DOI: 10.5061/dryad.0k6djhb3g
title: Supporting data for: Limited genetic differentiation of Mycetomoellerius mikromelanos in Parc National Soberanía, Panama: Implications for queen dispersal

description: The coevolutionary relationship between fungus-growing ants (Formicidae:
 Attini: Attina) and their symbionts has been well-studied in the
 Panamanian rainforests. To further understand the ecological context of
 these evolutionary relationships, we have examined the population genetic
 structure of the fungus-growing ant species
 Mycetomoellerius mikromelanos Cardenas, Schultz, & Adams
 2021, in the Panama Canal Zone. We specifically investigated the presence
 of population structure, the significance of geographic features (i.e.,
 creeks) limiting gene flow, and relatedness between ant colonies. To
 accomplish this, we genotyped 85 ant colonies from nine creeks across an
 approximately 30 km transect in Parque National Soberanía, Panama using
 double digest restriction-site associated DNA sequencing. We did not find
 distinct population structures using two genetic clustering methods;
 however, we did detect an effect of isolation by distance. Furthermore,
 related colonies were frequently detected on the same creek or neighboring
 creeks, and some at further geographic distances. Collectively, these
 findings demonstrate that new colonies tend to establish on natal creeks
 and occasionally on distant creeks following long-distance dispersal
 events. We discuss how population genetic patterns reveal the natural
 history of M. mikromelanos in Parque National Soberanía and how these
 results fit into the context of fungus-growing ant mutualisms.
description: DNA was extracted from a single
 worker from colonies of <em>Mycetomoellerius
 mikromelanos </em>found in Parque National Soberanía, Panama.
 Following the ddRADseq protocol of Peterson et al. (2012) digestion was
 performed with restriction site enzymes Msp1 and Spfl-HF (New England
 Biolabs, Inc., Ipswich, Massachusetts, USA). Genomic fragments of 250-600
 bp in length were selected and sequenced 150 bp paired-end reads at
 Nationwide Childrens Hospital in Columbus, Ohio USA on an Illumina HiSeq
 4000. SNP data were QC'd and trimmed (FastQC
 v0.11.7;<strong> </strong>Andrews 2018; trimmomatic v0.38;
 Bolger et al. 2014), and SNP discovery was performed with ipyrad (v0.9.31;
 Eaton & Overcast, 2020). Andrews, S. (2018).
 <em>FastQC</em> (v0.11.7). Barbraham Institute. https://github.com/s-andrews/FastQC/releases Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina sequence data. <em>Bioinformatics</em>, <em>30</em>(15), 2114–2120. https://doi.org/10.1093/bioinformatics/btu170 Eaton, D. A. R., & Overcast, I. (2020). ipyrad: Interactive assembly and analysis of RADseq datasets. <em>Bioinformatics 36</em>(8), 2592–2594. https://doi.org/10.1093/bioinformatics/btz966 Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., & Hoekstra, H. E. (2012). Double digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species. <em>PLoS ONE</em>, <em>7</em>(5), 1–11. https://doi.org/10.1371/journal.pone.0037135
description: *unix based CLI, python, R