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 binary species tree. The analysis detected robust evidence for multiple ancient introgression events affecting the nuclear genome, with introgression probabilities reaching 63%. We estimate population parameters and highlight the fact that species divergence times may be seriously underestimated if ancient cross-species gene flow is ignored in the analysis. We examine the assumptions and performance of HyDe, and demonstrate that it lacks power if gene flow occurs between sister lineages or if the mode of gene flow does not match the assumed hybrid speciation model with symmetrical population sizes. Our analyses highlight the power of likelihood-based inference of cross-species gene flow using genomic sequence data.

The files are plain text files. They are used to run the BPP program, which is available at https://github.com/bpp/Funding provided by: Biotechnology and Biological Sciences Research CouncilCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100000268Award Number: BB/T003502/1, BB/R01356X/1Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: NSFSBS- 2023723

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