Admixture and reproductive skew shape the conservation value of ex situ populations of the Critically Endangered eastern black rhino - microsatellite and mitochondrial genotype data

Small populations of endangered species risk losing already eroded genetic diversity, important for adaptive potential, through the effects of genetic drift. The magnitude of drift can be mitigated by maximising the effective population size, as is the goal of genetic management strategies. Different mating systems, specifically those leading to reproductive skew, exacerbate genetic drift by distorting contributions. In the absence of an active management strategy, reproductive skew will have long-term effects on the genetic composition of a population, particularly where admixture is present. Here we examine the contrasting effects of conservation management strategies in two ex situ populations of the Critically Endangered eastern black rhino (Diceros bicornis michaeli), one managed as a semi-wild population in South Africa (SAx), and one managed under a mean-kinship breeding strategy in European zoos. We use molecular data to reconstruct pedigrees for both populations and validate th..., Samples were collected from zoo animals, between 2017 and 2021, using non-invasive nasal swabs (N=75), or whole blood (N=10) where this could be obtained opportunistically. One muscle tissue sample from a deceased animal, preserved in 2ml absolute ethanol at -20°C, was also included. Nasal swabs were preserved using silica gel at room temperature and blood samples collected in EDTA tubes were frozen at -20°C. From the SAx population we extracted DNA from pinna offcuts preserved in sodium chloride. These were obtained during routine ear-notching operations performed to facilitate individual animal identification on the reserve. Samples used in this study dated up to 2018, but samples from historic assignments and some adults were not available. We sampled approximately 80% of the SAx and 85% of the Zoo population.
DNA was extracted using a QIAamp DNA mini kit (QIAGEN GMBH, Hilden, Germany). Mitochondrial DNA was amplified using D-loop primers mt15996L and mt16502H following Moodley et al..., , # Admixture and reproductive skew shape the conservation value of ex situ populations of the Critically Endangered eastern black rhino - microsatellite and mitochondrial genotype data

[https://doi.org/10.5061/dryad.69p8cz97p](https://doi.org/10.5061/dryad.69p8cz97p)

Mitochondrial d-loop genotypes and microsatellite genotypes for two *ex situ* populations of the Critically Endangered eastern black rhino. These were used to reconstruct the pedigree of a free-living population and predict the effectiveness of different management strategies at preserving genetic diversity.

## Description of the data and file structure

The first column carries the population identifier. The SAx population is freely mixing with natural mate choice and little intervention. Zoo animals are managed under the eastern black rhino EEP in European zoos. The next three columns include individual information. mtDNA haplotypes are included for all animals genotyped. Microsatellites genotypes are presented as two c...