The 2020 and 2021 results of the SWAMP eDNA Metabarcoding Monitoring and Analysis Project (SeMMAP) sampling efforts using Jonah Ventures aquatic eDNA kits and sequencing. Included are the locations, field measures and MiFish and 23S sequencing results of eDNA sampling for fish and phytoplankton communities respectively. 45 samples were taken between June 2020 and October of 2021.SeMMAP was created to explore the use of eDNA metabarcoding for surface water quality monitoring and how this method may achieve our main goals of monitoring more with less resources and integrating SWAMP programs through a single data source. We will be exploring a data management plan as well as the benefits of using volunteer and Tribal partners to collect the same quality data as our internal SWAMP programs. Our aim is to bring inclusion to the Water Boards by putting monitoring into the hands of those who have been marginalized by the Boards and other government agencies.This map is part of a larger engagement tool, the SeMMAP Portal which will serve as a site for external partners, regional partners, SWAMP program personnel and the public to view the pace and direction of the project and the collected data. The SeMMAP Portal contains data dashboards, maps, a partner project gallery for partners to view how each is using their eDNA to answer scientific questions and monitor water quality. The Portal also includes guides and instructions on best practices as well as the raw data and metadata.This content was created by Peter Houpt from the State Water Resources Control Boards, SWAMP eDNA Metabarcoding Monitoring and Analysis Project.

peter.houpt@waterboards.ca.gov oima-semmap@waterboards.ca.gov

The SWAMP environmental DNA Metabarcoding Monitoring and Analysis Project (SeMMAP) was created to explore the use of eDNA metabarcoding for surface water quality monitoring and how this method may achieve the project’s goals of monitoring more with less resources and integrating SWAMP programs through a single data source.

We are creating a data management plan and exploring the benefits of collaborating with volunteer and Tribal partners to collect the same quality data as our regional and internal SWAMP programs. eDNA metabarcoding is extremely cost effective compared to traditional methods and the simple collection process allows almost anyone to collect robust scientific data. The project's aim is to bring inclusion to the Water Boards by putting monitoring into the hands of those who have been marginalized by the Boards and other government agencies, while simultaneously outsourcing some of the more costly aspects of sampling in order to save taxpayer money and deliver high quality data. In short, "Science for the Stewards!"

We operate on the principles of Equity, Accountability and Transparency. To this effort, we have created the SeMMAP Data Resource Hub. The SeMMAP Hub will serve as a site for external partners, regional partners, SWAMP program personnel, decision makers and the public to view the pace and direction of the project. It also provides access to the raw data collected as well as data visualization tools to help users analyze and interpret the DNA sequencing results.

The SeMMAP Hub contains data dashboards, maps, and a partner project gallery for participants to share and view how they’re using their eDNA data to answer scientific questions and monitor water quality. The Hub also includes illustrated instructions for sample collection, guides on best practices, literature to help with study design, as well as the raw data and metadata standards.

The maps within display the 2020 and 2021 results of SeMMAP sampling efforts using Jonah Ventures aquatic eDNA kits. Included are the locations, field measures and MiFish and 23S sequencing results of eDNA sampling for fish and phytoplankton communities respectively. 45 samples were taken between June 2020 and October of 2021, at 30 unique sites.

This content was created by Peter Houpt from the State Water Resources Control Boards, SWAMP eDNA Metabarcoding Monitoring and Analysis Project.

peter.houpt@waterboards.ca.gov, oima-semmap@waterboards.ca.gov

This webmap is a collection of ecological overlay services from vegetation mapping work by the California Native Plant Society (CNPS), California Dept of Fish and Game (CDFG), Natureserve, and the USGS Gap Analysis ProgramThe CNPS Vegetation Program has worked for over 15 years to provide standards and tools for identifying and representing vegetation, as an important feature of California's natural heritage and biodiversity. Many knowledgeable ecologists and botanists support the program as volunteers and paid staff. Through grants, contracts, and grass-roots efforts, CNPS collects field data and compiles information into reports, manuals, and maps on California's vegetation, ecology and rare plants in order to better protect and manage them. We provide these services to governmental, non-governmental and other organizations, and we collaborate on vegetation resource assessment projects around the state. CNPS is also the publisher of the authoritative Manual of California Vegetation, you can purchase a copy HERE. To support the work of the CNPS, please JOIN NOW and become a member!The CDFG Vegetation Classification and Mapping Program develops and maintains California's expression of the National Vegetation Classification System. We implement its use through assessment and mapping projects in high-priority conservation and management areas, through training programs, and through working continuously on best management practices for field assessment, classification of vegetation data, and fine-scale vegetation mapping.HOW THE OVERLAY LAYERS WERE CREATED:Nserve and GapLC Sources: Early shortcomings in the NVC standard led to Natureserve's development of a mid-scale mapping-friendly "Ecological Systems" standard roughly corresponding to the "Group" level of the NVC, which facilitated NVC-based mapping of entire continents. Current scientific work is leading to the incorporation of Ecological Systems into the NVC as group and macrogroup concepts are revised. Natureserve and Gap Ecological Systems layers differ slightly even though both were created from 30m landsat data and both follow the NVC-related Ecological Systems Classification curated by Natureserve. In either case, the vector overlay was created by first enforcing a .3ha minimum mapping unit, that required deleting any classes consisting of fewer than 4 contiguous landsat cells either side-side or cornerwise. This got around the statistical problem of numerous single-cell classes with types that seemed improbable given their matrix, and would have been inaccurate to use as an n=1 sample compared to the weak but useable n=4 sample. A primary goal in this elimination was to best preserve riparian and road features that might only be one pixel wide, hence the use of cornerwise contiguous groupings. Eliminated cell groups were absorbed into whatever neighboring class they shared the longest boundary with. The remaining raster groups were vectorized with light simplification to smooth out the stairstep patterns of raster data and hopefully improve the fidelity of the boundaries with the landscape. The resultant vectors show a range of fidelity with the landscape, where there is less apparent fidelity it must be remembered that ecosystems are normally classified with a mixture of visible and non-visible characteristics including soil, elevation and slope. Boundaries can be assigned based on the difference between 10% shrub cover and 20% shrub cover. Often large landscape areas would create "godzilla" polygons of more than 50,000 vertices, which can affect performance. These were eliminated using SIMPLIFY POLYGONS to reduce vertex spacing from 30m down to 50-60m where possible. Where not possible DICE was used, which bisects all large polygons with arbitrary internal divisions until no polygon has more than 50,000 vertices. To create midscale layers, ecological systems were dissolved into the macrogroups that they belonged to and resymbolized on macrogroup. This was another frequent source for godzillas as larger landscape units were delineate, so simplify and dice were then run again. Where the base ecol system tiles could only be served up by individual partition tile, macrogroups typically exhibited a 10-1 or 20-1 reduction in feature count allowing them to be assembled into single integrated map services by region, ie NW, SW. CNPS / CDFW / National Park Service Sources: (see also base service definition page) Unlike the Landsat-based raster modelling of the Natureserve and Gap national ecological systems, the CNPS/CDFW/NPS data date back to the origin of the National Vegetation Classification effort to map the US national parks in the mid 1990's.
These mapping efforts are a hybrid of photo-interpretation, satellite and corollary data to create draft ecological land units, which are then sampled by field crews and traditional vegetation plot surveys to quantify and analyze vegetation composition and distribution into the final vector boundaries of the formal NVC classes identified and classified. As such these are much more accurate maps, but the tradeoff is they are only done on one field project area at a time so there is not yet a national or even statewide coverage of these detailed maps.
However, with almost 2/3d's of California already mapped, that time is approaching. The challenge in creating standard map layers for this wide diversity of projects over the 2 decades since NVC began is the extensive evolution in the NVC standard itself as well as evolution in the field techniques and tools. To create a consistent set of map layers, a master crosswalk table was built using every different classification known at the time each map was created and then crosswalking each as best as could be done into a master list of the currently-accepted classifications. This field is called the "NVC_NAME" in each of these layers, and it contains a mixture of scientific names and common names at many levels of the classification from association to division, whatever the ecologists were able to determine at the time. For further precision, this field is split out into scientific name equivalents and common name equivalents.MAP LAYER NAMING: The data sublayers in this webmap are all based on the US National Vegetation Classification, a partnership of the USGS GAP program, US Forest Service, Ecological Society of America and Natureserve, with adoption and support from many federal & state agencies and nonprofit conservation groups. The USNVC grew out of the US National Park Service Vegetation Mapping Program, a mid-1990's effort led by The Nature Conservancy, Esri and the University of California. The classification standard is now an international standard, with associated ecological mapping occurring around the world. NVC is a hierarchical taxonomy of 8 levels, from top down: Class, Subclass, Formation, Division, Macrogroup, Group, Alliance, Association. The layers in this webmap represent 4 distinct programs: 1. The California Native Plant Society/Calif Dept of Fish & Wildlife Vegetation Classification and Mapping Program (Full Description of these layers is at the CNPS MS10 Service Registration Page and Cnps MS10B Service Registration Page . 2. USGS Gap Protected Areas Database, full description at the PADUS registration page . 3. USGS Gap Landcover, full description below 4. Natureserve Ecological Systems, full description belowLAYER NAMING: All Layer names follow this pattern: Source - Program - Level - Scale - RegionSource - Program = who created the data: Nserve = Natureserve, GapLC = USGS Gap Program Landcover Data PADUS = USGS Gap Protected Areas of the USA program Cnps/Cdfw = California Native Plant Society/Calif Dept of Fish & Wildlife, often followed by the project name such as: SFhill = Sierra Foothills, Marin Open Space, MMWD = Marin Municipal Water District etc. National Parks are included and may be named by their standard 4-letter code ie YOSE = Yosemite, PORE = Point Reyes.Level: The level in the NVC Hierarchy which this layer is based on: Base = Alliances and Associations Mac = Macrogroups Sub = SubclassesScale: One of 3 basic scales at which this layer will appear: Base = base scale, approx 1:1k up to 1:36k Mid = 72k to about 500k Out = 1m to 10mRegion: The region that this layer covers, ie USA=USA, WEST= western USA,
Marin = Marin County. May not appear if redundant to the Source-Program text.LABEL & COLOR: These overlays utilize a separate labelling layer to make it easy to include or not include labels, as needed. These are named the same as the layer they label, with "LABEL" added, and often the color used for that label layer in order to help tell them apart on the map. Note there can be multiple different label layers for the same set of polygons, depending upon the attribute or naming style desired, ie scientific names or common names. Finally the order of these services in the sublayers of a map service is normally designed so that ALL of the label services appear above ANY/ALL of the vector services they refer to, to prevent a vector service writing on top of a label and obscuring it.MAPPING PROJECTS INCLUDED IN THIS WEBMAP:Southern San Joaquin Valley Habitat Linkage (CDFW) . (Detailed Description & Attributes FGDC Metadata ds1021) Anza Borrego Desert State Park (CDFW) (Detailed Description & Attributes FGDC Metadata ds165) Alliance level Central Valley Riparian and Sacramento Valley (Detailed Description & Attributes FGDC Metadata ds1000) Sequoia and Kings Canyon National Parks (NPS) (Detailed Description & Attributes FGDC Metadata)Western Riverside County (Detailed Description & Attributes FGDC Metadata ds170) Mojave Vegetation for the