DOI: 10.5061/dryad.hdr7sqvr7
title: Supplementary data for: Phylogenomics, male internal genitalia, a new species, and other notes on new world Stenopelmatus Jerusalem crickets (Orthoptera: Stenopelmatoidea: Stenopelmatini)

description: Based on past and expanded DNA sampling, the orthopteran families
 Stenopelmatidae and Anostostomatidae, as currently structured, are shown
 to be non-monophyletic. The splay-footed cricket genus Comicus, is
 confirmed to be genetically distinct from all Stenopelmatidae. We add two
 specimens to our previously published phylogenetic tree for New World
 Stenopelmatus Jerusalem cricket species and report the first multilocus
 DNA recovery for S. ater from Costa Rica. Male internal genitalia may be
 of systematic value in Jerusalem crickets, but we believe they should be
 analyzed when in their unfolded, “physiologically functional” state, where
 morphological characters can be seen in more detail when compared to their
 preserved, folded state. We describe Stenopelmatus nuevoguatemalae n. sp.
 from Guatemala.
description: We used the Orthoptera-specific target enrichment (OR-TE) probes
 (Shin <em>et al. </em>2024) to capture 1,828 loci from genomic
 DNA. See Weissman <em>et al. </em>(2021) and Shin <em>et
 al. </em>(2024) for DNA extraction, library preparation, hybrid
 capture, and data processing. We inferred the phylogeny using a
 coalescent-based species tree analysis in the program ASTRAL 5.7.3 (Zhang
 et al. 2018). Specifically, we created 1,236 individual datasets (one for
 each gene). The gene trees were generated from each gene-specific
 alignment in RAxML 8 (Stamatakis 2014) using 100 rapid bootstrap
 pseudoreplicates and the GTR GAMMA I model. We generated a summary species
 tree using the default options in ASTRAL.
description: # Supplementary Data for the manuscript titled, "Phylogenomics, male
 internal genitalia, a new species, and other notes on New World
 Stenopelmatus Jerusalem crickets (Orthoptera: Stenopelmatoidea:
 Stenopelmatini)"
 [https://doi.org/10.5061/dryad.hdr7sqvr7](https://doi.org/10.5061/dryad.hdr7sqvr7) This dataset includes processed data files for the ASTRAL analysis included in the manuscript, including alignment for 1237 loci, individual tree files, and the files used for the ASTRAL analysis. \## Description of the data and file structure The data are contained in three separate folders. 1\. phylip files This folder includes 1236 alignments in phylip format, each representing a locus captured using the Orthoptera-Specific Target Enrichment (OR-TE) probe set. We included only those loci that were recovered for at least 4 taxa. 2\. tree files This folder contains 1236 tree files in newick format. Each file presents a maximum likelihood gene tree inferred using RAxML. The model used for each analysis was GTR+G+I. 3\. Astral Analysis This folder contains the following files. JC_Steno_combined_BS.tre - This is a file that includes all 1236 trees into a single file. JC_Steno_combined_all_noBS.tre - This is a file that includes all 1236 trees, but with any node that has a bootstrap support of less than 10 collapsed to polytomy. JC_Steno_combined_all_noBS_final.tre - Result of the ASTRAL analysis JC_Steno_combined_all_noBS.log - Log file of the analysis JC_Steno_combined_all_noBS_final_renamed.tre - Result of the ASTRAL analysis with taxon name name.txt - a file used for converting ID numbers to taxon names. We used the following command to calculate the tree: java -jar -Xmx3000M astral.5.7.8.jar -i JC_Steno_combined_all_noBS.tre -o JC_Steno_combined_all_noBS_final.tre 2&gt; JC_Steno_combined_all_noBS.log These files all contain ID names for the terminals. To replace ID names to taxon names, we use the following command in Terminal. sed -f name.txt JC_Steno_combined_all_noBS_final.tre &gt; JC_Steno_combined_all_noBS_final_renamed.tre We have included name.txt which was used for this command.