Genetic structure and diversity in wild populations of the Light-footed Ridgway’s Rail reflect 20 years of augmentation through captive breeding and release

Captive breeding and release programs aimed at recovery of rare species can be informed by genetic data to help select high-diversity source populations, make pairing decisions to minimize inbreeding, and manage release strategies. We developed a set of 54 microsatellite loci to assess genetic structure and diversity across the United States range of the Light-footed Ridgway’s Rail (Rallus obsoletus levipes), a federally endangered marsh bird for which populations have been augmented by a captive breeding program annually since 2001. We identified three regional genetic clusters, with the highest genetic diversity reported in the central cluster, which included all sampled wetlands in north San Diego County. Recent (2019–24) captive-breeding adults all clustered within the northernmost cluster (Orange and Ventura Counties), which was expected given that this cluster included the source wetland for the captive breeding program. Gene flow rates, which approximate the proportions of individuals in a population originating from other populations, were relatively high among clusters (4–24 percent) and may have been enhanced through the release of captive-bred rails. Based on the genetic data analyzed in a genetic rescue decision framework, sourcing new breeding birds from the north San Diego County cluster could provide the greatest genetic diversity benefits. The northernmost cluster, which included Mugu Lagoon and all sampled Orange County wetlands, was considered the most in need of genetic rescue. Recent breeding pairs in the captive breeding program have comparatively low diversity and high interrelatedness. Sourcing birds from wetlands with high genetic diversity and population sizes, assessing genetic relatedness before pairing, and focusing releases in areas that have low estimates of genetic diversity could improve the distribution of genetic diversity across wild populations in the future.