange. Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19:1655–1664, 2009
3. H. Zhou, D. H. Alexander, and K. Lange. A quasi-Newton method for accelerating the convergence of iterative optimization algorithms. Statistics and Computing, 2009.
4. Alexander D. H., Lange K. (2011). Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics 12:246. doi: 10.1186/1471-2105-12-246.
5. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81.
6. WDIST is developed, tested, and documented primarily by Christopher Chang and Laurent Tellier at the BGI Cognitive Genomics Lab and Carson Chow, James Lee, and Shashaank Vattikuti at the NIH-NIDDK's Laboratory of Biological Modeling.
7. Solheim, Wilhelm G. Archaeology and culture in Southeast Asia : unraveling the Nusantao, (revised edition), Diliman, Quezon City : University of the Philippines Press, 2006.
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