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

J Comput Biol. 2008 Nov;15(9):1133-54. doi: 10.1089/cmb.2008.0065.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Chromosomes, Human, Y / genetics
  • DNA, Mitochondrial / genetics
  • Haplotypes
  • Humans
  • Models, Genetic*
  • Multigene Family
  • Phylogeny*
  • Polymorphism, Single Nucleotide*
  • Recombination, Genetic*

Substances

  • DNA, Mitochondrial