I had always wanted to do Denisovan comparisons with moderns, but ascertainment bias had always rendered the results of any such comparisons with moderns pretty much useless. As a result, I could never do any meaningful IBS comparisons, or put together a decent admixture calculator using Denisovans. Analysis using the the normal datasets in use were always giving weird results such as Europeans and Africans showing more similarity to Denisovans.

I dexided to put some time aside to see if I could overcome the problem with ascertainment bias, which is basically a problem of the SNPs sampled not being representative of the alleles in an individual. For example, the widely used Eurasian ascertained arrays, which are based on polymorphic loci that distinguish Eurasians, do not permit accurate comparisons with others with widely divergent histories from Eurasians, such as Africans, and archaics, such as Denisovan. Therefore the Eurasian ascertained arrays don't properly represent derived alleles uniquely attributed to Denisovans.

It appears that I now finally have a decent dataset that I can use as a backbone for future Denisovan comparisons. This may lead to the 1st decent GEDmatch Denisovan calculator. Here are some IBS results, sorted with highest similarity to Denisovans. The results seem quite reasonable, especially since I am not using whole genome data, as would be expected to get meaningful results for any such comparisons.

Immediately apparent, is Papuans, and other Austronesians scoring much higher similarity to Denisovan. I was also pleased to see that E Asians were on top and not in the bottom, and Africans in the bottom. All in all good news.

NOSAMPLE / POPDENISOVA1 IBS1Denisova_light100.00%2Denisovan98.74%3Vindija_light84.17%4Australian62.42%5Papuan62.40%6Bougainville62.22%7MA161.84%8Itelmen61.55%9Eskimo61.54%10Chukchi61.54%11Nganasan61.50%12Karitiana61.49%13Cambodian61.46%14Ami61.44%15Dai61.44%16GujaratiD61.43%17Kusunda61.42%18Japanese61.42%19Han61.42%20Mongola61.41%21GujaratiC61.36%22Uzbek61.35%23GujaratiB61.33%24Scottish61.32%25Kalash61.31%26GujaratiA61.29%27Bengali61.29%28English61.29%29Estonian61.28%30Norwegian61.28%31Balochi61.27%32Iranian61.27%33Greek61.26%34Loschbour61.26%35Pathan61.26%36Algerian61.23%37Sardinian61.23%38LBK61.23%39Spanish61.22%40Saudi61.22%41Egyptian61.19%42Armenian61.17%43Somali61.16%44Hadza61.09%45Khomani58.72%