Over the past two decades, researchers have documented the extent of natural hybridization between closely related species using genomic tools. Many species across the tree of life show evidence of past hybridization with their evolutionary relatives. In some cases, this hybridization is complex – involving gene flow between more than two species. While hybridization is common over evolutionary timescales, some researchers have proposed that it may be even more common in contemporary populations where anthropogenic disturbance has modified a myriad of aspects of the environments in which organisms live and reproduce. Here, we develop a flexible tool for local ancestry inference in hybrids derived from three source populations and describe a complex, recent hybridization event between distantly related swordtail fish lineages (Xiphophorus) and its potential links to anthropogenic disturbance.

The reference genomes were assembled as part of previous publications and were used for three-way ancestryinfer runs in Banerjee & Powell et al.

The ancestry informative markers and parental counts were developed and used for ancestryinfer runs in Banerjee & Powell et al. Please see methods and supporting information of Banerjee & Powell et al. for information about developing ancestry informative sites and parental counts.

Details for the ancestryinfer runs performed for Banerjee & Powell et al can be found at https://github.com/smbanerjee/Tlalica_three-way_hybrids and details for the program ancestryinfer can be found at https://github.com/Schumerlab/ancestryinfer. 

These files do not require specifc software to open or read.