Assessment of the impacts of anthropogenic hybridisation in a threatened non-model bird species through the development of genomic resources with implications for conservation

Interspecific hybridisation—the breeding between distinct species—can contribute to species extinction due to wasted reproductive potential, outbreeding depression, and introgression of genetic material mediated by backcrossing. Incomplete reproductive barriers can facilitate interspecific hybridisation as previously isolated species come into contact with one another. Interspecific hybridisation is relatively common among birds, but anthropogenic impacts that increase the incidence of such hybridisation between threatened native species and non-threatened species are of conservation concern due to the risks of genetic swamping, which at its most extreme may result in species extinction. While the impacts of interspecific hybridisation have previously been assessed using small numbers of genetic markers, new genomic sequencing developments now facilitate implementation of genome-wide reassessments providing greater resolution of analyses. The critically endangered kakī (black stilt; Himantopus novaezelandiae) is one such species that can benefit from these new genomic data. Anthropogenic habitat change and introduction of mammalian predators resulted in the decline of this Aotearoa New Zealand endemic wading bird during the 1900s. An intense population bottleneck resulting in an ephemeral sex-bias among the remaining kakī contributed to hybridisation with the self-introduced poaka (the Aotearoa New Zealand population of the Australian pied stilt; H. himantopus leucocephalus), a congeneric species previously thought to have diverged from a common ancestor with kakī one million years ago. Intensive conservation management including captive breeding for translocation and predator control has increased kakī numbers from ~23 adults in 1981 to approximately 169 wild adults in 2020. Previous genetic studies identified minimal evidence of introgression of poaka genetic material into kakī, and iv determined that moderate outbreeding depression in combination with stochastic processes likely limited introgression. These data informed the kakī captive breeding for translocation programme with the aim of maintaining genetic integrity. However, re-evaluation using genomic data was recommended for kakī. Using high-throughput sequencing techniques, I sequenced and assembled the first reference genomes for kakī and Australian pied stilts as tools for use in analyses of introgression. The kakī mitochondrial genome was also assembled to facilitate comparisons of contemporary and historic stilt diversity, showing that conservation management aimed at maximising genetic diversity has largely maintained mitochondrial diversity despite kakī decline, identifying three mitochondrial haplotypes present among contemporary kakī. Kakī and poaka are well-differentiated, and are estimated to have diverged from a common ancestor approximately 750,000 years ago based on Bayesian analysis of mitochondrial data. In addition, the analysis of high-resolution genomic markers generated from approximately 65% of contemporary wild kakī detected no introgression from poaka to kakī despite past hybridisation. These findings confirm the results of previous genetic analysis of introgression and the success of past conservation management. As kakī recovery continues, these combined findings will be used by the New Zealand Department of Conservation’s Kakī Recovery Programme to further maintain the genetic integrity of kakī. Overall, the genomic resources developed here have facilitated the transition from using genetic data to genomic data for kakī recovery, and contribute to our understanding of the impacts of anthropogenic hybridisation on a critically endangered taonga species