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Type: Journal article
Title: Estimating the ancestral recombinations graph (ARG) as compatible networks of SNP patterns
Author: 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.
Citation: Journal of Computational Biology, 2008; 15(9):1133-1153
Publisher: Mary Ann Liebert Inc Publ
Issue Date: 2008
ISSN: 1066-5277
Contributor: Cooper, Alan
Statement of
Laxmi Parida, Marta Mele, Francesc Calafell, Jaume Bertranpetit and The Genographic Consortium
Abstract: 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.
Keywords: Genographic Consortium
Chromosomes, Human, Y
DNA, Mitochondrial
Recombination, Genetic
Polymorphism, Single Nucleotide
Multigene Family
Models, Genetic
Description: Copyright © Mary Ann Liebert, Inc. University of Adelaide consortium member: Alan Cooper
DOI: 10.1089/cmb.2008.0065
Appears in Collections:Aurora harvest
Australian Centre for Ancient DNA publications
Earth and Environmental Sciences publications
Environment Institute Leaders publications

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