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

Parida, L.; Mele, M.; Calafell, F.; Bertranpetit, J.; Schurr, T.; Santos, F.; Quintana-Murci, L.; Comas, D.; Tyler-Smith, C.; Zalloua, P.; Balanovska, E.; Balanovsky, O.; Behar, D.; Mitchell, R.; Jin, L.; Soodyall, H.; Pitchappan, R.; Cooper, A.; Royyuru, A.; Rosset, S.; et al.; Cooper, Alan

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

2008

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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.

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Laxmi Parida, Marta Mele, Francesc Calafell, Jaume Bertranpetit and The Genographic Consortium

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