Substantial population substructure can be observed by the nonrandom grouping of population groups that extends through PC7.
These results indicate there is no substantial population substructure between American and French BMDs.
The authors raise several notes of caution, however, not least the fact that substantial geographical substructuring exists in vivax populations, which could confound efforts to find true associations between markers and traits.
With the exception of the Liverpool Lung Project, quantile quantile (Q Q) plots showed that there was minimal inflation of the test statistics, indicating that substantial cryptic population substructure or differential genotype calling between cases and controls was unlikely in each of the GWASs (Supplementary Material, Fig. S1).
These results as expected indicated substantially less substructure.
The association mapping panel was characterized by strong population substructure.
Old World populations of P. vivax showed substantial evidence of population substructure, with high sequence divergence among localities at both synonymous and nonsynonymous sites, while Brazilian isolates showed reduced diversity and little population substructure.
For WSar, the heterozygosity deficit implies a significant deviation from Hardy Weinberg equilibrium (P<0.001), that could possibly be related to a moderately high-inbreeding coefficient (FIS=0.162), but also to a substantial degree of population substructure (see Scandura et al., 2011b).
Such cytogenetic data are clearly needed even if chromosome counts appear regular [see also 43], since a deeper analysis of the genome and chromosome substructure can reveal substantial chromosome dosage deviation from expectation.
The genomic inflation factor lamda was calculated as 1.043, suggesting that the population substructure, if any, should not have a substantial effect on result.
