DOI: 10.5061/dryad.d7wm37q9c
title: UCE phylogenomics illuminate the evolutionary history and biogeography of Dorymyrmex pyramid ants

description: Latitudinal diversity gradients are one of the most widely discussed
 patterns in global biogeography, generally in the context of high
 diversity in tropical regions. In contrast, "amphitropical" or
 "inverse" distributions, once thought to be unusual, are
 increasingly recognized as common among many hymenopteran insects. One
 such group is the ant genus Dorymyrmex, which specializes in arid habitats
 throughout the Americas. To evaluate when and how Dorymyrmex acquired its
 present-day distribution, I sequenced partial genomes of 167 Dorymyrmex
 representing 69 species by targeting ultra-conserved elements (UCEs). A
 matrix of 870 genetic loci was used to infer maximum likelihood and
 Bayesian phylogenies, estimate divergence dates, and reconstruct
 hypothesized ancestral areas. These new analyses reveal that Dorymyrmex
 comprises four species groups, the D. flavescens, tener, wolffhuegeli, and
 pyramicus groups. The D. pyramicus group likely dispersed from South
 America to North America only once, via Central America. Like many
 Hymenoptera, this dispersal occurred before the traditional closure date
 of the Isthmus of Panama, corroborating and extending the results of
 previous studies. Finally, I discuss life history strategies of Dorymyrmex
 that may have contributed to the geographic and genetic radiation of the
 D. pyramicus group, detail significant insights into Dorymyrmex morphology
 and classical taxonomy with new comparative illustrations, and provide
 recommendations for future work.
description: # UCE phylogenomics illuminate the evolutionary history and biogeography
 of Dorymyrmex pyramid ants
 [https://doi.org/10.5061/dryad.d7wm37q9c](https://doi.org/10.5061/dryad.d7wm37q9c) ## Description of the data and file structure Targeted genomic sequence data (UCEs) were assembled into contigs in SPAdes and assembled into matrices in phyluce. Each matrix was aligned in MAFFT and downsampled for computational efficiency by removing loci that violate evolutionary model assumptions using IQ-TREE --symtest-remove-bad. Matrices were cleaned in the program spruceup to trim out poor quality sequence regions, then partitioned using the SWSC-EN algorithm. Partitions were merged in IQ-TREE using ModelFinder -m TESTMERGEONLY. Resulting matrices are *LFD-185t-part* and *D-Cono-150t-part.* Maximum likelihood phylogenies were inferred in IQ-TREE. Bayesian phylogenies were inferred in ExaBayes on the CIPRES Science Gateway. Divergence times were estimated in MCMCtree and visualized in MCMCtreeR. Biogeographic history (ancestral areas) were estimated in BioGeoBEARS. ### Files and variables #### File: MATRIX-D-Cono-150t-part\_134parts\_IQtreeSymtestGood-spruced-up.phy **Description:** Multiple sequence alignment for the 150-taxon ingroup "Conomyrma", with partitions split using SWSC-EN and merged with IQ-TREE ModelFinder #### File: MATRIX-LFD-185t-part\_870loci-IQtreeSymtestGood-spruced-up.phy **Description:** Multiple sequence alignment for the 185-taxon total clade "Leptomyrmex+Forelius+Dorymyrmex", with partitions split using SWSC-EN and merged with IQ-TREE ModelFinder #### File: BioGeoBEARS-input-78taxa-Dory-chronogram.tre **Description:** Chronogram pruned to 78 species-level lineages for input into BioGeoBEARS #### File: BioGeoBEARS-input-Ecoregion-matrix.txt **Description:** Ecoregions inhabited by each taxon, for input into BioGeoBEARS #### File: ExaBayes-input-LFD-185t-CONFIG\_exb\_11.conf **Description:** Configuration file for ExaBayes #### File: ExaBayes-output-LFD-185t\_870loci-122parts\_Mar26names\_PHYLO.contree **Description:** Output phylogeny from ExaBayes #### File: ExaBayes-input-LFD-185t-870loci-partitionmodels.best\_scheme **Description:** Partition file for data matrix LFD-185t-part, for input into ExaBayes #### File: IQtree-output\_D-Cono-150t\_134partitions\_IQtreeModelFinderModels\_MaxLikelihood.contree **Description:** Consensus maximum likelihood phylogeny of dataset D-Cono-150t-part (IQ-TREE) #### File: IQtree-output\_LFD-185t-870loci-122parts-IQT-Mar26names\_MaxLikelihood.contree **Description:** Consensus maximum likelihood phylogeny of dataset LFD-185t-part (IQ-TREE) #### File: MCMCtree-input-2calibs-x100-Mar23names.tre **Description:** Input cladogram for MCMCtree, with topology from ExaBayes output #### File: MCMCtree-input-CONFIG-rgene-sigma2-scaled10.ctl **Description:** Configuration file for MCMCtree #### File: MATRIX-D-Cono-150t-part\_134parts\_IQtreeModelFinder.best\_scheme.nex **Description:** Partition file for the data matrix D-Cono-150t-part, with partitions split using SWSC-EN and merged with IQ-TREE ModelFinder #### File: MATRIX-LFD-185t-part\_870loci-122partitions-IQtreeModelFinder.best\_model.nex **Description:** Partition file for the 185-taxon data matrix LFD-185t-part, with partitions split using SWSC-EN and merged with IQ-TREE ModelFinder #### File: MCMCtree-output-185taxa-chronogram.tre **Description:** MCMCtree output chronogram #### File: ExaBayes-output-LFD-185t-870loci-122parts-STDOUT.txt **Description:** Output log file from ExaBayes #### File: BioGeoBEARS-output-model-comparison-results.txt **Description:** Comparison of AIC and LRT scores for all models tested in BioGeoBEARS ## Code/software Data wrangling: * phyluce v1.7.3 * illumiprocessor v2.10 * trimmomatic v0.39 * MAFFT v7.475, L-INS-i algorithm * IQ-TREE v2.2.3, --symtest-remove-bad Analysis: * IQ-TREE v2.1.2, ModelFinder * AMAS (alignment statistics calculation) * ExaBayes v1.5.1, -M 3, on the CIPRES Science Gateway * consense (ExaBayes utility) * MCMCtree, in PAML v4.10.3 * BioGeoBEARS (in R) Visualization: * Tracer * FigTree * MCMCtreeR (in R) ## Access information Other publicly accessible locations of the data: * Raw sequence reads: [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA759281/](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA759281/) ## Usage notes * Data, config files, and partition files can be viewed using a standard plain text editor. * Tree files (.tre, .contree) can be viewed in FigTree. * *ExaBayes...STDOUT.txt* can be viewed in Tracer.