Abstract
Viruses are essential, but often overlooked, players in the formation, turnover, and maintenance of life on Earth. From influencing the genomic evolution of cellular life and regulating ecosystems and biogeochemical cycles to causing infectious disease outbreaks and aiding vaccine and drug development, these invisible parasites are embedded in every facet of biology. Yet, we know little about the true extent of viral diversity and ecology, especially in more isolated reaches of the planet. To expand this knowledge from the perspective of isolated ecosystems and explore the roles of novel viruses in emerging diseases, my thesis presents a comprehensive metatranscriptomic analysis of viromes across Aotearoa New Zealand and Antarctica. This research involved collecting and analysing various sample types from diverse host populations in remote and agricultural ecosystems. The geographic isolation and environmental shifts that have shaped New Zealand and Antarctica have also influenced the uncharacterised viromes in their culturally and economically significant species. Through this work, I investigated viral diversity, host associations, and ecological drivers in 24 aquatic and terrestrial hosts. On Rēkohu (Chatham Island), viromes of native New Zealand fish were highly diverse, expanding two recently proposed, divergent viral families. Common smelt, in particular, showed evidence of long-term virus-host codivergence with dsDNA viruses. Similarly, viral diversity in polar fish from the Ross Sea, Antarctica shed light on their unique evolutionary trajectories shaped by species radiations and extreme temperatures. Despite the low host diversity, polar fish viromes exhibited viral diversity comparable to more biodiverse aquatic ecosystems. Evidence of viral host-switching also raises questions about pathogen emergence and biodiversity loss in fragile marine environments. I also identified abundant apicomplexan parasites and novel viruses with evidence of cross-species transmission between native, introduced, and migratory birds on two islands in the Chatham Islands. These findings reveal implications for the conservation and monitoring of threatened populations across wider New Zealand. My research further examined two emerging diseases in agricultural species. In spiny lobsters, I detailed a novel crustavirus–Red rock lobster crustavirus–associated with tail fan necrosis, a classical shell disease affecting the health and economic viability of this species. Finally, I characterised the oral and faecal viromes of dairy calves experiencing an idiopathic ill-thrift syndrome, highlighting Pseudocowpox virus and Bovine bopivirus as being significantly associated with the symptoms of this condition. Across these studies, I discovered 83 endemic novel viruses, significantly broadening the known virosphere of these environments. This work uncovered patterns of viral diversity and evolution tied to host phylogeny, environmental change, and human-mediated farming and fishing practices. Furthermore, it emphasises the value of a cross-ecosystem approach to evolutionary virology and demonstrates the utility of integrating genomics into wildlife surveillance and disease investigations, particularly in understudied hosts.