Year: 2026
Type: preprint
Abstract: Pinpointing the genetic elements underlying a phenotype within a supergene can be difficult because hundreds of linked genes can show similar associations with phenotype. Rare recombination between supergene haplotypes can help identify those genetic elements by changing haplotype-phenotype combinations. Here we investigate the genetic underpinnings of colony queen number and body size in the ant Formica lemani . Throughout the Formica genus, single-queen colonies typically carry M haplotypes, while multi-queen colonies also carry P haplotypes. In F. lemani , we found two P haplotypes homologous to those described in the closely related F. cinerea , but unlike in F. cinerea , where P 1 is restricted to multi-queen colonies, F. lemani P 1 is common in both single- and multi-queen colonies. This deviation suggests that P 1 may carry novel SNP combinations allowing single queen colony compatibility. By comparing haplotypes within F. lemani and with Formica cinerea , we searched for candidate monogyny variants resulting from gene flux from the M onto the P 1 haplotype, or with P 1 -specific mutations. We found 82 genes associated with candidate variants, of which two are among the fourteen previously suggested candidates in other species, suggesting that several different genes may underlie queen number across the genus. We also identified a supergene associated with smaller queens and males, which is shared with F. cinerea and in interchromosomal linkage disequilibrium with the queen-number supergene. Together, these results provide a rare example of how an ancient supergene can change in function, and a step toward identifying the genes within a supergene responsible for its functions.
Institution: University of California, Riverside
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
Awards: G1476237564, SG: Evolutionary history and contemporary function of alternative supergene haplotypes, Research Infrastructure: MRI: Acquisition of a Big Data HPC Cluster for Interdisciplinary Research and Training, MRI: Acquisition of a Big Data Compute Cluster for Interdisciplinary Research, G5946491792, CAREER: Integrating genetic and ecological drivers of a social phenotype: dynamics of a social polymorphism and supergene, Graduate Research Fellowship Program (GRFP)
OpenAlex ID: W7221066991