Supplementary Material: Detectability of varied hybridization scenarios using genome-scale hybrid detection methods

Abstract: Hybridization events complicate the accurate reconstruction of phylogenies, as they lead to patterns of genetic heritability that are unexpected under traditional, bifurcating models of species trees. This phenomenon has led to the development of methods to infer these varied hybridization events, both methods that reconstruct networks directly, as well as summary methods that predict individual hybridization events from a subset of taxa. However, a lack of empirical comparisons between methods – especially those pertaining to large networks with varied hybridization scenarios – hinders their practical use. Here, we provide a comprehensive review of popular summary methods: TICR, MSC-quartets, HyDe, Patterson’s D-Statistic (ABBA-BABA), D3, and Dp. TICR and MSCquartets are based on quartet concordance factors gathered from gene tree topologies and HyDe, Patterson’s D-Statistic, D3, and Dp use site pattern frequencies to identify hybridization events between sets of three taxa. We then use simulated data to address questions of method accuracy and ideal use scenarios by testing methods against complex networks which depict gene flow events that differ in depth (timing), quantity (single vs. multiple, overlapping hybridizations), and rate of gene flow (γ). We find that deeper or multiple hybridization events may introduce noise and weaken the signal of hybridization, leading to higher relative false negative rates across all methods. Despite some forms of hybridization eluding quartet-based detection methods, MSCquartets displays high precision in most scenarios. While HyDe results in high false negative rates when tested on hybridizations involving extinct or unsampled ghost lineages, HyDe is the only method able to identify the direction of hybridization, distinguishing the source parental lineages from recipient hybrid lineages. Lastly, we test the methods on a dataset of ultraconserved elements from the bee subfamily Nomiinae, finding possible hybridization events between clades which correspond to regions of poor support in the species tree estimated in a previous study. Supplementary Material for the manuscript "Detectability of varied hybridization scenarios using genome-scale hybrid detection methods" contains: - visualizations of hybrid networks used for simulations, - summary tables describing differences between hybrid detection methods,- results of hybrid tests on simulated data presented at bonferroni-corrected significance levels, and- results of hybrid tests on real data presented at a significance level of 0.05.