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Quantifiable measurement of habitat restoration effects on salmonid reproductive performance is limited, although it is necessary for evaluating whether population responses follow management actions. We investigated using close‐kin mark‐recapture methods to partition restoration effects within standard monitoring metrics of juvenile emigrants leaving the natal reach. This approach allowed for statistical comparison of relative juvenile capture rates (recruitment) from Chinook Salmon (Oncorhynchus tshawytscha) naturally reproducing in gravel augmented (restored) and nonaugmented (unrestored) reaches of a highly managed California River. Genetic parentage techniques linked adult females that had spawned in augmented and nonaugmented spawning habitats with juvenile Chinook Salmon sampled the following spring at a trap located below the natal spawning area. Successful recruitment was documented from both augmented and nonaugmented habitats, with no statistical difference between the two habitat types. The capture rate per adult female was low (0.19–0.24 juveniles/female) compared to rates observed in other systems. Within the juvenile collections, most females in the study had 0 or 1 offspring observed; however, one female that spawned in a restored habitat had 25 offspring recovered at the trap. We modeled juvenile capture rates in relation to a range of biological and environmental variables including spawning habitat site, spawning habitat treatment (augmented and nonaugmented), annual spawner abundance, year spawned, female fork length, spawning and hatch day, and flow maximum and variance. There was an inverse relationship between annual adult abundance (escapement obtained from carcass surveys) and recruitment (juvenile recoveries at trap), suggesting habitat limitation may be creating density‐dependent effects. Additionally, female body size was positively associated with recruitment, while spawning day and mean daily temperature were inversely associated with recruitment, suggesting that both biological and environmental factors independent of habitat influenced reproduction potential. This study provides evidence that habitat restoration could have an additive (incremental) positive effect on recruitment rate, informing hatchery management and restoration activities related to population recovery. [ABSTRACT FROM AUTHOR]

Environmental DNA (eDNA) detection methods can complement traditional biomonitoring to yield new ecological insights in aquatic systems. However, the conceptual and methodological frameworks for aquatic eDNA detection and interpretation were developed primarily in freshwater environments and have not been well established for estuaries and marine environments that are by nature dynamic, turbid, and hydrologically complex. Environmental context and species life history are critical for successful application of eDNA methods, and the challenges associated with eDNA detection in estuaries were the subject of a symposium held at the University of California Davis on January 29, 2020 (https://marinescience.ucdavis.edu/engagement/past-events/edna). Here, we elaborate upon topics addressed in the symposium to evaluate eDNA methods in the context of monitoring and biodiversity studies in estuaries. We first provide a concise overview of eDNA science and methods, and then examine the San Francisco Estuary (SFE) as a case study to illustrate how eDNA detection can complement traditional monitoring programs and provide regional guidance on future potential eDNA applications. Additionally, we offer recommendations for enhancing communication between eDNA scientists and natural resource managers, which is essential for integrating eDNA methods into existing monitoring programs. Our intent is to create a resource that is accessible to those outside the field of eDNA, especially managers, without oversimplifying the challenges or advantages of these methods. [ABSTRACT FROM AUTHOR]

Introductions of non-native fish have the potential to cause substantial economic and ecological losses. In the western United States, non-native brook trout (Salvelinus fontinalis) are widely established and pose a threat to the persistence of bull trout (Salvelinus confluentus), a native char listed as threatened under the US Endangered Species Act, due to competition and hybridization. With brook trout identified as a factor limiting the recovery of ESA-listed bull trout in the Malheur Watershed of eastern Oregon, managers are pursuing brook trout eradication efforts. Key to the eradication efforts is reliable monitoring to ensure success. Traditional monitoring practices have included mechanical sampling methods such as seining, netting, and electrofishing, all of which are labor intensive and limited in reliability. Environmental DNA (eDNA) is genetic material naturally shed by organisms that can be found in bulk environmental samples without isolating individual organisms. Sampling for eDNA can often be done with less time and expense than traditional methods, making it ideal for effectiveness monitoring following fish eradication efforts. This study placed a single fish in a live-car where the species was not otherwise present and used eDNA sampling to infer the likelihood of detection downstream. Results suggest that a single fish can be detected reliably up to 500 m downstream when multiple samples are taken. This eDNA sampling method provides managers with the ability to conduct eradication effectiveness monitoring reliably and rapidly and may also be used to detect new fish invasions as well as rare or cryptic species. [ABSTRACT FROM AUTHOR]

The Giant Gartersnake (Thamnophis gigas) is a low density visually evasive species with a low detection probability based on standard field survey methods (e.g., traps, visual census). Habitat loss has resulted in extirpations or serious declines for T. gigas populations throughout the southern two thirds of its historic range. Uncertainty regarding its current distribution and occupancy present management challenges for the species. Enhancing survey sensitivity through development of environmental DNA sampling (eDNA) methods would improve compliance monitoring under the Endangered Species Act, recovery planning for T. gigas, and evaluation of California’s Central Valley tule marsh habitat on which this species depends. To address these needs, we designed and validated diagnostic quantitative Polymerase Chain Reaction (qPCR) assays for identifying portions of the Cytochrome B (CytB) and the Nicotinamide adenine dinucleotide (NADH) dehydrogenase subunit 4 (ND4) genes of the T. gigas mitochondrial genome. The designed ND4 qPCR assay was not specific to T. gigas DNA and amplified DNA from a closely related and spatially co-occurring Thamnophis species (T.s. fitchi). The CytB T. gigas qPCR assay proved specific to a species level with a sensitivity that reliably detected T. gigas DNA at a concentration of 2.0x10-5 ng μL-1. To assess detection range, coordinated field sampling was conducted at aquatic sites with an observed and documented population of T. gigas. The T. gigas qPCR assay reliably detected DNA from samples taken 300m downstream from the known source. We then used environmental eDNA sampling and qPCR analysis to augment unsuccessful trap surveys in the southern range of T. gigas and detected DNA in 28 of the 52 locations sampled, confirming that T. gigas was still present at some sites where physical trapping failed to identify presence. QPCR-based DNA detection coupled with eDNA sampling methods provides an effective means to obtain critical population metrics from this otherwise cryptic, federally protected and hard to study organism, offering great promise for elucidating patterns of occupancy with greater efficiency and at far less cost than trapping methods, particularly where detection probabilities are low. [ABSTRACT FROM AUTHOR]

Delta Smelt have collapsed demographically, but little is known about their current genetic status. We used 12 microsatellite loci to evaluate two measures of the effective population size (Ne) of Delta Smelt. Ne is a measure that offers predictive power regarding the loss of genetic diversity in a population over time, as well as the short and long-term genetic risks for loss of fitness resulting from low diversity. We found that the Ne of Delta Smelt is too high to accurately estimate with the data (upper 95% confidence intervals were infinity), but the lower confidence intervals of NeLD (linkage disequilibrium Ne) were above 1,000, while some of the lower confidence intervals of NeV (variance Ne) were below 1,000. We interpret this to indicate that Delta Smelt are not declining because of genetic factors, and are not at immediate risk of losing genetic diversity from low Ne. We caution that these estimates are from a shortterm data set estimated from a population that has already been declining for decades, and that it is likely that Delta Smelt have lost diversity. We suggest continuing efforts to maximize abundance to prevent further loss of genetic diversity. [ABSTRACT FROM AUTHOR]

Environmental DNA (eDNA) is an emerging sampling method that has been used successfully for detection of rare aquatic species. The Identification of sampling tools that are less stressful for target organisms has become increasingly important for rare and endangered species. A decline in abundance of the Southern Distinct Population Segment (DPS) of North American Green Sturgeon located in California’s Central Valley has led to its listing as Threatened under the Federal Endangered Species Act in 2006. While visual surveys of spawning Green Sturgeon in the Central Valley are effective at monitoring fish densities in concentrated pool habitats, results do not scale well to the watershed level, providing limited spatial and temporal context. Unlike most traditional survey methods, environmental DNA analysis provides a relatively quick, inexpensive tool that could efficiently monitor the presence and distribution of aquatic species. We positively identified Green Sturgeon DNA at two locations of known presence in the Sacramento River, proving that eDNA can be effective for monitoring the presence of adult sturgeon. While further study is needed to understand uncertainties of the sampling method, our study represents the first documented detection of Green Sturgeon eDNA, indicating that eDNA analysis could provide a new tool for monitoring Green Sturgeon distribution in the Central Valley, complimenting traditional on-going survey methods. [ABSTRACT FROM AUTHOR]

AbstractWe compared a length-at-date growth model to truss network (morphometric) models for classifying emigrating juvenile (age 0 through age 1) California Central Valley Chinook SalmonOncorhynchus tshawytschato three genetically identified races at upstream (salmon generally younger and smaller) and downstream (salmon generally older and larger) monitoring stations. Morphometric models including capture date and head to standard length ratio performed better than the growth model at distinguishing genetically assigned fall-run and late fall-run juveniles; prediction accuracy increased from 54.6% to 63.8% for upstream salmon and from 17% to 73% for downstream salmon. The growth model may over inflate downstream estimates of federally listed Chinook Salmon by misidentifying fall and late-fall runs (nonlisted) as winter and spring runs (both listed) as much as 83% of the time. Morphometric models did not improve run assignment for the listed runs; the growth model outperformed morphometric models at downstream stations. Morphometric models including head shape and sample date had similar accuracy measures to models, including multiple fish measurement ratios, suggesting head shape is the strongest predictor of the juvenile Central Valley Chinook Salmon race. Our results indicate morphometric modeling can improve identification of nonlisted juvenile Central Valley Chinook Salmon from federally listed runs, potentially benefitting monitoring, water management, and protection of sensitive species. Received May 5, 2014; accepted August 13, 2014 [ABSTRACT FROM AUTHOR]

Due to the challenges associated with monitoring in riverine environments, unbiased and precise spawner abundance estimates are often lacking for populations of Pacific salmonOncorhynchusspp. listed under the Federal Endangered Species Act. We investigated genetic approaches to estimate the 2009 spawner abundance for a population of Columbia River Chinook SalmonOncorhynchus tshawytschavia genetic mark–recapture and rarefaction curves. The marks were the genotyped carcasses collected from the spawning area during the first sampling event. The second sampling event consisted of a collection of juveniles from a downstream migrant trap located below the spawning area. The parents that assigned to the juveniles through parentage analysis were considered the recaptures, which was a subset of the genotypes captured in the second sample. Using the Petersen estimator, the genetic mark–recapture spawner abundance estimates based on the binomial and hypergeometric models were 910 and 945 Chinook Salmon, respectively. These results were in agreement with independently derived spawner abundance estimates based on redd counts, area-under-the-curve methods, and carcass tagging based on the Jolly–Seber model. Using a rarefaction curve approach, which required only the juvenile offspring sample, our estimate of successful breeders was 781 fish. Our genetic-based approaches provide new alternatives to estimate adult Pacific salmon abundance in challenging environmental conditions or for populations with poor or unknown estimates of precision. Received December 7, 2012; accepted July 17, 2013 [ABSTRACT FROM AUTHOR]

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We used pattern recognition algorithms and image processing to identify individual Chinook salmon Oncorhynchus tshawytscha. Using melanophore spot patterns located on the dorsal head region, algorithms ranked all database images against each other. We coupled this technology with a graphical user interface to visually confirm or reject top-ranked algorithm results and tested this process on 295 juvenile Chinook salmon in seven photo sessions over a 251-d period. Juveniles began developing spots, identifiable in photo images, between 167 and 197 d after conception (52.7-mm fork length [FL]). Unique spot patterns appeared 197–232 d from conception, beginning at approximately 104-mm FL. Of 254 fish surviving the experimental period, 106 (42%) demonstrated identifiable patterns, 102 (40%) developed spots but patterns were insufficient for identification, and 46 (18%) exhibited a complete lack of spots. Spot patterns continued developing on individual fish by study end. On average, fish that developed recognizable spot patterns did so at approximately 140-mm FL. Once they did, reidentification was 100% correct in up to four subsequent trials. Patterns remained identifiable even after a 25–32% size increase over a 55-d period and as juveniles went through smoltification. Although patterns occurred at sizes typically larger than salmon observed at some California Central Valley monitoring locations, this technique provides a potentially valuable, noninvasive method of identifying individual salmon during emigration. Improved image collection techniques and use of body areas exhibiting identifiable patterns at earlier developmental stages may increase fish available for pattern identification. These results demonstrate the indexing of a large database using pattern recognition algorithms for Chinook salmon. The utility of such an approach may be valuable for addressing specific biological questions associated with mass-produced (wild and hatchery), migratory salmonids, especially as individuals develop, grow, and move through the various habitats available to them. Received November 21, 2011; accepted March 22, 2012 [ABSTRACT FROM AUTHOR]

It is widely recognized that genetic diversity within species is shaped by dynamic habitats. The quantitative and molecular genetic patterns observed are the result of demographics, mutation, migration, and adaptation. The populations of rainbow trout Oncorhynchus mykiss in the Columbia River basin (including both resident and anadromous forms and various subspecies) present a special challenge to understanding the relative roles of those factors. Standardized microsatellite data were compiled for 226 collections (15,658 individuals) from throughout the Columbia and Snake River basins to evaluate the genetic patterns of structure and adaptation. The data were primarily from fish of the anadromous life history form, and we used a population grouping procedure based on principal components and hierarchical k-means clustering to cluster populations into eight aggregates or groups with similar allele frequencies. These aggregates approximated geographic regions, and the two largest principal components corresponded to ancestral lineages of Sacramento redband trout O. m. stonei, coastal rainbow trout O. m. irideus, and interior Columbia River redband trout O. m. gairdneri. Genetic data were partitioned among primary aggregates (lower Columbia, middle–upper Columbia, and Snake rivers), and the magnitude of genetic divergence relative to genetic diversity was analyzed (per locus) to test for evidence of selection and subsequent signals of adaptation. Two loci showed higher divergence than expected by chance (i.e., positive selection); however, both of these loci were on the fringe of the 99% confidence level and are potential false positives. Genetic patterns were also significantly correlated with certain environmental and habitat parameters (e.g., precipitation), but the extent to which those correlations are causal as opposed to effectual remains unclear. Despite the remaining questions, these data provide a foundation for more detailed investigations of harvest, admixture, and introgression between hatcheryand natural-origin fish and differences in reproductive success among individuals as well as monitoring trends in productivity. [ABSTRACT FROM AUTHOR]

Stochastic fluctuation in allele frequencies may reflect microevolutionary processes responsible for genetic change, such as small effective population size ( Ne), which is a legitimate concern for imperiled populations affected by environmental or anthropogenic factors. In salmonids, recent empirical studies have provided conflicting results regarding the consistency of within-population genetic variation over time. In the present study, we surveyed the genetic variation at 14 microsatellite loci in two endemic populations of summer steelhead (Tucannon and Touchet) for seven consecutive years and the Lyons Ferry Hatchery stock (LFH) for 4 years. The LFH (mitigation) stock is used to enhance fishing opportunities in southeastern Washington State and not to aid in the recovery of natural populations. We observed statistically significant differences in allele frequencies between replicated collections from the same location. One of twenty-one genic tests for the Tucannon River collections, 9 of 21 genic tests for the Touchet River collections, and all genic tests regarding LFH collections were statistically significant. Temporal variation was larger than spatial variation (0.86% and 0.44%, respectively). We also used genetic data to infer effective population sizes for natural steelhead populations and the LFH mitigation hatchery stock, with point estimates of 729.7, 599.4, and 266.7 for the Tucannon, Touchet, and LFH populations, respectively. Despite the temporal variation observed, relative genetic differentiation was stable over time, replicated collections tending to cluster together in factorial correspondence analyses of allele frequency data. However, the genetic data were consistent with the potential for gene flow between the Tucannon River and LFH populations. The potential benefits of stocking genetically differentiated hatchery fish to enhance fishing opportunities in the Tucannon River may be offset by the negative effects of hatchery introgression and the small Ne in hatchery fish. [ABSTRACT FROM AUTHOR]

Microsatellites, which have rapidly become the preferred markers in population genetics, reliably assign individual chinook salmon to the winter, fall, late-fall, or spring chinook runs in the Sacramento River in California's Central Valley (Banks et al. 2000<$REFLINK>. Can. J. Fish. Aquat. Sci. 57:915–927). A substantial proportion of this discriminatory power comes from Ots-2, a simple CA repeat, which is expected to evolve rapidly under the stepwise mutation model. We have sequenced a 300-bp region around this locus and typed 668 microsatellite-flanking sequence haplotypes to explore further the basis of this microsatellite divergence. Three sites of nucleotide polymorphism in the Ots-2 flanking sequence define five haplotypes that are shared by the Californian and Canadian populations. The Ots-2 microsatellite alleles are nonrandomly distributed among these five haplotypes in a pattern of gametic disequilibrium that is also shared among populations. Divergence between the winter run and other Central Valley stocks appears to be caused by a combination of surprisingly static evolution at Ots-2 within a context of more rapidly changing haplotype frequencies. [ABSTRACT FROM PUBLISHER]