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212 results for “fish ecology”
Interagency Ecological Program and US Fish and Wildlife Service: San Francisco Estuary Enhanced Delta Smelt Monitoring Program Data, 2016-2024
The Enhanced Delta Smelt Monitoring Program (EDSM) was initiated by the U.S. Fish and Wildlife Service in 2016. The main purpose of EDSM is to provide information about endemic Delta Smelt (Hypomesus transpacificus) population sizes and distributions within the upper San Francisco Estuary. To track the life cycle of this annual species, larval trawling with a fine-mesh (20 mm) net is conducted during the spring months, and Kodiak trawling for juveniles and adults occurs during the summer, fall, and winter months. Sampling sites are chosen via a stratified random sampling design. A minimum of two tows are conducted at each site, and field staff typically sample between 18 and 41 sites weekly. All fish collected are identified and enumerated, and a subset are measured for body length. Environmental data (water temperature, conductivity, dissolved oxygen, turbidity, depth) are also measured. In addition to Hypomesus spp., this long-term monitoring dataset can also be useful in evaluating the status and trends of other species of interest, especially pelagic fishes. For more information: https://www.fws.gov/office/lodi-fish-and-wildlife
Interagency Ecological Program: Fish catch and water quality data from the Sacramento River floodplain and tidal slough, collected by the Yolo Bypass Fish Monitoring Program, 1998-2024.
Largely supported by the Interagency Ecological Program (IEP), California Department of Water Resources (DWR) has operated a fish monitoring program in the Yolo Bypass, a seasonal floodplain and tidal slough, since 1998. The objectives of the Yolo Bypass Fish Monitoring Program (YBFMP) are to: 1. Collect baseline data on water quality, chlorophyll, lower trophic level biota, and fish in the Yolo Bypass to monitor spatial and temporal changes in trends and abundance. 2. Analyze and communicate Yolo Bypass data with interested parties and the scientific and management communities to address pertinent management-related questions. 3. Provide technical expertise on Yolo Bypass aquatic ecology and monitoring and sampling methods. The YBFMP operates a rotary screw trap and fyke trap and conducts biweekly beach seine and lower trophic surveys in addition to maintaining water quality instrumentation in the bypass. Only juvenile and adult fish catch with associated water quality are presented in this dataset. The rotary screw trap sampling objectives are to: (1) examine species abundance and life stage of juvenile outmigrants and resident small-bodied fishes, (2) identify temporal and spatial patterns in fish abundance and species composition, and (3) examine the effect of physical and environmental conditions on these patterns. The fyke trap sampling objectives are to: (1) examine abundance of migrating and resident adult fishes, (2) identify temporal and spatial patterns in fish abundance and species composition, especially with regard to anadromous species, (3) examine the effect of physical and environmental conditions on these patterns, and (4) provide data on the timing and duration of species captured in the Yolo Bypass for comparison to those captured in other Sacramento Valley tributaries. The beach seine surveys are conducted in the Yolo Bypass’s perennial channel (Toe Drain), inundated floodplain, disconnected inundated ponds, and perennial ponds. The objectives o
Interagency Ecological Program: Over four decades of juvenile fish monitoring data from the San Francisco Estuary, collected by the Delta Juvenile Fish Monitoring Program, 1976-2025
The United States Fish and Wildlife Service Delta Juvenile Fish Monitoring Program (DJFMP) has monitored juvenile Chinook Salmon Oncorhynchus tshawytscha and other fish species within the San Francisco Estuary (Estuary) since 1976 using a combination of surface trawls and beach seines. Since 2000, three trawl sites and 58 beach seine sites have been sampled weekly or biweekly within the Estuary and lower Sacramento and San Joaquin Rivers. As part of the Interagency Ecological Program (IEP) that manages the Estuary, the DJFMP has tracked the relative abundance and distribution of naturally and hatchery produced juvenile Chinook Salmon of all races as they outmigrate through the Sacramento-San Joaquin Delta for over four decades. The data that DJFMP collected has been used not only to help inform the management of Chinook Salmon, but also to monitor the status of native species of interest such as the previously listed Sacramento Splittail Pogonichthys macrolepidotus and invasive species such as Mississippi Silverside Menidia audens and Largemouth Bass Micropterus salmoides. DATA CORRECTION/UPDATE: Previous data versions 244.6, 244.7, and 244.8 contained an error and resulted in duplicated records of hatchery Chinook Salmon in the datasets. These datasets were removed from the data repository and the error was corrected in version 244.9 and after. DNA Data: Full more details of the DNA methods and results for juvenile Chinook salmon included in this dataset, please check out Blankenship, S.M., J. Israel, E. Buttermore, and K. Reece. 2021. Knights Landing, California Department of Fish and Wildlife, Genetic Determination of Population of Origin 2017 through 2019 ver 1. Environmental Data Initiative. https://doi.org/10.6073/pasta/85fbc988c0b1362e84c318e69c7a939e. For more information on the Delta Juvenile Fish Monitoring Program: https://www.fws.gov/project/delta-juvenile-fish-monitoring-program
Interagency Ecological Program: Zooplankton catch and water quality data from the Sacramento River floodplain and tidal slough, collected by the Yolo Bypass Fish Monitoring Program, 1998-2018
Largely supported by the Interagency Ecological Program (IEP), the California Department of Water Resources (DWR) has operated a fisheries and invertebrate monitoring program in the Yolo Bypass since 1998. The main objectives of the Yolo Bypass Fish Monitoring Program (YBFMP) are to collect baseline data on lower trophic levels (phytoplankton, zooplankton and insect drift), juvenile and adult fish, hydrology, and water quality parameters. As the Yolo Bypass has been identified as a high restoration priority by numerous regulatory agencies, these baseline data are critical for evaluating success of future restoration projects. In addition, the data have already served to increase our understanding of the role of the Yolo Bypass in the life history of native fishes, and its ecological function in the San Francisco Estuary. Zooplankton are an important component in the diet of larval, juvenile, and small adult fishes within the San Francisco Estuary, including Delta Smelt, juvenile Chinook Salmon, Striped Bass, and Sacramento Splittail. The YBFMP collects zooplankton year-round from two sites. Since 2011, samples have been collected biweekly (every other week) to weekly (during floodplain inundation) using 150- and 50- micrometer mesh plankton nets. Zooplankton are identified and enumerated by contractors (currently BSA Environmental Services). The goals of the zooplankton monitoring program are to compare the seasonal variation in species densities and trends between (1) the Sacramento River channel, and (2) the Yolo Bypass, the river’s seasonal floodplain. Data on zooplankton catch and associated water quality parameters are presented in this dataset.
Interagency Ecological Program: Water quality, fish, and zooplankton monitoring and modeling to support the 2018 Suisun Marsh Salinity Control Gates Summer Action
In summer 2018 we used a unique water control structure in the San Francisco Estuary (SFE) to direct a managed flow pulse into Suisun Marsh, one of the largest contiguous tidal marshes on the west coast of the United States. The action was designed to increase habitat suitability for the endangered Delta Smelt Hypomesus transpacificus, a small osmerid fish endemic to the upper SFE. The approach was to operate the Suisun Marsh Salinity Control Gates (SMSCG) in conjunction with increased Sacramento River tributary inflow to direct an estimated 160 x 10^6 m3 pulse of low salinity water into Suisun Marsh during August, a critical time period for juvenile Delta Smelt rearing. This dataset includes physical and biological monitoring data collected for the action. Datasets include Delta Smelt catch from the USFWS Enhanced Delta Smelt Monitoring program, zooplankton and Microcystis abundance from the Environmental Monitoring Program, historic Delta Smelt catch from the Summer Townet Survey, Delta Outflow from the Dayflow model, extent of Delta Smelt habitat from the UnTRIM Bay-Delta model, and water quality (Salinity, Temperature, Chlorophyll, and Turibidity) collected at continuous sondes at three locations. These data are associated with the manuscript "Evaluation of a large-scale flow manipulation to the upper San Francisco Estuary: Response of habitat conditions for an endangered native fish," by Dr. Ted Sommer, et al. 2020 PLOS One, in review.
Interagency Ecological Program: Drift invertebrate and ichthyoplankton catch and water quality from the Sacramento River channel, and Sacramento River floodplain and tidal slough, collected by the Yolo Bypass Fish Monitoring Program, 1998-2022
Largely supported by the Interagency Ecological Program (IEP), California Department of Water Resources (DWR) has operated a fish monitoring program in the Yolo Bypass, a seasonal floodplain and tidal slough, since 1998. The objectives of the Yolo Bypass Fish Monitoring Program (YBFMP) are to: 1. Collect baseline data on water quality, chlorophyll, lower trophic level biota, and fish in the Yolo Bypass to monitor spatial and temporal changes in trends and abundance. 2. Analyze and communicate Yolo Bypass data with interested parties and the scientific and management communities to address pertinent management-related questions. 3. Provide technical expertise on Yolo Bypass aquatic ecology and monitoring and sampling methods. Aquatic and terrestrial insects are an important component in the diet of juvenile and adult fishes within the San Francisco Estuary, including two important native fishes: juvenile Chinook Salmon and Sacramento Splittail. The YBFMP collects drift invertebrates year-round from two sites. Currently, samples are collected biweekly (every other week) to weekly (during floodplain inundation) using a rectangular aquatic drift net that sits at the surface of the water. Invertebrates are identified and enumerated by contractors (currently EcoAnalysts, Inc.). The goals of the monitoring program are to compare the seasonal variations in densities and species trends of aquatic and terrestrial insects/non-insects within the Sacramento River channel and the Yolo Bypass, the river’s seasonal floodplain. Drift invertebrate Key findings to date include: (1) Chinook Salmon sampled in the floodplain had diets comprised of 90% Dipterans and zooplankton, with Chironomidae being the dominant Diptera family (Sommer et al., 2001), (2) The floodplain of the Yolo Bypass contains significantly higher densities of Diptera (Diptera densities being positively associated with flow) and terrestrial invertebrates than the adjacent Sacramento River (Sommer et al. 2001b: Sommer
Interagency Ecological Program and US Fish and Wildlife Service: Juvenile/Larval Fish and Zooplankton collections at Liberty Island, California 2002-2005 & 2013-2019
The U.S. Fish and Wildlife Service (USFWS) Lodi Fish and Wildlife Office (LFWO) Delta Juvenile Fish Monitoring Program (DJFMP) has intermittently sampled Liberty Island with various equipment since 2002. Liberty Island was a reclaimed agricultural island until it flooded in 1997-1998 and we subsequently left to passively restore as a tidally influenced wetland. Larval trawls and beach were the only sampling methods used during both early (2002-2005) and late (2009-2019) sampling periods. The main purpose of the sampling was to gather information about fish presence and abundance in Liberty Island during the passive restoration, with an emphasis on reproductive and early life-stages of native species. Larval trawls, or tow nets, were used to catch larval fish in 2004-2005 and again from 2013-2019. Zooplankton nets were used 2013-2019. Water quality measurements were collected alongside each tow.
Interagency Ecological Program: Discrete water quality and phytoplankton data from the Sacramento River floodplain and Yolo Bypass tidal slough, collected by the Yolo Bypass Fish Monitoring Program, 1998 - 2022
The Yolo Bypass Fish Monitoring Program (YBFMP) operates a rotary screw trap and fyke trap and conducts biweekly beach seine and lower trophic surveys in addition to maintaining water quality instrumentation in the bypass. The YBFMP serves to fill information gaps regarding environmental conditions in the bypass that trigger migrations and enhanced survival and growth of native fishes, as well as provide data for IEP synthesis efforts. YBFMP staff also conduct analyses of YBFMP monitoring data to address pertinent management related questions as identified by IEP. The Yolo Bypass has been identified as a high restoration priority by the National Marine Fisheries Service and US Fish and Wildlife Service Biological Opinions for Delta Smelt, Winter and Spring-run Chinook salmon and by California EcoRestore. The YBFMP informs the restoration actions that are mandated or recommended in these plans and provides critical baseline data on the ecology of the bypass and how it interacts with the broader San Francisco Estuary. Program objectives include: Collecting baseline data on water quality, chlorophyll, lower trophic level biota, and fish in the Yolo Bypass to monitor spatial and temporal changes in trends and abundance; Analyzing and communicating Yolo Bypass data with stakeholders and the scientific and management communities to address pertinent management related questions; Providing technical expertise on Yolo Bypass aquatic ecology and monitoring and sampling methods. We collect discrete water quality data using a YSI ProDSS and sample phytoplankton, chlorophyll and nutrients as discrete water grabs taken biweekly (or weekly during Yolo Bypass inundation) along with lower trophic tows. Water is sampled at three sites along the Yolo Bypass and Sacramento River, then processed and analyzed by an internal DWR laboratory.
Interagency Ecological Program: Summer Townet Survey for Young Pelagic Fishes in the San Francisco Estuary
The Interagency Ecological Program’s (IEP) Summer Townet Survey (STN) is a long-term effort to monitor the annual recruitment success of young pelagic fishes in the upper San Francisco Estuary (California, United States). Conducted by the California Department of Fish and Wildlife (CDFW) since 1959, STN has sampled fixed locations from Eastern San Pablo Bay to Rio Vista on the Sacramento River, and to Stockton on the San Joaquin River; and a single station in the lower Napa River. The study area was expanded in 2011 to include the Sacramento Deep Water Ship Channel (SDWSC) and Cache Slough (CS). Currently, 40 stations are sampled as a “survey” every other week June through August for 6 surveys. A conical net, lashed to a fixed metal “D” frame, is pulled obliquely through the water column 2 to 3 times at each station. All fish and macro-invertebrates are identified and enumerated from each tow, with fork lengths (mm) of the first 50 of each fish species also recorded. Fish catch, length-frequency, and catch-per-unit-effort (CPUE) among stations is available with data visualization tools on the study website for all species (https://wildlife.ca.gov/Conservation/Delta/Townet-Survey). Data collected at historic 31 stations are used to calculate annual relative abundance indices for age-0 Striped Bass (Morone saxatilis) and Delta Smelt (Hypomesus transpacificus). The remaining 9 stations are sampled to expand our sampling range further upriver and increase our understanding of larval and juvenile fish abundance and distribution in the lower Napa River and the North Delta. A meso-zooplankton net targeting copepods and cladocerans is also used in parallel to assess fish food resources at each station and a subset of the fish collected are retained for diet analysis by CDFW researchers (beginning 2005, see STN and FMWT zooplankton data on EDI). The STN also measures habitat conditions via water temperature (°C), water clarity (Secchi disk depth in cm), Turbidity (NTU) and s
Interagency Ecological Program: Fish catch and associated water quality for the Fall Midwater Trawl Survey, Sacramento-San Joaquin Delta, 1967-2024
The Interagency Ecological Program’s (IEP) Fall Midwater Trawl Survey (FMWT) is a long-term monitoring survey conducted by the California Department of Fish and Wildlife (CDFW) and has sampled annually since its inception in 1967, with the exceptions of 1974 and 1979, when sampling was not conducted. The FMWT was initiated to determine the relative abundance and distribution of age-0 Striped Bass (Morone saxatilis) in the San Francisco Estuary (California, United States), but the data has also been used for other upper estuary pelagic species, including Delta Smelt (Hypomesus transpacificus), Longfin Smelt (Spirinchus thaleichthys), American Shad (Alosa sapidissima), Splittail (Pogonichthys macrolepidotus), and Threadfin Shad (Dorosoma petenense). The FMWT currently samples 130 stations each month from September to December and a subset of this data is used to calculate an annual abundance index. These 130 stations range from San Pablo Bay upstream to Stockton on the San Joaquin River, and West Sacramento on the Sacramento Deep Water Ship Channel. FMWT sampling data includes 193 unique station locations throughout the San Francisco Estuary; 63 are not currently sampled. Most stations no longer sampled occur in South and Central San Francisco Bay (1968-1979), with others located in San Pablo Bay and upstream into the Delta. There are catch records for stations that were sampled only once. Data users are encouraged to look at station frequency over time to understand when and where sampling occurred. Sampling takes approximately 14 days per month to complete. Historically, FMWT sampling occasionally began as early as July (1972) or August (1968-1973, 1993-1994, 1996-1997) and sometimes continued past December to March (1968-1973, 1978, 1991-2001) or beyond (1992-1995). The Spring Midwater Trawl (SMWT) was a modified survey created to continue sampling January-March to track movements of mature adult delta smelt from 1991-2001. SMWT was replaced in 2002 with the more e
Interagency Ecological Program and US Fish and Wildlife Service: Beach Seine Efficiency Study, collected by the Delta Juvenile Fish Monitoring Program, 2013-2018
Within the San Francisco Estuary, beach seining has been used since the 1970s by the U.S. Fish and Wildlife Service's Delta Juvenile Fish Monitoring Program (DJFMP) to monitor the relative abundance and distribution of juvenile Chinook salmon and other fishes of management concern occurring in near shore habitats. Over 2,000 seine samples are currently being collected throughout the San Francisco Estuary annually. Data from these surveys are used to make various water operation decisions and help inform managers on the status of fish populations within the San Francisco Estuary. By not accounting for the variability of species- and size-specific efficiency of beach seines across environmental gradients, the metrics developed by the DJFMP are likely underestimated and biased to an unknown extent. Consequently, the ability of the DJFMP to document the true occupancy of fishes for water operations and population vicissitude may be inhibited. Therefore, the first objective of this study is to estimate the species- and size-specific capture efficiency of DJFMP beach seines for fishes occurring in near shore habitats within the San Francisco Estuary. The second objective is to model the observed efficiency estimates using habitat variables to allow managers to account for incomplete detection when estimating fish abundance and occupancy from DJFMP beach seine data.
Interagency Ecological Program: San Francisco Bay Study Survey for Fish and Mobile Crustaceans 1980-2024
The San Francisco Bay Study (Bay Study) was established in 1980 to determine the effects of freshwater outflow on the abundance and distribution of fish and mobile crustaceans (brachyuran crabs and caridean shrimp) in the San Francisco Estuary, mainly downstream of the Sacramento-San Joaquin Delta. The Bay Study survey currently samples 52 open-water stations monthly from a research vessel with two types of trawl gear: a midwater trawl to sample pelagic fishes, and an otter trawl to sample demersal fishes, crabs, and shrimp. Historically, the study also included plankton sampling (1980-1989) for larval fish and crustaceans. Fish collected by the otter and midwater trawl are identified to species, counted, and a representative subsample is measured. In addition, crabs from the otter trawl are identified, counted, sexed, and measured, and gelatinous zooplankton from the midwater trawl are identified and counted. Shrimp are retained from each otter trawl sample and returned to the laboratory for processing, which includes identification, counts, sex, and length. Additional data collected at each station includes water depth, Secchi, and a water column profile of temperature and conductivity. This data publication includes fish, crab, shrimp, gelatinous zooplankton (jellies), and water quality data. Metadata related to the plankton sampling will be included in the future when this data is published.
Interagency Ecological Program and US Fish and Wildlife Service: Enhanced Delta Smelt Monitoring Program Experimental Larval Survey Data 2018-2019
The United States Fish and Wildlife Service’s (USFWS) Experimental Larval Survey was designed and implemented by the Enhanced Delta Smelt Monitoring Program to assess alternative sampling methods for monitoring the larval life stages of the federally endangered Delta Smelt (Hypomesus transpacificus) within the San Francisco Estuary, California, USA. From 2018 to 2019, four different sampling methods (Beach Seine, Manta Trawl Net, 20-mm Surface Trawl Net, 20-mm Midwater Trawl Net) nested in time and space were used to estimate the occupancy rate, relative density, and size distribution of larval Delta Smelt across sampling methods and water depth strata within the San Francisco Estuary. For more information on the Lodi USFWS Office and the Enhanced Delta Smelt Monitoring Program: https://www.fws.gov/lodi/.
Fig. 7 in Fishermen's local ecological knowledge on Southeastern Brazilian coastal fishes: contributions to research, conservation, and management
Fig. 7. Ordination plot of the correspondence analysis (first two axes) based on fishermen's answers about fishing season of the nine studied fish species in the southeastern Brazilian coast: Absa = Abudefduf saxatilis; Boru = Bodianus rufus; Cala = Caranx latus; Epma = Epinephelus marginatus; Haau = Haemulon aurolineatum; Heba = Hemiramphus balao; Kysp = Kyphosus spp.; Mifu = Micropogonias furnieri; Sesp = Seriola spp.
Fig. 6 in Fishermen's local ecological knowledge on Southeastern Brazilian coastal fishes: contributions to research, conservation, and management
Fig. 6. Ordination plot of the correspondence analysis (first two axes) based on fishermen's answers about migratory routes of the nine studied fish species in the southeastern Brazilian coast: Absa = Abudefduf saxatilis; Boru = Bodianus rufus; Cala = Caranx latus; Epma = Epinephelus marginatus; Haau = Haemulon aurolineatum; Heba = Hemiramphus balao; Kysp = Kyphosus spp.; Mifu = Micropogonias furnieri; Sesp = Seriola spp.
Fig. 4 in Fishermen's local ecological knowledge on Southeastern Brazilian coastal fishes: contributions to research, conservation, and management
Fig. 4. Trophic chain based on those food items and predators most cited by fishermen in the southeastern Brazilian coast for a) reef fishes and b) pelagic fishes. Numbers are percent of interviewed fishermen who mentioned each feeding interaction. Fish sizes are not in scale. Those feeding interactions that agree with reported feeding habits of these fishes in the biological literature are marked *(Randall, 1967; Berkeley & Houde, 1978; Menezes & Figueiredo, 1980; Sazima, 1986; Pipitone & Andaloro, 1995; Barreiros & Santos, 1998; Vasconcellos & Gasalla, 2001; Silvano, 2001; Silvano & Güth, 2006; Figueiredo & Vieira, 2005; Gibran, 2007).
Fig. 3 in Fishermen's local ecological knowledge on Southeastern Brazilian coastal fishes: contributions to research, conservation, and management
Fig. 3. Main habitats of fishes according to fishermen in the southeastern Brazilian coast: percentages of fishermen who mentioned each habitat category are in Appendix 1. Double-headed arrows indicate that fishes occur in both habitats in horizontal space (e.g. open ocean and reefs), up and down arrows indicate that fishes occur in both habitats in vertical space (e.g., near the bottom and at the surface). Fish sizes are not in scale.
Fig. 1 in Fishermen's local ecological knowledge on Southeastern Brazilian coastal fishes: contributions to research, conservation, and management
Fig. 1. Ordination plot of the correspondence analysis (first two axes) based on fishermen answers about uses of the nine studied fish species in the southeastern Brazilian coast: Absa = Abudefduf saxatilis; Boru = Bodianus rufus; Cala = Caranx latus; Epma = Epinephelus marginatus; Haau = Haemulon aurolineatum; Heba = Hemiramphus balao; Kysp = Kyphosus spp.; Mifu = Micropogonias furnieri; Sesp = Seriola spp.
Fig. 2 in Fishermen's local ecological knowledge on Southeastern Brazilian coastal fishes: contributions to research, conservation, and management
Fig. 2. Ordination plots of the correspondence analysis (first two axes) based on fishermen answers about fishing methods and baits of the nine studied fish species in the southeastern Brazilian coast: Absa = Abudefduf saxatilis; Boru = Bodianus rufus; Cala = Caranx latus; Epma = Epinephelus marginatus; Haau = Haemulon aurolineatum; Heba = Hemiramphus balao; Kysp = Kyphosus spp.; Mifu = Micropogonias furnieri; Sesp = Seriola spp.
Fig. 8 in Fishermen's local ecological knowledge on Southeastern Brazilian coastal fishes: contributions to research, conservation, and management
Fig. 8. Ordination plot of the correspondence analysis (first two axes) based on fishermen's answers about reproductive (spawning) season of the nine studied fish species in the southeastern Brazilian coast: Absa = Abudefduf saxatilis; Boru = Bodianus rufus; Cala = Caranx latus; Epma = Epinephelus marginatus; Haau = Haemulon aurolineatum; Heba = Hemiramphus balao; Kysp = Kyphosus spp.; Mifu = Micropogonias furnieri; Sesp = Seriola spp.
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