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 hypothe..., , , # 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

[https://doi.org/10.5061/dryad.x0k6djhwf](https://doi.org/10.5061/dryad.x0k6djhwf)

## Description of the data and file structure

These data were collected and generated as part of phylogenetic network analysis of various species in the New Zealand cicada genera *Kikihia* and *Maoricicada*.

### Files and variables

#### File: output.zip

**Description:** This compressed folder contains output files for all analyses used in this study. The folder contains its own README detailing the included files and folders.

#### File: data.zip

**Description:** This compressed folder contains input sequence data as well as data generated by intermediate steps of the TICR pipeline. The folder contains its own README detailing the included files and folders.

#### File: data_snaq_2_mrbayes_output_Maoricicada_wMi...,