Comparing Inference under the MSC versus the MSC-with-Recombination

Accurate inference of population parameters plays a pivotal role in unravelling the evolutionary histories. While recombination has been universally accepted as a fundamental process in the evolution of sexually reproducing organisms, it remains challenging to model it exactly. Thus, existing coalescent-based approaches make different assumptions or approximations to facilitate phylogenetic inference, which can potentially bring about biases in estimates of evolutionary parameters when recombination is present. In this article, we evaluate the performance of population parameters estimation using three classes of methods: StarBEAST2, SNAPP, and diCal2. We performed whole-genome simulations in which recombination rates, mutation rates, and levels of ILS were varied. We show that StarBEAST2 using short or medium-sized loci is robust to realistic rates of recombination, which is in agreement with previous studies. SNAPP, as expected, is generally unaffected by recombination events. Most surprisingly, diCal2, a method that is designed to explicitly account for recombination, performs considerably worse than other methods under comparison.