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  1. Article ; Online: Striped bass (Morone saxatilis) migration timing driven by estuary outflow and sea surface temperature in the San Francisco Bay-Delta, California

    Pascale Goertler / Brian Mahardja / Ted Sommer

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Volume 11

    Abstract: Abstract The influence of climate on the timing of large-scale animal migrations is a major ecological and resource management concern. Anadromous fish migrations can have broad scale impacts on human communities and marine, aquatic and terrestrial food ... ...

    Abstract Abstract The influence of climate on the timing of large-scale animal migrations is a major ecological and resource management concern. Anadromous fish migrations can have broad scale impacts on human communities and marine, aquatic and terrestrial food webs. However, isolating the effects of climate change on the timing of life stage transitions for anadromous fish species is challenging. Striped bass (Morone saxatilis) exhibit striking variation in migration patterns within their natural range, including migratory behaviors that change with latitude, and climate-induced temperature changes are predicted to drive future habitat and distribution changes. Here we explore the linkages between migration and multiple components of coastal and inland aquatic ecosystems impacted by climate change. By leveraging environmental and fisheries monitoring which began in 1969, we describe the upstream migration timing of non-native adult Striped bass influenced by estuary outflow and sea surface temperature in the San Francisco Bay-Delta, California. Striped bass migrated later in years when Delta outflow was greater and sea surface temperature was cooler. It is likely that temperature thresholds in the ocean during the springtime provide a cue for Striped bass to initiate migration, but sea surface temperature may also represent composite climatic trends influencing Striped bass. Further, the observed variation in migration timing of adult Striped bass has implications for predation risk on the seaward-migration of juvenile Chinook salmon.
    Keywords Medicine ; R ; Science ; Q
    Subject code 333
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. 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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  3. Article ; Online: Role of freshwater floodplain-tidal slough complex in the persistence of the endangered delta smelt.

    Brian Mahardja / James A Hobbs / Naoaki Ikemiyagi / Alyssa Benjamin / Amanda J Finger

    PLoS ONE, Vol 14, Iss 1, p e

    2019  Volume 0208084

    Abstract: Seasonal floodplain wetland is one of the most variable and diverse habitats found in coastal ecosystems, yet it is also one of the most highly altered by humans. The Yolo Bypass, the primary floodplain of the Sacramento River in California's Central ... ...

    Abstract Seasonal floodplain wetland is one of the most variable and diverse habitats found in coastal ecosystems, yet it is also one of the most highly altered by humans. The Yolo Bypass, the primary floodplain of the Sacramento River in California's Central Valley, USA, has been shown to provide various benefits to native fishes when inundated. However, the Yolo Bypass exists as a tidal dead-end slough during dry periods and its value to native fishes has been less studied in this state. During the recent drought (2012-2016), we found higher abundance of the endangered Delta Smelt (Hypomesus transpacificus), than the previous 14 years of fish monitoring within the Yolo Bypass. Meanwhile, Delta Smelt abundance elsewhere in the estuary was at record lows during this time. To determine the value of the Yolo Bypass as a nursery habitat for Delta Smelt, we compared growth, hatch dates, and diets of juvenile Delta Smelt collected within the Yolo Bypass with fish collected among other putative nursery habitats in the San Francisco Estuary between 2010 and 2016. Our results indicated that when compared to other areas of the estuary, fish in the Yolo Bypass spawned earlier, and offspring experienced both higher quality feeding conditions and growth rates. The occurrence of healthy juvenile Delta Smelt in the Yolo Bypass suggested that the region may have acted as a refuge for the species during the drought years of 2012-2016. However, our results also demonstrated that no single region provided the best rearing habitat for juvenile Delta Smelt. It will likely require a mosaic of habitats that incorporates floodplain-tidal sloughs in order to promote the resilience of this declining estuarine fish species.
    Keywords Medicine ; R ; Science ; Q
    Subject code 590
    Language English
    Publishing date 2019-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Evidence of a Shift in the Littoral Fish Community of the Sacramento-San Joaquin Delta.

    Brian Mahardja / Mary Jade Farruggia / Brian Schreier / Ted Sommer

    PLoS ONE, Vol 12, Iss 1, p e

    2017  Volume 0170683

    Abstract: Many estuarine and freshwater ecosystems worldwide have undergone substantial changes due to multiple anthropogenic stressors. Over the past two decades, the Sacramento-San Joaquin Delta (Delta) in California, USA, saw a severe decline in pelagic fishes, ...

    Abstract Many estuarine and freshwater ecosystems worldwide have undergone substantial changes due to multiple anthropogenic stressors. Over the past two decades, the Sacramento-San Joaquin Delta (Delta) in California, USA, saw a severe decline in pelagic fishes, a shift in zooplankton community composition, and a rapid expansion of invasive aquatic vegetation. To evaluate whether major changes have also occurred in the littoral fish community, we analyzed a beach seine survey dataset collected from 1995 to 2015 from 26 sites within the Delta. We examined changes in the Delta fish community at three different ecological scales (species, community, and biomass), using clustering analyses, trend tests, and change-point analyses. We found that the annual catch per effort for many introduced species and some native species have increased since 1995, while few experienced a decline. We also observed a steady pattern of change over time in annual fish community composition, driven primarily by a steady increase in non-native Centrarchid species. Lastly, we found that littoral fish biomass has essentially doubled over the 21-year study period, with Mississippi Silverside Menidia audens and fishes in the Centrarchidae family driving most of this increase. The changes in the catch per effort, fish community composition, and biomass per volume indicate that a shift has occurred in the Delta littoral fish community and that the same factors affecting the Delta's pelagic food web may have been a key driver of change.
    Keywords Medicine ; R ; Science ; Q
    Subject code 333
    Language English
    Publishing date 2017-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Abundance Trends, Distribution, and Habitat Associations of the Invasive Mississippi Silverside ( Menidia audens ) in the Sacramento–San Joaquin Delta, California, USA

    Brian Mahardja / J. Louise Conrad / Lester Lusher / Brian Schreier

    San Francisco Estuary and Watershed Science, Vol 14, Iss

    2016  Volume 1

    Abstract: doi: http://dx.doi.org/10.15447/sfews.2016v14iss1art2 Although many alien fish species have colonized the Sacramento–San Joaquin Delta (Delta), few are as pervasive and abundant as Mississippi Silversides ( Menidia audens ). Moreover, Mississippi ... ...

    Abstract doi: http://dx.doi.org/10.15447/sfews.2016v14iss1art2 Although many alien fish species have colonized the Sacramento–San Joaquin Delta (Delta), few are as pervasive and abundant as Mississippi Silversides ( Menidia audens ). Moreover, Mississippi Silversides are hypothesized to be an intra-guild predator of the endangered Delta Smelt ( Hypomesus transpacificus ). Because of their prevalence in the Delta and poten-tial predation on Delta Smelt, Mississippi Silversides may have far-reaching effects on both the aquatic ecosystem and conservation management policies of the region. Yet little is known about how Mississippi Silverside abundance and distribution have changed within the Delta, or how they respond to various habitat attributes such as temperature, turbidity, and flow. We examined 19 years of beach seine survey data to evaluate how the abundance and distribution of Mississippi Silversides has changed over the years, characterize their habitat associations, and determine the environmental factors that predict their annual cohort strength. Concurrent with the decline of sev-eral pelagic fish species in the San Francisco Estuary in the early 2000s, we observed a significant increase in Mississippi Silverside catch that was accompanied by a moderate distributional shift in which densi-ties increased in the western Delta region. We also found that the occurrence of this highly prolific alien species was associated with higher water tempera-ture, higher turbidity, relatively low conductivity, and moderate to high levels of dissolved oxygen. Lastly, we demonstrated that freshwater input to the Sacramento–San Joaquin Delta during the summer and water exports during the spring months were both negatively correlated with the annual cohort size of Mississippi Silversides in the region. Our study identified the environmental variables deserv-ing additional attention in future studies involving Mississippi Silverside and suggests that the species favors habitat conditions that are likely to be detri-mental for pelagic ...
    Keywords Mississippi Silverside ; Menidia audens ; invasive species biology ; littoral fish ; life history ; Environmental sciences ; GE1-350
    Subject code 333
    Language English
    Publishing date 2016-03-01T00:00:00Z
    Publisher eScholarship Publishing, University of California
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article: Use of single nucleotide polymorphisms identifies backcrossing and species misidentifications among three San Francisco estuary osmerids

    Benjamin, Alyssa / Amanda J. Finger / Brian Mahardja / İsmail K. Sağlam / James Hobbs / Tien-Chieh Hung

    Conservation genetics. 2018 June, v. 19, no. 3

    2018  

    Abstract: Two threatened osmerid species native to the San Francisco Estuary (SFE)—Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys)—are subject to broad human influence, including significant habitat alteration and the presence of ...

    Abstract Two threatened osmerid species native to the San Francisco Estuary (SFE)—Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys)—are subject to broad human influence, including significant habitat alteration and the presence of the introduced osmerid, Wakasagi (Hypomesus nipponensis). The identification of these closely related species and their hybrids is difficult in field collected specimens which are subject to damage through handling and may be difficult to identify morphologically, especially when young. In addition, it is known that these three species hybridize, but the extent and effect of hybridization is difficult to quantify and monitor. We developed assays for 24 species-specific single nucleotide polymorphisms (SNPs) that identify whether a sample is a pure species (Delta Smelt, Longfin Smelt, or Wakasagi), a first generation (F1) hybrid, or a backcross. We used this SNP panel to genetically identify wild osmerids collected in Yolo Bypass from 2010 to 2016 and detected nine Delta Smelt × Wakasagi F1 hybrids and two Wakasagi × (Delta Smelt × Wakasagi) backcross hybrids; all assayed hybrids had Wakasagi as the maternal parent. The backcrossing into Wakasagi suggests that hybridization may only occur in one direction and thus preclude introgression to Delta Smelt. We also found substantial morphological field misidentifications (32.7%) in the Yolo Bypass samples resulting in more Wakasagi and fewer Delta Smelt than previously recorded when based on morphology. The SNP panel described in this study constitutes a valuable resource for monitoring hybridization in the SFE and assigning species identifications with accuracy and efficiency.
    Keywords backcrossing ; estuaries ; habitat destruction ; humans ; hybrids ; Hypomesus nipponensis ; Hypomesus transpacificus ; indigenous species ; introgression ; monitoring ; single nucleotide polymorphism ; Spirinchus thaleichthys
    Language English
    Dates of publication 2018-06
    Size p. 701-712.
    Publishing place Springer Netherlands
    Document type Article
    ZDB-ID 2059560-8
    ISSN 1572-9737 ; 1566-0621
    ISSN (online) 1572-9737
    ISSN 1566-0621
    DOI 10.1007/s10592-018-1048-9
    Database NAL-Catalogue (AGRICOLA)

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  7. Article: Hierarchical patterns of population structure in the endangered Fraser River white sturgeon (Acipenser transmontanus) and implications for conservation

    Schreier, Andrea Drauch / Bernie May / Brian Mahardja

    Canadian journal of fisheries and aquatic sciences. 2012 Nov. 16, v. 69, no. 12

    2012  

    Abstract: The Fraser River system consists of five white sturgeon (Acipenser transmontanus) management units, two of which are listed as endangered populations under Canada’s Species at Risk Act. The delineation of these management units was based primarily on ... ...

    Abstract The Fraser River system consists of five white sturgeon (Acipenser transmontanus) management units, two of which are listed as endangered populations under Canada’s Species at Risk Act. The delineation of these management units was based primarily on population genetic analysis with samples parsed by collection location. We used polysomic microsatellite markers to examine population structure in the Fraser River system with samples parsed by collection location and with a genetic clustering algorithm. Strong levels of genetic divergence were revealed above and below Hells Gate, a narrowing of the Fraser canyon further obstructed by a rockslide in 1913. Additional analyses revealed population substructure on the Fraser River above Hells Gate. The Middle Fraser River (SG-3) and Nechako River were found to be distinct populations, while the Upper Fraser River, although currently listed as an endangered population, represented a mixing area for white sturgeon originating from SG-3 and Nechako. Differences between these results and previous genetic investigations may be attributed to the detection of population mixing when genetic clustering is used to infer population structure.
    Keywords Acipenser transmontanus ; algorithms ; genetic analysis ; genetic markers ; genetic variation ; mixing ; population structure ; risk ; rivers ; rockfalls ; Canada
    Language English
    Dates of publication 2012-1116
    Size p. 1968-1980.
    Publishing place NRC Research Press
    Document type Article
    ZDB-ID 1473089-3
    ISSN 1205-7533 ; 0706-652X
    ISSN (online) 1205-7533
    ISSN 0706-652X
    DOI 10.1139/f2012-120
    Database NAL-Catalogue (AGRICOLA)

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  8. Article: Metapopulation structure of a semi-anadromous fish in a dynamic environment

    Feyrer, Frederick / Brian Mahardja / James Hobbs / Lenny Grimaldo / Melinda Baerwald / Rachel C. Johnson / Shawn Acuna / Swee Teh

    Canadian journal of fisheries and aquatic sciences. 2015 Jan. 8, v. 72, no. 5

    2015  

    Abstract: The Sacramento splittail (Pogonichthys macrolepidotus) is a relatively large (400 mm), long-lived (8 years) demersal cyprinid of conservation importance endemic to the San Francisco Estuary (SFE), California, USA. It exhibits a semi-anadromous life cycle ...

    Abstract The Sacramento splittail (Pogonichthys macrolepidotus) is a relatively large (400 mm), long-lived (8 years) demersal cyprinid of conservation importance endemic to the San Francisco Estuary (SFE), California, USA. It exhibits a semi-anadromous life cycle spending adult life in low to moderate salinity (0–12) habitat with migrations into upstream freshwater rivers and floodplains for spawning during winter–spring. The species persists as two genetically distinguishable populations — one dominant and one subordinate — separated by discrete spawning habitats that we suggest resemble an island–mainland metapopulation structure. The populations overlap in distribution in the SFE, yet segregation is maintained with individuals tending to aggregate or school with others of similar population heritage and natal origin. The populations are spatially connected via dispersal of the dominant population into the subordinate population’s spawning habitat when climate patterns produce freshwater outflow sufficient to form a bridge of suitable low salinity habitat across the upper SFE. Habitat affinities of the two populations, hydrodynamic modeling studies, and historical outflow records together suggest such conditions occur in approximately 1/3 of years overall with an irregular frequency. This dynamic pattern of spatial connectivity controlled by climate variability may be an important driver of gene flow between the two populations.
    Keywords adults ; climate ; estuaries ; fish ; floodplains ; freshwater ; gene flow ; habitats ; hydrologic models ; Pogonichthys macrolepidotus ; rivers ; salinity ; spawning ; California
    Language English
    Dates of publication 2015-0108
    Size p. 709-721.
    Publishing place NRC Research Press
    Document type Article
    ZDB-ID 1473089-3
    ISSN 1205-7533 ; 0706-652X
    ISSN (online) 1205-7533
    ISSN 0706-652X
    DOI 10.1139/cjfas-2014-0433
    Database NAL-Catalogue (AGRICOLA)

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