DOI: 10.5061/dryad.3d31q
title: Data from: The acacia ants revisited: convergent evolution and biogeographic context in an iconic ant/plant mutualism

description: Phylogenetic and biogeographic analyses can enhance our understanding of
 multispecies interactions by placing the origin and evolution of such
 interactions in a temporal and geographical context. We use a phylogenomic
 approach—ultraconserved element sequence capture—to investigate the
 evolutionary history of an iconic multispecies mutualism: Neotropical
 acacia ants (Pseudomyrmex ferrugineus group) and their associated
 Vachellia hostplants. In this system, the ants receive shelter and food
 from the host plant, and they aggressively defend the plant against
 herbivores and competing plants. We confirm the existence of two separate
 lineages of obligate acacia ants that convergently occupied Vachellia and
 evolved plant-protecting behaviour, from timid ancestors inhabiting dead
 twigs in rainforest. The more diverse of the two clades is inferred to
 have arisen in the Late Miocene in northern Mesoamerica, and subsequently
 expanded its range throughout much of Central America. The other lineage
 is estimated to have originated in southern Mesoamerica about 3 Myr later,
 apparently piggy-backing on the pre-existing mutualism. Initiation of the
 Pseudomyrmex/Vachellia interaction involved a shift in the ants from
 closed to open habitats, into an environment with more intense plant
 herbivory. Comparative studies of the two lineages of mutualists should
 provide insight into the essential features binding this mutualism.
description: Complete set of aligned
 UCE contigsThe file includes the
 complete set of 2448 aligned, untrimmed UCE contigs. The alignments are
 provided as individual files in FASTA format.uce-contigs-aligned-untrimmed.zipRaw sequence reads (SRA PRJNA357470)Raw illumina reads in FASTQ format for all samples sequenced in this study. Samples were enriched for ultra-conserved element loci.Concatenated matrix of aligned UCE lociThe primary DNA sequence matrix analyzed in this study. The matrix contains 1672 aligned, filtered, and trimmed UCE loci. Includes by-locus character partitions.concatenated-matrix-with-1672loci.nexusData tablesThe complete set of data tables included in the main text and supplemental materials of this study. Provided in csv and xlsx formats.all-tables-in-csv-xlsx-formats.zipBEAST xml data filesAll BEAST xml data files used in this study. Includes one file for the 29 sample analysis, and two files for the 18 sample analyses (topologies 1 and 2).beast-xml-files.zipBioGeoBEARS analysis filesBioGeoBEARS analysis files for all of the Pseudomyrmex and Vachellia biogeographic analyses.BioGeoBEARS-files.zipTree filesMain phylogenetic tree results provided in NEXUS and PDF formats. Includes best RAxML trees with bootstrap scores, ExaBayes consensus trees with posterior probabilities, ASTRAL species trees with bootstrap scores, and BEAST chronograms.all-trees-in-nexus-pdf-formats.zipTrait reconstruction analysis filesR scripts and trait data for inferring habitat and nesting ancestral states.Trait-Reconstruction.zipPartition files in RAxML formatPartitioning schemes for by-locus, hcluster, and kmeans partitioned analyses. All files in RAxML-style format.partitioning-files-raxml-format.zip