Data from: Phylogenomic insights and geographic distribution of the New World genus Amphibolips Reinhard (Hymenoptera: Cynipidae, Cynipini) using ultraconserved elements
Data files
Dec 05, 2024 version files 146.33 MB
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Phylogenomics_of_New_World_Amphibolips.zip
146.33 MB
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README.md
2.28 KB
Abstract
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.
README: 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
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
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
Access information
Data was derived from the following sources:
- NCBI Short Read Archive under BioProject accession number PRJNA1149323.