DOI: 10.5061/dryad.js509
title: Data from: The fire ant social chromosome supergene variant Sb shows low diversity but high divergence from SB

description: Variation in social behavior is common yet little is known about the
 genetic architectures underpinning its evolution. A rare exception is in
 the fire ant Solenopsis invicta: Alternative variants of a supergene
 region determine whether a colony will have exactly one or up to dozens of
 queens. The two variants of this region are carried by a pair of “social
 chromosomes”, SB and Sb, which resemble a pair of sex chromosomes.
 Recombination is suppressed between the two chromosomes in the supergene
 region. While the X-like SB can recombine with itself in SB/SB queens,
 recombination is effectively absent in the Y-like Sb because Sb/Sb queens
 die before reproducing. Here, we analyze whole genome sequences of eight
 haploid SB males and eight haploid Sb males. We find extensive SB-Sb
 di↵erentiation throughout the &gt;19Mb long supergene region. We find
 no evidence of “evolutionary strata” with different levels of divergence
 comparable to those reported in several sex chromosomes. A high proportion
 of substitutions between the SB and Sb haplotypes are nonsynonymous,
 suggesting inefficacy of purifying selection in Sb sequences, similar to
 that for Y-linked sequences in XY systems. Finally, we show that the Sb
 haplotype of the supergene region has 635-fold less nucleotide diversity
 than the rest of the genome. We discuss how this reduction could be due to
 a recent selective sweep affecting Sb specifically or associated with a
 population bottleneck during the invasion of North America by the sampled
 population.
description: dS, dN and dN/dS values
 between Atta cephalotes and Acromyrmex echinatiorCalculated by codeml
 from one-to-one orthologs (see article methods for
 details)atta-acro-dnds.csvSubstitutions between the SB and Sb social chromosome variants in 403 protein coding genesSubstitutions between the SB and Sb variants in 403 protein coding genes in the social chromosome supergene region of the fire ant Solenopsis invicta. The table includes gene name, gene length, the number of synonymous and nonsynonymous substitutions (syn_substitutions and nonsyn_substitutions) and their rate (ds and dn).genes.txtconsensus-bbConsensus DNA sequence of 403 protein coding genes in the SB variant of the fire ant social chromosome supergene.consensus-bb.cdsConsensus amino acid sequence of 403 protein-coding genes in the SB variant of the fire ant Solenopsis invicta social chromosome supergene.consensus-lbConsensus DNA sequence of 403 protein-coding genes in the Sb variant of the fire ant Solenopsis invicta social chromosome supergene.consensus-lb.cdsConsensus amino acid sequence of 403 protein-coding genes in the Sb variant of the fire ant Solenopsis invicta social chromosome supergene.Genotypes of B and b haploid males.Filtered VCF file with variants called from whole-genome sequences of 16 Solenopsis invicta haploid males with Cortex. 8 samples have the Gp-9B genotype (f1_B to f7_B, gdo10), 8 samples have the Gp-9b genotype (f1b to f7b, gdo10).all-filtered.vcf.bgzSAMN00014755Reads from sequencing a Gp-9B maleSRX206834Reads from sequencing a Gp-9 b maleSRP017317Reads from sequencing 7 Gp-9B and 7 Gp-9b males