DOI: 10.5061/dryad.qnk98sfkp
title: Biogeography and evolution of social parasitism in Australian Myrmecia bulldog ants revealed by phylogenomics

description: Studying the historical biogeography and life history transitions from
 eusocial colony life to social parasitism contributes to our understanding
 of the evolutionary mechanisms generating biodiversity in eusocial
 insects. The bulldog ants in the genus Myrmecia are a well-suited system
 for testing competing evolutionary hypotheses about how their species
 diversity was assembled through time because the genus is endemic to
 Australia with the single exception of the species Myrmecia apicalis
 inhabiting the Pacific Island of New Caledonia and because at least one
 social parasite species exists in the genus. However, the evolutionary
 mechanisms underlying the disjunct biogeographic distribution of M.
 apicalis and the life history transition(s) to social parasitism remain
 unexplored. To study the biogeographic origin of the isolated, oceanic
 species M. apicalis and to reveal the origin and evolutionary history of
 social parasitism in the genus, we reconstructed a comprehensive phylogeny
 of the ant subfamily Myrmeciinae. We utilized Ultra Conserved Elements
 (UCEs) as molecular markers to generate a comprehensive molecular genetic
 dataset consisting of 2,287 loci per taxon on average for 66 out of the 93
 known Myrmecia species as well as for the sister lineage Nothomyrmecia
 macrops and selected outgroup taxa. Our time-calibrated phylogeny inferred
 that: (i) stem myrmeciine ants originated during the Paleocene ~58 Ma ago;
 (ii) the current disjunct biogeographic distribution of M. apicalis was
 driven by long-distance dispersal from Australia to New Caledonia during
 the Miocene ~14 Ma ago; (iii) the single social parasite species, M.
 inquilina, exploits three host species and evolved directly from one of
 the known host species, M. nigriceps, most likely via the intraspecific
 route of social parasite evolution in sympatry; and (iv) 5 of the 9
 previously established taxonomic species groups are non-monophyletic. We
 suggest minor changes to reconcile the molecular phylogenetic results with
 the taxonomic classification. Our study enhances our understanding of the
 evolution and biogeography of Australian bulldog ants in the genus
 Myrmecia, contributes to our knowledge about the evolution of social
 parasitism in ants, and provides a solid phylogenetic foundation for
 future inquiries 
description: <strong>Molecular data generation</strong>
 We used Ultra Conserved Elements (UCEs) as molecular markers.
 UCEs have been widely used as a reliable source for inferring molecular
 phylogenies in several taxa including ants (Barrera et al. 2022; Borowiec
 et al. 2021; Branstetter et al. 2017; Camacho et al. 2022; Faircloth et
 al. 2015; Hanisch et al. 2022; van Elst et al. 2021; Zhang et al. 2019).
 UCEs can be extracted from museum vouchers that are old and/or have not
 been preserved in optimal conditions (Blaimer et al. 2016; Borowiec et al.
 2021), which was the case for most of our samples. Ant
 DNA was extracted using the Qiagen DNeasy Blood and Tissue Kit (Qiagen,
 GmbH) following the manufacturer’s protocol. We extracted DNA from the
 three right legs of the ants when the specimens were longer than 15 mm.
 When the ants were smaller, we extracted DNA non-destructively without
 removing any appendages. After the DNA extractions, the specimens were
 re-mounted and preserved as vouchers in their corresponding biological
 collections. When DNA was extracted from the legs, the
 three right legs (including the coxae) were removed and placed in 1.5 ml
 tubes along with a sterilized stainless-steel bead that facilitated
 pulverization of the tissue before DNA extraction. Samples were pulverized
 with a tissue lyser where disruption was carried out at a frequency of 25
 Hz for 30 seconds. When DNA was extracted non-destructively from entire
 specimens, we poked two small holes into the right side of the mesosoma to
 allow the lysis buffer and enzymes to enter the specimen. Each sample was
 incubated in a solution of proteinase K and lysis buffer for ~24 hours.
 For the rest of the extraction, we followed the manufacturer’s protocol.
 50–100 ng of DNA were sheared by sonication (Qsonica) to an average
 fragment size of ~600 bp and used for the library preparation (Kapa Hyper
 Prep Library Kit, Kapa Biosystems) incorporating "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 by Faircloth et
 al. (2015) and modified by Branstetter et al. (2017).
 Libraries were pooled for target enrichment using the hym-v2 set
 of ant-specific RNA probes (MYcroarray), which target 2,590 UCE loci in
 ants (Branstetter et al. 2017). The enrichment protocol followed Faircloth
 et al. (2015) and modifications described in Branstetter et al. (2017)
 with the following changes suggested in Prebus (2021): We (1) used iTru
 blockers instead of the standard blockers, (2) conducted a post-enrichment
 PCR of the samples, (3) left enriched DNA bound to the streptavidin beads
 during post-enrichment PCR, (4) cleaned the resulting pools using
 Speed-Bead magnetic carboxylate beads (Rohland and Reich, 2012), and (5)
 adjusted the final volume to 22 μl. 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. In total, we sequenced two lanes submitted as two final pools of
 samples. One of the lanes was sequenced at the High Throughput Genomics
 Core Facility at the University of Utah and the second lane was sequenced
 at the Novogene Corporation Inc.
description: # Biogeography and evolution of social parasitism in Australian *Myrmecia*
 bulldog ants revealed by phylogenomics
 [https://doi.org/10.5061/dryad.qnk98sfkp](https://doi.org/10.5061/dryad.qnk98sfkp) #### UCE contigs  Contigs assembled in SPAdes. #### How to download the data Download the zip folder with the compressed file. Then, upload this file to your cluster and decompress it. You will get all the contigs listed in fasta format. #### How to use it Use the contigs if you are interested in reproducing our study or if you want to add these sequences to your phylogenetic project. #### Suggested citation Mera-Rodríguez, D. 2022. Biogeography and evolution of social parasitism in Australian *Myrmecia* bulldog ants revealed by a phylogenomic reconstruction, Dryad, Dataset, [https://doi.org/10.5061/dryad.qnk98sfkp](https://doi.org/10.5061/dryad.qnk98sfkp)