Ecology, epidemiology and evolution of enteric microbes in fragmented populations of the endangered takahe (Porphyrio hochstetteri) : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Manawatū, New Zealand

Abstract

Pathogenic diseases are increasingly recognised as a challenge to the conservation of wildlife. Complex host-pathogen relationships and transmission dynamics in wild populations can limit our understanding of how pathogens contribute to the decline and endangerment of wildlife. Endangered wildlife populations maintained in reserves present a unique opportunity to investigate wildlife host-microbe relationships in a controlled semi-natural environment where diversity, abundance and the movement of species are restricted. The aim of this study was to investigate the prevalence and molecular differentiation of enteric bacteria carried by endangered takahe (𝘗𝘰𝘳𝘱𝘩𝘺𝘳𝘪𝘰 𝘩𝘰𝘤𝘩𝘴𝘵𝘦𝘵𝘵𝘦𝘳𝘪). Through the use of network analysis and molecular epidemiology, the study explored the effects of geographic isolation and translocation on the prevalence, transmission and evolution of 𝘊𝘢𝘮𝘱𝘺𝘭𝘰𝘣𝘢𝘤𝘵𝘦𝘳 and 𝘚𝘢𝘭𝘮𝘰𝘯𝘦𝘭𝘭𝘢 spp. within fragmented populations of takahe.

Translocation and conservation management has created a dynamic network of takahe populations which vary in their likelihood to maintain and transmit pathogens. My study suggests that range expansion following a significant bottleneck and intensive conservation management of takahe has had unforeseen consequences on microbial diversity. The management of takahe in different environmental settings has influenced the carriage of 𝘊𝘢𝘮𝘱𝘺𝘭𝘰𝘣𝘢𝘤𝘵𝘦𝘳 𝘫𝘦𝘫𝘶𝘯𝘪 and 𝘊𝘢𝘮𝘱𝘺𝘭𝘰𝘣𝘢𝘤𝘵𝘦𝘳 𝘤𝘰𝘭𝘪. A newly discovered rail-associated 𝘊𝘢𝘮𝘱𝘺𝘭𝘰𝘣𝘢𝘤𝘵𝘦𝘳 𝘴𝘱. 𝘯𝘰𝘷𝘢 1 was prevalent in all populations. However, more discriminatory whole genome analysis of isolates detected a significant biogeographic variation in 𝘊. 𝘴𝘱. 𝘯𝘰𝘷𝘢 1 genotypes. Possible explanations for the observed pattern include the spatial expansion and isolation of hosts resulting in reduced gene flow of 𝘊𝘢𝘮𝘱𝘺𝘭𝘰𝘣𝘢𝘤𝘵𝘦𝘳 𝘴𝘱𝘱. and allopatric speciation, and the presence of heterogeneous environmental attributes or cross-species transmission of 𝘊𝘢𝘮𝘱𝘺𝘭𝘰𝘣𝘢𝘤𝘵𝘦𝘳 𝘴𝘱𝘱. from sympatric reservoir hosts. An assessment of vertebrate reservoirs in an island ecosystem indicated cross-species transmission of 𝘊𝘢𝘮𝘱𝘺𝘭𝘰𝘣𝘢𝘤𝘵𝘦𝘳 𝘴𝘱𝘱. was not likely to be a factor contributing to the maintenance and phylogeographical distribution of 𝘊𝘢𝘮𝘱𝘺𝘭𝘰𝘣𝘢𝘤𝘵𝘦𝘳 𝘴𝘱𝘱. in takahe. This study was the first of its kind to explore microbial dynamics in a large proportion of a well-described but fragmented population of a wild bird. Results suggest historic and current management practices may be having unforeseen influences on enteric microbes, the consequences of which are unknown but could be detrimental to the health of translocated populations of takahe.