Genetic structure, inbreeding and effective population size in an endangered island cockatoo, following management-led recovery

Island populations are particularly vulnerable to genetic risk. The glossy black-cockatoo Calyptorhynchus lathami halmaturinus has been restricted to Kangaroo Island, South Australia, since the mid-20th century and had declined to a few hundred individuals before management-led recovery. To understand how this population bottleneck might have affected population structure, genetic diversity and inbreeding, we analyzed single nucleotide polymorphisms (SNPs), principally generated from feather samples collected from nestlings during two breeding seasons. We investigated differences in genetic variability between population ‘flocks’ across the island. Overall F IS was 0.02 and mean allelic richness was 1.84. Low pairwise F ST values (-0.001-0.04) indicated genetic connectivity between the flocks, however, genetic differentiation (P ≤ 0.004) between all but the two eastern flocks suggests some limitations to gene flow. Seventeen per cent of individuals were highly inbred, with more than a third of these individuals from the most eastern flock. While there was no substantial population structure, analysis indicated some differentiation of the currently expanding eastern flock. Spatial autocorrelation found stronger than random relatedness amongst nestlings in nesting clusters, confirming suggestions from previous studies. The estimated effective population size ( N e ) was 122, above the minimum ( N e ≥ 50 ) commonly thought needed to avoid inbreeding depression in the short term, with N e values for two flocks also above this level. Our study highlights the importance of focussing on population genetics as well as numerical recovery when developing actions to manage threatened populations.