Genetic tools for the conservation of New Zealand birds, with a focus on the Chatham Island taiko (Pterodroma magentae)

Abstract

In this age of mass extinction, genetic methods have become powerful tools to solve previously intractable questions and inform conservation management strategies. By utilising genetic markers which vary in both their modes of inheritance and rates of mutation, insight can be gained into many different issues of conservation importance. The value of such information is increasingly being recognised in New Zealand, where introduced predators have decimated the native avifauna so that today 80% of species are threatened or at risk. The identification of specimens or bird remains to the species level from morphologically unidentifiable samples such as blood, feathers or bone is one issue of conservation concern that can be addressed using genetic tools. DNA barcoding utilises a standardised 648bp region of the mitochondrial cytochrome oxidase 1 (COI) gene to do just this. I curated and analysed 1416 sequences from 211 New Zealand bird species to determine the efficacy of DNA barcoding within our unique avifauna. Additional specimens collected from outside New Zealand were included in the analysis to increase sampling of geographic variation and evaluate the accuracy of the method to distinguish closely related species. DNA barcoding proved effective at identifying the majority (88%) of species. Most of the 13 taxa that could not be distinguished were recently diverged indicating incomplete lineage sorting and in some cases hybridisation. Within 16 species there was evidence of divergent lineages, some of which are recognised subspecies separated by large geographic distances. The reference database and analysis presented will provide a valuable conservation and management tool for New Zealand’s endangered birds. I also developed nuclear genetic markers to answer questions specific to the Chatham Island taiko (Pterodroma magentae), one of the world’s rarest seabirds and the focus of considerable conservation efforts. An elusive species, individual taiko are difficult to observe and locate and as a result many questions regarding kinship remain unanswered. To address such questions, I used next-generation sequencing to isolate 18 polymorphic microsatellite loci specific to taiko. Genotyping individuals at these loci and two others previously shown to be polymorphic in taiko provided sufficient power to assign first-degree relationships for many individuals. From analysis of population structure and relatedness it appears that all sampled taiko (n = 157) belong to a single breeding colony. Some individuals were offspring of known breeders and some of these breeders were likely breeding for over 20 years prior to the discovery of their burrow. There was also strong evidence that active burrows remain undiscovered, justifying ongoing efforts to locate them. Additionally, there was evidence that inbreeding is occurring as on average breeding pairs are more closely related than expected by chance (average rXY = 0.13). This is likely a consequence of a reduced population size combined with strong natal philopatry. These findings will have important implications for current and future conservation management of taiko.