A case for genetic parentage assignment in captive group housing

Captive animals are commonly housed in groups to make efficient use of limited resources and allow for natural social behaviour. Captive management relies on accurate pedigrees to estimate various population genetic parameters, such as genetic contributions of breeders, but pedigrees of group-housed offspring can be uncertain. Pedigree analysis software incorporates genetic information from multiple putative parents (“MULT”). Molecular pedigree reconstruction to resolve pedigree uncertainties can be costly. We quantify the need for molecular parentage assignment by comparing predicted offspring contributions (based on uncertain “MULT” pedigrees) to contributions obtained from a molecular genetic pedigree reconstruction. Parentage of 81 insurance population Tasmanian devils (Sarcophilus harrisii) born in free-range enclosures from 2011 to 2017 was resolved using 891 single nucleotide polymorphisms. We observed large discrepancies between the MULT pedigree and molecular pedigree data, revealing both overestimates and underestimates of genetic contributions of individuals, and different pedigree-based effective population sizes (102 vs. 158 respectively). The molecular data revealed that reproductive skew (proportion of adults that failed to breed) was high for both sexes. Over half of the wild-born individuals in our dataset were found to have not bred. If undetected, variation in breeding success undermines the utility of pedigree management and may threaten the success of captive breeding. Molecular techniques are increasingly cost-effective, and our data demonstrate that they are critical to devil management. Where feasible, we recommend molecular management of group-housed species in captivity to avoid inaccurate estimates of genetic diversity and to identify non-breeding individuals, in particular founders, for targeted breeding.