Data from: Unexpected absence of a multiple-queen supergene haplotype from supercolonial populations of Formica ants
Data files
Mar 20, 2025 version files 53.23 MB
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JEB_2025.zip
53.23 MB
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README.md
2.77 KB
Abstract
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.
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