DOI: 10.5061/dryad.4qrfj6qmm
title: Data from: Unexpected absence of a multiple-queen supergene haplotype from supercolonial populations of Formica ants

description: Ants exhibit many complex social organization strategies. One particularly
 elaborate strategy is supercoloniality, in which a colony consists of many
 interconnected nests (=polydomy) with many queens (=polygyny). In many
 species of Formica ants, an ancient queen number supergene determines
 whether a colony is monogyne (=headed by single queen) or polygyne. The
 presence of the rearranged P haplotype typically leads colonies
 to be polygyne. However, the presence and function of this supergene
 polymorphism have not been examined in supercolonial populations. Here, we
 use genomic data from species in the Formica rufa group to
 determine whether the P haplotype leads to supercoloniality. In a
 Formica paralugubris population, we find that nests are polygyne, despite
 the absence of the P haplotype in workers. We find spatial genetic
 ancestry patterns in nests consistent with supercolonial organization.
 Additionally, we find that the P haplotype is also absent in workers from
 supercolonial Formica aquilonia, and Formica aquilonia x polyctena hybrid
 populations, but is present in some Formica polyctena workers. We conclude
 that the P haplotype is not necessary for supercoloniality in the Formica
 rufa group, despite its longstanding association with non-supercolonial
 polygyny across the Formica genus.
description: # Unexpected absence of a multiple-queen supergene haplotype from
 supercolonial populations of Formica ants
 [https://doi.org/10.5061/dryad.4qrfj6qmm](https://doi.org/10.5061/dryad.4qrfj6qmm) ## Description of the data and file structure To explore the genetics underlying complex social organization strategies in the ant genus *Formica*, we generated genomic sequence data for up to four workers per nest in a population. We used population genetics methods to explore nest social organization strategies and the potential genetics underlying nest queen number. ### Files and variables #### File: JEB\_2025.zip All files are text files that are viewable in any text edittor or directly in R. Files for Figure 2: Eigenvec files for generating PCAs. * Figure2A_noScaffold03_00_wRADs_wTruncwgs.eigenvec.txt * Figure2B_Scaffold03Figure1A_RADs_wTruncwgs.eigenvec Files for Figure 3: Relatedness estimates for generating intra-nest pairwise relatedness for each species. * Figure3_aqu_RelatednessEstimates * Figure3_paralug_RelatednessEstimates * Figure3_trunc_RelatednessEstimates Files for Figure 4: Admixture proportions for generating plots. * Figure4A_admixture_paralug_colonies_nochr3_k3.txt * Figure4B_admixture_paralug_nochr3_k3.txt Files for Figure 5: Eigenvec and heterozygosity files for generating plots. * Figure5A_nouhaud-woodant-chr03.eigenvec * Figure5B_nouhaud-nonref-allelefreq.012 **Description:**  Figure 2: Files neccessary to generate Figure 2. This figure consists of principal component analysis of the genome excluding chromosome 3 and solely chromosome 3 for the species collected for this study. Figure 3: Files neccessary to generate Figure 3. This figure shows the intra-species pairwise relatedness for each nest. Figure 4: Files neccessary to generate Figure 4. This figures shows the genetic admixture proportions workers from each nest plotted against their geographical locations and individual nest proportions. Figure 5: Files neccessary to generate Figure 5. This figure leverages public data to show heterozygosity and of principal component analysis of chromosome 3 in other *Formica* species. Supplemental_Figures: Files neccessary to generate all the supplemental figures. VCFs: Filtered SNP data for *Formica paralugubris*, *Formica aquilonia*, and *Formica* *truncorum*. It also includes a combined VCF for all the species. ## Code/software manuscript_figures.R: The necessary R code to reproduce all the figures in the manuscript. ## Access information Data was derived from the following sources: * SpecIAnt. (2022). *Genotypes from two wood ant species and three hybrid populations*. [Dataset] figshare. [https://doi.org/10.6084/m9.figshare.20464383.v1](https://doi.org/10.6084/m9.figshare.20464383.v1)