DOI: 10.5061/dryad.b464m
title: Data from: Insights into the evolution, biogeography and natural history of the acorn ants, genus Temnothorax Mayr (Hymenoptera: Formicidae)

description: Background: Temnothorax (Formicidae: Myrmicinae) is a diverse genus of
 ants found in a broad spectrum of ecosystems across the northern
 hemisphere. These diminutive ants have long served as models for social
 insect behavior, leading to discoveries about social learning and
 inspiring hypotheses about the process of speciation and the evolution of
 social parasitism. This genus is highly morphologically and behaviorally
 diverse, and this has caused a great deal of taxonomic confusion in recent
 years. Past efforts to estimate the phylogeny of this genus have been
 limited in taxonomic scope, leaving the broader evolutionary patterns in
 Temnothorax unclear. To establish the monophyly of Temnothorax, resolve
 the evolutionary relationships, and investigate trends in the evolution of
 key traits, I generated, assembled, and analyzed two molecular datasets: a
 traditional multi-locus Sanger sequencing dataset, and an ultra-conserved
 element (UCE) dataset. Using maximum likelihood, Bayesian and
 summary-coalescent based approaches, I analyzed 22 data subsets consisting
 of 103 ingroup taxa and a maximum of 1.8 million base pairs in 2,485 loci.
 Results: The results of this study suggest an origin of Temnothorax at the
 Eocene-Oligocene transition, concerted transitions to arboreality in the
 Oligocene in several clades, coinciding with ancient global cooling, and
 several convergent origins of social parasitism in the Pliocene. As with
 other Holarctic taxa, Temnothorax has a history of migration across
 Beringia during the Miocene. Conclusions: Temnothorax is corroborated as a
 natural group, and the notion that many of the historical subgeneric and
 species group concepts are artificial is reinforced. The strict form of
 Emery's Rule, in which a socially parasitic species is sister to its
 host species, is not well supported in Temnothorax.
description: Complete set of aligned
 UCE lociThis file contains the
 complete set of 2510 aligned, untrimmed ultraconserved element loci in
 FASTA formatuce-contigs-aligned-untrimmed.tar.gz10-gene Sanger sequencing datasetThis file contains a broad selection of data files for analyses of the 10 gene Sanger sequencing dataset, including constrained and unconstrained analyses, BEAST xml files, and input for BUCKy, MrBayes, IQ-TREE, and RAxML.10-gene-dataset.tar.gzUCE ASTRAL analysis input filesThis file contains the binned, weighted input files for the ASTRAL species tree analysis of the ultraconserved element dataset.ASTRAL.tar.gzUCE analysis input filesThis file contains the 'min90' and 'coding' ultraconserved elements alignments and their associated partition files.UCE-datasets.tar.gzBioGeoBEARSThis file contains the input files for the BioGeoBEARS analysis of the empirical data, as well as a script for model-averaging BioGeoBEARS output.HiSSE scriptsThis file contains the scripts and input files for the HiSSE analysis of arboreality and parasitism in Temnothorax.HiSSE.tar.gzData matrices and tree files for the 'min90' UCE and 10-gene Sanger datasetsThis links to matrices and trees associated with Figures 2 and 3 in the main article.Raw sequence reads (SRA PRJNA393044)Raw illumina reads in FASTQ format for all samples sequenced in this study. Samples were enriched for ultra-conserved element loci.