Data from: The fire ant social chromosome supergene variant Sb shows low diversity but high divergence from SB

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 >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.