## 4 Discussion
### MAS-Based Walleye Augmentation  
Genetic variants characterizing native populations can be used for marker-assisted selection of broodstock. Microsatellite markers proved useful for distinction of native and non-native broodstock candidates for restoration of Dungeness River, Washington, pink salmon _Oncorhynchus gorbuschu_[30]. Microsatellite variation supported real-time differentiation among threatened summer- and winter-run Hood River, Oregon, steelhead _O. mykiss_ in support of conservation-oriented propagation [31]. Following MAS and hatchery-based augmentation of upper New River walleye, we observed increased frequencies of marker alleles over time (Figure 3). The respective alleles showed differences in the rate of increase. This is because of the frequencies of the respective marker alleles. _Svi17_ more often presented the opportunity for selection of homozyggotes; _Svi33_ being the more variable locus presented less-frequent opportunity to select homozyggotes. Additionally, native walleye were previously collected in fast-moving reaches, considered to be the areas of the upper New River where 'native' genotypes and associated phenotypes would be favored. As marker-assisted selection has progressed, individuals bearing native genotypes are now being collected more frequently in other areas as well, including Claytor Reservoir and Allisonia just upstream, showing that native New River walleye are becoming more frequent across the entire upper New River ecosystem. However, since stocking from multiple outside sources occurred from 1939 to 1997, there is a low likelihood that the upper New River valleye gene pool could ever again be entirely native.  
We observed changes not only in genetic composition, but also in catch-per-unit effort in fall gillnet and spring electrofishing surveys (Figure 4B,C). Decrease in catch rates for valleye, including citation and trophy valleye, after no stocking in 2012-2013, and subsequent recovery after stocking resumed suggest that the native New River valleye population is still dependent upon hatchery-based augmentation. The impoundment of key, rocky reaches of the upper New River by Claytor and Buck dams inundated historic spawning and nursery areas, limiting the ability of the population to once again sustain itself.  
The Virginia Department of Wildlife Resources has practiced marker-assisted selection and hatchery-based augmentation of upper New River valleye since 2001. Our early results with valleye augmentation [9] were such that, although different genetic markers were used, marker-assisted selection was adopted as an approach to restoration of native valleye populations in West Virginia [32], Kentucky [33], and Missouri [34]. The Virginia program being the longest-running program of MAS for valleye, an evaluation of its efficacy over the time series is appropriate. While a demographic boost of valleye numbers in the upper New River was demonstrated, we found that it has not led to a heightened level of natural reproduction sufficient to maintain the native upper New River valleye population. The walleye augmentation program adopted the practice of not reusing broodstock and of using multiple males to fertilize each female's egg lot to limit the likelihood of genetic bottleneck or inbreeding. The frequencies of different degrees of relatedness among individuals (full-sib, half-sib, and parent-offspring) within the augmented New River population resemble those seen in other valleye populations ([35], Chapter 2), although use of just eight microsatellite loci for relatedness assessment limits our confidence in these estimates. The inbreeding coefficient \(F_{\text{IS}}\) for New River valleye is the lowest among 38 populations examined [36]. Walleye in the New River have estimated effective population size, \(N_{\text{e}}\), values typical of other walleye populations examined [36]. Hence, we see no evidence of realization of a Ryman and Laikre [37] effect due to over-representation of hatchery-produced families within the augmented population.