A next-generation genotyping process to balance demographic goals and genetic health for the Paddlefish (Polyodon spathula)

Abstract Captive rearing and reintroduction programs are essential for many wild populations, but they are often associated with negative genetic outcomes, including the loss of diversity and adaptation to captivity. Optimizing practices to prevent negative impacts to wild populations requires accurate and cost-effective genetic monitoring. We developed and tested a microsatellite panel for Paddlefish ( Polyodon spathula ) designed for next generation sequencing. We then used the panel to evaluate the genetic diversity of paddlefish stocked in 2022 and compared results to a similar investigation from 2017, when the hatchery released paddlefish at a later stage in development. The new panel successfully assigned parentage to the 2022 broodstock parents ( n = 29) and a sample of their offspring ( n = 250). Fifty markers satisfied our error rate threshold (< 0.25) and Hardy-Weinberg Equilibrium expectations in two wild populations. Comparison of 2022 results to results from 2017 suggest that earlier stocking increases the effective to census population size ratio ( N e / N ) of the captive population and likely reduces adaptation to captivity. Our genotyping method circumvented complex bioinformatics tasks typically required to filter out paralogous loci in species with recent genome duplications, like Paddlefish. Further, the use of existing bioinformatics tools and maximum likelihood assignment methods that allow genotyping error made genotyping and assignment easy to implement quickly for conservation and management investigations.