Aligning gene trees with family trees

Abstract

Relatedness between individuals can be measured at the genealogical level (by describing shared ancestors in a pedigree) or at a genetic level (by describing shared haplotypes across the genome). The shared haplotype structure can be conveniently summarized as a sequence of trees along the genome, where each tree describes the last shared genetic ancestors between individuals at a locus. While many tools exist to infer tree sequences from genetic data, and many large pedigree datasets are available, few tools exist to identify the relationship between the two - finding which genetic ancestor corresponds to which pedigree ancestor, and conversely. In this paper, we propose an algorithm to solve this problem by providing, for each genetic tree, the list of all consistent ancestry paths within a genealogical tree. We also provide variants of the algorithm with moderate robustness to both tree sequence and pedigree errors. We demonstrate the scalability of our approach on the BALSAC genealogical dataset, which includes millions of individuals in Quebec, Canada. We find that 20 carriers usually provide enough information to reliably identify a common ancestor 15 generations ago or find the parent of origin of alleles among probands, but the number of possible ancestry paths within the pedigree can remain large. We apply the method to reconstruct the inheritance of a causal allele for type 1 myotonic dystrophy.