Ancestral haplotype reconstruction in endogamous populations using identity-by-descent
Fig 4
(A) Let individuals 1–8 be the genotyped individuals of this pedigree. Let C = {1, 2, 5, 7, 8} (orange individuals) be the cohort sharing IBD segment I. Note that this pedigree contains two loops, since c and f share recent ancestors p and q, and d and e share recent ancestor ℓ. The multiset Mp for each ancestral individual p is shown below the node name. Mp is formed by concatenating the multisets of p’s children, and it represents the number of paths from ancestor p to each member of the cohort. (B) After trimming redundant ancestors and merging couples, we obtain a set of putative sources for the IBD segment. In this case, we have three potential sources: S = {gh, ℓ, pq}. We begin the iterative phase by selecting the source with the fewest descendance paths, which in this case is gh (starred). We place the IBD segment in individuals that are on all paths from gh to the cohort. In this case we would add the IBD segment to individuals b, c, and d (light orange).