Abstract

Abstract An alternative way of constructing ancestral graphs, which is different from the coalescent-based approach, is proposed using population linkage disequilibrium (LD) data. The main difference from the existing method is the construction of the ancestral graphs based on var-iants instead of individual sequences. Therefore, the key of the proposed method is to use the order of allele ages in the graphs. Distinct from the previous age-esti-mation methods, allele ages are estimated from full hap-lotype information by examining the number of gen-erations from the initial complete LD to the current de-cayed state for each two variants depending on the di-rection of LD decay between variants. Using a simple algorithmic procedure, an ancestral graph can be de-rived from the expected allele ages and current LD de-cay status. This method is different in many ways from previous methods, and, with further improvement, it might be a good replacement for the current appro-aches.Keywords: allele age, ancestral graph, haplotypes, link-age disequilibrium, recombination

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