Effective population size and Ne/N ratio for two populations of Northern chamois (Rupicapra rupicapra) on the edge of the species’ distribution range

Abstract Background Effective population size (N e ) is a fundamental parameter in conservation genetics, providing relevant information on the adaptability and long-term viability of populations. In contrast, wildlife management strategies, particularly for hunted species, often rely on estimates of abundance (N) without incorporating genetic data. Accounting for N e in wildlife management concepts could add important information on population viability, especially for species that are regulated mainly by humans. The iconic mountain dwelling chamois (Rupicapra rupicapra ) is widespread throughout the Alps, and many populations are influenced by human activities, including hunting. Results We derived N e using genetic data from 16 microsatellite loci for two chamois populations in the Bavarian Alps, Germany. Estimates of N based on Bayesian spatial capture-recapture (SCR) from a previous study allowed us to calculate the N e /N ratio. N e values per generation in the two study areas were 514 (CI 342–949) and 179 (CI 129–266). Estimated median N e /N ratios were similar in both study areas but had large confidence intervals: 0.56 (CI 0.34–0.96) and 0.58 (CI 0.39–0.88). Confidence intervals of N e estimates varied between the two study areas, and sample size had a substantial influence on the precision of the estimates, as expected from previous studies. We discuss the challenges in obtaining robust N e /N estimates, which are crucial when N e and N are applied for conservation purposes. Conclusion N e /N ratios were similar between the two study areas, but confidence intervals were wide, reflecting substantial uncertainty. Even with extensive data, accurately estimating these ratios remains challenging, highlighting potential limitations for their use in population monitoring and management.