Acknowledgements

We are grateful to the Kākāpō125+ Project led by the New Zealand Department of Conservation (DOC) in partnership with Te Rūnanga o Ngāi Tahu (TRONT). The generation and availability of the short-read data used in this study is owed to the following additional parties: Genetic Rescue Foundation, University of Otago, New Zealand Genomics Limited, Rockefeller Institute, Duke University, Science Exchange and Experiment.com. We also thank DOC and TRONT for providing the opportunity to explore structural variants in kākāpō using both short- and long-read data. JRW and TES are grateful to the Shorebirds Trust, DOC, Genomics Aotearoa, and the University of Canterbury (UC) for their financial support and also extend their thanks to the UC Conservation, Systematics and Evolution Research Team (ConSERT), the UC Research Computational Cluster, especially Francois Bissey, and the New Zealand eScience Infrastructure for support in accessing the computational resources necessary for generating this manuscript. We are also grateful for three anonymous reviewers for their constructive feedback on earlier versions of this work.