Diagnosis at ANC was based on linkage to HIV test results in PMTCT testing registers, or prior VCT.
This program is based on linkage desequilibrium, neutrality tests and substitution distribution along the locus.
Statistical methods (based on linkage desequilibrium, neutrality tests and substitution distribution along the locus) are still too rudimentary to precisely describe the recombination events in the set of ITS sequences found in I. canariensis.
Two tests of gene flow, one based on linkage disequilibrium and a MCMC analysis based on coalescence, suggest that the two species might be exchanging alleles at the per locus.
However, an alternative explanation is that comparisons with the chimpanzee - an evolutionarily closed outlier; have less statistical power than comparisons with the rhesus monkey and therefore, our data may be also compatible with a more recent action of natural selection, though not recent enough to be detected using neutrality tests based on linkage disequilibrium [33].
Besides these methods, selection can be detected using Poisson random-field models [ 28- 30], and tests based on linkage disequilibrium, haplotype structure and population differentiation [ 31- 36].
Unlike FST and Peddrift, tests based on linkage disequilibrium, such as the extended haplotype homozygosity (EHH) statistic and its derivatives, are dependent on SNP spacing and frequency, as they are multi-marker tests.
Thus, a significant homozygote excess (Pearson's X2 for deviation from Hardy-Weinberg expectations = 21.18, P < 0.0001) was found among the parents that were a priori believed to be QTL homozygous based on linkage analysis (i.e. on the earlier test for QTL based on challenge-tested offspring).
We pruned the dataset based on linkage disequilibrium (LD) to reduce the number of tests performed.
These sets were chosen to eliminate any dependency in each test between the two half data sets based on linkage disequilibrium.
