In the current post, I explore this issue further by using the SNP ascertainment panels released by Patterson et al. (2012). In particular, I use panel #3, which involves 48,531 SNPs ascertained in a Papuan individual.
MbutiPygmy French ; Denisova Chimp 0.0234 2.597
Yoruba French ; Denisova Chimp 0.0303 3.970
San French ; Denisova Chimp 0.0334 3.475
BantuKenya French ; Denisova Chimp 0.0206 2.625
MbutiPygmy Sardinian ; Denisova Chimp 0.0224 2.413
Yoruba Sardinian ; Denisova Chimp 0.0293 3.683
San Sardinian ; Denisova Chimp 0.0324 3.319
BantuKenya Sardinian ; Denisova Chimp 0.0196 2.399
MbutiPygmy Dai ; Denisova Chimp 0.0331 3.347
Yoruba Dai ; Denisova Chimp 0.0401 4.694
San Dai ; Denisova Chimp 0.0428 4.265
BantuKenya Dai ; Denisova Chimp 0.0307 3.524
MbutiPygmy Japanese ; Denisova Chimp 0.0366 3.833
Yoruba Japanese ; Denisova Chimp 0.0436 5.256
San Japanese ; Denisova Chimp 0.0463 4.724
BantuKenya Japanese ; Denisova Chimp 0.0342 4.070
MbutiPygmy Karitiana ; Denisova Chimp 0.0187 1.611
Yoruba Karitiana ; Denisova Chimp 0.0252 2.320
San Karitiana ; Denisova Chimp 0.0287 2.457
BantuKenya Karitiana ; Denisova Chimp 0.0158 1.461
MbutiPygmy Surui ; Denisova Chimp 0.0303 2.486
Yoruba Surui ; Denisova Chimp 0.0368 3.260
San Surui ; Denisova Chimp 0.0398 3.265
BantuKenya Surui ; Denisova Chimp 0.0275 2.429
All of these are positive, and many of them are significant with a Z-score greater than 3. Africans appear more "Denisovan" than West/East Eurasians and Amerindians using this panel. So, perhaps, this is another indication of the "surprising link" I discovered in my previous post.
This link may have been overlooked in previous analyses which found that Africans are less Denisovan than all Eurasian groups. But, as I argue in my previous post, this is potentially due to introgression of archaic African alleles into living Sub-Saharan Africans which shifted them away from Denisovans. So, the African story may involve admixture between a population somehow related to Denisovans (whether due to an early Out-of-Africa that affected them, or due to an Into-Africa event), and divergent native Palaeoafrican populations.
It would be worthwhile to follow up on these observations using the high-quality Denisovan genome recently published, to see how they might hold up.