Abstract
Accurate identification of evolutionarily significant units of rare and threatened organisms provides a foundation for effective management and conservation. Up to seven subspecies of the critically endangered Yellow-crested Cockatoo (Cacatua sulphurea) have been described, four of which were commonly recognised pre-2014. In the absence of genotypic data, C. sulphurea subspecies delimitation has been based on morphology, behaviour and biogeography. To clarify genetic relationships and shed light on the diversification of this parrot radiation, whole genomes were sequenced for 16 museum specimens, covering the geographic range of the proposed seven subspecies as well as one C. galerita galerita. Combined with four museum-derived wild Cacatua sequences from NCBI, the results indicate there are three distinct C. sulphurea subspecies clusters centred in different biogeographic subregions of Wallacea (Timor; Sumba; as well as the Sulawesi Region and the main Lesser Sunda chain), separated by shallow genetic distances (d(a) < 0.148%). The results raise questions about the recent species-level elevation of the phenotypically most distinct subspecies, C. s. citrinocristata, and about the origins of C. s. abbotti, the only subspecies west of Wallace's Line. Our analyses suggest C. s. abbotti is unlikely to be embedded within C. sulphurea, suggesting its origin on the remote Masalembu islands may be due to human translocation via historical trade routes. These genomic results inform the prioritisation and streamlining of conservation measures for the critically endangered C. sulphurea by identifying and delimiting likely conservation units.