Has gene expression neofunctionalization in the fire ant antennae contributed to queen discrimination behavior?

Genome-Wide Analysis of the Odorant Receptor Gene Family in Solenopsis invicta, Ooceraea biroi, and Monomorium pharaonis (Hymenoptera: Formicidae)

Olfactory systems in eusocial insects play a vital role in the discrimination of various chemical cues. Odorant receptors (ORs) are critical for odorant detection, and this family has undergone extensive expansion in ants. In this study, we re-annotated the OR genes from the most destructive invasive ant species Solenopsis invicta and 2 other Formicidae species, Ooceraea biroi and Monomorium pharaonis, with the aim of systematically comparing and analyzing the evolution and the functions of the ORs in ant species, identifying 356, 298, and 306 potential functional ORs, respectively. The evolutionary analysis of these ORs showed that ants had undergone chromosomal rearrangements and that tandem duplication may be the main contributor to the expansion of the OR gene family in S. invicta. Our further analysis revealed that 9-exon ORs had biased chromosome localization patterns in all three ant species and that a 9-exon OR cluster (SinvOR4–8) in S. invicta was under strong positive selection (Ka/Ks = 1.32). Moreover, we identified 5 S. invicta OR genes, namely SinvOR89, SinvOR102, SinvOR352, SinvOR327, and SinvOR135, with high sequence similarity (>70%) to the orthologs in O. biroi and M. pharaonis. An RT-PCR analysis was used to verify the antennal expression levels of these ORs, which showed caste-specific expression. The subsequent analysis of the antennal expression profiles of the ORs of the S. invicta workers from the polygyne and monogyne social forms indicated that SinvOR35 and SinvOR252 were expressed at much higher levels in the monogyne workers than in the polygyne workers and that SinvOR21 was expressed at higher levels in polygyne workers. Our study has contributed to the identification and analysis of the OR gene family in ants and expanded the understanding of the evolution and functions of the ORs in Formicidae species.

Direct and indirect genetic effects of a social supergene

Indirect genetic effects describe phenotypic variation that results from differences in the genotypic composition of social partners. Such effects represent heritable sources of environmental variation in eusocial organisms because individuals are typically reared by their siblings. In the fire ant Solenopsis invicta, a social supergene exhibits striking indirect genetic effects on worker regulation of colony queen number, such that the genotypic composition of workers at the supergene determines whether colonies contain a single or multiple queens. We assessed the direct and indirect genetic effects of this supergene on gene expression in brains and abdominal tissues from laboratory-reared workers and compared these with previously published data from field-collected prereproductive queens. We found that direct genetic effects caused larger gene expression changes and were more consistent across tissue types and castes than indirect genetic effects. Indirect genetic effects influenced the expression of many loci but were generally restricted to the abdominal tissues. Further, indirect genetic effects were only detected when the genotypic composition of social partners differed throughout the development and adult life of focal workers, and were often only significant with relatively lenient statistical cutoffs. Our study provides insight into direct and indirect genetic effects of a social supergene on gene regulatory dynamics across tissues and castes in a complex society.

Iterative evolution of supergene-based social polymorphism in ants

Species commonly exhibit alternative morphs, with individual fate being determined during development by either genetic factors, environmental cues or a combination thereof. Ants offer an interesting case study because many species are polymorphic in their social structure. Some colonies contain one queen while others contain many queens. This variation in queen number is generally associated with a suite of phenotypic and life-history traits, including mode of colony founding, queen lifespan, queen-worker dimorphism and colony size. The basis of this social polymorphism has been studied in five ant lineages, and remarkably social morph seems to be determined by a supergene in all cases. These 'social supergenes' tend to be large, having formed through serial inversions, and to comprise hundreds of linked genes. They have persisted over long evolutionary timescales, in multiple lineages following speciation events, and have spread between closely related species via introgression. Their evolutionary dynamics are unusually complex, combining recessive lethality, spatially variable selection, selfish genetic elements and non-random mating. Here, we synthesize the five cases of supergene-based social polymorphism in ants, highlighting interesting commonalities, idiosyncrasies and implications for the evolution of polymorphisms in general. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.

Characterization of Queen Supergene Pheromone in the Red Imported Fire Ant Using Worker Discrimination Assays

Ants use chemical signals to communicate for various purposes related to colony function. Social organization in the red imported fire ant, Solenopsis invicta, is determined by the Sb supergene, with colonies of the monogyne (single-queen) form lacking the element and colonies of the polygyne (multiple-queen) form possessing it. Polygyne workers accept new reproductive queens in their nest, but only those carrying Sb; young winged queens lacking this genetic element are executed as they mature sexually in their natal nest or as they attempt to enter a foreign nest to initiate reproduction after mating and shedding their wings. It has been suggested that queen supergene genotype status is signaled to workers by unsaturated cuticular hydrocarbons, while queen reproductive status is signaled by piperidines (venom alkaloids). We used high-throughput behavioral assays to study worker acceptance of paper dummies dosed with fractions of extracts of polygyne queens, or blends of synthetic counterparts of queen cuticular compounds. We show that the queen supergene pheromone comprises a blend of monoene and diene unsaturated hydrocarbons. Our assays also reveal that unsaturated hydrocarbons elicit discrimination by polygyne workers only when associated with additional compounds that signal queen fertility. This synergistic effect was obtained with a polar fraction of queen extracts, but not by the piperidine alkaloids, suggesting that the chemical(s) indicating queen reproductive status are compounds more polar than cuticular hydrocarbons but are not the piperidine alkaloids. Our results advance understanding of the role of chemical signaling that is central to the regulation of social organization in an important invasive pest and model ant species.

The maintenance of polymorphism in an ancient social supergene

Supergenes, regions of the genome with suppressed recombination between sets of functional mutations, contribute to the evolution of complex phenotypes in diverse systems. Excluding sex chromosomes, most supergenes discovered so far appear to be young, being found in one species or a few closely related species. Here, we investigate how a chromosome harbouring an ancient supergene has evolved over about 30 million years (Ma). The Formica supergene underlies variation in colony queen number in at least five species. We expand previous analyses of sequence divergence on this chromosome to encompass about 90 species spanning the Formica phylogeny. Within the nonrecombining region, the gene knockout contains 22 single nucleotide polymorphisms (SNPs) that are consistently differentiated between two alternative supergene haplotypes in divergent European Formica species, and we show that these same SNPs are present in most Formica clades. In these clades, including an early diverging Nearctic Formica clade, individuals with alternative genotypes at knockout also have higher differentiation in other portions of this chromosome. We identify hotspots of SNPs along this chromosome that are present in multiple Formica clades to detect genes that may have contributed to the emergence and maintenance of the genetic polymorphism. Finally, we infer three gene duplications on one haplotype, based on apparent heterozygosity within these genes in the genomes of haploid males. This study strengthens the evidence that this supergene originated early in the evolution of Formica and that just a few loci in this large region of suppressed recombination retain strongly differentiated alleles across contemporary Formica lineages.

Simple inheritance, complex regulation: Supergene-mediated fire ant queen polymorphism

The fire ant Solenopsis invicta exists in two alternate social forms: monogyne nests contain a single reproductive queen and polygyne nests contain multiple reproductive queens. This colony-level social polymorphism corresponds with individual differences in queen physiology, queen dispersal patterns and worker discrimination behaviours, all evidently regulated by an inversion-based supergene that spans more than 13 Mb of a "social chromosome," contains over 400 protein-coding genes and rarely undergoes recombination. The specific mechanisms by which this supergene influences expression of the many distinctive features that characterize the alternate forms remain almost wholly unknown. To advance our understanding of these mechanisms, we explore the effects of social chromosome genotype and natal colony social form on gene expression in queens sampled as they embarked on nuptial flights, using RNA-sequencing of brains and ovaries. We observe a large effect of natal social form, that is, of the social/developmental environment, on gene expression profiles, with similarly substantial effects of genotype, including: (a) supergene-associated gene upregulation, (b) allele-specific expression and (c) pronounced extra-supergene trans-regulatory effects. These findings, along with observed spatial variation in differential and allele-specific expression within the supergene region, highlight the complex gene regulatory landscape that emerged following divergence of the inversion-mediated Sb haplotype from its homologue, which presumably largely retained the ancestral gene order. The distinctive supergene-associated gene expression trajectories we document at the onset of a queen's reproductive life expand the known record of relevant molecular correlates of a complex social polymorphism and point to putative genetic factors underpinning the alternate social syndromes.