Data from: Phylogenomic insights into helmet evolution in Neotropical treehoppers (Hemiptera: Membracidae): Conserved morphological complexity across five subfamilies
Data files
Oct 02, 2025 version files 42.01 GB
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assembly.conf
4.76 KB
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FastQfileIDQ30.xlsx
11.87 KB
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illumiprocessor.conf
5.72 KB
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mafft-nexus-internal-trimmed-gblocks-clean-75p-Mrbayes.nexus
29.19 MB
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mafft-nexus-internal-trimmed-gblocks-clean-75p-raxml.charsets
182.50 KB
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mafft-nexus-internal-trimmed-gblocks-clean-75p-raxml.phylip
29.01 MB
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nexustreenew
1.53 KB
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RAW_UCE_Treehoppers.zip
41.96 GB
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README.md
2.96 KB
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taxon-set.conf_
503 B
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TPS_Dorsal_pronoto.TPS
36.29 KB
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TPS_Frontal_pronoto.TPS
37.15 KB
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TPS_lateral_pronoto.TPS
57.08 KB
Abstract
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.
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.
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.
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.
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
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
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
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. PLoS computational biology, 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. Syst Biol 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. Molecular ecology resources, 15(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. Genome Res 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. Systematic biology, 61(3), 539-542. https://doi.org/10.1093/sysbio/sys029
Wickham H (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4, https://ggplot2.tidyverse.org.