isolation with migration

Mailund T, Halager AE, Westergaard N, Dutheil JY, Munch K, Andersen LN, Lunter G, Prüfer K, Scally A, Hobolth A & Schierup MH 2012 A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. PLoS Genet 8:e1003125.

• we also apply the model to the Homo/Pan speciation event and find that the most likely scenario involves an extended period of gene flow during speciation

• for the constant population size coalescent, the total branch length in the ancestry of a sample set grows logarithmically with the number of samples, but linearly in the number of loci
• most statistical methods for exploring the evolution of closely related species therefore employ multiple loci with small sample sizes
• these methods, however, typically assume loci are sufficiently short and widely separated that recombination is negligible within them and occurs freely between them
• one notable exception is the MIMAR model, which does allow recombination within loci but still assumes free recombination between loci

• when recombination is present, however, the likelihood computations quickly become computationally infeasible since the process is not Markovian across loci
• reasonable approximations can be made, however, by assuming the Markov property across loci