DOI: 10.5061/dryad.x0k6djhwf
title: 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

description: 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.
description: # 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_wMito.zip **Description:** This compressed folder is an overflow folder too large to include in data.zip. It contains the compressed output files for all *Maoricicada* nuclear genes and mitochondrial genomes generated by the MrBayes step of the TICR pipeline used to prepare the SNaQ analyses. The output files are sorted into compressed folders based on file extension; the "runs_t.zip" compressed folder contains the sampled gene trees used as input for subsequent steps in the TICR pipeline. #### File: data_snaq_2_mrbayes_output_Kikihia_wMito.zip **Description:** This compressed folder is an overflow folder too large to include in data.zip. It contains the compressed output files for all *Kikihia* nuclear genes and mitochondrial genomes generated by the MrBayes step of the TICR pipeline used to prepare the SNaQ analyses. The output files are sorted into compressed folders based on file extension; the "runs_t.zip" compressed folder contains the sampled gene trees used as input for subsequent steps in the TICR pipeline. ## Code/software #### scripts.zip Description: This compressed folder contains the data processing and analysis scripts used to generate the intermediate data files and analysis results from the input sequence alignments. The folder contains its own README file with information about each script. ## Access information Data was derived from the following sources: * Input sequence alignments were obtained and re-formatted from the following Dryad repository: [https://datadryad.org/dataset/doi:10.5061/dryad.t1g1jwt7v](https://datadryad.org/dataset/doi:10.5061/dryad.t1g1jwt7v)