There has been much discussion relating to the current biodiversity crisis, with the loss of species now at an unprecedented rate. Using augmentation and/or reintroduction to minimize the loss of species in the wild is becoming more prominent. Zoological institutions have been traditionally involved in the management of insurance populations providing a range of species for release to the wild. Insurance populations can be costly, both in resources and behavioural changes, and so should aim to be maintained for as short a time as possible, with a maximum of 40 years. A Tasmanian devil Sarcophilus harrisii insurance population was established in 2006 with the arrival of devil facial tumour disease, and was founded with 120 individuals sourced predominantly from the west coast of Tasmania. Here the challenges of establishing and managing an insurance population in an already genetically depauperate species in the presence of a contagious cancer are discussed. The Tasmanian devil insurance metapopulation now includes a continuum of management scenarios (from intensive zoo‐based facilities, through free‐range enclosures, to an island and fenced peninsula) and consists of over 700 devils representing at least 180 founders. The lessons learned in regard to this programme are presented, including the issues surrounding reduced genetic diversity and how we are striving to improve the long‐term management of the insurance metapopulation through a combination of molecular genetics, modelling and on‐the‐ground management. The tools and technologies that have been developed in this programme are directly applicable to the recovery and management of a suite of other threatened fauna.

Conservation breeding programmes have become widespread as natural habitats shrink, and have been historically managed using pedigree data and an assumption that population founders are unrelated. Molecular genotyping is able to determine founder relatedness, but is rarely used. To empirically test the impact of assuming founders to be unrelated, we utilized data from 203 founding individuals and 11 subsequent years of breeding records for the Tasmanian devil (Sarcophilus harrisii) insurance population. We integrated molecular data (N = 119 founders) and detailed trapping information (N = 203 founders) to test how founder relationship assumptions impacted the genetic characteristics of the population over time (N = 942 unique individuals). We developed a method to combine molecular kinship (using the TrioML estimator), year of birth and trapping location, and integrated the resulting empirical kinship estimates into population management software. We tested the effect of using pedigree data only, versus our integrated approach, on population outcomes. Inbreeding coefficients evaluated using the integrated approach were significantly higher than pedigree-only inbreeding coefficients in the first few years following population establishment. A geographic distanceonly approach showed an association between kinship and probability of successful breeding. Our results show the value in using field and/or molecular data combined with pedigree data in conservation breeding programmes to provide new information for managing crucial populations and improving their success. We caution population managers against commencing expensive conservation breeding programmes in the absence of understanding founder relatedness, especially when wild augmentation is a goal. Long-term costs of assuming founders are unrelated include financial costs, reduced productivity and release of potentially highly inbred individuals.