DOI: 10.5061/dryad.3ffbg79tk
title: Data from: Phylogenomic insights and geographic distribution of the New World genus Amphibolips Reinhard (Hymenoptera: Cynipidae, Cynipini) using ultraconserved elements

description: AbstractIn recent years, new wasp species and genera of Cynipidae have
 been described, and their species delimitation and evolutionary
 relationships have been supported using molecular markers. However, few
 studies have included comprehensive and extensive sampling of specimens
 across the complete distribution of a single genus. In this study, we
 analysed the phylogenetic relationships of the genus Amphibolips
 throughout its range using ultraconserved elements (UCEs). We collected
 520 adult wasps from 401 sites in various geographic locations,
 predominantly in Mexico, and used 78 wasps for UCE analysis. Our results
 demonstrate that Amphibolips forms a monophyletic clade. Amphibolips can
 be further subdivided into four genetically well‐differentiated clades.
 Each clade had morphological traits that could be collectively
 characterised. Species delimitation using molecular sequencing highlights
 the taxonomic complexity involved in separating and assigning species
 using exclusively morphological criteria. This approach offers an
 opportunity to refine current morphological taxonomic criteria or propose
 new criteria to establish more accurate classifications. The rich
 diversity of host species and geographic regions in Mexico represents a
 biodiversity hotspot for Amphibolips. The number of undescribed species
 remains high. This study facilitates the determination of appropriate
 boundaries for putative new Amphibolips species.
description: # Phylogenomic insights and geographic distribution of the New World genus
 Amphibolips Reinhard (Hymenoptera: Cynipidae, Cynipini) using
 ultraconserved elements (UCEs)
 [https://doi.org/10.5061/dryad.3ffbg79tk](https://doi.org/10.5061/dryad.3ffbg79tk) ### Files #### File: Phylogenomics\_of\_New\_World\_Amphibolips.zip **Description:** This folder contains three folders inside. The first of these folders is called `alignments`. It contains the alignments in phylip and nexus format for each data matrix used during the analyses. The second folder is called `individual_uce_trees_passed_symmetry_test`. It contains two individual tree files of UCEs that passed the symmetry test in IQ-TREE. These files are needed to use molecular species delimitation with SODA. The third folder is called `trees_supplementary_material`. It contains the .tree files of the trees that are left as supplementary material in the manuscript. **Abbreviations used for file names:** * Amphi: Refers to the *Amphibolips* genus. * \#p: Completeness matrix of the specified number. * spruce97: Result obtained after using the spruceup program with the 97% quartile. * BS10: Result after collapsing nodes with support values equal to or less than 10% using Newick utilities. * FS#: Supplementary Figure and its corresponding number in the manuscript. * unpart: Resulting tree without considering partitions. * sym: Resulting tree of the UCEs that passed the IQ-TREE symmetry test. * SWSC: Resulting tree from the analysis using the SWSC-EN algorithm. * astral#: Resulting tree from the ASTRAL-III analysis and the completeness matrix used. * concord: Resulting tree from the IQ-TREE concordance test. ## Software ###### The software used for the analyses is the following: Phyluce version 1.7.1 SPAdes IQ-TREE v 2.2.2.6 PFinderUCE-SWSC-EN PartitionFinder2 ASTRAL-III Newick_utils Bayesian Poisson Tree Processes - bPTP Species bOundry Delimitation using Astral - SODA FigTree Adobe Photoshop ###### Some of these programs include other programs within their operation that are already included in the installation of these same programs. ## Access information Data was derived from the following sources: * NCBI Short Read Archive under BioProject accession number PRJNA1149323.