Estimating the ancestral recombinations graph (ARG) as compatible networks of SNP patterns

Traditionally nonrecombinant genome, i.e., mtDNA or Y chromosome, has been used for phylogeography, notably for ease of analysis. The topology of the phylogeny structure in this case is an acyclic graph, which is often a tree, is easy to comprehend and is somewhat easy to infer. However, recombination is an undeniable genetic fact for most part of the genome. Driven by the need for a more complete analysis, we address the problem of estimating the ancestral recombination graph (ARG) from a collection of extant sequences. We exploit the coherence that is observed in the human haplotypes as patterns and present a network model of patterns to reconstruct the ARG. We test our model on simulations that closely mimic the observed haplotypes and observe promising results. © Mary Ann Liebert, Inc. 2008.