Supergene genotypes and associated phenotypes in Formica cinerea samples

Antagonistic selection has long been considered a major driver of the formation and expansion of sex chromosomes. For example, sexually antagonistic variation on an autosome can select for suppressed recombination between that autosome and the sex chromosome, leading to a neo-sex chromosome. Autosomal supergenes, chromosomal regions containing tightly linked variants affecting the same complex trait, share similarities with sex chromosomes, raising the possibility that sex chromosome evolution models can explain the evolution of genome structure and recombination in other contexts.  We tested this premise in a Formica ant species wherein we identified four supergene haplotypes on chromosome 3 underlying colony social organization and sex ratio. We discovered a novel rearranged supergene variant (9r) on chromosome 9 underlying queen miniaturization. The 9r is in strong linkage disequilibrium with one chromosome 3 haplotype (P2) found in multi-queen (polygyne) colonies. We suggest that qu..., Sample collection
Formica cinerea is a socially polymorphic species with a wide distribution across Europe63. This species nests preferentially along sand and gravel banks of rivers and open sand dunes. We collected F. cinerea workers and alates (gynes and males) from colonies in northern Italy (Aosta Valley and Piedmont) in June-July across several years, 2014, 2018-2021 (Table S1). Whenever possible, we sampled up to 10 gynes and males, and about 15 workers from each colony, and noted the observed sex-ratio. When multiple mature queens were found within colonies, we also sampled a subset of them. During 2019-2021, we collected newly mated wingless queens that were either looking for suitable locations to start new colonies or were under stones in self-dug chambers with none to few eggs. We stored samples in 96-100% ethanol.
Library preparation
We extracted DNA from the head and thorax of workers, and only the head of gynes and males. For the 2014 and 2018-2020 samples, we used the QIA..., , # Overview of Formica cinerea samples

[https://doi.org/10.5061/dryad.02v6wwq8s](https://doi.org/10.5061/dryad.02v6wwq8s)

The table \"Overview of Formica cinerea samples\" shows information for each of the 1415 individuals analyzed in the paper titled '**Social antagonism facilitates supergene expansion in ants'**. In the paper, we describe a supergene on chromosome 3 with 4 alternative haplotypes (MA, MD, P1, P2) underlying the number of colony queens and sex ratio. A second supergene on chromosome 9 with two alternative haplotypes (9a, 9r) controls queen and male body size.

## Description of the data and file structure

For each sample we report the specimen ID (SAMPPLE ID coulmn), the caste they belong to (CASTE column), colony of origin (COLONY column), the year they have been collected (YEAR coulmn), the bacth number the samples have been sequenced (BATCH column), the supergene genotype on chromosome 3 (GENOTYPES CHR3 column), the supergene genotype on chromosome 9 (GENOTYPES CHR9 ...