title: Reconstructing past changes in locus-specific recombination rates.
abstract: BACKGROUND
  Recombination rates vary at the level of the species, population and individual. Now recognized as a transient feature of the genome, recombination rates at a given locus can change markedly over time. Existing inferential methods, predominantly based on linkage disequilibrium patterns, return a long-term average estimate of past recombination rates. Such estimates can be misleading, but no analytical framework to infer recombination rates that have changed over time is currently available.
  
  
  RESULTS
  We apply coalescent modeling in conjunction with a suite of summary statistics to show that the recombination history of a locus can be reconstructed from a time series of genetic samples. More usefully, we describe a new method, based on n-tuple dataset subsampling, to infer past changes in recombination rate from DNA sequences taken at a single time point. This subsampling strategy can correctly assign simulated loci to constant, increasing and decreasing recombination models with an accuracy of 84%.
  
  
  CONCLUSIONS
  While providing an important stepping-stone to determining past recombination rates, n-tuple subsampling still exhibits a moderate error rate. Theoretical limitations indicated by coalescent theory suggest that highly accurate inference of past recombination rates will remain challenging. Nevertheless, we show for the first time that reconstructing historic recombination rates is possible in principle.
authors: Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand. m.p.cox@massey.ac.nz
authors: Murray P
authors: MP
authors: Cox
authors: Barbara R
authors: BR
authors: Holland
authors: Matthew C
authors: MC
authors: Wilkins
authors: Jan
authors: J
authors: Schmid
mesh_terms: D000818:Animals; D005796:Genes; D006801:Humans; D008957:Models, Genetic; D009154:Mutation; D011995:Recombination, Genetic