title: The fire ant social chromosome supergene variant Sb shows low diversity but high divergence from SB.
abstract: Variation in social behaviour 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 analyse whole-genome sequences of eight haploid SB males and eight haploid Sb males. We find extensive SB-Sb differentiation throughout the >19-Mb-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.
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
authors.forename: Rodrigo
authors.identifier: http://orcid.org/0000-0003-2492-4067
authors.initials: R
authors.lastname: Pracana
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
authors.forename: Anurag
authors.initials: A
authors.lastname: Priyam
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
authors.forename: Ilya
authors.initials: I
authors.lastname: Levantis
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
authors.forename: Richard A
authors.identifier: http://orcid.org/0000-0002-4801-9312
authors.initials: RA
authors.lastname: Nichols
authors.affiliation: School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
authors.forename: Yannick
authors.identifier: http://orcid.org/0000-0002-3140-2809
authors.initials: Y
authors.lastname: Wurm
mesh_terms: D000818:Animals; D001000:Ants / Q000235:genetics*; D002875:Chromosomes / Q000235:genetics*; D017344:Genes, Insect; D014644:Genetic Variation; D006238:Haploidy; D008297:Male; D009656:North America; D017422:Sequence Analysis, DNA; D012919:Social Behavior
keywords: Solenopsis invicta; diversity in supergene variants; evolutionary strata; queen number in ants; social chromosomes