DOI: 10.5061/dryad.sn02v6xkc
title: UCE phylogenomics improves the classification of the cosmopolitan pit-building antlion tribe Myrmeleontini (Neuroptera: Myrmeleontidae: Myrmeleontinae)

description: This dataset provides raw genome assemblies, a lineage-specific
 ultraconserved element (UCE) probe set, and derived phylogenomic data for
 the antlion tribe Myrmeleontini (Neuroptera: Myrmeleontidae). The files
 include scaffold-level genome assemblies used for probe design, the UCE
 probe set Myrmeleontidae_v1 (156,272 probes targeting 8,537 loci), UCE
 loci filtered to 90% taxon occupancy (uceMYR90; 3,027 loci), a
 concatenated supermatrix alignment, and inputs/outputs for concatenated
 maximum-likelihood and coalescent-based (ASTRAL) phylogenetic inference,
 including partitioning and support-assessment results. Support and
 conflict are summarized using IQ-TREE concordance factors (gCF and sCF)
 and Quartet Sampling metrics (QC, QD, QI).
description: # UCE phylogenomics improves the classification of the cosmopolitan
 pit-building antlion tribe Myrmeleontini (Neuroptera: Myrmeleontidae:
 Myrmeleontinae) Dataset DOI:
 [10.5061/dryad.sn02v6xkc](https://doi.org/10.5061/dryad.sn02v6xkc) ##
 Description of the data and file structure README – Phylogenomic dataset
 for Myrmeleontini (Neuroptera: Myrmeleontidae) 1\. Overview This Dryad
 submission provides data used for phylogenomic analyses of Myrmeleontini
 based on ultraconserved elements (UCEs). The dataset includes (all in
 Myrmeleontini_upload.zip): (1) scaffold-level genome assemblies used for
 probe design (“original scaffold”) (2) a lineage-specific UCE probe set
 (“Myrmeleontidae_v1.fasta”) (3) UCE loci filtered for 90% completeness
 (“90 UCEs data”; uceMYR90) (4) a concatenated UCE supermatrix
 (“FcC_supermatrix.fas”) (5) files for concatenated maximum-likelihood (ML)
 inference and partitioning (“ML”) (6) original ASTRAL inputs/outputs
 (“astral”) (7) support and conflict assessment results for ML and ASTRAL
 trees (“16-1-concordane_factors”, “17-quetetsampling”,
 “16-2-as-concordane_factors”, “17-as-quetetsampling”) All files are
 provided as plain text or standard phylogenetic formats (FASTA,
 Newick/Nexus, and program output text files). 2\. Directory and file
 inventory 2.1 **original scaffold**/ Contents: de novo assembled genomes
 (scaffold-level assemblies) used to design the UCE probe set. File type:
 FASTA (.fa/.fasta; may be gzip-compressed).\ Each file in the “original
 scaffold” folder is a raw genome assembly, and the file name corresponds
 to the voucher/specimen ID (the associated species information for each
 voucher is provided in Table S1 of the manuscript). 2.2
 **Myrmeleontidae_v1.fasta** Contents: Lineage-specific UCE probe sequences
 used for locus extraction. File type: FASTA. Key values: 156,272 probes
 targeting 8,537 loci. 2.3 **90 UCEs data**/ Contents: UCE loci filtered to
 90% taxon occupancy (uceMYR90; 3,027 loci), including locus alignments
 used for downstream analyses. Typical file types: aligned loci in
 FASTA/PHYLIP (depending on export), and/or per-locus alignment files. File
 naming convention (90% UCE loci) Files in the folder “90 UCEs data/” are
 named automatically by the pipeline and follow this pattern:
 uce-.treeshrink. where: \- is
 an internal, sequential UCE locus identifier assigned by the
 extraction/processing scripts. It is used only to uniquely label and track
 loci across files and does not encode biological meaning. \- “treeshrink”
 indicates that the locus alignment was processed with TreeShrink to
 identify and remove outlier long-branch sequences. \- 
 indicates the file format (e.g., “fas” = FASTA alignment). Example: \-
 uce-340.treeshrink.fas FASTA alignment for UCE locus 340 after TreeShrink
 filtering. Notes: Alignments were produced with MAFFT and trimmed with
 ClipKit; potential alignment errors were filtered using TAPER; outlier
 sequences were filtered using TreeShrink prior to matrix generation. 2.4
 **ML/** Contents:\ Files for the concatenated maximum-likelihood (ML)
 analysis based on the 90% completeness UCE supermatrix. ML/partition/
 Folder containing files used for partitioning the concatenated alignment.
 \- FcC_supermatri.csv: Partition table (see file for details) used to
 define/record partition blocks for the concatenated matrix. \-
 FcC_supermatri_entropy_partition_finder.cfg: Configuration file for
 entropy-based partitioning of UCE loci (used to generate/guide the
 partition scheme). ML/FcC_supermatrix.fas Concatenated alignment
 (supermatrix) of UCE loci filtered to 90% taxon occupancy. How to reuse:
 This file can be used directly in concatenated phylogenetic inference
 programs (e.g., IQ-TREE), together with the corresponding partition
 file(s) provided under the “ML” folder. ML/ML.tre Maximum-likelihood
 phylogenetic tree inferred from the concatenated supermatrix under the
 partitioned model. 2.6 **astral/** Contents: 1\) all.gene.tre Plain-text
 Newick gene trees used as the ASTRAL input. This file contains 3,027 gene
 trees (one tree per UCE locus; one tree per line). Internal node labels
 are bootstrap-like support values (0–100) and branch lengths are included.
 2\) astral.tre The ASTRAL species tree output in Newick format. This is
 the direct ASTRAL output tree with branch lengths and node support values
 (as written in the file; values are in the 0–1 range). 3\)
 species_tree.tre The same ASTRAL species tree as in astral.tre, written
 with an alternative rooting/ordering for readability (Apexz is placed as
 the outgroup in this representation). Branch lengths and the same node
 support values are retained. 4\) log.txt Console log of the ASTRAL run,
 including the program/version information, input summary (e.g., number of
 gene trees and species), threading, and the final inferred tree/score
 reported by ASTRAL. 2.7 **16-1-concordane_factors/** (ML support
 assessment) Contents: IQ-TREE concordance factor results computed on the
 concatenated-tree framework. Typical outputs include tables reporting gCF
 and sCF values per internal branch. gCF (gene concordance factor) =
 percentage of gene trees supporting a given internal branch of the
 reference tree. sCF (site concordance factor) = percentage of alignment
 sites supporting a given internal branch of the reference tree.
 Definitions: \- gCF (gene concordance factor): percentage of gene trees
 supporting a given internal branch. Concordance factors (gCF/sCF) –
 ML-tree based (IQ-TREE) FcC_supermatrix_partition_myr.contree The
 partitioned maximum-likelihood (ML) tree inferred from the concatenated
 UCE supermatrix. This tree was used as the reference tree for concordance
 factor calculations. rerooted.tre The same ML reference tree after
 re-rooting using the designated outgroup taxa, provided for visualization
 and consistency in downstream interpretation. all.gene.tre Input gene
 trees used for concordance factor (gCF) calculations. This file contains
 the set of per-locus ML gene trees corresponding to the UCE loci retained
 in the 90% occupancy dataset (one tree per locus; Newick format).
 concord90.log IQ-TREE log file for the concordance factor run, recording
 the command line, settings, and run summary. concord90.cf.tre The
 reference tree annotated with concordance factor values produced by
 IQ-TREE (Newick format with node/branch annotations). concord90.cf.tre.nex
 NEXUS-format version of the concordance-factor annotated tree (same
 information as concord90.cf.tre), provided for compatibility with software
 that prefers NEXUS. concord90.cf.branch Tab-delimited branch-by-branch
 concordance factor output from IQ-TREE, listing gCF/sCF and related branch
 information. **concord90.cf.stat** **Final summary table of concordance
 factors (gCF and sCF) for the ML reference tree. This is the definitive
 results file for downstream use and interpretation.** \- sCF (site
 concordance factor): percentage of alignment sites supporting a given
 internal branch. alignment/ Folder containing the filtered and aligned UCE
 locus sequences used for concordance factor calculations (one alignment
 per locus; generated from the 90% occupancy UCE dataset after filtering
 and alignment). rerooted.tre The reference maximum-likelihood tree after
 re-rooting using the designated outgroup taxa, used for visualization and
 consistent interpretation. concord.best_scheme Best-fit partitioning
 scheme selected/used by IQ-TREE for the concordance factor analysis
 (plain-text summary). concord.best_scheme.nex NEXUS-format representation
 of the best-fit partitioning scheme (same information as
 concord.best_scheme), provided for compatibility. concord.model.gz
 Model/partition summary file produced by IQ-TREE (plain-text).
 concord.best_model.nex NEXUS-format version of the model/partition summary
 (same information as concord.best_model). concord.model.gz Compressed file
 containing model/partition-related outputs generated by IQ-TREE
 (gzip-compressed). concord.ckp.gz\ Checkpoint file produced by IQ-TREE,
 which can be used to resume the run if needed. concord.treefile Reference
 tree file produced/used by IQ-TREE for this run (Newick format).
 concord.cf.tre Reference tree annotated with concordance factor values
 produced by IQ-TREE (Newick format with node/branch annotations).
 concord.cf.tre.nex NEXUS-format version of concord.cf.tre (same
 concordance-factor annotations), provided for compatibility.
 concord.cf.branch Tab-delimited branch-by-branch concordance factor output
 from IQ-TREE, listing sCF (and associated statistics) for each branch.
 **concord.cf.stat** **Final summary table of site concordance factor
 results for the reference tree. This is the definitive results file for
 downstream use and interpretation.** concord.iqtree IQ-TREE report file
 summarizing run settings, chosen models/partitions, and key results.
 concord.ckp.gz Compressed checkpoint file produced by IQ-TREE
 (gzip-compressed), enabling the run to be resumed if needed. concord.log
 Plain-text log file for the concordance factor run, recording the command
 line and run progress. 2.8 **16-2-as-concordane_factors/** (ASTRAL support
 assessment) Contents: Concordance-factor summaries mapped to the ASTRAL
 species-tree framework. Definitions: similar as Section 2.7 (gCF and sCF).
 \- gCF (gene concordance factor): percentage of gene trees supporting a
 given internal branch.\ Concordance factors (gCF/sCF) – ASTRAL
 species-tree based species_tree.tre The ASTRAL-inferred species tree
 (Newick format) used as the reference tree for concordance factor
 calculations in the ASTRAL framework. asrerooted.tre The ASTRAL species
 tree after re-rooting using the designated outgroup taxa, provided for
 visualization and consistent interpretation. all.gene.tre Input gene trees
 used for concordance factor calculations under the ASTRAL framework (one
 gene tree per UCE locus; Newick format). These are the per-locus trees
 summarized by ASTRAL to infer the species tree. concord90.log Log file for
 the concordance factor run, recording the command line, settings, and run
 summary. concord90.cf.tree The ASTRAL reference tree annotated with
 concordance factor values (Newick format with node/branch annotations).
 concord90.cf.tree.nex NEXUS-format version of concord90.cf.tree (same
 concordance-factor annotations), provided for compatibility.
 concord90.cf.branch Tab-delimited branch-by-branch concordance factor
 output, listing concordance factor values and related statistics for each
 branch of the ASTRAL reference tree. **concord90.cf.stat** **Final summary
 table of concordance factor results for the ASTRAL reference tree. This is
 the definitive results file for downstream use and interpretation.** \-
 sCF (site concordance factor): percentage of alignment sites supporting a
 given internal branch. alignment/ Folder containing the filtered and
 aligned UCE locus sequences used for site concordance factor calculations
 (one alignment per locus; derived from the 90% occupancy UCE dataset).
 asrerooted.tre The ASTRAL species tree after re-rooting using the
 designated outgroup taxa, used as the reference tree for this sCF analysis
 and for visualization. concord.best_scheme Best-fit partitioning scheme
 selected/used by IQ-TREE for this concordance factor run (plain-text
 summary). concord.best_scheme.nex NEXUS-format version of the best-fit
 partitioning scheme (same information as concord.best_scheme), provided
 for compatibility. concord.model.gz Model/partition summary file produced
 by IQ-TREE (plain-text). concord.ckp\ Checkpoint file produced by IQ-TREE,
 which can be used to resume the run if needed. concord.best_model.nex
 NEXUS-format version of the model/partition summary (same information as
 concord.best_model). concord.model.gz Compressed file containing
 model/partition-related outputs generated by IQ-TREE (gzip-compressed).
 concord.treefile Reference tree file used by IQ-TREE for the sCF
 computation (Newick format). concord.cf.tree ASTRAL reference tree
 annotated with site concordance factor values (Newick format with
 node/branch annotations). concord.cf.tree.nex NEXUS-format version of
 concord.cf.tree (same sCF annotations), provided for compatibility.
 concord.cf.branch Tab-delimited branch-by-branch site concordance factor
 output, reporting sCF (and associated statistics) for each branch of the
 reference tree. **concord.cf.stat** **Final summary table of site
 concordance factor results for the ASTRAL reference tree. This is the
 definitive results file for downstream use and interpretation.**
 concord.iqtree IQ-TREE report file summarizing run settings, chosen
 models/partitions, and key results. concord.ckp.gz Compressed checkpoint
 file produced by IQ-TREE (gzip-compressed), enabling the run to be resumed
 if needed. concord.log Plain-text log file for the concordance factor run,
 recording the command line and run progress. 2.9 **17-quetetsampling/**
 (ML support assessment) Notes: \- QC (quartet concordance): values near 1
 indicate strong concordance; values near -1 indicate strong discordance.
 \- QD (quartet differential): values near 1 indicate discordant
 alternatives are similarly frequent; values near 0 indicate one discordant
 alternative dominates. \- QI (quartet informativeness): proportion of
 informative replicates; 1 means all replicates informative, 0 means none.
 Contents: Quartet Sampling outputs mapped to the ASTRAL species tree.
 Quartet Sampling (QC/QD/QI) – input and output files
 FcC_supermatrix_partition_myr.txt Partition file used in the phylogenetic
 analysis of the concatenated UCE supermatrix. This file defines the
 partition blocks (and associated models/settings, if specified) used for
 tree inference. rerooted.tre The phylogenetic tree used as the reference
 for Quartet Sampling, re-rooted using the designated outgroup taxa for
 consistent interpretation. RESULT.node.counts.csv Quartet Sampling output
 table reporting, for each internal node, the counts/frequencies of
 concordant and discordant quartet topologies across replicates.
 **RESULT.node.scores.csv** **Final Quartet Sampling results table
 reporting node-level scores. This is the definitive results file to use
 for downstream interpretation (including QC, QD, and QI values).**
 RESULT.labeled.figtree Tree file formatted for visualization in FigTree,
 with Quartet Sampling results mapped/annotated on the reference tree.
 RESULT.labeled.tre Newick tree annotated with Quartet Sampling results
 (node labels/metadata), suitable for downstream plotting or inspection.
 RESULT.labeled.tre.freq Supplementary output containing quartet topology
 frequencies associated with the annotated tree. RESULT.labeled.tre.qc
 Supplementary output containing QC (quartet concordance) values mapped to
 the annotated tree. RESULT.labeled.tre.qd Supplementary output containing
 QD (quartet differential) values mapped to the annotated tree.
 RESULT.labeled.tre.qi Supplementary output containing QI (quartet
 informativeness) values mapped to the annotated tree. RESULT.run.stats Run
 statistics and summary information produced during Quartet Sampling (e.g.,
 number of replicates and run diagnostics). 2.10 **17-as-quetetsampling/**
 (ASTRAL support assessment) Contents: Quartet Sampling outputs computed on
 the ML/concatenated tree. FcC_supermatrix_partition_myr.txt Partition file
 used in the phylogenetic analysis of the concatenated UCE supermatrix.
 This file defines the partition blocks (and associated models/settings, if
 specified) used for tree inference. asrerooted.tre The ASTRAL species tree
 used as the reference for Quartet Sampling, re-rooted using the designated
 outgroup taxa for consistent interpretation. RESULT.node.counts.csv
 Quartet Sampling output table reporting, for each internal node, the
 counts/frequencies of concordant and discordant quartet topologies across
 replicates. **RESULT.node.scores.csv** **Final Quartet Sampling results
 table reporting node-level scores. This is the definitive results file to
 use for downstream interpretation (including QC, QD, and QI values).**
 RESULT.labeled.figtree Tree file formatted for visualization in FigTree,
 with Quartet Sampling results mapped/annotated on the reference tree.
 RESULT.labeled.tre Newick tree annotated with Quartet Sampling results
 (node labels/metadata), suitable for downstream plotting or inspection.
 RESULT.labeled.tre.freq Supplementary output containing quartet topology
 frequencies associated with the annotated tree. RESULT.labeled.tre.qc
 Supplementary output containing QC (quartet concordance) values mapped to
 the annotated tree. RESULT.labeled.tre.qd Supplementary output containing
 QD (quartet differential) values mapped to the annotated tree.
 RESULT.labeled.tre.qi Supplementary output containing QI (quartet
 informativeness) values mapped to the annotated tree. RESULT.run.stats Run
 statistics and summary information produced during Quartet Sampling (e.g.,
 number of replicates and run diagnostics). 3\. Recommended free/open
 software to view and reuse the data General file viewing: \- Any text
 editor (e.g., VS Code, Notepad++, TextEdit) \- gzip/gunzip or 7-Zip (for
 .gz compressed files) Sequence and alignment viewing: \- AliView, MEGA, or
 UGENE (free tools for FASTA/alignment viewing) Phylogenetic inference and
 tree viewing: \- IQ-TREE 2 (concatenated ML inference; reading partition
 files and producing output trees) \- ASTRAL (species-tree inference from
 gene trees) \- FigTree or iTOL (tree visualization; iTOL is web-based)
 Alignment utilities (if reprocessing is desired): \- MAFFT (alignment) \-
 ClipKit (trimming) \- TAPER (alignment error filtering) \- TreeShrink
 (outlier long-branch filtering) 4\. Notes on data reuse Users can
 reproduce the main phylogenomic analyses by: (1) using
 “FcC_supermatrix.fas” with the partition file(s) in “ML/” to rerun
 concatenated ML analyses (IQ-TREE) (2) using the per-locus gene trees in
 “astral/” to rerun ASTRAL and compare species-tree estimates (3) using
 concordance-factor and Quartet Sampling folders to quantify support and
 discordance across alternative trees 5\. Legal and ethical considerations
 This dataset contains no human subject data. Specimens represent insects
 (Myrmeleontidae). Information on specimen provenance, sampling
 permissions, museum loans, and any applicable legal considerations (e.g.,
 collecting permits and access and benefit-sharing where relevant) is
 documented in the associated manuscript and supporting materials. 6\.
 Contact For questions about the dataset, please contact: Name: Yuchen
 Zheng Email:
 [zhengyuchenantlion@gmail.com](mailto:zhengyuchenantlion@gmail.com)
 Affiliation: Institute of Zoology, Chinese Academy of Sciences ##
 Code/software Please see the material and methods ## Access information
 Other publicly accessible locations of the data: * NCBI (Bioproject:
 PRJNA1403738) (uploading) Data was derived from the following sources: *
 the research of "**UCE phylogenomics improves the classification of
 the cosmopolitan pit-building antlion tribe Myrmeleontini (Neuroptera:
 Myrmeleontidae: Myrmeleontinae)**" (proofing)