Epigenetic changes and an extensive rewiring of the transcriptome underlie worker size distribution in the Florida carpenter ant [BiSulfite-seq]
Variation in continuous traits, such as height, is a complex output of genetic and environmental factors. In the Florida carpenter ant, workers are 75% genetically related but exhibit a wide range of lengths that broadly categorizes them into minor or major subcastes with specific roles within the colony. While initial studies have suggested that epigenetic changes can mediate the influence of the environment in the differential development of minor and major ants, no study has comprehensively studied ant size as a continuous phenotype with genome-wide approaches. Here, we exploit the entire continuous spectrum of ant size, mRNA expression, microRNA expression, and DNA methylation – in combination with genomic sequencing – to identify the molecular and epigenetic factors driving the determination of body size. We report dramatic changes in gene expression in key genes linked to sugar metabolism as well as the correlation of expression of a large proportion of the transcriptome to size, involving pathways related to DNA replication, muscle growth, and neuronal development. We further identify  and investigate the correlation of the expression of microRNAs and levels of DNA methylation with size, as well as their link to histone modifications, which together, might sculpt differential gene expression profiles. Together, this study unveils a coordinated molecular and epigenetic regulatory network determining body size, offering valuable insights into developmental biology and the molecular contributions to body size in the context of C. floridanus and beyond. Overall design: Here, we applied a comprehensive multimodal omics approach to evaluate the molecular contributors to C. floridanus worker size by constructing combined genome-wide DNA sequence variation, DNA methylation, gene expression, and microRNA expression profiles, each from every individual ant across 48 terminal-stage larvae whose sizes span the complete range of larval lengths