We propose a heuristic algorithm, called ARG4WG, to build plausible ancestral recombination graphs (ARGs) from thousands of whole genome samples. By using the longest shared end for recombination inference, ARG4WG constructs ARGs with small numbers of recombination events that perform well in association mapping on genome-wide association studies.
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Foreshadowing haplotype-based methods of the genomics era, it is an old observation that the "junction" between two distinct haplotypes produced by recombination is inherited as a Mendelian marker. In a genealogical context, this recombination-mediated information reflects the persistence of ancestral haplotypes across local genealogical trees in which they do not represent coalescences. We show how these non-coalescing haplotypes ("locally-unary nodes") may be inserted into ancestral recombination graphs (ARGs), a compact but information-rich data structure describing the genealogical relationships among recombinant sequences.
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