Résumé
Maintaining the genetic diversity of populations is important in conservation because it strongly influences the ability to adapt to changing environments. We characterised the genetic structure of the endemic and endangered New Zealand (NZ) long-tailed bat (Chalinolobus tuberculatus) in two valleys in Fiordland, NZ. Fiordland is one of the last strongholds of the species, which has drastically declined throughout NZ. C. tuberculatus has suffered from recent habitat fragmentation and episodic predation by exotic mammals over the last 150 years. Gene flow and structuring were measured using nine nuclear microsatellite loci. In addition, the hyper-variable domain HVI of the mitochondrial control region was sequenced to analyse population structure at the maternal level. Our results show that the nine colonies studied have retained high genetic diversity, with moderate signs of genetic bottlenecks. Furthermore, low F-ST and F-IS values indicated that all colonies are still connected by gene flow and do not show signs of inbreeding. Substantial gene flow among colonies was also demonstrated by Bayesian clustering and PCA analysis. At the mitochondrial level, substantial differentiation between colonies has resulted from strong natal philopatry in females. Overall, our results indicate that genetic diversity is maintained in the Fiordland population of C. tuberculatus despite regular population crashes and habitat fragmentation. Management should ensure that remaining habitat linkages are preserved and further predator-induced population bottlenecks are prevented so that current genetic diversity is maintained in the long-term.