Systematic and taxonomic revision of Emerald and Tigertail dragonflies (Anisoptera: Synthemistidae & Corduliidae)
Data files
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README.md
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Supplemental_Information.zip
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Jul 02, 2025 version files 6.55 GB
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README.md
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Supplemental_Information.zip
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Abstract
Libelluloidea is the most speciose superfamily within dragonflies (Odonata: Anisoptera), yet intrafamilial relationships have remained contested for the past 150 years. Here we present a phylogenetic hypothesis for two families within Libelluloidea, Corduliidae (Emeralds), and Synthemistidae (Tigertails) based on comprehensive taxon sampling (Corduliidae: 141/165 species, Synthemistidae: 123/150) for which we generated Anchored Hybrid Enrichment (AHE) high-throughput molecular sequences (10 - 1054 loci). Furthermore, we combined our molecular dataset with 100 discrete morphological characters based on wing, body, nymphal and genitalic characters. Using our molecular data, and an evaluation of morphological characters via ancestral character state reconstruction, we propose a new classification for these taxa. Here, three new families are erected: Lauromacromiidae fam. nov.,; Macromidiidae fam. nov.,; Aeschnosomatidae fam. nov.. and the status is revised for six families: Pseudocorduliidae stat. rev., Lohmann, 1996; Gomphomacromiidae stat. rev., Tillyard & Fraser, 1940; Austrocorduliidae stat. rev., Lohmann, 1996; Idomacromiidae stat. rev., Tillyard & Fraser 1940; Idionychidae stat. rev., Tillyard & Fraser, 1940; Neophyidae stat. rev., Tillyard & Fraser, 1940. Furthermore, we sink the genus Procordulia Martin, 1907 into the genus Hemicordulia Selys, 1870. Finally, we recover five enigmatic taxa (Archaeophya Fraser, 1959, Libellulosoma Martin, 1907, Austrophya Tillyard, 1909, Apocordulia Watson ,1980, and Cordulisantosia Fleck and Costa, 2007) for which no molecular data was previously available within these new families with high support using a total-evidence approach. Character state reconstructions revealed widespread homology among traditional characters used to identify groups within each family. We estimate the ancestral Libelluloidea possessed a compact anal loop, prominent uniform labial dentition in the nymphs, and a reduced ovipositor. Finally, time-divergence analyses estimate Libelluloidea to have originated within the Late Jurassic, with subsequent families diversifying throughout the Cenozoic.
We have submitted:
Specimen provenance data including locality, date, author, collector, determiner, sequencing code, and if scored for morphology of species used in phylogeny (Supplemental_Table_S1.csv)
Specimen loci count, sequencing dataset (500kb or 20kb), and if removed in downstream post-hoc analyses of species used in phylogeny (Supplemental_Table_S2.csv)
Raw AHE reads of Corduliidae and Synthemistidae species + outgroups from our AHE pipeline. We followed methods outlined in Breinholt et al. (2018) to assemble and assign orthology to each target capture locus (1_Assemblies).
Supplemental files, figures, and job files of phylogenetic analyses conducted within our manuscript (2_Phylogenetic_Analysis)
Output files from different morphological scoring analyses in order infer the degree of influence morphological characters possess in topological and branch length differences in our molecular phylogeny, using taxa retained after ad-hoc pruning (3_Morphological_Analysis)
Output files from our total-evidence (Morphology + sequences) phylogenetic analysis to infer the placement of species which we failed to amplify sequences for (4_Total_Evidence_Analysis)
Output from our time-divergence MCMCtree analysis (5_Time_Divergence_Analysis)
Data Formats
Excel/csv files:
- .csv: Utilized for organizing metadata of specimens used in phylogenetic sequencing, including taxonomy, author, locality, longitude, latitude, institution, and collection (Supplemental_Table_S1.csv)
Text Files:
- .txt: Contains output from parameter settings/output files from our phylogenetic analyses and divergence analyses (mcmc.txt)
Python/Shell/perl Scripts:
- .py/.sh/.pl: Python or bash scripts for running phylogenetic analyses (See Breinholt et al. 2018) (FASconCAT_v1.11.pl)
Cluster Job Files:
- .job: SLURM job script submitted to the cluster, contains parameters of various phylogenetic (ML) analyses (combined_analysis.job)
Phylogenetic Files:
- .tre: Output phylogenetic trees generated from IQ-tree, can be viewed using Figtree (http://tree.bio.ed.ac.uk/software/figtree/) (Astral_tree.tre)
- .newick: Output phylogenetic trees generated from IQ-tree can be viewed using Figtree (http://tree.bio.ed.ac.uk/software/figtree/) (ML_Tree_Renamed.newick)
- .phy: Input alignment file in phylip format of AHE sequences used for sequences, can be opened using Aliview (https://ormbunkar.se/aliview/), or Mesquite (https://www.mesquiteproject.org/) (dna.phy, wings.phy)
- .fasta: Input unaligned Raw AHE reads of Corduliidae and Synthemistidae species + outgroups, can be opened using Aliview (https://ormbunkar.se/aliview/), or Mesquite (https://www.mesquiteproject.org/) (GEODE_17697_Corduliidae_Antipodochlora_braueri_targets_ORTHO.fasta)
Time-Divergence Files:
- .ctl: Control files which define parameters for creating time-divergence analyses using the MCMCtree package in PAML (mcmctree.ctl)
- .BV: Pre-computed branch lengths and their associated variances for the specified tree topology in our time-divergence analysis (out.BV)
Additional Files:
- .out: Standard output file generated by jobs run on a SLURM-managed cluster. Provides inputted parameters for phylogenetic analyses and produced output files (slurm-3619918.out)
- .nex: Nexus format data generated to store both molecular and morphological-data in text format (partition.nex).
- .bionj/.gz/.iqtree/.log/.mldist/.parstree/.ufboot/.ckp/.mcmc/.parts/.p/.t/.probs/.tstat/.vstat/.txt/emf: various output files generated from Maximum Likelihood (IQ-tree) phylogenetic analyses
Recommended Software for Data Analysis
In order to run/reproduce analyses from 1_Assemblies, requires the use of bioconda (https://bioconda.github.io/) with the packages MAFFT v.7.475, trimAI v1.2, and FASconCAT v1.11
In order to run/reproduce analyses from 2_Phylogenetic_Analysis requires the use of iqtree2 (http://www.iqtree.org/)
In order to run/reproduce analyses from 3_Morphological_Analysis and 4_Total_Evidence_Analysis requires the use of iqtree2 (http://www.iqtree.org/), Mesquite v.3.81 (https://www.mesquiteproject.org/), R and RStudio (https://posit.co/download/rstudio-desktop/)
In order to run/reproduce analyses from 5_Time_Divergence_Analysis requires the PAML command line package (http://abacus.gene.ucl.ac.uk/software/paml.html), using the MCMCtree command
Usage, Compatibility, and Accessibility
This dataset encompasses a wide breadth of file formats, due to the span of analyses conducted within this manuscript, ranging from phylogenetic, morphological, and divergence.
The majority of these files can be viewed using a standard text editing software such as BBedit (https://www.barebones.com/products/bbedit/index.html), as well as tree view software Figtree (https://github.com/rambaut/figtree/releases) and all programs, code, and data are publicly available, and free to use.
Researchers are encouraged use original data formats, repeat analyses using our data for reliability and accuracy, and to email the corresponding author for any additional questions or confusions.
We are committed to providing support, clarity, and guidance to facilitate the effective use of these data, with the hopeful prospect of instilling curiosity and future analyses with not only our data, but with phylogenomic datasets.
Version changes
11-jun-2011: Added additional locality information to Supplemental_Table_S1.csv after review of manuscript by co-authors, and renamed the family-level underscores of the Specimen column from Supplemental_Table_S2.csv to reflect the new taxonomy from the manuscript
Descriptions
Supplemental_Table_S1.csv
- Sequencing Code: Sequencing code used for specimen upon extraction of DNA from the hind leg and subsequent submission to RapidGenomics. NOTE, lines with NA represent unsequenced specimens, but still scored for morphology
- Family: Taxonomic rank of specimen at the family level
- Genus: Taxonomic rank of specimen at the genus level
- Species: Taxonomic rank of specimen at the species level (species epithet)
- Author: Author who first described the species
- Country: Country where specimen was captured, NA indicates that information was not present on label
- State/Province/Region: State/Province/Region where specimen was captured, NA indicates that information was not present on label
- County/Parish/Prefecture: County/Parish/Prefecture where specimen was captured, NA indicates that information was not present on label
- Locality: Descriptive locality where specimen was captured, NA indicates that information was not present on label
- Latitude: Latitude coordinate where specimen was captured, NA indicates that information was not present on label
- Longitude: Longitude coordinate where specimen was captured, NA indicates that information was not present on label
- Altitude: Altitude where specimen was captured, NA indicates that information was not present on label
- Sex: Sex of specimen (Male/Female), NA indicates that information was not present on label
- Day: Calendar day of specimen capture (1 - 31), NA indicates that information was not present on label
- Month: Calendar month of specimen capture (Specimen roman numeral notation, I - XII), NA indicates that information was not present on label
- Year: Calendar year of specimen origin (1939 - 2018), NA indicates that information was not present on label
- Collector: Collector of specimen, NA indicates that information was not present on label
- Det: Determiner of species identification, NA indicates that information was not present on label
- Institution: Institution where specimen is housed (FSCA, BYU, RMNH), NA indicates that information was not present on label
- Collection: Collection of specimen (If researcher donated specimens to museum, that specimen is part of that collection, D.R. Paulson Collection), NA indicates that information was not present on label
- Processed by: Processor of specimen into database of museum, NA indicates that information was not present on label
- Type: Specimen type status (Holotype, Paratype, Lectotype etc.), NA indicates that information was not present on label
- Notes: Additional notes on label for specimen which does not fit into aforementioned categories, NA indicates that information was not present on label
- Scored for Morphology: If the specimen was scored using our 100 discrete morphological matrix (See 3_Morphological_Analysis and 4_Total_Evidence_Analysis)
Supplemental_Table_S2.csv
- Specimen: Sequencing code, family, genus, and species of specimen used for extraction of dna from hind leg and subsequent submission to RapidGenomics
- Loci Count: Number of successful loci amplified and sequenced from that specimen
- AHE_Dataset: Probe set used to amplify loci for specimen (500kb = 1000+ loci, while 20kb = 92 loci probe set)
1_Assemblies:
File Naming Convention
Each file name follows a structured format that encodes metadata about the sample and data type:
Components
- GEODE_####: A unique AHE (Anchored Hybrid Enrichment) project identifier assigned to the specimen. The number (e.g.,
17697) corresponds to the sample ID used in sequencing and tracking. - : The taxonomic family of the specimen (e.g.,
Corduliidae). - : The genus of the specimen (e.g.,
Antipodochlora). - : The species epithet of the specimen (e.g.,
braueri). - : Describes the sequence content:
targets_ORTHO: Raw AHE reads targeting the 500kb probe region only.targetsFULL_ORTHO: Raw AHE reads including both the 500kb probe region and the surrounding flanking regions.- (For the 20kb dataset, the same naming convention applies, and details can be cross-referenced in Supplemental_Table_S2.csv.)
Examples
- GEODE_17697_Corduliidae_Antipodochlora_braueri_targets_ORTHO.fasta: Raw AHE reads of 500kb loci probe set of the species Antipodochlora braueri.
- GEODE_17697_Corduliidae_Antipodochlora_braueri_targetsFULL_ORTHO.fasta: Raw AHE reads of 500kb loci probe + flanking region set of the species Antipodochlora braueri. NOTE: remaining taxa follow same file formatting and naming, both for 500kb and 20kb dataset (see Supplemental_Table_S2.csv)
2_Phylogenetic_Analysis
Unaltered_iqtree: Here you will find all the maximum likelihood (IQTREE) phylogenetic analyses conducted after removing sequences of 'uncertain placement'. Consider these our phylogeny of all taxa prior to ad-hoc modifications
- Astral_tree.tre: The species tree inferred using ASTRAL, which estimates a consensus tree from multiple gene trees while accounting for incomplete lineage sorting.
- concord.cf.branch: Contains branch-specific concordance factors, showing how much of the data (e.g., gene trees or sites) supports each internal branch.
- concord.cf.stat: Summary statistics of concordance factors, including mean, variance, and distribution across branches.
- concord.cf.tree: A phylogenetic tree in Newick format annotated with concordance factor values for each branch.
- concord.cf.tree.nex: Same as concord.cf.tree, but in NEXUS format for visualization in software like FigTree or PAUP*.
- concord.log: Log file from the concordance factor analysis process; records steps taken and any errors or warnings.
- extract_partition_file_from_fcc.py: A Python script used to extract partitioning information from FASconCAT or similar concatenated datasets.
- FASconCAT_v1.11.pl: A Perl script used to concatenate multiple gene alignments into a supermatrix and generate partition files for phylogenetic analysis.
- FcC_info.xls: Excel spreadsheet generated by FASconCAT containing summary statistics about the concatenated alignments, such as the number of characters per gene, missing data percentages, and taxon coverage.
- FcC_smatrix.fas: FASTA-formatted supermatrix of concatenated gene alignments produced by FASconCAT. Unaltered version of FcC_smatrix_N.fas.
- FcC_smatrix_N.fas: The concatenated supermatrix alignment in FASTA format, created by FASconCAT, used for tree inference or model selection, with dashes (-) replaced with N
- iqtree_model_selection_and_tree_search.job: A job script (likely for SLURM or another scheduler) to run IQ-TREE for model selection and tree inference.
- iqtree2: The IQ-TREE 2 binary executable or a symbolic link to it. This is the program used for phylogenetic inference under maximum likelihood.
- loci_count.txt: Plain text file listing the number of loci recovered per taxon, useful for assessing completeness and data coverage across samples.
- odo_concat.best_model.nex: Contains the best-fitting substitution model selected for the concatenated dataset, formatted for NEXUS compatibility.
- odo_concat.best_scheme: The partitioning scheme inferred to best fit the concatenated dataset, listing genes or regions and their respective models.
- odo_concat.best_scheme.nex: NEXUS format version of the best partitioning scheme, usable by software requiring this format.
- odo_concat.bionj: A neighbor-joining tree used as the starting tree for maximum likelihood inference in IQ-TREE.
- odo_concat.ckp.gz: A compressed checkpoint file used to resume interrupted IQ-TREE runs without starting from scratch.
- odo_concat.contree: The consensus tree from a bootstrap or posterior distribution, summarizing common features across replicates.
- odo_concat.iqtree: Summary output file containing the results of the tree inference, including model selection, likelihood scores, and support values.
- odo_concat.log: Log file from IQ-TREE, detailing the process of model selection and tree inference, including run time, warnings, and performance stats.
- odo_concat.mldist: A matrix of pairwise maximum likelihood distances between all taxa in the alignment.
- odo_concat.model.gz: Compressed file containing the model settings and substitution matrices used for the analysis.
- odo_concat.splits.nex: A splits graph in NEXUS format showing alternative topologies or conflicting phylogenetic signals.
- odo_concat.treefile: The final maximum likelihood tree produced by IQ-TREE, including branch lengths and support values.
- odo_concat.ufboot: Contains ultrafast bootstrap replicate trees, used to assess support for branches in the ML tree.
- odo_gene.best_scheme: The best partitioning scheme inferred for the per-gene dataset.
- odo_gene.best_scheme.nex: The same per-gene partition scheme formatted in NEXUS for compatibility with other programs.
- odo_gene.ckp.gz: Compressed checkpoint file for the gene-partitioned analysis, allowing restart from the last saved point.
- odo_gene.log: Log file of the IQ-TREE run on the gene-partitioned dataset, recording model fitting and tree inference steps.
- odo_gene.model.gz: Compressed model information file for the gene-partitioned dataset.
- odo_gene.parstree: A tree inferred using parsimony, typically used as an alternative starting tree or for comparison with the ML tree.
- odo_gene.treefile: Maximum likelihood tree for the gene-partitioned dataset, with branch support values.
- odo_partition.best_model.nex: The best substitution models selected for each partition in the partitioned dataset, formatted for NEXUS.
- odo_partition.best_scheme: The inferred optimal partitioning scheme, listing regions and their corresponding models.
- odo_partition.best_scheme.nex: NEXUS format version of the optimal partitioning scheme for compatibility with other tools.
- odo_partition.ckp.gz: Checkpoint file from the partitioned analysis, useful for resuming IQ-TREE if the run was stopped.
- odo_partition.iqtree: Main summary file for the partitioned IQ-TREE run, detailing selected models, tree stats, and branch supports.
- odo_partition.log: Log output from the partitioned tree inference, including warnings, progress, and resource usage.
- odo_partition.model.gz: Gzipped file storing model configurations used for each partition during the analysis.
- odo_partition.treefile: Maximum likelihood tree for the partitioned dataset, typically considered the final phylogeny result.
- partition_def.txt: The partition definition file, listing the alignment regions and their associated genes or data blocks.
- slurm-4301735.out: Standard output file from a SLURM job submission. Contains run-time messages, errors, or print statements from the job script.
- taxa_list.txt: A list of taxon names included in the analysis, typically used for filtering, labeling, or cross-referencing in phylogenetic workflows.
Pruned_iqtree: Here you will find all the maximum likelihood (IQTREE) phylogenetic analyses conducted after removing sequences of 'uncertain placement' (i.e. taxa which recovered to incorrect places within our Unaltered_iqtree), NOTE: all file outputs, names, and files are the same as Unaltered_iqtree
3_Morphological_Analysis
Distance_Metrics.R: Code used to calculate differences in tree topology (RF distance) and branch length (Euclidian Distance) of our pruned iqtree (See odo_concat.contree from Pruned_iqtree) to that of our total-evidence trees calculated with different subsets of morphological data
Morphology_Scores_Sequenced_Taxa.nex: Species scored from our pruned phylogeny, using our full 100 discrete character matrix consisting of characters from wings, external body, external genitalic, penile, and nymphal. Nexus file contains information and character states of each morphological character
ML_Tree_Renamed.newick: Maximum-likelihood (ML) tree generated using our pruned iqtree (211 taxa) in newick format. Note ML_Tree_Renamed.newick is the same as odo_concat.contree from Pruned_iqtree, however names have been changed to remove sequencing code (i.e. GEODEXXXX, or RMNH.XXXX), family name (i.e. Synthemistidae)
1_Wings_Scorings: Output from Total-Evidence (Morphology + Sequences) Phylogenetic analysis using our concatenated sequence matrix of our pruned species + subset of morphological matrix of just wing characters
- odo_concat.best_scheme: The best-fit partitioning scheme selected for the concatenated dataset, listing data blocks and the corresponding models applied to each.
- combined_analysis.job: A job script (likely for SLURM or similar HPC job schedulers) that executes total-evidence analysis, such as model selection and tree inference using IQ-TREE.
- dna.phy: A PHYLIP-formatted DNA alignment file used as input for phylogenetic analyses. This file contains aligned sequences of all taxa.
- iqtree2: The IQ-TREE 2 executable or symbolic link to it. Used for performing model selection and maximum likelihood phylogenetic inference.
- odo_concat.best_model.nex: A NEXUS-format file listing the best-fitting substitution models selected for each partition in the concatenated dataset.
- odo_concat.best_scheme.nex: NEXUS version of the partitioning scheme, including data blocks and associated substitution models, formatted for compatibility with downstream programs.
- odo_concat.bionj: A BioNJ tree, which is a distance-based neighbor-joining tree used as a starting topology for the maximum likelihood search in IQ-TREE.
- odo_concat.ckp.gz: A compressed checkpoint file generated during the IQ-TREE run. Allows resuming the analysis from the last saved state if interrupted.
- odo_concat.contree: The consensus tree resulting from the bootstrap analysis. It summarizes the bootstrap replicates to show the most supported branches.
- odo_concat.iqtree: The main IQ-TREE output file. It includes detailed results such as model selection, log-likelihood scores, branch supports, and partition statistics.
- odo_concat.log: Log file that records all steps of the IQ-TREE analysis. Useful for tracking progress, runtime, model decisions, and troubleshooting.
- odo_concat.mldist: Pairwise maximum likelihood distance matrix among all taxa, based on the input alignment and selected model(s).
- odo_concat.model.gz: A compressed file storing the substitution models and parameters used for each partition during the analysis.
- odo_concat.parstree: A parsimony-based tree generated as an alternative starting point or for comparison with the ML tree.
- odo_concat.splits.nex: A splits graph in NEXUS format showing alternative groupings or conflicting signals among taxa; useful for visualizing phylogenetic uncertainty.
- odo_concat.treefile: The final maximum likelihood tree inferred by IQ-TREE, containing branch lengths and support values. This is the primary output tree.
- odo_concat.ufboot: Ultrafast bootstrap replicate trees. This file is used to calculate branch support values for the consensus tree.
- partition.nex: A NEXUS-format partition file defining the start and end positions of each data block for use in partitioned analysis. NOTE: wings.phy is added as a partition, using MK+ASC model.
- slurm-3991242.out: Output file from a SLURM job submission. Includes standard output from the job script, such as command progress, warnings, or errors.
- wings.phy: A PHYLIP-format alignment file containing only wing-related morphological scores. Used in a targeted phylogenetic analysis.
2_External_Body_Scorings: Output from Total-Evidence (Morphology + Sequences) Phylogenetic analysis using our concatenated sequence matrix of our pruned species + subset of morphological matrix of just external-body characters. NOTE: all file outputs are the same as 1_Wings_Scorings
- External_body.phy: A PHYLIP-format alignment file containing only external body morphological scores. Used in a targeted phylogenetic analysis.
- partition.nex: A NEXUS-format partition file defining the start and end positions of each data block for use in partitioned analysis. NOTE: External_body.phy is added as a partition, using MK+ASC model.
3_External_Genitalic_Scorings: Output from Total-Evidence (Morphology + Sequences) Phylogenetic analysis using our concatenated sequence matrix of our pruned species + subset of morphological matrix of just external-genitalic characters. NOTE: all file outputs are the same as 1_Wings_Scorings
- External_genitalic.phy: A PHYLIP-format alignment file containing only external genitalic-related morphological scores. Used in a targeted phylogenetic analysis.
- partition.nex: A NEXUS-format partition file defining the start and end positions of each data block for use in partitioned analysis. NOTE: External_genitalic.phy is added as a partition, using MK+ASC model.
4_Larval_Scorings: Output from Total-Evidence (Morphology + Sequences) Phylogenetic analysis using our concatenated sequence matrix of our pruned species + subset of morphological matrix of just nymphal characters. NOTE: all file outputs are the same as 1_Wings_Scorings
- larval.phy: A PHYLIP-format alignment file containing only larval-related morphological scores. Used in a targeted phylogenetic analysis.
- partition.nex: A NEXUS-format partition file defining the start and end positions of each data block for use in partitioned analysis. NOTE: larval.phy is added as a partition, using MK+ASC model.
5_Genitalic_Scorings: Output from Total-Evidence (Morphology + Sequences) Phylogenetic analysis using our concatenated sequence matrix of our pruned species + subset of morphological matrix of just penile characters. NOTE: all file outputs are the same as 1_Wings_Scorings
- larval.phy: A PHYLIP-format alignment file containing only penile-related morphological scores. Used in a targeted phylogenetic analysis.
- partition.nex: A NEXUS-format partition file defining the start and end positions of each data block for use in partitioned analysis. NOTE: genitalic.phy is added as a partition, using MK+ASC model.
All_Scores_Analysis: Output from Total-Evidence (Morphology + Sequences) Phylogenetic analysis using our concatenated sequence matrix of our pruned species + all characters from morphological matrix. NOTE: all file outputs are the same as 1_Wings_Scorings
- MORPH.phy: A PHYLIP-format alignment file containing all morphological scores (100). Used in a targeted phylogenetic analysis.
- partition.nex: A NEXUS-format partition file defining the start and end positions of each data block for use in partitioned analysis. NOTE: MORPH.phy is added as a partition, using MK+ASC model.
4_Total_Evidence_Analysis
Morphology_Matrix_All_Taxa.nex: All species scored (including taxa of 'uncertain placement'), using our full 100 discrete character matrix consisting of characters from wings, external body, external genitalic, penile, and nymphal. Nexus file contains information and character states of each morphological character. Also includes our Total Evidence Phylogeny and pruned ML phylogeny
Total_Evidence_renamed.newick: Total-evidence phylogenetic analysis including taxa of 'uncertain placement' but scored for morphology. Note Total_Evidence_renamed.newick is the same as odo_concat.contree from Total_Analysis_2, as this tree possessed the highest likelihood (i.e. lowest log likelihood score)
ML_Tree_Renamed.newick: Maximum-likelihood (ML) tree generated using our pruned iqtree (211 taxa) in newick format. Note ML_Tree_Renamed.newick is the same as odo_concat.contree from Pruned_iqtree, however names have been changed to remove sequencing code (i.e. GEODEXXXX, or RMNH.XXXX), family name (i.e. Synthemistidae)
Consistency_Indices.csv: A CSV document containing the consistency index, retention index, and rescaled consistency index (CI * RI) of each morphological character using our pruned ML tree
- Character: Sequential Character Number (i.e. 1, 2, 3)
- Category: Morphological category based on subset (i.e. Wings, External Body)
- Consistency Index: Consistency index value for that character
- Retention Index: Retention index value for that character
- Rescaled Consistency Index: Rescaled Consisteny Index index value for that character
Rescaled Consistency Index: R code used to calculate Analysis of Variance (ANOVA) to determine if particular subsets possess statistical significance in taxonomic importance
Total_Analysis_1: First iteration (run) of Total-evidence phylogenetic analysis including taxa of 'uncertain placement' but scored for morphology. NOTE: all file outputs are the same as 1_Wings_Scorings
- MORPH.phy: A PHYLIP-format alignment file containing all morphological scores (100) of both pruned and 'uncertain placement' taxa Used in a targeted phylogenetic analysis.
- partition.nex: A NEXUS-format partition file defining the start and end positions of each data block for use in partitioned analysis. NOTE: MORPH.phy is added as a partition, using MK+ASC model.
Total_Analysis_2: Second iteration (run) of Total-evidence phylogenetic analysis including taxa of 'uncertain placement' but scored for morphology. NOTE: all file outputs are the same as Total_Analysis_1:
Total_Analysis_3: Third iteration (run) of Total-evidence phylogenetic analysis including taxa of 'uncertain placement' but scored for morphology. NOTE: all file outputs are the same as Total_Analysis_1:
Total_Analysis_4: Fourth iteration (run) of Total-evidence phylogenetic analysis including taxa of 'uncertain placement' but scored for morphology. NOTE: all file outputs are the same as Total_Analysis_1:
Total_Analysis_5: Fifth iteration (run) of Total-evidence phylogenetic analysis including taxa of 'uncertain placement' but scored for morphology. NOTE: all file outputs are the same as Total_Analysis_1:
5\Time\Divergence_Analysis
- 2base.t: Time unit conversion file used in MCMCTree, typically converting between substitution units and real-time units (e.g., million years).
- FcC_smatrix_N.phy: Input alignment file of AHE sequences used for ML tree (FcC_smatrix_N.fas in Pruned_iqtree)
- lnf: Log file recording the log-likelihood values during MCMC sampling. Used to assess convergence and stability of the run.
- mcmctree.ctl: Control file specifying settings for the MCMCTree run, including priors, clock model, and input/output file names.
- mcmctree.job: Job script (likely for SLURM or a similar scheduler) used to submit the MCMCTree analysis to a computing cluster.
- No_Fossil.newick: Input tree not including Somatochlora brisaci, Neophya legrandi, or Paleophya argentina as fossil calibration point, tree is ultrametric where nodes are labeled with fossil ages (Used ML_Tree_Renamed.newick)
- out: The main MCMCTree output file. Contains the posterior means, credibility intervals, and other results for divergence times.
- out.BV: Branch variance file, containing variances of divergence times along each branch. Useful for assessing uncertainty.
- rst: A file containing ancestral reconstructions or summary statistics depending on the model settings. May include estimated substitution rates or states.
- rst1: A first version of the * rst file. MCMCTree may output multiple such files during different steps of the process.
- rst2: A second version of the * rst file. Contains additional or alternative reconstructions, depending on the analysis mode.
- rub: Temporary or intermediate file created during the MCMC run. Often used internally by MCMCTree.
- SeedUsed: Records the random seed used in the MCMC analysis for reproducibility.
- slurm-4413588.out: SLURM job output file containing standard output from the MCMCTree job, such as progress updates and error messages.
- tmp0001.ctl: A temporary control file automatically generated during the MCMCTree run, often for internal checkpointing.
- tmp0001.out: Output file corresponding to the temporary control file. May include logs or results from a checkpointed phase.
- tmp0001.trees: Sampled trees from the MCMC posterior, useful for summarizing tree topology and divergence times.
- tmp0001.txt: Text-formatted version of summary results for easy viewing, often includes posterior means and credibility intervals for node ages.
approx01: First Run of from MCMCtree analysis
- No_Fossil_divergence.tre: Dated tree output, with estimated divergence times for nodes, posterior means or medians of node ages, with branch lengths scaled according to these times
- No_Fossil.newick: Input tree not including Somatochlora brisaci, Neophya legrandi, or Paleophya argentina as fossil calibration point, tree is ultrametric where nodes are labeled with fossil ages (Used ML_Tree_Renamed.newick)
- FcC_smatrix_N.phy: Input alignment file of AHE sequences used for ML tree (FcC_smatrix_N.fas in Pruned_iqtree)
- in.BV: Pre-computed branch lengths and their associated variances for the specified tree topology. This information is derived from the maximum likelihood estimation of branch lengths and rate parameters based on the sequence data
- mcmc.txt: Raw MCMC samples from the posterior distribution
- mcmctree.ctl: Control file for the MCMCTree analysis, containing the tree topology or starting tree, MCMC parameters (e.g., burn-in, chain length, sample frequency), and priors for divergence times, clock models, and rates
- mcmctree.job: SLURM job script submitted to the cluster, Contains: Job configuration (e.g., wall time, memory, CPUs), and the command to run MCMCTree.
- out: main output log summarizing the MCMC run, includes details on priors, posterior estimates, acceptance rates, and summary statistics (means, medians, 95% HPDs for parameters like node ages)
- SeedUsed: A log of the random seed used for the analysis
- slurm-4413775.out: Standard output logs from SLURM, the job scheduler, contains messages from the MCMCTree run including command-line arguments, progress information (e.g., burn-in completion, sampling progress), and potential errors or warnings
approx02: Second Run of from MCMCtree analysis. NOTE, same output files as approx01
Taxon Sampling
We acquired specimens of Corduliidae and Synthemistidae and our outgroups from both freshly caught field-collected and museum specimens. Specimens were hand caught using aerial nets within New South Wales and Victoria Australia during the summer months of January and February 2023. Specimens were placed in glassine envelopes and submerged in acetone for preservation and were transported to the American Museum of Natural History for molecular and morphological analysis. However, most specimens used in our work were sourced from natural history collections. Specimens were sampled from collections in the American Museum of Natural History (AMNH), Florida State Collection of Arthropods (FSCA), Naturalis Biodiversity Center, Natural History Museum (NMNH), Brigham Young University, Monte L. Bean Life Sciences Museum (BYU), Natural History Museum, London UK (NHMUK), the Australian Museum (AM), and the United States National Museum of Natural History (USNM). In total, we sampled 141 of the 165 species of Corduliidae (85%) and 123 of the 150 species of Synthemistidae (82%). We also sampled 9 additional Libelluloidea taxa from other families (Libellulidae: Pantala, Libellula, Orthetrum, Macromiidae: Macromia, Epophthalmia), and families within Cavilabiata (Chlorogomphidae: Chlorogomphus, Cordulegastridae: Cordulegaster, Anotogaster, Neopetaliidae: Neopetalia punctata). Specimen provenance data including locality, date, author, collector, determiner, and sequencing code are listed in Supplemental Table S1.
DNA Extraction and Sequencing:
We removed the hind leg from each field-collected or museum acquired specimen using sterilized forceps, and extracted DNA using ZYMOBIOMICS DNA miniprep kits (Irvine, CA). We quantified DNA yield using a Qubit 4 fluorometer, and sent to RAPID Genomics (Gainesville, Florida) for library preparation and sequencing. Loci were amplified using modified Anchored Hybrid Enrichment (AHE) probes first implemented in Bybee et al. (2021); the modified probe set consists of 1,306 loci covering approximately 500 kilobases (Goodman et al. 2023). We sequenced loci for representatives of each genus using the full 1,306 probe set (herein referred to as 500kb set), while a subset of 92 loci (herein referred to as 20kb probe set) were sequenced for the remaining species (See Supplemental Table S2)(500kb: 60%, 20kb: 40% of taxa). We re-sequenced several monotypic genera (Synthemistidae: Archaeophya, Austrophya, Apocordulia, Corduliidae: Williamsonia, Cordulisantosia) using the 20kb loci probe set due to failed assembly during the first round of 500kb sequencing.
AHE Assembly and Analysis
We trimmed adaptors from raw reads using fastp (Tang and Wong 2001), and checked for quality using multiQC (Ewels et al. 2016). We followed methods outlined in Breinholt et al. (2018) to assemble and assess orthology for each target capture locus. In brief, we assembled each locus individually using iterative baited assembly with SPAdes (Prjibelski et al. 2020) and a chromosome-length genome assembly of Tanypteryx hageni (Petaluridae) as reference (Tolman et al. 2023). We then screened each locus for orthology by first ensuring that the locus did not have multiple BLAST hits in the reference genome and, secondly, by ensuring best reciprocal hits between the reference and the query sequence.
Phylogenetic Analysis:
We generated multiple sequence alignments for each locus using the ‘MAFFT-linsi’ algorithm in MAFFT v.7.475 (Katoh and Standley 2013) and trimmed alignments using a 0.75 threshold cutoff using trimAI v1.2 (Capella-Gutiérrez et al. 2009). We concatenated the alignment using FASconCAT v1.11 (Kück and Meusemann 2010), and generated an optimal partitioning scheme using relaxed clustering with the model fixed to GTR + G for each subset in IQtree v2.1.3 (Minh et al. 2020). We then selected the best nucleotide substitution model for each subset in the partitioning scheme using ModelFinder (Kalyaanamoorthy et al. 2017) and estimated a maximum likelihood tree (ML). We estimated branch support using SH-like approximate likelihood ratio tests (SH-aLRT) and 1,000 ultrafast bootstrap replicates (UFboot) in IQtree v2.1.3 (Guindon et al. 2010, Minh et al. 2020). Finally, to assess the degree of incomplete lineage sorting, we performed a coalescent-based species tree estimation in ASTRALIII v5.6.1 and estimated branch support using local posterior probabilities (LPP) (Mirarab and Warnow 2015). We identify nodes of high support possessing ML and SH-aLRT values > 95, and LPP values >0.95 We rooted the tree using Neopetalia punctata (Neopetaliidae).
Post-Hoc Modifications to Phylogeny:
Preliminary analyses recovered 38 taxa of varying genera and families that clustered together, forming several odd clades in our phylogeny (See Supplemental Information). These taxa were misplacements (herein referred to as ‘uncertain status’ taxa), and these have been observed in other, previous AHE datasets and are the result of low locus count, low overlap among recovered loci across taxa, contamination, or a combination of factors (Goodman et al. 2025, Goodman et al. 2023). When contamination was exhibited based on other information, those sequences were removed. To improve resolution in our analysis, we omitted those taxa for which there was little to no overlap in recovered loci as several taxa possessed fewer than 10 loci that were recovered among congenerics with high support. After omitting these taxa, our family and genus-level representation decreased, with four monotypic genera no longer present in our analyses (Austrophya, Archaeophya, Apocordulia, and Cordulisantosia). Preliminary phylogenies recovered sequences of Archaeophya and Cordulisantosia within Neocordulia, while sequences of Apocordulia recovered within Idionyx and Somatochlora, and sequences of Austrophya recovered within Libellulidae and sister to Tonyosynthemis; we also observed short fragments and unusual gene alignments. Visual inspection of gene trees suggested other ‘uncertain status’ taxa that were grouping within Neocordulia and Somatochlora, most likely due to contamination. Our final, filtered data set included 211 taxa, down from the 249 taxa originally sequenced (See Supplemental Table S2).
Morphological Analysis:
We collected morphological data from approximately 430 specimens to characterize the variability in states among individuals and across sexes; for all our species we examined at least two specimens unless only one was available (Fig. 1 – 4). When different specimens from a single species varied in their character state, we coded all possible states present in the specimens for that species. We scored 30 wing venation (Fig. 1), 13 external body, 13 accessory genitalic (Fig. 2), 23 nymphal (Fig. 3), and 11 penile characters from Ware (2008) (Fig. 4); we further expanded on this dataset with an additional 10 de novo penile characters described herein totaling 100 characters. Wing-vein terminology followed Riek and Kukalová-Peck (1984); characters were based on previously published characters from Needham and Broughton (1927), Fraser (1957), Miller (1991), Carle (1995), Needham et al. (2000), and Garrison et al. (2006), as well as unpublished characters from Tennessen and May. When we lacked specimens to examine for particular species, we scored adult or nymphal characters from the literature (Theischinger and Watson 1978, 1984, Theischinger 1999, Theischinger and Hawking 2000, Carvalho et al. 2004, Machado 2005a, b, Theischinger and Hawking 2006, Carvalho et al. 2008, Fleck 2008, Theischinger 2009, Pinto and Carvalho 2010, Pinto and Lamas 2010, Fleck 2012a, Fleck 2012b, Fleck and Neiss 2012b, a, Machado 2012, Fleck and Legrand 2013, Theischinger and Endersby 2014b, Fleck 2017, Neiss et al. 2018, Fleck and Juillerat 2019, Roberts et al. 2019, Tennessen 2019, Ehlert and Parise Pinto 2020, Fleck and Haber 2022, Pinto et al. 2022). We mapped characters onto our ML tree under parsimony using the Trace Character option in Mesquite v3.4 (Maddison and Maddison 2007). We were unable to estimate character evolution under maximum likelihood due to the morphological characters possessing more than two states, prompting us to utilize parsimony-based character mapping only.
Further, to assess the degree of impact that specific parts of our morphological dataset had on relationships in a combined molecular and morphological topology, we first subdivided our morphological characters into discrete groups (wing venation, external body, accessory genitalic, nymphal, and penile), then performed total-evidence Maximum Likelihood phylogenetic analysis combining our molecular dataset with each individual character subset. We applied an MK model of discrete character evolution for our morphology partitions in our ML analyses otherwise using parameters as described above (Lewis 2001) (See supplementary Information). We compared topological differences for each of our trees using Robinson-Foulds (RF) Distance (Robinson and Foulds 1981), and branch length differences using Euclidian Distance (Felsenstein 1984). We then used analysis of variance (ANOVA) to determine statistical differences in topology and branch length between character subsets. In particular, to determine the degree of homoplasy and variation among our morphological data matrix, we compared the rescaled consistency index (Farris 1989) for each character using an ANOVA.
Fossil Selection and Time Divergence Analysis:
We employed fossils as calibrations for divergence time estimation following the best practices outlined by Parham et al. (2012). However, choosing fossils for calibration of odonate divergence time estimation analyses can be challenging due to the restricted suites of characters that are present in most fossils. The taxonomy of odonate fossils relies predominantly on wing characters due to their high preservation potential, and litany of wing venation traits (Fraser and Tillyard 1957). However, wing venation is highly prone to convergence and should be used in conjunction with other traits if available (Fraser and Tillyard 1957, Gloyd 1959, Hennig 1981, Fleck et al. 2008). Amber fossils of adult and nymphal Odonata are rare in the fossil record (Wighton and Wilson 1986, Bechly 1996a, Karr and Clapham 2015, Schädel and Bechly 2016, Zheng and Jarzembowski 2020, Boudet et al. 2023)(See table 1 in Schaedel et al. (2020))(paleodb.com), limiting the possibility for analyses including accessory genitalic, thoracic, penile, or nymphal traits. Kohli et al. (2016) published a list of vetted fossil calibrations for Odonata, as part of the Fossil Calibration Database (fossilcalibrations.org), providing recommendations for fossil selection in our phylogeny; these were updated and expanded upon in Kohli et al. (2021). We employed fossil calibrations for the crown nodes from Kohli et al (2021) for Cavilabiata, Chlorogomphidae + Cordulegastridae, Macromiidae, Corduliidae, Libellulidae, and Corduliidae + Libellulidae. Phylogenetic and age justifications for divergence time estimation of our fossils are outlined in detail in Kohli et al. (2016) and Kohli et al. (2021).
Fossil Validation
We surveyed five additional putative fossils proposed to belong in Synthemistidae as calibration points, extending our sampling beyond Kohli et al. (2021). We used the five principles outlined by Parham et al. (2012) and Ksepka et al. (2015) as best calibration practices. In brief, the five criteria are as follows: 1. Fossil accession number for fossil and referrals, 2. Apomorphy-based or phylogenetic analysis, 3. Reconciliation of morphological and molecular data, 4. Locality and stratigraphic data for fossil taxa 5. Radioisotopic age or numeric age references for fossil (See Table 1 in Goodman et al. (2025) for fossil calibrations).
Two putative fossils were originally assigned to the defunct subfamily Gomphomacromiinae as defined by Tillyard and Fraser (1940), both being estimated as late Jurassic/Early Cretaceous (113 – 125mya) in origin. Mesocordulia boreala, Ren and Guo, 1996 is from Western Liaoning Province, China. The holotype consists of an adult female with all four wings, head, thorax, and abdomen, as well as the paratype consisting of a complete hindwing. Mesocordulia boreala was subsequently placed within the extinct family Araripelibellulidae by Bechly (1996b), in the subfamily Mesocorduliinae. A new specimen of M. boreala was recently described, possessing exceptional preservation of both the forewings and hindwings, as well as several body, head, and external genitalic characters (Nel et al. 2024); several new diagnostic characters identified by Nel prompted the elevation of Mesocorduliinae to family-level. A second fossil is Eocordulia cretacea, Pritykina, 1985 from Western Mongolia. The holotype consists of fragmentary fore and hindwings, there is a paratype of an adult female, and paratypes consisting of the hind wing of an adult male, and posterior end of the abdomen with appendages of an adult male. Eocordulia cretacea was placed within the extinct family Eocorduliidae by Bechly (2007), but not peer-reviewed. Although both taxa exhibit very similar wing venation traits to Synthemistidae, such as a compact (Eocordulia cretacea) or smoothly curving uninflated anal loop (Mesocordulia boreala), both taxa possess unfused sectors of the arculus, a trait present only in non-libelluloid Cavilabiata (Cordulegastridae + Neopetaliidae)(Nel et al. 2024). As such, we chose to exclude these two fossils as calibration points within our time-divergence analysis.
Two other putative fossils for calibration belong to the defunct subfamily Cordulephyidae as defined by Lohmann (1996b). The older fossil is Paleophya argentina, Petrulevičius and Nel 2009, from northwest Argentina and is estimated to be from the early Paleogene (58.7 - 55.8 mya). The holotype consists of a very fragmented hind wing, with anterior and posterior portions missing except between the arculus, anal loop, bridge, and the third postnodal crossvein. The second fossil, Neophya legrandi Nel and Fleck 2013, is from the late Eocene (33.9 – 33.8 mya) from the Isle of Wright. The holotype only consists of the base of the hindwing, between the first antenodal crossvein and the pterostigma, and above the triangle. Paratypes consist of the hindwing base, the costo-apical part of either the fore or hindwing, and the wing apex of the fore or hindwing.
Lastly, Somatochlora brisaci (Nel et al. 1996) is significantly younger, with a Miocene origin (8.7 – 5.3 Ma), discovered in a deposit from Southeastern France. The fossil is a near-complete hindwing except for a few posterior regions of the wing margin missing near the third and fourth medial veins, the cubital (C) and anal (A) veins. Although previous morphological analysis of the wings of S. brisaci failed to recover it within Somatochlora (Goodman et al. 2025), this is an appropriate fossil within Corduliidae.
To determine the utility of these fossil taxa as calibration points, we scored wing-trait data for Neophya legrandi, Paleophya argentina, and Somatochlora brisaci, and performed a total evidence ML phylogeny consisting of our molecular + all morphological characters. Furthermore, we included morphological data for our ‘uncertain status’ taxa for which we had ambiguous molecular placement (n=40) including Austrophya, Archaeophya, Apocordulia, and Cordulisantosia. Finally, we scored the Malagasy species Libellulosoma to infer their placement within Libelluloidea. Previous research has hypothesized its relationship as close to the South American and Australian taxa Aeschnosoma and Pentathemis respectively (Corduliidae)(Fleck and Legrand 2013, Roberts et al. 2019).
All divergence time analyses were conducted on the nucleotide dataset in MCMCtree as implemented in the software package PAML v.4.7a Yang (2007) using an ultrametric (equal branch lengths) version of our ML tree as input. We used our full unpartitioned dataset due to computational limits since our dataset consists of over 1000 loci and 90 partitions were suggested by PartitionFinder. Fossil calibrations were set using uniform prior distributions with hard upper and lower bounds. Our root maximum age was set at 158.1 million years, based on the earliest fossil within Cavilabiata (Juralibellula ningchengensis) (Huang and Nel 2007). We set default parameters for defining prior distribution and used the General Time Reversible (GTR) nucleotide substitution model for calculating the hessian matrix for our dataset. For each scenario, we performed two independent MCMC runs with 500,000 iterations, sampling every 100 trees with a 2000 tree burn-in, and checked for convergence using Tracer v. 1.6 (Drummond and Rambaut 2007). Finally, we examined the prior distributions of each run to ensure reasonable fossil choices and placement on the tree (Warnock et al. 2012). Divergence time estimates, distributions, and outputs are provided in our Supplemental Information.
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