High-throughput DNA metabarcoding of mitochondrial 12S rRNA and Cyt b gene sequences was coupled with a morphology-based identification tool to assess ichthyoplankton community structure in Oujiang River Estuary, China. The performances of 12S and Cyt b barcoding markers were compared in terms of taxonomic resolution, detection and coverage, and their suitability was established for use as a quick and powerful ichthyoplankton assessment tool. A total of 30,138 ichthyoplankton (2462 eggs and 27,676 larvae) samples were collected from April to August 2015 and identified to 145 taxa belonging to 57 families and 105 genera. June and July were the main spawning months. Ichthyoplankton were more abundant around Lingkun and Qidu Islands and the upper parts of Oujiang River Estuary. The 12S gene marker presented higher species coverage and detection rate than Cyt b. DNA metabarcoding exhibited more representative species identification power than morphology. The findings reported in this study provided a key attempt towards the development of time-efficient and cost-effective ichthyoplankton identification and assessment tool.

The woundfin Plagopterus argentissimus is imperiled as a result of habitat destruction, water diversion, and the introduction of nonnative species. Augmentation of wild woundfin populations in the Utah portion of the Virgin River with fish from Dexter National Fish Hatchery and Technology Center (Dexter Hatchery) began in 2003. We used 10 microsatellite DNA loci to determine whether captive woundfins are contributing to recruitment in the Virgin River. Admixture analyses based on moment estimators, maximum likelihood, frequency, and Bayesian approaches indicated that the genetic contribution of Dexter Hatchery's woundfin augmentation stocking to 2005 recruitment in the Virgin River was 35–46% in the Washington Fields Diversion reach and 43–59% in the area of the Quail Creek Reservoir inflow. Salvaged wild parental stock was mixed with the captive broodstock at Dexter Hatchery in 2004 and had a genetic contribution of 26–49% to the offspring reared at Dexter Hatchery in 2005. Care must be taken to ensure the genetic integrity of stocked fish as the potential impact on the augmented population can be substantial. These results demonstrate that genetic markers used to infer gene flow (via admixture analysis) from the captive population to the wild population can be applied to determine the effectiveness of hatchery propagation programs and to monitor genetic similarity between wild and stocked fish.