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The coexistence of different mating strategies, whereby a species can reproduce both by selfing and outcrossing, is an evolutionary enigma. Theory predicts two predominant stable mating states: outcrossing with strong inbreeding depression or selfing with weak inbreeding depression. As these two mating strategies are subject to opposing selective forces, mixed breeding systems are thought to be a rare transitory state yet can persist even after multiple speciation events. We hypothesise that if each mating strategy plays a distinctive role during some part of the species life history, opposing selective pressures could be balanced, permitting the stable co-existence of selfing and outcrossing sexual morphs. In this scenario, we would expect each morph to be specialised in their respective roles. Here we show, using behavioural, physiological and gene expression studies, that the selfing (hermaphrodite) and outcrossing (female) sexual morphs of the trioecious nematode Auanema freiburgensis have distinct adaptations optimised for their different roles during the life cycle. A. freiburgensis hermaphrodites are known to be produced under stressful conditions and are specialised for dispersal to new habitat patches. Here we show that they exhibit metabolic and intestinal changes enabling them to meet the cost of dispersal and reproduction. In contrast, A. freiburgensis females are produced in favourable conditions and facilitate rapid population growth. We found that females compensate for the lack of reproductive assurance by reallocating resources from intestinal development to mate-finding behaviour. The specialisation of each mating system for its role in the life cycle could balance opposing selective forces allowing the stable maintenance of both mating systems in A. freiburgensis.

Hamilton���s rule has helped to reframe how we look at evolutionary biology. Incorporating inclusive fitness into our understanding of species interactions has helped define altruistic, selfish, spiteful and mutalistic interactions. While there is a strong theoretical understanding of these types of interactions, how they manifest molecularly is poorly understood. This thesis attempts to investigate some of the molecular mechanisms driven by Hamilton���s rule and the issues that have to be resolved so that these interactions can be fully understood. To understand the issues identifying molecular mechanisms in genomic conflict, I determined the problems with calling allele-specific expression and how it is not a good estimate for genomic imprinting. Looking at conflict at the species level I found a potential mechanism for sperm activation in Nasonia vitripenis that potentially allows for controlled sex allocation in response to kin selection mating pressures. To understand how altruistic behaviour is controlled in social insects I conducted a comparative analysis exploring RNA editing and its relation to reproductive phenotypic plasticity in Hymenoptera. This work identified a correlation between editing and reproductive flexibility, however this could be conflated with genome quality and therefore needs further study. Finally to understand the problems in investigating mutalistic relationships I determine how environmental pollutants can affect the wild Bombus terrestris microbiome. A correlation between several pollutants and core bacteria from the B. terrestris was identified but future studies will be needed to identify any affects on bee health. Overall this thesis identifies new avenues of exploration for understanding the molecular mechanisms driven by Hamilton���s rule.

The protein farnesyltransferase (FTase) mediates posttranslational modification of proteins with isoprenoid lipids. FTase is a heterodimer and although the beta subunit harbors the active site, it requires the a subunit for its activity. Here we explore the other functions of the FTase alpha subunit in addition to its established role in protein prenylation. We found that in the absence of the beta subunit, the alpha subunit of FTase forms a stable autonomous dimeric structure in solution. We identify interactors of FTase alpha using mass spectrometry, followed by rapid in vitro analysis using the Leishmania tarentolae cell - free system. Vps4A was validated for direct binding to the FTase alpha subunit both in vitro and in vivo. Analysis of the interaction with Vps4A in Hek 293 cells demonstrated that FTase alpha controls trafficking of transferrin receptor upstream of this protein. These results point to the existence of previously undetected biological functions of the FTase alpha subunit that includes control of intracellular membrane trafficking. Refereed/Peer-reviewed