Genomic and transcriptomic bases of nutrient uptake in facultative and obligate ant-plant symbioses

Mutualisms are widespread across life and vary in their degree of dependence, ranging from facultative associations to specialised obligate relationships. The drivers and consequences of mutualistic dependence remain poorly understood, especially in ‘macro’-mutualism such as ant-plant symbioses. Ant-plant systems are well suited to addressing these questions because partner presence can be experimentally manipulated (ants can be added or excluded), the symbiosis spans a continuous spectrum from facultative to obligate association across closely related specie, and partner exchange is spatially localised to a discrete structure, the domatium, making the physiological and transcriptomic consequences of dependence experimentally tractable in a way that is difficult to achieve in more diffuse or intracellular mutualisms such as microbiome or endosymbiont systems.
In this thesis, I integrate genomics, experiments and transcriptomics to investigate how shifts toward obligate dependence reshape ant-plant function, using epiphytic Rubiaceae ant-plants (Hydnophytinae) as a model system. In chapter 2, I generated high-quality reference genomes for the obligate ant-plant Myrmecodia beccarii and the facultative Hydnophytum moseleyanum establishing a duplication-aware genomic framework that supports orthology inference and transcriptome mapping. This provides the genomic resources needed to interpret nitrogen-related candidates in a gene- and copy-aware manner across dependence levels.
In chapter 3, I established a controlled greenhouse symbiosis system between ghost ants (Tapinoma melanocephalum) and both Hydnophytinae species. Using a 15N isotope feeding assay, I show that ghost ants form nutritional mutualisms with both plants, and ant-derived fertilisation patterns match field observations, validating the system.
In chapter 4, I manipulated ant presence and nutrient availability to test whether nitrogen-uptake genes are expressed more constitutively in M. beccarii but remain inducible in H. moseleyanum. This identifies candidate genes involved in nitrogen-based nutritional symbiosis and supports a shift from inducible to constitutive expression associated with the evolution of obligate dependence.