DOI: 10.5061/dryad.k0p2ngfh6
title: Data from: Phylogenomic approach to integrative taxonomy resolves a century-old taxonomic puzzle and the evolutionary history of the Acromyrmex octospinosus species complex

description: Accurately delimiting species boundaries is essential for understanding
 biodiversity. Here, we assessed the taxonomy of the leaf-cutting ants in
 the Acromyrmex octospinosus species complex using an integrative approach
 incorporating morphological, population genetic, phylogenetic, and
 biogeographical data. We sampled populations across the species complex’
 biogeographic distribution and reconstructed their evolutionary
 relationships using ultraconserved elements (UCEs) as molecular markers.
 We evaluated traditional morphological characters used to distinguish
 putative taxa and performed species delimitation analyses to investigate
 divergence between evolutionary lineages. Our results support the
 hypothesis that the A. octospinosus species complex consists of two
 species: the widely distributed and polymorphic species A. octospinosus
 and its inquiline social parasite A. insinuator. We consider A. echinatior
 syn. nov. and A. volcanus syn. nov. as well as the subspecies A.
 octospinosus cubanus syn. nov., A. octospinosus ekchuah syn. nov., and A.
 octospinosus inti syn. nov. as junior synonyms of A. octospinosus. We also
 investigated the biogeographic history of the species complex and the
 evolutionary origin of the social parasite A. insinuator. We inferred that
 A. octospinosus originated during the late Miocene ~6.9 Ma ago in the
 Neotropical rainforest. Acromyrmex insinuator shared a common ancestor
 with A. octospinosus ~3.4 Ma ago, with a crown-group age of ~0.9 Ma. Our
 phylogeny supports the hypothesis that the inquiline social parasite
 speciated via the intra-specific route of social parasite evolution in
 direct sympatry from its host. Our findings reshape our understanding of
 the A. octospinosus species complex and provide a foundation for future
 studies of Acromyrmex leaf-cutting ants.
description: DNA was extracted non-destructively from adult ants using a
 DNeasy Blood and Tissue Kit (Quiagen, Inc.) following the manufacturer’s
 protocol. After DNA extraction, the specimens were re-mounted and
 preserved as vouchers in our entomological collection.
 A total of 50–100 ng of DNA was sheared by sonication (Qsonica)
 to a target fragment size of 400–600 bp and used as input for genomic DNA
 library preparation for targeted enrichment of ultraconserved elements
 (UCEs) (Kapa Hyper Prep Library Kit, Kapa Biosystems). We incorporated
 "with-bead" (SeaPure) cleaning steps (Fisher et al., 2011). Each
 library was associated with a unique combination of iTru adapters (Gnirke
 et al., 2009). We followed the protocol for library preparation as
 described in Faircloth et al., (2015) and modified by Branstetter et al.,
 (2017a). Libraries were pooled for target enrichment using the hym-v2 set
 of ant-specific RNA probes (MYcroarray), which target 2,590 UCE loci in
 the Formicidae. The enrichment protocol followed Faircloth et al., (2015)
 and modifications described in Branstetter et al., (2017a) and Borowiec et
 al., (2021). After the enrichment, we performed
 quantitative PCR to reliably estimate DNA concentration for the enriched
 pools. We used a SYBR® FAST qPCR kit (Kapa Biosystems) and a Bio-Rad CFX96
 RT-PCR thermal cycler (Bio-Rad Laboratories). Finally, we combined all
 samples into an equimolar final pool. Final pools for each lane were
 sequenced at the High Throughput Genomics Core Facility at the University
 of Utah, Novogene Corporation Inc., and Admera Health Biopharma.
description: # Phylogenomics resolve a century-old taxonomic puzzle and reveal
 evolutionary history of the Acromyrmex octospinosus species complex
 [https://doi.org/10.5061/dryad.k0p2ngfh6](https://doi.org/10.5061/dryad.k0p2ngfh6) ## Description of the data and file structure Download the Acromyrmex_octospinosus.zip folder. Upload this file to your cluster and decompress it. This folder contains two subfolders. The first one is called **Acromyrmex octospinosus contigs**. This folder contains 74 files in fasta format. Each file contains the ultraconserved element assemblies for each individual sequenced. The name of the file corresponds to species name and extraction code. Use this contigs if you are interested in reproducing our study or if you want to add these sequences to your phylogenetic project. The second folder is called **Alignments and tree files**, and contains the alignments, SNP data, partitioning schemes, dated and undated trees, as well as gene trees used in our study.