DOI: 10.5061/dryad.hhmgqnkrw
title: Data from: Phylogenomic insights into helmet evolution in Neotropical treehoppers (Hemiptera: Membracidae): Conserved morphological complexity across five subfamilies

description: We analyzed genomic data from 2,539 nuclear loci (580,110 aligned
 nucleotides) to investigate phylogenetic relationships among selected
 treehopper lineages (Hemiptera: Membracidae), with a focus on helmet
 morphology. Using geometric morphometric and comparative methods, we found
 that helmet shape—but not size—exhibits strong phylogenetic signal,
 indicating that shape is highly conserved across evolutionary lineages.
 Similar morphologies were more common among closely related taxa,
 particularly within genera and tribes. Our results support the monophyly
 of major clades (e.g., Centrotinae + Nicomiinae; Membracinae + Darninae +
 Similiinae), demonstrating the power of UCE-derived nuclear data to
 resolve relationships within Membracidae. Additionally, patterns of shape
 variation suggest the evolution of pronotal modularity across lineages.
description: Data sequences and processing Ultraconserved
 elements (UCEs) are highly conserved regions of organismal genomes shared
 among evolutionary distant taxa (McCormack et al. 2012; Faircloth et al.
 2012). We use a bait designs targeting UCEs for Hemiptera (40,207 baits
 for 2,731 UCEs) to recover UCE from Membracidae (Treehoppers). We use
 phyluce and illumiprocessor software to help analyze data (Faircloth,
 2013; Faircloth et al. 2012; Faircloth et al., 2015). 
 Phylogenetic analysis<br> Phylogenetic analysis was
 conducted using RAxML-NG version 0.9.0 (Kozlov et al., 2019) for Maximum
 Likelihood and MrBayes version 3.2.6 (Ronquist et al., 2012) for Bayesian
 Inference. Phylogenetic calibration was estimated using a 17 Ma
 Stegaspidinae fossil and a normal distribution in BEAST 2 (Bouckaert et
 al., 2019). Photography and image processing<br>
 Photographs were taken with a Rebel XT camera and processed using Adobe
 Photoshop Lightroom version 24.1.0 (Adobe Systems Software Ireland Ltd.
 2023). Geometric morphometrics<br> Landmarks were
 placed using tpsRelw (v1.75) and tpsDig (v2.33) software (SB
 Morphometrics, NY, USA). Centroid size was estimated using MorphoJ
 (v1.08.0) (Klingenberg Lab, MC, UK). PCA visualizations were performed
 using the MorphoJ (v1.08.0) and R Statistical Software (v4.1.2), along
 with the ape, phytools, and ggplot2 packages (Revell, 2012; Wickham, 2016;
 R Core Team, 2021). Procrustes ANOVA by taxonomic rank (genus, tribe, and
 species), using a 1000-permutation test, was also performed in MorphoJ
 (v1.08.0) (Klingenberg Lab, MC, UK).
 References  Bouckaert R., Vaughan T.G.,
 Barido-Sottani J., Duchêne S., Fourment M., Gavryushkina A., et al. (2019)
 BEAST 2.5: An advanced software platform for Bayesian evolutionary
 analysis. <em>PLoS computational biology</em>, 15(4),
 e1006650. Faircloth BC, McCormack JE, Crawford NG,
 Harvey MG, Brumfield RT, Glenn TC. 2012. Ultraconserved Elements Anchor
 Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales.
 <em>Syst Biol</em> 61:717-726. pmid: 22232343
 doi:10.1093/sysbio/sys004. Faircloth, B. C.,
 Branstetter, M. G., White, N. D., & Brady, S. G. (2015). Target
 enrichment of ultraconserved elements from arthropods provides a genomic
 perspective on relationships among Hymenoptera. <em>Molecular
 ecology resources</em>, <em>15</em>(3), 489-501. https://doi.org/10.1111/1755-0998.12328 Faircloth, BC. 2013. illumiprocessor: a trimmomatic wrapper for parallel adapter and quality trimming. http://dx.doi.org/10.6079/J9ILL. Kozlov, Diego Darriba, Tomáš Flouri, Benoit Morel, and Alexandros Stamatakis (2019) RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics, 35 (21), 4453-4455 https://doi.org/10.1093/bioinformatics/btz305 McCormack JE, Faircloth BC, Crawford NG, Gowaty PA, Brumfield RT, Glenn TC. 2012. Ultraconserved Elements Are Novel Phylogenomic Markers that Resolve Placental Mammal Phylogeny when Combined with Species Tree Analysis. <em>Genome Res</em> 22: 746–754. pmid: 22207614 doi: 10.1101/gr.125864.111. R Core Team (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/. Revell, L. J. (2012). phytools: An R package for phylogenetic comparative biology (and other thing*s). In Methods in Ecology and Evolution *(Vol. 3, pp. 217–223). https://doi.org/10.1111/j.2041-210X.2011.00169.x Ronquist, F., Teslenko, M., Van Der Mark, P., Ayres, D. L., Darling, A., Höhna, S., ... & Huelsenbeck, J. P. (2012). MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. <em>Systematic biology</em>, <em>61</em>(3), 539-542. https://doi.org/10.1093/sysbio/sys029 Wickham H (2016). ggplot2: Elegant Graphics for Data Analysis. <em>Springer-Verlag New York.</em> ISBN 978-3-319-24277-4, https://ggplot2.tidyverse.org.
description: # Data from: Phylogenomic insights into helmet evolution in Neotropical
 treehoppers (Hemiptera: Membracidae): Conserved morphological complexity
 across five subfamilies
 [https://doi.org/10.5061/dryad.hhmgqnkrw](https://doi.org/10.5061/dryad.hhmgqnkrw) ## Description of the data and file structure ### Files and variables #### File: taxon-set.conf\_ **Description:** This is the configuration file containing the IDs of the taxa used for phylogenetic estimation. #### File: FastQfileIDQ30.xlsx **Description:** This is a table with quality of the fastq files. #### File: RAW_UCE_Treehoppers.zip **Description:** This is a raw sequence data file generated by Illumina HiSeq using paired-end reads. It contains all sample files. #### File: TPS_lateral_pronoto.TPS **Description:** Landmark data for lateral shape of treehopper pronota. #### File: TPS_Frontal_pronoto.TPS **Description:** Landmark data for frontal shape of treehopper pronota. #### File: nexustreenew **Description:** Phylogenetic tree used for mapped helmet shape of the treehoppers #### File: TPS_Dorsal_pronoto.TPS **Description:** Landmark data for dorsal shape of treehopper pronota. #### File: phyluce.conf **Description:** conf file  #### File: taxon-set.conf\_ **Description:** configuration file used to indicate the taxa for extracting UCE loci #### File: assembly.conf **Description:** configuration file used to assemble the data with spades in phyluce #### File: illumiprocessor.conf **Description:** configuration file used to clean the raw data sequence with illumiprocessor #### File: mafft-nexus-internal-trimmed-gblocks-clean-75p-raxml.charsets **Description:** Text file used in MAFFT, it specifies regions of the sequences that should be treated differently during the alignment process. #### File: mafft-nexus-internal-trimmed-gblocks-clean-75p-raxml.phylip **Description:** Sequence data used for the phylogenetic analysis. #### File: mafft-nexus-internal-trimmed-gblocks-clean-75p-Mrbayes.nexus **Description:** Sequence data used for the phylogenetic analysis using Bayesian Inference ## Code/software We used Illumiprocessor, a program for the automated cleaning of FASTQ files from sequencing. All UCE sequence data were processed using the phyluce program and its tutorial: [https://phyluce.readthedocs.io/en/latest/tutorials/tutorial-1.html](https://phyluce.readthedocs.io/en/latest/tutorials/tutorial-1.html). To perform the phylogenetic analysis, we used RAxML (Raxml-ng v0.9.) for maximum likelihood (ML) estimation and MrBayes (MrBayes v3.2.6) for Bayesian inference. Morphological data were obtained and analyzed using tpsUtil and tpsDig: [https://www.sbmorphometrics.org/index.html](https://www.sbmorphometrics.org/index.html). PCR, CVA, and phylogenetic signal were estimated and plotted using R Statistical Software (v4.1.2; R Core Team 2021), with the following packages: phytools, morpho, ape, and ggplot2.