Methodological Bias in Estimates of Strain Composition and Straying of Hatchery‐Produced Steelhead in Lake Michigan Tributaries

Steelhead Oncorhynchus mykiss were first introduced into the Great Lakes in the late 1800s. Subsequently, natural recruitment of steelhead from spawning runs in streams across the basin has been regularly supplemented by hatchery production of strains derived from widely dispersed locales within the species’ native range. Estimates of hatchery contributions to the spawning runs of naturalized populations may be underrepresented by observations of marked fish, as not all hatchery fish are marked prior to release. To assess the potential bias in estimates of the hatchery contribution to steelhead spawning runs in four major rivers in Michigan, we used scale pattern analysis (SPA) to identify nonmarked hatchery fish and multilocus genotypes to estimate the proportional contributions of each hatchery strain to spawning runs. The four hatchery strains currently stocked are significantly genetically distinct (mean FST = 0.077), making it possible to identify specific strains by use of likelihood‐based assignment tests. The differences between direct (mark observations) and indirect (SPA and genetic analysis) estimates of hatchery contribution were mainly due to variations in the percentage of hatchery fish marked by states prior to release and the potential for confusion between certain marks and injuries. By combining direct and indirect assessment methodologies, we estimated that the percentage of hatchery fish returning to the four rivers ranged from 13% to 31% of total spawning runs. The large contribution of hatchery fish to nonstocked rivers differed significantly from expectations of strain‐specific stocking rates across the Lake Michigan basin and for individual streams, indicating high amounts of straying into Michigan streams.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141020/1/nafm1288.pd

Evidence of Limited Recruitment of Pallid Sturgeon in the Lower Missouri River

Pallid Sturgeon Scaphirhynchus albus are endemic to the Missouri and Mississippi river basins and are rare throughout their range. The species was listed as federally endangered with little to no evidence of natural recruitment. Since population augmentation was initiated as a recovery objective in the early 1990s, thousands of hatchery-origin Pallid Sturgeon have been stocked in the lower Missouri River (Gavins Point Dam [river kilometer 1,305.1] to the confluence of the Mississippi River [river kilometer 0.0]). Efforts to discriminate natural reproduction and recruitment of wild-origin Pallid Sturgeon from hatchery-origin fish has been hampered by tag loss in hatchery-origin sturgeon, inconsistent documentation of hatchery parental crosses, and the failure to collect tissue samples for genotyping all broodstock. However, the recent reconstruction of missing parental genotypes from known hatchery-origin progeny and from cryopreserved milt made it possible to examine Pallid Sturgeon recruitment. Therefore, our objectives were to 1) determine the likelihood that unmarked Pallid Sturgeon captured from the lower Missouri River were the result of natural recruitment and 2) examine the length distribution of wild- and hatchery-origin fish to determine if a difference exists by origin and examine the life-stage distribution. Genetic analysis showed that from 2003 to 2015, 358 ‘‘presumptive wild-origin’’ Pallid Sturgeon were captured in the lower Missouri River and the comparison between the length distributions of wild- and hatchery-origin fish did not provide any additional clarification into potential wildorigin fish. Low recruitment may be due to a small breeding population, high mortality of early life stages, hybridization with Shovelnose Sturgeon Scaphirhynchus platorynchus, or transport of drifting free embryos or larvae into inhospitable habitats. Determining what factors are limiting recruitment is the important next step for the recovery of Pallid Sturgeon in the lower Missouri River

Session B7- Evaluating brook trout genetic response to population isolation

Brook trout (Salvelinus fontinalis) reside in a range of habitats including headwater streams where populations may become periodically isolated. Demographic consequences of population isolation include increased potential for localized extinction. Genetic consequences for population isolation, or populations of sustained small numbers, include increasing susceptibility to inbreeding, the expression of negative fitness traits, and overall loss of genetic variability, which may increase the risk of localized extinction. Reestablishment of connectivity -with larger populations through periodic gene flow into these small populations may act to offset loss of genetic diversity. Restoring population connectivity and degraded headwater habitats, especially those that historically harbored wild brook trout populations has been a focus of restoration efforts. To understand the degree of genetic isolation among headwater brook trout populations, we examined how variability in connectivity between brook trout populations bas resulted in the partitioning of genetic variation within a number of headwater brook trout populations in two locations: Nash Stream, New Hampshire, and Pennsylvania. Both locations bad multiple headwater brook trout populations, but varied by how populations were potentially isolated. In Nash Stream, potential causes of isolation were culverts or waterfalls. In Pennsylvania, isolation could be due to larger geographic distance, culverts or dams, or areas of poor stream quality. In both locations, overall estimates of variation in allele frequency among populations were high, indicating that populations were significantly genetically different, but the effect of the different barrier types varied based on the likely amount of gene flow allowed. For example, in Pennsylvania, significant correlations of genetic diversity were only observed with the presence of impaired stream sections, but not geographic distance or barrier effect. Understanding the effects of barriers on genetic diversity and gene flow can be useful to guide efforts to restore connectivity between populations

Minimal Captive Introgression in Wild Brook Trout (Salvelinus fontinalis) Populations in the Loyalsock Creek Watershed, Pennsylvania

Due to increased anthropogenic pressures on many fish populations, stocking wild populations with hatchery individuals has become a common management practice. Stocking has been the subject of much controversy due, in large part, to the potential for captive individuals to breed with wild stocks. By modulating the abundance of locally adapted gene complexes and introducing maladaptive genotypes, genetic introgression can cause declines in wild population fitness, resiliency, and accelerate local population extirpation. However, the rate of introgression in highly stocked river systems has not been rigorously evaluated, and so the relative risk of genetic erosion from stocking is unknown. We quantified the proportion of introgressed individuals in 30 populations of wild brook trout (Salvelinus fontinalis) distributed throughout the Loyalsock Creek watershed in Pennsylvania. Genetic assignment tests were used to determine the origin (wild vs. captive) for 1748 wild-caught and 300 hatchery brook trout. These assignment tests generated the probability of an individual fish belonging to either a simulated wild or simulated hatchery population. Fish with intermediate probabilities of wild descent were classified as introgressed, with cutoff values determined through simulation of first-generation crosses between wild and hatchery individuals. Even though streams in Loyalsock Creek are annually stocked with high densities of adult trout, we found minimal evidence for genetic introgression in the populations studied. Over 93% of all wild-caught individuals assigned to wild origin, and only 5% of wild-caught fish showed evidence of recent introgression. There was variation in introgression across populations; however, average within-site wild probability was 97%. Our results suggest that introgression with hatchery fish can occur at low rates, even in heavily managed ecosystems. However, results from this study should be viewed cautiously. Higher rates of introgression are not uncommon in other species of salmonids, and introgression may be more common under different environmental conditions. Further, we did not evaluate potential declines in wild brook trout fitness from competition with hatchery individuals, and so negative effects of stocking could still occur despite limited introgression

Data from: Limited hatchery introgression into wild brook trout (Salvelinus fontinalis) populations despite reoccurring stocking

Due to increased anthropogenic pressures on many fish populations, supplementing wild populations with captive-raised individuals has become an increasingly common management practice. Stocking programs can be controversial due to uncertainty about the long-term fitness effects of genetic introgression on wild populations. In particular, introgression between hatchery and wild individuals can cause declines in wild population fitness, resiliency, and adaptive potential, and contribute to local population extirpation. However, low survival and fitness of captive-raised individuals can minimize the long-term genetic consequences of stocking in wild populations, and to date the prevalence of introgression in actively stocked ecosystems has not been rigorously evaluated. We quantified the extent of introgression in 30 populations of wild brook trout (Salvelinus fontinalis) in a Pennsylvania watershed, and examined the correlation between introgression and 11 environmental covariates. Genetic assignment tests were used to determine the origin (wild vs. captive-raised) for 1742 wild-caught and 300 hatchery brook trout. To avoid assignment biases, individuals were assigned to two simulated populations that represented the average allele frequencies in wild and hatchery groups. Fish with intermediate probabilities of wild ancestry were classified as introgressed, with threshold values determined through simulation. Even with reoccurring stocking at most sites, over 93% of wild-caught individuals probabilistically assigned to wild origin, and only 6% of wild-caught fish assigned to introgressed. Models examining environmental drivers of introgression explained less than 3% of the among-population variability, and all estimated effects were highly uncertain. This was not surprising given overall low introgression observed in this study. Our results suggest that introgression of hatchery-derived genotypes can occur at low rates, even in actively stocked ecosystems and across a range of habitats. However, a cautious approach to stocking may still be warranted, as the potential effects of stocking on wild population fitness and the mechanisms limiting introgression are not known

Development and validation of two environmental DNA assays for American Eel (Anguilla rostrata)

Abstract We developed and validated two species‐specific qPCR markers to detect American Eel environmental DNA. Marker validation included assay design, specificity and sensitivity testing, and in vivo laboratory and field experiments. Markers AME1 and AME2 targeted 116 and 129 bp fragments of the mitochondrial NADH dehydrogenase subunit 2 and cytochrome b genes, respectively. Markers were 94%–100% homologous for all 49 aligned American Eel sequences. Specificity tests, with known DNA obtained from 149 individuals spanning 81 fish species, amplified DNA derived from American Eel tissue exclusively. Each marker also had high sensitivity with LOD and LOQ values of 2.8–50 copies. For each marker, pilot testing of American Eel in aquaria at increasing densities (n = 0, 1, 5, 10 eels) showed a significant (p < 0.03) negative relationship between mean qPCR cycle threshold value and number of eels per tank. Our in situ testing of water samples collected from 35 sites on the East Coast (from as far south as Maryland to as far north as Maine) revealed that sites known to contain populations of American Eel (n = 11) were all positive for American Eel DNA, while sites where American Eel were presumed absent (n = 24) failed to amplify American Eel DNA. In three cases, our assays produced positive detections in the lower portion of a watershed but failed to detect American Eel upstream of a presumed impassible barrier in each of the same watersheds (all internal positive controls indicated no evidence of PCR inhibition in our field samples and all negative controls indicated no evidence of contamination). Our encouraging results of in vitro and in situ validation demonstrate the utility of using eDNA as a tool to aid in American Eel conservation efforts