Simulation of 'hitch-hiking' genealogies

J Math Biol. 2001 Jan;42(1):41-70. doi: 10.1007/pl00000072.

Abstract

An ancestral influence graph is derived, an analogue of the coalescent and a composite of Griffiths' (1991) two-locus ancestral graph and Krone and Neuhauser's (1997) ancestral selection graph. This generalizes their use of branching-coalescing random graphs so as to incorporate both selection and recombination into gene genealogies. Qualitative understanding of a 'hitch-hiking' effect on genealogies is pursued via diagrammatic representation of the genealogical process in a two-locus, two-allele haploid model. Extending the simulation technique of Griffiths and Tavare (1996), computational estimation of expected times to the most recent common ancestor of samples of n genes under recombination and selection in two-locus, two-allele haploid and diploid models are presented. Such times are conditional on sample configuration. Monte Carlo simulations show that 'hitch-hiking' is a subtle effect that alters the conditional expected depth of the genealogy at the linked neutral locus depending on a mutation-selection-recombination balance.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Alleles
  • Animals
  • Biological Evolution
  • Computer Simulation*
  • Diploidy
  • Genetic Linkage
  • Haploidy
  • Models, Genetic*
  • Monte Carlo Method
  • Mutation
  • Pedigree*
  • Recombination, Genetic
  • Selection, Genetic