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.