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Supplementary data for: Phylogenomics, male internal genitalia, a new species, and other notes on new world Stenopelmatus Jerusalem crickets (Orthoptera: Stenopelmatoidea: Stenopelmatini)

Cite this dataset

Weissman, David; Song, Hojun; Vadergast, Amy (2024). Supplementary data for: Phylogenomics, male internal genitalia, a new species, and other notes on new world Stenopelmatus Jerusalem crickets (Orthoptera: Stenopelmatoidea: Stenopelmatini) [Dataset]. Dryad. https://doi.org/10.5061/dryad.hdr7sqvr7

Abstract

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.

README: 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

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> 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 > JC_Steno_combined_all_noBS_final_renamed.tre

We have included name.txt which was used for this command.

Methods

We used the Orthoptera-specific target enrichment (OR-TE) probes (Shin et al. 2024) to capture 1,828 loci from genomic DNA. See Weissman et al. (2021) and Shin et al. (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.

Funding

National Science Foundation, Award: DEB-1937815, DEB