Power of Bayesian and heuristic tests to detect cross-species introgression with reference to gene flow in the Tamias quadrivittatus group of North American chipmunks

In the past two decades genomic data have been widely used to detect historical gene flow between species in a variety of plants and animals. The Tamias quadrivittatus group of North America chipmunks, which originated through a series of rapid speciation events, are known to undergo massive amounts of mitochondrial introgression. Yet in a recent analysis of targeted nuclear loci from the group, no evidence for cross-species introgression was detected, indicating widespread cytonuclear discordance. The study used the heuristic method HyDe to detect gene flow, which may suffer from low power. Here we use the Bayesian method implemented in the program bpp to reanalyze these data. We develop a Bayesian test of introgression, calculating the Bayes factor via the Savage-Dickey density ratio using the Markov chain Monte Carlo (MCMC) sample under the model of introgression. We take a stepwise approach to constructing an introgression model by adding introgression events onto a well-supported b..., Please see the accompanying published article: 
Ji J, Jackson DJ, Leache AD, Yang Z. (2023) Power of Bayesian and heuristic tests to detect cross-species introgression with reference to gene flow in the Tamias quadrivittatus group of North American chipmunks. Systematic Biology 72:446-465.  https://doi.org/10.1093/sysbio/syac077, The files are plain text files.  They are used to run the BPP program, which is available at 
https://github.com/bpp/