coalescent with epistasis
Barton NH & Navarro A 2002 Extending the coalescent to multilocus systems: the case of balancing selection. Genet Res 79:129-139.
- structured coalescent approach breaks down when the number of backgrounds approaches the population size
- because of stochastic fluctuations in background frequencies
- a new method is needed to extend the structured coalescent to cases with large numbers of backgrounds
- a general analytical method that extends the structured coalescent to any situation where selection is strong enough (i.e. Ns is large enough) for background frequencies to be constant
- in principle, one could consider genealogies conditioning on the random series of background frequencies and then average over these sequences
- applying the same strategy to multilocus balancing selection is difficult for several reasons
- a proper analysis must take simultaneously into account fluctuations in all the backgrounds
- taking into account the whole population all time, rather than only the favoured allele for just a few generations
- one must account for the loss and recovery of backgrounds by drift and recombination
