These methods, instrumentation and/or protocols apply to all data in this dataset:| Methods and protocols used in the collection of this data package |
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| Description: | 1.1 Nearshore survey of largemouth bass and submersed aquatic vegetation
This two-year study was completed as a collaboration among several research laboratories at the University of California-Davis and was funded by the Interagency Ecological Program. Thirty-three sites were sampled for fishes via electrofishing and for SAV via rake pulls every two months from October 2008 to October 2010. Criteria for location selection included the following: (1) SAV detected within the site at least once by annual aerial hyperspectral imagery of the Delta during 2004-2008 and (2) water depth no greater than 3 m. Each electrofishing transect was approximately 300 m, and the same transects were revisited at each sampling event. After electrofishing, SAV was sampled every 60 m at six points along the transect. SAV samples were collected with a collapsible 16-foot double-headed metal thatch rake. The rake was lowered straight down the water column, rotated 360° while in contact with the bottom, and continually rotated while raising it straight up the water column. This protocol provided a sampling method standardized for surface area (0.101 m2), allowing an estimation of the SAV biomass density. The SAV sampling procedure was repeated at a series of four parallel points up to 60 m away from the transect in either direction. In sloughs that were less than 60 m in width, off-transect points were taken a minimum of 40 m away from the transect or not collected at all. This protocol yielded up to 14 SAV points for each transect. However, as most transects are located directly adjacent to the shoreline, only one set of off-transect points were acquired for the majority of sites, for a total of 10 points. In the laboratory, SAV from each rake sample was separated by species and rinsed prior to recording wet weights for each species. Species-specific wet to dry mass regressions based on previous work were used to estimate dry mass from wet mass for each SAV species.
For more information about this study, see the following publication:
J. Louise Conrad, Andrew J. Bibian, Kelly L. Weinersmith, Denise De Carion, Matthew J. Young, Patrick Crain, Erin L. Hestir, Maria J. Santos & Andrew Sih (2016) Novel Species Interactions in a Highly Modified Estuary: Association of Largemouth Bass with Brazilian Waterweed Egeria densa, Transactions of the American Fisheries Society, 145:2, 249-263, https://doi.org/10.1080/00028487.2015.1114521.
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| | Description: | 1.2 Delta Smelt Resiliency Strategy Aquatic Weed Control Action
Fluridone was applied at two of the sites (Decker Island, Little Hastings), and the other two sites served as non-treated reference sites (Fisherman’s Cut, French Island). Biomass and species composition of SAV was monitored at Little Hastings, French Island, and Decker Island during the two weeks prior to the first fluridone applications (May 25 to June 7, 2017) to determine baseline conditions of the sites. Then, sites were sampled every two months until December 2018, after the last fluridone applications were completed (10 sampling events total). Sampling at Fisherman’s Cut was initiated in April 2018 (5 sampling events).
A point intercept sampling method was used. ArcGIS was used to randomly select a set of stations at each site for SAV sampling, specifying a minimum of 30 m between any two points (except Fisherman’s Cut because of its small size). During 2017, 40 stations per site were sampled. During 2018, sampling was reduced to 20 stations per site (a random subset of the original 40 stations), based on a power analysis of the 2017 biomass data. A sample was generally collected within a ~20-m radius of its corresponding station. This approach prevented the removal of vegetation for one sample from affecting biomass of samples collected in subsequent months.
Samples were collected using the following protocol: (1) lower a long-handled, double-headed thatch rake vertically to the bottom (rake head width of 35 cm with fourteen 5.5-cm-long metal teeth on either side), (2) turn the rake three times on its vertical axis while in contact with the bottom, (3) pull the rake straight up to the surface while continuing to rotate it. In high density SAV areas, the maximum capacity of the rake was sometimes exceeded, and therefore biomass may have been underestimated in some instances. Percent of total sample volume that each SAV species comprised was recorded to the nearest 10%. Samples were transported in garbage bags at ambient temperatures during the one-hour drive to the laboratory where they were stored for up to a week in a refrigerator prior to processing.
Samples were processed to estimate biomass using the following protocol. Samples were rinsed to remove sediment and macroinvertebrates. Once water ran clear through the sample, it was placed into an 18.9-L salad spinner and rotated 20 times (1 revolution per sec) to remove excess water. Total wet biomass was measured with a bench scale. Species specific wet mass was estimated by multiplying sample total wet mass by the percent cover of each species on the rake.
For more details, see the open access peer-reviewed article published in Estuaries and Coasts.
https://link.springer.com/article/10.1007/s12237-022-01079-5.
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| | | Description: | 1.3 Franks Tract submersed aquatic vegetation survey
In 2006, the California Department of Parks and Recreation Division of Boating and Waterways and the SePRO Corporation began a collaborative effort to monitor and manage SAV in Franks Tract using the herbicide fluridone. However, only data for 2014 – 2021 were available for inclusion in this data set. They monitor changes in SAV community composition using point-intercept surveys conducted on one date annually in the fall. Sampling points are chosen by generating a grid of evenly spaced points projected over the full area of Franks Tract. The number of sampling points varies among years but is usually 100 (range: 50–200 samples). Most surveys have been conducted in mid-October (range: October 1–October 13). To sample each point, they use a weighted, double-headed, 0.33-meter-wide rake head attached to a rope, which is dragged for approximately 3 m along the bottom and then pulled up to the boat for analysis. All SAV present on the rake is identified to species and species-specific abundances are estimated based on the percentage of the rake head each covers. Abundances are recorded using ordinal scores. During 2014-2018, there were four ordinal scores (0 = 0%, 1 = 1–24%, 2 = 25–49%, 3 = 50–74%, 4 = 75–100%), while during 2019-2021, there were five ordinal scores (0 = 0%1 = 1–19%, 2 = 20–39%, 3 = 40–59%, 4 = 60–79%, 5 = 80–100%).
For more information, see the following publication:
Jeffrey Caudill, Ajay R. Jones, Lars Anderson, John D. Madsen, Patricia Gilbert, Scott Shuler and Mark A. Heilman. 2019. Aquatic plant community restoration following the long-term management of invasive Egeria densa with fluridone treatments. Management of Biological Invasions 10(3):473–485. https://www.reabic.net/journals/mbi/2019/3/MBI_2019_Caudill_etal.pdf
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| | Description: | 1.4 Center for Spatial Technologies and Remote Sensing field survey
During 2007-2008 and 2014-2021, field data were collected in the Sacramento - San Joaquin Delta for the purpose of training and validating invasive species maps derived from remote sensing imagery over the Delta. SAV was sampled using thatching rakes with 34 teeth tethered to a long rope. The rake was thrown off the side of the boat into the patch and allowed to sink to the bottom of the water column and then dragged in and pulled up. The species on the rake were identified and their percent cover on the rake was estimated to the nearest 10%. Then the sample was dropped back into the water. Note that empty samples (ie, no SAV) are not currently included in this data set.
These data were not collected randomly. The study area was not sampled uniformly through the years. In 2016, 2017, 2018, and 2019 spring, only a third of the Delta was sampled. Some flooded islands within the Delta were difficult to access hence they were accessed some years but not others. If airboats were available, access was easier than if all fieldwork was only done on motorboats. Some species only appeared for the first time during this period and might have been missed or misidentified in the first year of appearance. For example, Richardson's pondweed (Potamogeton richardsonii) might have been misidentified in earlier years as curlyleaf pondweed (Potamogeton crispus). Species that could not be effectively differentiated in the field were recorded by the name of the most abundant species e.g. Stukenia pectinata (Sago Pondweed) for S. pectinata, S. filiformis and P. foliolus.
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| | | Description: | 2 Data integration
Data integration was completed in R version 4.2.1 (R Core Team 2022). All code for integrating data sets is available online in the GitHub repository:
https://github.com/InteragencyEcologicalProgram/AquaticVegetationPWT/tree/main/MasterDataSet_SAV
2.1 Data formatting
Prior to creating the combined data set in sav_integrated_dataset_2023-03-16.csv, data sets were formatted for consistency by utilizing standardized species name codes, renaming column names, converting units, and pivoting all datasets to the “long” format where each row contains abundance metrics for each taxon within each sample.
For each sample, a row was included for every species recorded in the entire survey. If a species was recorded in a specific sample, species_incidence was reported as 1 and the appropriate abundance metric(s) was provided. If a species was not recorded in a sample, species_incidence was reported as 0 and all abundance metrics are “NA”. Note that not all species were recorded in all surveys, which could be due to the species absence, misidentification, or undersampling. Therefore, the specific set of species included as rows for samples differs among surveys.
2.1 Abundance metrics
The only way to utilize data from all surveys is to use presence-absence because no abundance metric is available across all of them.
The CSTARS and DSRS data sets both record species abundances by estimating the percentage of a rake head covered by each species to the nearly 10% (column: species_rake_cover_percent). These rake samples are not collected in exactly the same way and therefore might not be perfectly comparable. CSTARS dragged a rake head attached to a rope through the water, while DSRS spun a rake head attached to a handle in a fixed location.
The Franks Tract survey records species abundances using ordinal scores based on the percentage of rake head covered by the biomass of each species (column: species_rake_cover_ordinal). The CSTARS and DSRS data collected as rake head percentages are converted to ordinal scores in this column for ease of cross survey comparisons. The Franks Tract and CSTARS samples are both collected using a rake head attached to a rope, so the ordinal scores should be comparable. As noted above, the DSRS samples were collected with a rake head on a handle, so the ordinal scores for this survey may be less comparable to the other two surveys.
For the bass study, SAV abundances were recorded as fresh mass of each species in a sample (column: species_mass_fresh_g). From the fresh mass, dry mass was estimated (column: species_mass_dry_estimated_g) using previously developed fresh to dry mass equations. Fresh mass and estimated dry mass were divided by the surface area sampled by the rake head (0.101 m2) to calculate mass density (columns: species_density_fresh_g_m2, species_density_dry_estimated_g_m2). None of these four abundance metrics can be compared to abundance metrics of the other surveys.
The DSRS survey estimated species specific fresh mass by multiplying total SAV fresh mass by estimated percent of cover of the rake by a species, but this probably is not comparable enough to the bass study approach.
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| | Description: | 3 Taxonomy
Standardized species codes were implemented in the integrated data set. These codes generally consisted of the first three letters of the genus and first three letters of the specific epithet. The taxonomy_all_summary.csv file provides a crosswalk between the species codes and scientific names. The scientific names as well as the taxonomic family names were derived from ITIS. This file also indicates whether a species is native to the Delta and summarizes the number of samples in which each species was recorded for each survey.
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| | Description: | 4 Wet to dry mass conversions
The file sav_wet_dry_equations.csv provides the intercept and slope for the line that describes the species-specific relationship between wet mass and dry mass. These equations were developed by Erin Hestir and Maria Santos from the Center for Spatial Technologies and Remote Sensing lab of the University of California-Davis. Note that these equations are not available for all species.
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