Maintenance of mitogenomic diversity despite recent population decline in a critically endangered Aotearoa New Zealand bird

Abstract Mitochondrial genomes (mitogenomes) represent a relatively cost-effective tool for comparing diversity between contemporary and historical populations to assess impacts of past population processes, or the outcomes of conservation management. The Aotearoa New Zealand endemic kakī | black stilt (Himantopus novaezelandiae) is a critically endangered wading bird. Anthropogenic impacts contributed to kakī declining to ~ 23 individuals in 1981 and promoted interspecific hybridisation with their more common congener, the poaka | pied stilt (H. himantopus leucocephalus). Conservation management of kakī has resulted in the population increasing to 169 wild adults today. Here we use mitogenomes to enable comparisons of diversity between contemporary and historical (pre-1970s) stilts, and to understand the impacts of past interspecific hybridisation. We assemble a mitogenome for kakī and use this as a reference to facilitate downstream comparisons of mitochondrial diversity among kakī and poaka through time. Mitogenome haplotypes clearly differentiate kakī from poaka, and thus contribute to the behavioural, ecological, morphological and genetic evidence that conservation action has maintained the species integrity of this critically endangered bird. Furthermore, these results indicate conservation management aiming to maintain genetic diversity has been successful.