A MARKOV-CHAIN MODEL OF COALESCENCE WITH RECOMBINATION

Trees that describe the ancestry of DNA sequences sampled from a popul ation may differ between loci because of genetic recombination. We see k to understand the relationship between such trees for loci that are linked with non-zero recombination rate. We consider a coalescent proc ess model with recombination, as described by Hudson (1983; 1990). For two loci and a sample size of two sequences, a detailed analysis of t his process yields the joint distribution of the two trees (one at eac h locus). A number of interesting results follow from this analysis, i ncluding the distribution of the number of recombination events in the history of the sample. For the general case of rn loci and samples of size n, we describe an algorithm for simulating the tree building pro cess. Because analytic results are difficult to obtain in this case, w e use simulation to study properties of trees at multiple linked loci such as total tree time and number of recombination events. (C) 1997 A cademic Press.