DOI: 10.5061/dryad.3bk3j9kx3
title: Phasing in and out of phytophagy: Phylogeny and evolution of the family Eurytomidae (Hymenoptera: Chalcidoidea) based on Ultraconserved Elements

description: We present the first global molecular phylogenetic hypothesis for the
 family Eurytomidae, a group of chalcidoid wasps with diverse biology, with
 a representative sampling (197 ingroups and 11 outgroups) that covers all
 described subfamilies, and 70% of the known genera. Analyses of 962
 Ultra-Conserved Elements (UCEs) with concatenation (IQ-TREE) and
 multispecies coalescent approaches (ASTRAL) resulted in highly supported
 topologies in recovering the monophyly of Eurytomidae and its four
 subfamilies. The taxonomy of Eurytomidae, and in particular the large
 subfamily Eurytominae, needs major revisions as most large genera are
 recovered as para- or polyphyletic, and the erection of multiple new
 genera is required in the future to accommodate these taxa. Here, we
 synonymize the genera Cathilaria (C. certa, C. globiventris, C. opuntiae,
 and C. rigidae) and the monotypic Aiolomorphus rhopaloides within
 Tetramesa syn. nov., Parabruchophagus (P. kazakhstanicus, P. nikolskaji,
 P. rasnitsyni, P. saxatilis, and P. tauricus) and Exeurytoma (E.
 anatolica, E. caraganae, and E. kebanensis) within Bruchophagus syn. nov..
 We also provide 137 DNA barcode COI fragments extracted from the UCE
 contigs to aid in future identifications of Eurytomidae using this popular
 genetic marker. Eurytomidae most likely originated in South America with
 an estimated crown age of 83.37 Ma. Ancestral state reconstruction
 indicates that secondary phytophagy has evolved at least seven times
 within the subfamily Eurytominae, showcasing the evolutionary flexibility
 of these vastly understudied wasps.
description: # Phasing in and out of phytophagy: Phylogeny and evolution of the family
 Eurytomidae (Hymenoptera: Chalcidoidea) based on Ultraconserved Elements
 [https://doi.org/10.5061/dryad.b2rbnzsnt](https://doi.org/10.5061/dryad.b2rbnzsnt) This repository is associated with Zhang YM, Delvare G, Blaimer BB, Cruaud A, Rasplus J-Y, Brady SG, Gates MW. (2025). Phasing in and out of phytophagy: phylogeny and evolution of the family Eurytomidae (Hymenoptera: Chalcidoidea) based on Ultraconserved Elements. Systematic Entomology, *In Press*. [https://doi.org/10.1111/syen.12682](https://doi.org/10.1111/syen.12682) In this study we used Ultraconserved Elements (UCEs) to reconstruct the phylogeny of Eurytomidae. We performed a series of analyses in IQ-TREE (regular analysis, filtered using SRH + concordance factors, and PMSF models for amino acid datasets) and ASTRAL-III (individual gene trees calculated using IQ-TREE) on a total of four matrices: 50% complete and 70% complete matrix for nucleotide data, as well as 50% and 70% for amino acid. We also performed a divergence dating analysis using fossil calibrations in MCMCTree, using the 70% SWSC tree as input guide tree. ### **Assembled Contigs:** Eurytomidae_assembled_contigs.tar.gz: Assembled contigs for new assemblies generated in this study. ### **Alignments:** Eury50p_spruce99.phylip: Matrix for nucleotide 50 percent complete matrix, trimmed using Spruceup at 99% Weibull distribution. Eury70p_spruce99.phylip: Matrix for nucleotide 70 percent complete matrix, trimmed using Spruceup at 99% Weibull distribution. Eury50p_aa_spruceup99.phylip: Matrix for amino acid 50 percent complete matrix, trimmed using Spruceup at 99% Weibull distribution. Eury70p_aa_spruceup99.phylip: Matrix for amino acid 70 percent complete matrix, trimmed using Spruceup at 99% Weibull distribution. Eury50p_loci.part: Partition file by locus for Eury50p_spruce99.phylip Eury70p_loci.part: Partition file by locus for Eury70p_spruce99.phylip Eury50p_swsc.part: Partition file by Sliding Winodw Site Characteristics (SWSC) for Eury50p_spruce99.phylip Eury70p_swsc.part: Partition file by SWSC for Eury70p_spruce99.phylip Eury50p_aa.part: Partition file by locus for Eury50p_aa_spruceup99.phylip Eury70p_aa.part: Partition file by locus for Eury70p_aa_spruceup99.phylip ### **Trees:** Eury_50p_BS10_ASTRAL.treefile: Output tree from ASTRAL for the 50 percent complete matrix. Eury_50p_concord.cf.treefile: Output tree from IQTREE for 50 percent complete matrix, with concordance factors and filtered using SRH test. Eury_50p_loci.treefile: Output individual gene trees from IQTREE for amino acid 50 percent complete matrix. Eury_50p_swsc.treefile: Output tree from IQTREE for 50 percent complete matrix, using SWSC partitioning. Eury_70p_BS10_ASTRAL.treefile: Output tree from ASTRAL for the 70 percent complete matrix. Eury_70p_concord.cf.treefile: Output tree from IQTREE for 70 percent complete matrix, with concordance factors and filtered using SRH test. Eury_70p_loci.treefile: Output individual gene trees from IQTREE for amino acid 70 percent complete matrix. Eury_70p_swsc.treefile: Output tree from IQTREE for 70 percent complete matrix, using SWSC partitioning. Eury_aa50p_PMSF_C60.treefile: Output tree from IQTREE for amino acid 50 percent complete matrix, using PMSF C60 model, and Eury_50p_swsc.treefile as guide tree. Eury_aa70p_PMSF_C60.treefile: Output tree from IQTREE for amino acid 70 percent complete matrix, using PMSF C60 model, and Eury_70p_swsc.treefile as guide tree. ### **Dating:** Eury70p_guidetree.tre: Input guide tree for MCMCTree, a modified version of the Eury_70p_swsc.treefile. Eury70p_MCMCTree.tre: Output tree from MCMCTree. mcmctree.ctl: Control file for MCMCTree. in.BV: Normal approximation file used by MCMCTree. mcmctreer.r: R script used to generate final figure. ### **Biogeography:** Eurytomidae_BGB_script_constrained.r: R script used for biogeographic analysis. Eurytomidae_geog.data: Coding of biogeographic distribution used for biogeographic analysis. Eury_biogeo_modified.nwk: Pruned input tree from Eury_70p_swsc.treefile for biogeographic analysis. manual_dispersal_multipliers.txt: Dispersal rate scaler used for biogeographic analysis. timeperiods.txt: Time periods used for biogeographic analysis. ### **ASR:** Eury_ASR.csv: Coding of feeding biology for ancestral state reconstruction. State "0" is Parasitoid, "1" is Phytophagous, "?" is Unknown. corHMM.r: R script used for ancestral state reconstruction. #### Version changes **11-Apr-2025:** Removed redundant files and fixed small mistake in the README file regarding the published version.