population history

Strasburg JL & Rieseberg LH 2010 How robust are "Isolation with Migration" analyses to violations of the IM model? A simulation study. Mol Biol Evol, in press.
doi:10.1093/molbev/msp233

• the effects of a number of violations of the "Isolation with Migration" (IM) model, including intralocus recombination, population structure, gene flow from an unsampled species, linkage among loci, and divergent selection, on demographic parameter estimates made using the program IM_A
• the effect of having data that fits a nucleotide substitution model other than the two relatively simple models available in IM_A
• IM_A estimates are generally quite robust to small to moderate violations of the IM model assumptions
• population structure within species, a condition encountered to some degree in virtually all species, has little effect on parameter estimates even for fairly high levels of structure
• most parameter estimates are robust to significant levels of recombination when datasets are pared down to apparently non-recombining blocks
• a poor fit to the nucleotide substitution model can result in an increased error rate, in some cases due to a predictable bias and in other cases due to an increase in variance in parameter estimates among datasets simulated under the same conditions