29 August 2026: This article has been temporarily removed from Wiley Online Library during the course of an investigation of the underlying data by the society and the publisher.

Conservation management of endangered species increasingly relies on genomic approaches to understand how long‐term small population sizes affect the fitness of extant individuals. However, despite the growing investment in genomic resources by conservation programmes, the impact that sequencing methods have on the ability to detect inbreeding‐related phenomena has been largely overlooked. Here, we compare the use of whole‐gen...