DOI: 10.5061/dryad.c59zw3rhg
title: Phylogenomics resolve the systematics and biogeography of the ant tribe Myrmicini and tribal relationships within the hyperdiverse ant subfamily Myrmicinae

description: Ants are a globally distributed and highly diverse group of eusocial
 animals, playing key ecological roles in most of the world’s terrestrial
 ecosystems. Our understanding of the processes involved in the evolution
 this diverse family is contingent upon our knowledge of the phylogeny of
 the ants. While relationships among most subfamilies have come into
 resolution recently, several of the tribal relationships within the
 hyperdiverse subfamily Myrmicinae persistently conflict between or within
 studies, mirroring the controversial relationships of the Leptanillinae
 and Martialinae to the remaining ant subfamilies. Another persistent issue
 of debate in ant phylogenetics is the timing of major evolutionary events
 as inferred via divergence dating. Here, we test the topology of the
 myrmicine tribes using genome scale data, inspect gene tree-species tree
 concordance, and use posterior predictive checks and tests of
 compositional heterogeneity to infer sequence characteristics which
 potentially introduce systematic bias in myrmicine tribal topology.
 Furthermore, we test the placement of the fossil †Manica andrannae by
 integrating phylogenomic and morphological data from nearly all species
 within the genus Manica, and a broad sampling of its sister genus Myrmica.
 Subsequently, we demonstrate the effect of fossil placement on overall
 divergence times in the Myrmicinae. We then re-evaluate the historical
 biogeography of the Myrmicini and Pogonomyrmecini considering newly
 generated genetic data and insights from our phylogenomic results. We find
 that our current understanding of tribal topology in the Myrmicinae is
 strongly supported, but this topology is highly sensitive to compositional
 heterogeneity and gene-tree species-tree conflict. Our fossil placement
 analyses strongly suggest that †Manica andrannae is a stem Manica species,
 and that placement of this fossil in the crown group affects not only
 divergence dates within the tribe Myrmicini, but also has broad
 implications for divergence times throughout the formicoid clade. The
 results of our biogeographic reconstructions indicate a South American
 origin for the Pogonomyrmecini + Myrmicini, with the MRCA of Myrmica
 inhabiting the western Nearctic in the early Miocene prior to repeated
 dispersal across Beringia throughout the Miocene and Pliocene. The MRCA of
 Manica, on the other hand, was inferred to have a Holarctic range prior to
 vicariance during the Pliocene. Unexpectedly, we found strong support in
 the Pogonomyrmecini for three coordinated dispersal events from South to
 Central America during the early Miocene, which has been previously
 proposed as an early biotic interchange event prior to the more commonly
 accepted 3.5 Ma closure of the Isthmus of Panama.
description: ## Supplementary materials for "Phylogenomics resolve the systematics
 and biogeography of the ant tribe Myrmicini and tribal relationships
 within the hyperdiverse ant subfamily Myrmicinae"
 [https://doi.org/10.5061/dryad.c59zw3rhg](https://doi.org/10.5061/dryad.c59zw3rhg) --- Authors: Matthew Prebus & Christian Rabeling Year: 2025 Contact: Matthew Prebus, [mprebus@gmail.com](mailto:mprebus@gmail.com) --- ### Description of the data and file structure This dataset contains three compressed directories: `model_adequacy.zip` `morphometrics.zip` `phylogenies.zip` --- The file structure of `model_adequacy.zip` is as follows: ``` model_adequacy ├── matrices │   ├── full_matrix │   ├── max_PD_pass │   ├── mean_GC_pass │   ├── p4_corrected │   ├── p4_uncorrected │   └── var_GC_pass └── posterior_predictive_checks ├── data │   ├── GTR_Gamma │   ├── GTR_Inv │   ├── HKY_Gamma │   ├── HKY_Inv │   ├── JC_Gamma │   ├── JC_Inv │   ├── K80_Gamma │   ├── K80_Inv │   ├── K81_Gamma │   ├── K81_Inv │   ├── TIM_Gamma │   ├── TIM_Inv │   ├── TrN_Gamma │   ├── TrN_Inv │   ├── TVM_Gamma │   └── TVM_Inv └── scripts ``` This directory contains all scripts, matrices, and results used for posterior predictive checks on the Myrmicinae_176t dataset: `matrices` contains data and results of phylogenetic analyses of datasets filtered following posterior predictive checks or analysis of compositional heterogeneity: * `full_matrix` contains the full unfiltered Myrmicinae_176t dataset. * `max_PD_pass` contains the Myrmicinae_176t dataset filtered to include only loci that passed the max PD statistic. * `max_GC_pass` contains the Myrmicinae_176t dataset filtered to include only loci that passed the max GC statistic. * `p4_corrected` contains the Myrmicinae_176t dataset filtered to include only loci that passed the phylogeny-corrected p4 analysis. * `p4_uncorrected*` contains the Myrmicinae_176t dataset filtered to include only loci that passed the standard chi-squared p4 analysis. * `var_GC_pass` contains the Myrmicinae_176t dataset filtered to include only loci that passed the var GC statistic. Each directory in `matrices` contains four files: * `*_b10.trees`: Newick formatted gene partition trees estimated with *IQTREE v2.1.1*; all nodes with &lt; 10 bootstrap support have been collapsed into polytomies using *newick_utils*. * `*_models.nex`: NEXUS formatted matrix partitions with associated substitution models estimated with *IQTREE2*. * `*.trees`: Newick formatted gene partition trees estimated with *IQTREE*. * `*.nex`: NEXUS formatted ultraconserved elements (UCE) nucleotide sequence alignments. `posterior_predictive_checks` contains data and scripts used to run posterior predictive checks on UCE alignments. * `data` contains subdirectories named by best-fitting nucleotide substitution model inferred with ModelTest in *IQTREE*, with each directory containing UCE alignments in FASTA (`*.fas`) format that have been partitioned with the SWSC-EN algorithm. * `rb_pps_batch.sh` is a bash file used to run posterior predictive checks with *RevBayes v1.2.1*. * `scripts` contains all *RevBayes* and *R v4.1.3* scripts used to run posterior predictive checks. --- The file structure for `morphometrics.zip` is as follows: ``` morphometrics ├── morphometrics_HW_scaled_pca.R ├── morphometrics_HW_scaled.csv ├── morphometrics.csv └── morphometrics.R ``` This directory contains all scripts and datasets used to generate figures S2 and S3 in `Supplementary_File_1_extended_methods_morphometrics.pdf`: `morphometrics_HW_scaled_pca.R`: an R script for principal components analysis of morphometric data from extant *Manica*, extant *Myrmica*, and the fossil †*Manica andrannae* scaled to head width. `morphometrics_HW_scaled.csv`: morphometric data from 63 samples of extant *Manica*, extant *Myrmica*, and the fossil †*Manica andrannae* scaled to head width. The fields in this file are as follows: * **SpecimenCode**: a unique alphanumeric code physically associated with an individual specimen, primarily used for databasing. * **Genus**: genus of the specimen. * **Species**: species of the specimen. * **DNA extract**: a unique alphanumeric code physically associated with an individual specimen if DNA has been extracted from it for analysis. The following measurements were taken in millimeters: * **HL**: head length: the head must be carefully tilted to the position, providing the true maximum. If excavations of the posterior margin of the head capsule and/or anterior margin of the clypeus are present, then the measurement is taken from an imaginary line that spans the excavations from the posterior- or anterior-most margins. * **HW**: head width: maximum width of the head, measured directly behind the compound eyes. * **FW**: frontal lobe width: the maximum width measured between the frontal lobes; * **MdL**: mandible length: length of the masticatory margin of the mandible. * **SL**: scape length: maximum scape length, excluding the basal neck and the articular condyle. * **PdL**: antennal pedicel length, excluding basal condyle. * **FI1**: the length of the first flagellomere. * **FI2**: the length of the second flagellomere. * **OL**: ocular length: the maximum diameter of the compound eye. * **WL**: Weber’s length: distance between the caudal most point of propodeal lobe to the inflection point between the pronotal neck and the pronotal declivity. * **PrdH**: propodeum height: the height of the propodeum in profile, measured as the orthogonal distance from the ventral edge of the metapleuron to the highest point of the propodeum. * **ESL**: propodeal spine length: distance between the center of the propodeal spiracle and tip of the propodeal spine. * **PtL**: petiole length: diagonal petiolar length in lateral view; measured from anterior corner of subpetiolar process to dorso-caudal corner of caudal cylinder. * **PtH**: petiole height: the height of the petiolar node in profile, measured as the perpendicular distance from an imaginary line joining the base of the subpetiolar tooth and the ventral junction of the petiole and postpetiole to the highest point of the petiolar node. * **PPL**: postpetiole length: the longest distance, perpendicular to the posterior margin of the postpetiole, between the posterior postpetiolar margin and the anterior postpetiolar margin. * **PPH**: postpetiole height: the height of the postpetiole in profile, measured as the perpendicular distance from the ventral edge to the highest point of the postpetiole. * **PNW**: pronotum width: the maximum width of the pronotum in dorsal view. * **PrdL**: propodeum length: the maximum length of the propodeum in dorsal view, excluding the propodeal lobes. * **ESD**: propodeal spine distance: distance between the tips of propodeal tubercles/spines in dorsal view. * **PtW**: petiole width: the maximum width of the petiolar node in dorsal view. * **PPW**: postpetiole width: the maximum width of the postpetiole in dorsal view. * **HFL**: hind femur length: the maximum length of hind femur, measured in dorsal view. * **HTL**: hind tibia length: the maximum length of hind tibia, measured in dorsal view, excluding the proximal condyle. The following are indices calculated from the above measurements: * **CI**: cephalic index: HL/HW*100. * **SI1**: scape length index 1: SL/HL*100. * **SI2**: scape length index 2: SL/HW*100. * **FLI**: frontal lobe index: FW/HW*100. * **OI1**: ocular index 1: OL/HL*100. * **OI2**: ocular index 2: OL/HW*100. * **PI1**: petiole height index: PtL/PtH*100. * **PI2**: petiole width index: PtL/PtW*100. * **PPI1**: postpetiole height index: PPL/PPH*100. * **PPI2**: postpetiole width index: PPH/PPW*100. * **PPI3**: postpetiole-petiole index: PPW/PtW*100. * **ESLI**: propodeal spine length index: ESL/HW*100. * **ESDI**: propodeal spine distance index: ESD/HW*100. * **MI**: mesosoma index: WL/PNW*100. * **PRI**: propodeum index: PrdL/PrdH*100. The following are binary characters: * **antennal club count** &gt; 3: 1; ≤ 3: 0. * **mandibular teeth** &gt; 10: 1; ≤ 10: 0. `morphometrics.csv`: raw morphometric data from 63 samples of extant *Manica*, extant *Myrmica*, and the fossil †*Manica andrannae*. The variables in this dataset are identical to those in `morphometrics_HW_scaled.csv`, but raw measurements and indices are not scaled to head width. `morphometrics.R`: an R script for comparison of mean morphometrics between extant *Manica*, extant *Myrmica*, and the fossil †*Manica andrannae*. --- The file structure for `phylogenies.zip` is as follows: ``` phylogenies ├── astral ├── iqtree ├── mcmctree │   ├── MandrannaeManica_mcmctree │   └── MandrannaeMyessensis_mcmctree ├── mrbayes └── revbayes ├── biogeography_ase_v1_no_dispersal │   ├── data │   ├── output │   └── scripts ├── biogeography_ase_v2_dispersal │   ├── data │   ├── output │   └── scripts ├── divergence_dating │   ├── data │   ├── output │   └── scripts └── topology ├── data ├── output └── scripts ``` This directory contains all scripts and datasets used to generate the phylogenies in this study. `astral` contains input data used to generate summary coalescent trees with *ASTRAL III v5.7.4* as well as the output trees. * `Myrmicinae_176t_2255l_BS10_astral.tre`: a Newick tree file containing summary coalescent analysis output from ASTRAL inferred from 176 taxa in the Myrmicinae with 2255 UCE loci. Node support is in local posterior probability. * `Myrmicinae_176t_2255l_BS10.tre`: a Newick tree file containing 2255 UCE trees, one for each locus, inferred from 176 taxa in the Myrmicinae with *IQTREE*. Nodes supported by a maximum likelihood bootstrap score of less than 10 were collapsed into polytomies using *newick_utils*. * `Myrmicini_62t_2177l_BS10.tre`: a Newick tree file containing summary coalescent analysis output from ASTRAL inferred from 62 taxa in the Myrmicini with 2177 UCE loci. Node support is in local posterior probability. * `Myrmicini_62t_2177l_BS10.tre`: a Newick tree file containing 2177 UCE trees, one for each locus, inferred from 176 taxa in the Myrmicinae with *IQTREE*. Nodes supported by a maximum likelihood bootstrap score of less than 10 were collapsed into polytomies using *newick_utils*. `iqtree` contains input data for *IQTREE* used to generate, as well as output trees from the analyses: * the constrained trees for the topology test analysis of the Myrmicinae dataset (files beginning with `Myrmicinae_176t_2255l*`). Constraint trees used to compare topologies are denoted with the author names from each relevant study (Branstetter et al. 2017; Romiguier et al. 2022; Ward et al. 2015). They consist of two files: `*_constraint.tre` is the constraint file used in the analysis of the `Myrmicinae_176t_2255l.nex` alignment with the `Myrmicinae_176t_2255l_SWSCEN_partitions.txt.best_scheme.nex` partition scheme, which resulted in the second file: `*_constrained.tre`. `Myrmicinae_176t_2255l_SWSCEN_partitions.txt` is a partition file used to find the best partitioning scheme in an unconstrained analysis of the `Myrmicinae_176t_2255l.nex` alignment, which resulted in `Myrmicinae_176t_2255l.contree`. * comparison of the topology of the full dataset 62 taxon dataset (files beginning with `Myrmicini_62t_2177l*`) and reduced dataset (files beginning with `Myrmicini_62t_50l*`). Three files are associated with each analysis: `*_SWSCEN_partitions.txt` are UCE partitions found by the SWSC-EN algorithm; `*.nex` are the UCE alignments; `*.contree` are the resulting trees. `mcmctree` contains input data used as input for *MCMCTREE* to generate divergence dating trees for the Myrmicinae comparing alternate fossil calibrations. * `MandrannaeManica_mcmctree` contains a branch variation file `in.BV` generated by mcmctree and the mcmctree control file `mcmctree.ctl` to run the divergence dating analysis assuming that the fossil †*Manica andrannae* was a stem *Manica* species. `MandrannaeManica_mcmctree.tre` is the resulting divergence dated tree. * `MandrannaeMyessensis_mcmctree` contains a branch variation file `in.BV` generated by mcmctree and the mcmctree control file `mcmctree.ctl` to run the divergence dating analysis assuming that the fossil †*Manica andrannae* is sister to *Manica yessensis*. `MandrannaeMyessensis_mcmctree.tre` is the resulting divergence dated tree. * `Myrmicinae_176t_50_best.phy` is a phylip file containing the 50 best performing UCE loci in the 176 taxon Myrmicinae dataset found using *SortaDate*. * `Myrmicinae_176t_50l_SWSCEN_partitions_calibrated_MandrannaeMyessensis.tre` is a Newick tree file used as input for the `MandrannaeMyessensis_mcmctree` analysis. * `Myrmicinae_176t_50l_SWSCEN_partitions_calibrated.tre` is a Newick tree file used as input for the `MandrannaeManica_mcmctree` analysis. `mrbayes` contains nexus formatted input files used to generate the fossil placement analyses for †*Manica andrannae* with *MRBAYES v3.2.6*, as well as their output trees, all of which end in `*.con.tre`. * `Myrmicini_9t_50l_combined_igr_mrbayes.nex` is used to infer the diversified sampling analysis for fossil placement using a cutoff of 9 Ma. * `Myrmicini_13t_50l_combined_igr_mrbayes.nex` is used to infer the diversified sampling analysis for fossil placement using a cutoff of 5 Ma. * `Myrmicini_62t_50l_mrbayes.nex` is used to infer the topology of extant *Manica* and *Myrmica* using only molecular data, without a clock. * `Myrmicini_63t_50l_combined_igr_mrbayes_MandrannaeManica.nex` is a combined DNA sequence and morphology alignment used to infer divergence dates constraining †*Manica andrannae* to be a stem species of *Manica*. * `Myrmicini_63t_50l_combined_igr_mrbayes_MandrannaeMyessensis.nex` is a combined DNA sequence and morphology alignment used to infer divergence dates constraining †*Manica andrannae* to be sister to *Manica yessensis*. * `Myrmicini_63t_50l_combined_igr_mrbayes_unconstrained.nex` is a combined DNA sequence and morphology alignment used to infer divergence dates without constraining †*Manica andrannae* to any position. * `Myrmicini_63t_50l_combined_mrbayes_no_clock.nex` is used to infer the topology of extant *Manica*, *Myrmica*, and the fossil species †*Manica andrannae* using molecular and morphological data, without a clock. * `Myrmicini_63t_50l_morphology.nex` is used to infer the topology of extant *Manica*, *Myrmica*, and the fossil species †*Manica andrannae* using only morphological data, without a clock. `revbayes` contains input data used to generate the historical biogeography analyses for the Myrmicini and Pogonomyrmecini using *RevBayes*. * `biogeography_ase_v1_no_dispersal` contains files used in the analysis of historical biogeography without over-water dispersal; it contains two subdirectories. * `data` contains files used as input for running an epoch model using 10 time periods. * `myrmicini_pogonomyrmecini_biogeo_dating.mcc.tre` is a Newick file containing the results of the divergence dating analysis (see below). * `myrmicini_pogonomyrmecini_bioregions.nex` is a nexus file containing bioregion occupancy data for each taxon in the analysis. * `myrmicini_pogonomyrmecini_divergence_dating.mcc.tre` is a Newick file containing the results of the divergence dating analysis (see below), without node posterior probability or confidence intervals. * files beginning with `myrmicini_pogonomyrmecini.connectivity.*` are landmass connectivity files, one for each time period. * files beginning with `myrmicini_pogonomyrmecini.distances.*` are landmass distance files, one for each time period * `myrmicini_pogonomyrmecini.range_colors.txt` contains unique colors for each bioregion (or combination of bioregions) in the analysis. * `myrmicini_pogonomyrmecini.times.txt` defines each time period used in the epoch analysis. * `output` contains the raw ancestral state estimation tree output. * `scripts` contains files used for running and analyzing the analysis. * `make_anc_state.Rev` is a *RevBayes* script used to analyze the output of `Myrmicini_Pogonomyrmecini_run_epoch.Rev`. * `Myrmicini_Pogonomyrmecini_run_epoch.Rev` runs the epoch model with *RevBayes*. * `plot_anc_range.epoch_phy.R` is an *R* script that plots the results of `Myrmicini_Pogonomyrmecini_run_epoch.Rev` and `make_anc_state.Rev`. * `plot_anc_range.util.R` is a utility script used by `plot_anc_range.epoch_phy.R`. * `biogeography_ase_v2_dispersal` contains files used in the analysis of historical biogeography with over-water dispersal; it is structured identically to the `biogeography_ase_v1_no_dispersal` directory above. * `divergence_dating` contains files used to generate the divergence dated tree used as input for the two historical biogeography analyses above. * `data` contains nexus formatted DNA sequence alignment files, each named for the best-fitting nucleotide substitution model found by ModelFinder in *IQTREE2* for that alignment. * `output` contains the divergence dating tree output. * `scripts` contains *RevBayes* scripts called by the `Myrmicini_Pogonomyrmecini_dating_master.Rev` script. * `myrmicini_pogonomyrmecini_181t_substitution_partitioned.Rev` specifies the nucleotide substitution models used in the analysis. * `myrmicini_pogonomyrmecini_clock.Rev` specifies the molecular clock. * `Myrmicini_Pogonomyrmecini_dating_master.Rev` is a *RevBayes* script used to run the divergence dating analysis. * `myrmicini_pogonomyrmecini_tree.Rev` specifies the tree model. * `topology` files used to infer the topology of the Myrmicini and Pogonomyrmecini tree without a molecular clock. * `data` contains nexus formatted DNA sequence alignment files, each named for the best-fitting nucleotide substitution model found by ModelFinder in *IQTREE2* for that alignment. * `output` contains the topology tree output * `scripts` contains: * `Myrmicini_Pogonomyrmecini_topology.Rev` is a *RevBayes* script that runs the analysis.