Henry, Millicent Frances2025-11-052025-11-052025https://mro.massey.ac.nz/handle/10179/73761The New Zealand Huntaway and Heading Dog are vital to the success of New Zealand’s livestock farming industry. This study presents one of the first large-scale genomic analyses of these two unique working breeds. Utilising phylogenetic and population structure methodology, the primary objectives of this research were to investigate the genetic relationships of the New Zealand Huntaway and Heading Dog with international dog breeds, formalise the major historical breed contributions that have shaped their development, and assess their population structure and diversity. This study utilised a dataset of 1,735 individuals, representing 129 dog breeds and three wild canid species, and included 211 Huntaways and 246 Heading Dog genomic datasets generated as part of this project. Genomic analyses revealed that both breeds can be traced back to ancestral UK rural working dog populations, occupying positions within the UK rural subclade on the domestic canine phylogeny. Baseline inbreeding scores suggest that neither the New Zealand Huntaway or Heading Dog populations express significantly high inbreeding levels, and the scores obtained are similar to those seen in other formally recognised dog breeds. A list of genes under putative positive selection in both populations is presented and could be used for future genetic selection in these dog populations. This study highlights the Huntaway and Heading Dog as genetically distinct breeds adapted to the unique demands of New Zealand’s pastoral farming systems. These results not only contribute to the current understanding of breed development in geographically isolated environments such as New Zealand but also highlights the opportunity of integrating genomics into working dog management and breeding practices. The genetic resources generated through this study will serve as a valuable reference for future research in the “Right Dog for the Job” project, aimed at preserving the health, diversity and functionality of the New Zealand Huntaway and Heading Dog.enThe authorThesis310410 Phylogeny and comparative analysis310509 Genomics