The loss of biological diversity within species has the potential to significantly reduce resilience in the face of environmental change. Conservation of genetic variation needs to consider all available sources of diversity within a species, and approaches are required to integrate population management across traditionally separate wild and captive population domains. Here we report on a study that utilises different types of genetic analysis at different taxonomic scales and across an in situ-ex situ transition to support conservation planning for the Japanese golden eagle, a subspecies in serious regional decline. Mitochondrial DNA sequencing and nuclear DNA profiling are used to investigate subspecies differentiation and diversity in the natural population, revealing relatively high levels of variation in Japan. These results are compared with data from a newly established conservation breeding programme that indicates good representation of wild genetic variation in the captive founders. However, subsequent population viability analysis (PVA) to examine the demographic and genetic future of the captive population demonstrates the severe effects of existing reproductive skews, suggesting that this population is not sustainable without intensive genetic management. Lastly, the use of available molecular tools to validate and reconstruct pedigrees in Japanese golden eagle are evaluated and discussed in the context of captive and wild conservation management. The paper highlights the importance of producing and utilising comparative molecular genetic data across the population management spectrum and the benefits of PVA to support the implementation of integrated conservation plans.

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