Genetic analyses reveal hybridization but no hybrid swarm in one of the world’s rarest birds

Abstract Hybridization facilitated by human activities has dramatically altered the evolutionary trajectories of threatened taxa around the globe. Whereas introduced mammalian predators and widespread habitat loss and degradation clearly imperil the recovery and survival of the New Zealand endemic black stilt or kakī ( Himantopus novaezelandiae ), the risk associated with hybridization between this critically endangered endemic and its self‐introduced congener, the pied stilt or poaka ( Himantopus himantopus leucocephalus ) is less clear. Here, we combine Bayesian admixture analyses of microsatellite data with mitochondrial DNA sequence data to assess the levels of hybridization and introgression between kakī and poaka. We show that birds classified as hybrids on the basis of adult plumage are indeed of hybrid origin and that hybridization between kakī and poaka is both extensive and bidirectional. Despite this, we found almost no evidence for introgression from poaka to kakī, thus negating the popular belief that kakī represent a hybrid swarm. To our knowledge, ours represents the first comprehensive study to document a lack of widespread introgression for a species at risk despite a recent history of extensive bidirectional human‐induced hybridization. We attribute this rather surprising result, in part, to reduced reproductive success in female hybrids combined with a transient male‐biased kakī sex ratio. To maximize the evolutionary potential of kakī, we use these data to recommend conservation management activities aimed to maintain the genetic integrity and to maximize the genetic diversity of this iconic rare bird.