Dynamics of cross-species transmission in SIV

Extensive divergence makes sitewise measures of genetic linkage ineffective

For pairs of biallelic sites (ignoring rare variants), R2 was used to estimate how strongly the allele in one site predicts the allele in the second site, with values of 0 indicating no linkage and 1 indicating perfect linkage. The mean value of R2 was 0.044, indicating very low levels of linkage overall.