Introduction

In a supergene, different allelic combinations at tightly linked loci determine different morphs in a population. Classical crossing studies initially led to the discovery of several such systems including supergenes controlling shell colour in the snail Cepaea nemoralis (Cain et al. 1960), wing pattern in Papilio butterflies (Clarke & Sheppard 1971) and heterostyly in the self‐incompatibility system of Primula (Mather 1950; Dowrick 1956). Recent advances in sequencing technology have allowed more rapid discovery and description of supergene regions, including those controlling the wing pattern mimicry of a butterfly species (Joron et al. 2011), alternate forms of social organization in ants (Wang et al. 2013; Purcell et al. 2014), reproductive morphs in birds (Küpper et al. 2015; Lamichhaney et al. 2015; Tuttle et al. 2016) and ecotypes in a flowering plant (Lowry & Willis 2010). Supergene evolution is thought to involve selection on alleles at two or more loci (Bull 1983). This selection acts to prevent the formation of disadvantageous combinations of alleles by suppressing recombination within the supergene region, for example by favouring the spread of inversions (Linksvayer et al. 2013; Schwander et al. 2014; Thompson & Jiggins 2014).

In this study, we focus on the evolution of a chromosome system responsible for two forms of social organization in the fire ant Solenopsis invicta (Wang et al. 2013). Colonies have either exactly one queen or up to dozens of reproductive queens, with multiple physiological, morphological and behavioural traits differing between the two social forms (Ross & Keller 1995; DeHeer et al. 1999; Keller & Ross 1999; Goodisman et al. 2000; DeHeer 2002; Buechel et al. 2014; Huang & Wang 2014). Queens that will form their own single‐queen colony typically disperse over greater distances and can effectively colonize newly available habitats. In contrast, multiple‐queen colonies can outcompete single‐queen colonies in saturated habitats and harsh environments and can split by budding (Herbers 1986; Nonacs 1993; Bourke & Heinze 1994; Ross & Keller 1995). These patterns of selection likely maintain both social forms within the species (Nonacs 1993; Ross & Keller 1995). The social dimorphism is genetically determined by a single Mendelian element (Keller & Ross 1998; Ross & Keller 1998; Krieger & Ross 2002; Ross & Keller 2002), recently shown to be a large (∼13 Mb) chromosome region (Wang et al. 2013). Recombination is suppressed between the two variants of this region which are carried by a pair of ‘social chromosomes’, SB and Sb. The region spans approximately 55% of the chromosomes and includes up to 600 protein‐coding genes (based on the genome sequence of an SB male; Wang et al. 2013). The two chromosomes differ by one large inversion affecting most of the region, and at least one further smaller inversion (48 kb) within the region. Recombination between SB and Sb is thought to have been lost relatively recently (less than 500 000 years ago; Wang et al. 2013). Indeed, SB and Sb contain largely the same protein‐coding gene content, although it is unclear how much allelic divergence there is between the two variants (Wang et al. 2013). The features of the region are consistent with it being a supergene. Although we use this term, we note two caveats: First, experimental evidence demonstrating that two or more loci contribute to differences between social forms is still lacking. Additionally, the mutations responsible for these differences may have occurred after the evolution of suppressed recombination in the region.

In single‐queen colonies, all workers and the queen have the SB/SB genotype. In contrast, multiple‐queen colonies include SB/SB and SB/Sb workers, but all reproductive queens are SB/Sb because workers kill SB/SB queens reaching reproductive maturity (Keller & Ross 1998; Ross & Keller 1998, 2002; Wang et al. 2013). Recombination occurs only in queens because fire ant workers are completely sterile and males are haploid (Tschinkel 2006). The recombination of the supergene region has two additional restrictions. First, the supergene region of SB is thought to recombine only in homozygous SB/SB queens of single‐queen colonies because the region does not recombine in heterozygote queens. A second restriction on recombination occurs because Sb/Sb queens die before reproducing (Ross 1997; DeHeer et al. 1999; Keller & Ross 1999; Gotzek & Ross 2007). If this genotype is always lethal, recombinants between two Sb haplotypes cannot be transmitted to the next generation (Wang et al. 2013). These restrictions on recombination are comparable to those affecting an X/Y sex chromosome system in a diploid species, with SB resembling an X chromosome, Sb resembling a nonrecombining Y chromosome, and the region outside the supergene resembling a pseudo‐autosomal region. Sb is the only part of the genome that is present exclusively in multiple‐queen colonies, whereas gene flow occurs extensively between colony types in the rest of the genome (albeit with a possible directional bias from single‐queen to multiple‐queen colonies; Ross 1992; Ross & Shoemaker 1993; Shoemaker & Ross 1996; Ross et al. 1997). The evolutionary effects of reduced recombination and lower effective population size compared to typical autosomes (Charlesworth & Charlesworth 2000) have been extensively studied in sex chromosomes, which can be seen as special cases of supergenes (Charlesworth 2016). These findings generate predictions for the fire ant system which can be tested by comparisons within and among SB and Sb genomes.

Fire ants have a haplo‐diploid sex determination system (Tschinkel 2006), and thus, it is possible to unambiguously distinguish SB and Sb haplotypes by sequencing haploid males. Here, we compare whole‐genome sequences of eight SB and eight Sb males to test predictions based on our understanding of supergene and sex chromosome evolution. First, we test whether there is sequence differentiation between the two chromosomes over the whole extent of the supergene region, indicating long‐term inhibition of recombination over the entire region. This would contrast with several large genomic inversions in Drosophila melanogaster (>7 Mb; Corbett‐Detig & Hartl 2012; Huang et al. 2014; Kapun et al. 2014) where recombination is suppressed in the regions near the breakpoints, but recombination in the form of gene conversion and double crossover events can occur in most of the inverted region (Navarro et al. 1997; Kapun et al. 2014). Second, we investigate whether the supergene region has lower genetic diversity than the rest of the genome, expecting a mild reduction in the X‐like SB due to its decreased effective population size (Betancourt et al. 2004; Hutter et al. 2007; Keinan et al. 2009; Vicoso & Charlesworth 2009; Hammer et al. 2010; Lambert et al. 2010; Arbiza et al. 2014), and a much stronger reduction in the Y‐like Sb due to strong Hill–Robertson effects in the absence of recombination (Kaiser & Charlesworth 2009; Wilson Sayres et al. 2014). These effects could also have led to degeneration of Sb – comparable to that observed in Y (or W) chromosomes, which can be detected by comparison of genomic sequence between chromosomes and among species (Charlesworth & Charlesworth 2000; Charlesworth et al. 2005; Bergero & Charlesworth 2009; Bachtrog 2013). The social chromosome supergene system may give insight into the early stages of degeneration of a nonrecombining region (Zhou et al. 2012) given the relatively young age of the system (Wang et al. 2013). Finally, we test whether the supergene region can be divided into strata with different levels of divergence between SB and Sb. In sex chromosome systems, strata are understood to represent discrete increases in the size of the sex‐linked region, possibly through the fixation of new structural mutations (Bergero & Charlesworth 2009). Strata have been documented in mammalian and avian sex chromosomes of relatively ancient origin (Lahn & Page 1999; Handley et al. 2004; Cortez et al. 2014; Wright et al. 2014; Zhou et al. 2014), and also in younger sex chromosomes in plants (Bergero et al. 2007; Wang et al. 2012; Papadopulos et al. 2015). The discovery of strata could be valuable in reconstructing the evolution of the social chromosome, particularly if an older ‘core’ region could be identified, as that would be expected to contain loci playing key roles in the determination of social form.