In this case, ancestral "surface" populations are not isolated geographically from populations exploiting the novel cave niche [ 68, 71].
In our case, ancestral ranges were assumed to include no more than two areas since all extant species in the Ampelopsis clade are restricted into only one area.
Out of 1143 unique SNPs, disease-associated alleles were ancestral in 499 cases and derived in 644 cases.
These admixture proportions represent a tested individual in the space of K putative ancestral populations (for example, in case of K = 9, the ancestral populations are North-East Asian, Mediterranean, South African, South-West Asian, Native American, Oceanian, South-East Asian, Northern European, Sub-Saharan African).
For PCA method, classical principal components analysis is first applied to genotype data to model ancestral differences between cases and controls, which are then used to correct allele frequency variations at candidate loci across ancestral populations [8].
To confirm the results achieved through Structure 2.2, we further tested population stratification in our sample using EIGENSTRAT software that uses principal component analysis approach to model ancestral differences between cases and controls [23].
This supports the use of more general ancestral models in cases where a genome sequence, or specific model, or both are lacking.
cP-value obtained from testing the Native American, African and European ancestral contributions in cases and controls using Pearson's X test.
In both these cases ancestral allele determination is difficult taking only chimpanzee base position as a reference, and a three-way analysis including macaque genome can resolve the ambiguity [ 43].
