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  1. Article ; Online: Evaluating environmental DNA detection of a rare fish in turbid water using field and experimental approaches

    Ann E. Holmes / Melinda R. Baerwald / Jeff Rodzen / Brian M. Schreier / Brian Mahardja / Amanda J. Finger

    PeerJ, Vol 12, p e

    2024  Volume 16453

    Abstract: Detection sensitivity of aquatic species using environmental DNA (eDNA) generally decreases in turbid water but is poorly characterized. In this study, eDNA detection targeted delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish ...

    Abstract Detection sensitivity of aquatic species using environmental DNA (eDNA) generally decreases in turbid water but is poorly characterized. In this study, eDNA detection targeted delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish associated with turbid water. eDNA sampling in the field was first paired with a trawl survey. Species-specific detection using a Taqman qPCR assay showed concordance between the methods, but a weak eDNA signal. Informed by the results of field sampling, an experiment was designed to assess how turbidity and filtration methods influence detection of a rare target. Water from non-turbid (5 NTU) and turbid (50 NTU) estuarine sites was spiked with small volumes (0.5 and 1 mL) of water from a delta smelt tank to generate low eDNA concentrations. Samples were filtered using four filter types: cartridge filters (pore size 0.45 μm) and 47 mm filters (glass fiber, pore size 1.6 μm and polycarbonate, pore sizes 5 and 10 μm). Prefiltration was also tested as an addition to the filtration protocol for turbid water samples. eDNA copy numbers were analyzed using a censored data method for qPCR data. The assay limits and lack of PCR inhibition indicated an optimized assay. Glass fiber filters yielded the highest detection rates and eDNA copies in non-turbid and turbid water. Prefiltration improved detection in turbid water only when used with cartridge and polycarbonate filters. Statistical analysis identified turbidity as a significant effect on detection probability and eDNA copies detected; filter type and an interaction between filter type and prefilter were significant effects on eDNA copies detected, suggesting that particulate-filter interactions can affect detection sensitivity. Pilot experiments and transparent criteria for positive detection could improve eDNA surveys of rare species in turbid environments.
    Keywords Conservation ; Delta smelt ; Endangered species ; Estuary ; Environmental DNA ; Particulate matter ; Medicine ; R ; Biology (General) ; QH301-705.5
    Subject code 333
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher PeerJ Inc.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Captive-reared Delta Smelt (Hypomesus transpacificus) exhibit high survival in natural conditions using in situ enclosures.

    Melinda R Baerwald / Nicole Kwan / Catarina Pien / Grace Auringer / Evan W Carson / Dennis E Cocherell / Luke Ellison / Nann A Fangue / Amanda J Finger / Daphne A Gille / Haley Hudson / Tien-Chieh Hung / Ted Sommer / Troy Stevenson / Brian M Schreier

    PLoS ONE, Vol 18, Iss 5, p e

    2023  Volume 0286027

    Abstract: Conservation of endangered fishes commonly includes captive breeding, applied research, and management. Since 1996, a captive breeding program has existed for the federally threatened and California endangered Delta Smelt Hypomesus transpacificus, an ... ...

    Abstract Conservation of endangered fishes commonly includes captive breeding, applied research, and management. Since 1996, a captive breeding program has existed for the federally threatened and California endangered Delta Smelt Hypomesus transpacificus, an osmerid fish endemic to the upper San Francisco Estuary. Although this program serves as a captive refuge population, with experimental releases being initiated to supplement the wild population, it was uncertain how individuals would survive, feed, and maintain condition outside hatchery conditions. We evaluated this and the effects of three enclosure designs (41% open, 63% open, and 63% open with partial outer mesh wrap) on growth, survival, and feeding efficacy of cultured Delta Smelt at two locations (Sacramento River near Rio Vista, CA and in Sacramento River Deepwater Ship Channel) in the wild. Enclosures exposed fish to semi-natural conditions (ambient environmental fluctuations and wild food resources) but prevented escape and predation. After four weeks, survival was high for all enclosure types (94-100%) at both locations. The change in condition and weight was variable between sites, increasing at the first location but decreasing at the second location. Gut content analysis showed that fish consumed wild zooplankton that came into the enclosures. Cumulatively, results show that captive-reared Delta Smelt can survive and forage successfully when housed in enclosures under semi-natural conditions in the wild. When comparing enclosure types, we observed no significant difference in fish weight changes (p = 0.58-0.81 across sites). The success of housing captive-reared Delta Smelt in enclosures in the wild provides preliminary evidence that these fish may be suitable to supplement the wild population in the San Francisco Estuary. Furthermore, these enclosures are a new tool to test the efficacy of habitat management actions or to acclimate fish to wild conditions as a soft release strategy for recently initiated supplementation efforts.
    Keywords Medicine ; R ; Science ; Q
    Subject code 333
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: Seasonal floodplain‐tidal slough complex supports size variation for juvenile Chinook salmon (Oncorhynchus tshawytscha)

    Goertler, Pascale A.L / Brian M. Schreier / Ted R. Sommer / William H. Satterthwaite

    Ecology of freshwater fish. 2018 Apr., v. 27, no. 2

    2018  

    Abstract: Population diversity is a mechanism for resilience and has been identified as a critical issue for fisheries management, but restoration ecologists lack evidence for specific habitat features or processes that promote phenotypic diversity. Since habitat ... ...

    Abstract Population diversity is a mechanism for resilience and has been identified as a critical issue for fisheries management, but restoration ecologists lack evidence for specific habitat features or processes that promote phenotypic diversity. Since habitat complexity may affect population diversity, it is important to understand how population diversity is partitioned across landscapes and among populations. In this study, we examined life history diversity based on size distributions of juvenile Central Valley Chinook salmon (Oncorhynchus tshawytscha) within the Yolo Bypass, a remnant transitional habitat from floodplain to tidal sloughs in the upper San Francisco Estuary (SFE). We used a generalized least squares model with an autoregressive (AR1) correlation structure to describe the distribution of variation in fish size from 1998 to 2014, and tested the effect of two possible drivers of the observed variation: (i) environmental/seasonal drivers within the Yolo Bypass, and (ii) the juvenile Chinook source population within the Sacramento River and northern SFE. We found that the duration of floodplain inundation, water temperature variation, season, and sampling effort influenced the observed time‐specific size distribution of juvenile Chinook salmon in the Yolo Bypass. Given the lack of seasonally inundated habitat and low thermal heterogeneity in the adjacent Sacramento River, these drivers of juvenile size diversification are primarily available to salmon utilizing the Yolo Bypass. Therefore, enhancement of river floodplain‐tidal slough complexes and inundation regimes may support the resilience of imperiled Central Valley Chinook salmon.
    Keywords estuaries ; fisheries management ; floodplains ; habitats ; juveniles ; landscapes ; life history ; models ; Oncorhynchus tshawytscha ; phenotypic variation ; rivers ; salmon ; water temperature ; Sacramento River
    Language English
    Dates of publication 2018-04
    Size p. 580-593.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 913011-1
    ISSN 0906-6691
    ISSN 0906-6691
    DOI 10.1111/eff.12372
    Database NAL-Catalogue (AGRICOLA)

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  4. Article: Rearing and migration of juvenile Chinook salmon (Oncorhynchus tshawytscha) in a large river floodplain

    Takata, Lynn / Ted R. Sommer / J. Louise Conrad / Brian M. Schreier

    Environmental biology of fishes. 2017 Sept., v. 100, no. 9

    2017  

    Abstract: Off-channel habitat has become increasingly recognized as key for migratory fishes such as juvenile Chinook salmon (Oncorhynchus tshawytscha). Hence, floodplain habitat has been identified as critical for the continued persistence of California’s ... ...

    Abstract Off-channel habitat has become increasingly recognized as key for migratory fishes such as juvenile Chinook salmon (Oncorhynchus tshawytscha). Hence, floodplain habitat has been identified as critical for the continued persistence of California’s Central Valley salmon, particularly the Yolo Bypass, the primary floodplain of the Sacramento River. To provide insight into factors supporting juvenile salmon use of this 240 km², partially leveed floodplain, we examined inter- and intra-annual relationships between environmental correlates and residency time, apparent growth, emigration, migratory phenotype, and survival over more than a decade for natural-origin (“wild”) fish and experimentally-released hatchery fish. Flood duration was positively associated with hatchery juveniles residing longer and achieving larger size. Wild juveniles grew larger and emigrated later with cumulative temperature experience (accumulated thermal units) and warmer average annual temperatures during flood years. Within years, both wild and hatchery salmon departed the floodplain as flood waters receded. Parr-sized juveniles dominated outmigrant composition, though fry and smolt-sized juveniles were also consistently observed. Survival to the ocean fishery was not significantly different between hatchery fish that reared in the Yolo Bypass versus those that reared in the main stem Sacramento River. Our study indicates improved frequency and duration of connectivity between the Sacramento River and the Yolo Bypass could increase off-channel rearing opportunities that expand the life history diversity portfolio for Central Valley Chinook salmon.
    Keywords Oncorhynchus tshawytscha ; fisheries ; floodplains ; habitats ; hatcheries ; heat sums ; juveniles ; life history ; migratory behavior ; phenotype ; rearing ; rivers ; salmon ; temperature ; California ; Sacramento River
    Language English
    Dates of publication 2017-09
    Size p. 1105-1120.
    Publishing place Springer Netherlands
    Document type Article
    ZDB-ID 196790-3
    ISSN 1573-5133 ; 0378-1909
    ISSN (online) 1573-5133
    ISSN 0378-1909
    DOI 10.1007/s10641-017-0631-0
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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  5. Article: Generation of Quantitative Polymerase Chain Reaction Detectability Half-Lives and Comparison of Sampling Protocols for Genetic Diet Studies of San Francisco Estuary Fishes

    Brandl, Scott C / Bernie May / Brian M. Schreier / J. Louise Conrad / Melinda R. Baerwald

    Transactions of the American Fisheries Society. 2016 May 3, v. 145, no. 3

    2016  

    Abstract: Several factors affect the probability of genetic analyses to detect prey in predator gut contents, including biological differences in the prey and predator species as well as differences in sampling and laboratory methodologies. Understanding these ... ...

    Abstract Several factors affect the probability of genetic analyses to detect prey in predator gut contents, including biological differences in the prey and predator species as well as differences in sampling and laboratory methodologies. Understanding these biases allows researchers to more appropriately put genetic prey detections in an ecological context. In this study, we determined the detectability half-lives of DNA from two prey species in the guts of two predators. The half-life detectability of juvenile Chinook Salmon Oncorhynchus tshawytscha in Striped Bass Morone saxatilis was 66.2 h, and that of larval Delta Smelt Hypomesus transpacificus in Mississippi Silverside Menidia audens was 26.4 h. Additionally, we performed a series of laboratory trials to examine the effects of variables in sample collection and preservation methodologies on the detectability of prey. Differences between methodologies were minimal, providing confidence that laboratory analyses will not be greatly affected by inconsistencies in field sampling procedures. Injecting a 95% solution of ethanol into the stomach via the esophagus immediately following collection and placing the fish on ice in the field prior to freezing at –20°C in the laboratory is a protocol readily applied in the field that will provide consistent results. Received August 19, 2015; accepted December 3, 2015 Published online April 11, 2016
    Keywords diet study techniques ; DNA ; esophagus ; estuaries ; ethanol ; fish ; freezing ; half life ; Hypomesus transpacificus ; ice ; juveniles ; laboratory experimentation ; larvae ; Menidia audens ; Morone saxatilis ; Oncorhynchus tshawytscha ; predators ; probability ; quantitative polymerase chain reaction ; researchers ; stomach
    Language English
    Dates of publication 2016-0503
    Size p. 441-449.
    Publishing place Taylor & Francis
    Document type Article
    ISSN 1548-8659
    DOI 10.1080/00028487.2015.1131745
    Database NAL-Catalogue (AGRICOLA)

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