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

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. leucocephalus). Conservation management of kakī has resulted in the population increasing to 169 wild adults at the end of the 2023–2024 breeding season. Here we use mitogenomes to enable comparisons of diversity between contemporary and historical (pre-1960s) 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 across a period of population decline and subsequent conservation management for kakī. Mitogenome haplotype data provides no evidence of introgression from poaka into kakī despite past hybridisation. This contributes 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 that mitochondrial diversity has been maintained in kakī across a period of species decline and subsequent conservation management. [ABSTRACT FROM AUTHOR]