Consequences of intra-locus recombination for branch-length-based inference of gene flow

Phylogenomic methods provide a powerful way to study introgression across broad clades of the tree of life, because they can test for gene flow from gene trees without requiring population-level resequencing data. These methods generally assume that each locus can be represented by a single non-recombining genealogy, which may be violated when recombination occurs within loci. Here, we used coalescent simulations to evaluate how intra-locus recombination affects gene-flow inferences in Aphid, a method using branch lengths to distinguish gene flow from incomplete lineage sorting in species triplets. Across the conditions tested, Aphid accurately recovered the proportion of loci affected by recent and intermediate gene flow, while recombination reduced the underestimation observed when gene flow is ancient. It also retained a relative timing signal, with accuracy decreasing as gene flow became older. We then applied this relative-timing framework to 456 African cichlid exon trees, where proposed gene flow involving Coptodon was consistently associated with intermediate-to-old rather than recent coalescence signals. Overall, our simulations suggest that intra-locus recombination does not increase error in Aphid's inference of the prevalence of gene flow under the conditions tested, but can reduce temporal resolution for intermediate and ancestral events. The cichlid application shows that this loss of resolution still permits recent and older gene-flow signals to be distinguished in an empirical dataset.