Estimating the correlation of non-allele descents along chromosomes

The pattern of the correlation of non-allele descents among linked sites is an important aspect for an insight into the genomic evolution at the population level. Here, we present a new statistical method for estimating two types of non-allele descent correlations. One is the standardized parental descent disequilibrium termed by Cockerham & Weir (1973), the other is the standardized disequilibrium between non-allele descent segments from the same chromosome. Essential to this analysis is the partitioning of the joint identity-by-state probability for a random pair of non-allele gametes into the different components of identity by descents at the two or three sites. We consider the samples of phased haplotypes of single nucleotide polymorphism (SNP) markers and the weighted least square method for fast parameter estimation. Monte Carlo simulations demonstrate that robustly unbiased estimates with appropriate precisions can be obtained with certain sample sizes, ~100 diploids, under the impacts of allele frequency distributions and linkage disequilibrium. This method can be used to construct the maps of non-allele descent correlation blocks for the population whose genetic pedigree is not required on a prior basis.