Data and code from: Using phylogenetic network methods for genomic data exploration and hypothesis generation fails to untangle a confusing history of hybridization in New Zealand cicadas

Rapid species radiations make hybridization among species more likely. Detecting and reconstructing hybridization is, therefore, critical for understanding species relationships in many cases. We explored the relative performance of two phylogenetic network methods, SNaQ, a gene tree-based method, and PhyNEST, a site pattern-based method, in evaluating the plausibility of proposed past hybridization hypotheses. As our study system, we used the New Zealand cicada genera Kikihia and Maoricicada. Previous phylogenomic work on these two species' radiations suggested multiple hybridization events. We generated hypotheses for specific hybridization events based on observed hybrid mating songs and patterns of mito-nuclear discordance. We inferred phylogenetic networks using SNaQ and PhyNEST and a phylogenomic dataset of over 500 nuclear Anchored Hybrid Enrichment genes along with mitochondrial genomes to determine whether the two methods recovered plausible networks with respect to our hypothesized hybridization events. We also examined how the D-statistic performed in identifying our predicted hybridization events. We found that both SNaQ and PhyNEST, along with the D-statistic, recovered an extensive history of reticulate evolution in New Zealand cicadas which broadly matched our predictions. We found differences between networks inferred by the two network programs that may reflect differences in the inference methods or result from using site patterns versus gene trees as input data. Finally, we discuss considerations for users applying these methods to targeted enrichment data and suggest improvements for network method developers.