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USGS2015

Book review: Analysis of capture–recapture data

Analysis of Capture–Recapture Data by McCrea and Morgan is an excellent, easy to read monograph about capture–recapture models. In this book, the authors provide a concise overview of traditional closed population capture–recapture models (Models M0, Mb, Mh, etc.), individual covariate models, and open population models such as the Cormack–Jolly–Seber, Jolly–Seber models, multi-state models, and more recent developments such as occupancy models, state-space models, and integrated population models. The authors write “In this book we aim to cover the many modern developments in the area of capture–recapture and related models, and to set them in historical context of relevant research over the past 100 years.” The book does a good job of achieving this objective. And it is a very easy to read because it is well organized and the writing is clear and concise. I would recommend this book as a reference for the quantitative ecologist or statistician interested in knowing what’s out there. Review info: Analysis of Capture–Recapture Data. By Rachel S. McCrea and Byron J. T. Morgan, 2015. ISBN: 978-14398-6590, xx+292 pp.

Journal of Agricultural, Biological, and Environme↗

USGS2002

Ontogenetic behavior and migration of Volga River Russian sturgeon, Acipenser gueldenstaedtii, with a note on adaptive significance of body color

We conducted laboratory experiments with Volga River Russian sturgeon, Acipenser gueldenstaedtii, to develop a conceptual model of early behavior. We daily observed fish from day-0 (embryos, first life interval after hatching) to day-29 feeding larvae for preference of bright habitat and cover, swimming distance above the bottom, up- and downstream movement, and diel activity. Hatchling embryos initiated a downstream migration, which suggests that predation risk of embryos at spawning sites is high. Migration peaked on days 0-5 and ceased on day 7 (8-day migration). Migrants preferred bright, open habitat and early migrants swam-up far above the bottom (maximum daily median, 140 cm) in a vertical swim tube. Post-migrant embryos did not prefer bright illumination but continued to prefer white substrate, increased use of cover habitat, and swam on the bottom. Larvae initiated feeding on day 10 after 170.6 cumulative temperature degree-days. Larvae did not migrate, weakly preferred bright illumination, preferred white substrate and open habitat, and swam near the bottom (daily median 5-78 cm). The lack of a strong preference by larvae for bright illumination suggests foraging relies more on olfaction than vision for locating prey. A short migration by embryos would disperse wild sturgeon from a spawning area, but larvae did not migrate, so a second later migration by juveniles disperses young sturgeon to the sea (2-step migration). Embryo and larva body color was light tan and tail color was black. The migration, behavior, and light body color of Russian sturgeon embryos was similar to species of Acipenser and Scaphirhynchus in North America and to Acipenser in Asia that migrate after hatching as embryos. The similarity in migration style and body color among species with diverse phylogenies likely reflects convergence for common adaptations across biogeographic regions. ?? 2002 Kluwer Academic Publishers.

Environmental Biology of Fishes↗

USGS2000

Seagrass responses to and recovery (?) from seven years of brown tide

Most harmful algal blooms are relatively short, violent paroxysms to aquatic systems. The Texas brown tide was unique in its 7-year domination of upper Laguna Madre wherein it reduced light penetrating 1 m from 31 to 63% on an annual basis between June 1990 and May 1997. In response, seagrasses declined in biomass in deep areas for two years. Over the next three years, bare areas opened up in the deepest areas of the seagrass meadow and the outer seagrass boundary retreated landward. In the last two years of the brown tide, regression of the dominant species, Halodule wrightii, slowed and stopped, and Halophila engelmanni, a previously minor species, revegetated some areas. Subsequent to cessation of meadow retreat, water clarity improved to pre-brown tide levels, consistent with the hypothesis that regeneration of nutrients from retreating seagrass meadow may have been the source of the nutrient subsidy required to sustain the brown tide at high concentration. However, after a short interlude of clear water and Halodule recovery, a resurgence of the bloom occurred and areas of regrowth succumbed. Although human activities did not seem to be involved in initiation or persistence of the brown tide, nutrients brought in by runoff from agricultural lands may have contributed to the return of bloom conditions.

Texas↗

USGS1994

Water resources activities in Kentucky, 1993-94

The U.S. Geological Survey (USGS) is the principal Federal water-resources data collection and investigation agency. Through the Water Resources Division District Office in Kentucky, the USGS investigates the occurrence, distribution, quantity, movement, and chemical and biological quality of surface and ground water in the State. The mission of this program is to collect, interpret, and publish information on water resources. Almost all research and data collection is a cooperative effort in which planning and financial support are shared by State and local agencies and governments. Other activities are funded by other Federal agencies or by direct Congressional appropriation. This report is intended to inform the public and cooperating agencies, vitally interested in the water resources of Kentucky, as to the current status of the Distfict's data collection and investigation program. Included in the report are summaries of water-resources activities in Kentucky conducted by the USGS. Also included is a description of the USGS mission and program, District organization, funding sources and cooperating agencies, and a list of USGS publications relevant to the water resources of the State.

Open-File Report↗

USGS2013

National Park Service Vegetation Inventory Program, Cuyahoga Valley National Park, Ohio

The National Park Service (NPS) Vegetation Inventory Program (VIP) is an effort to classify, describe, and map existing vegetation of national park units for the NPS Natural Resource Inventory and Monitoring (I&M) Program. The NPS VIP is managed by the NPS Biological Resources Management Division and provides baseline vegetation information to the NPS Natural Resource I&M Program. The U.S. Geological Survey (USGS) Vegetation Characterization Program lends a cooperative role in the NPS VIP. The USGS Upper Midwest Environmental Sciences Center, NatureServe, and NPS Cuyahoga Valley National Park (CUVA) have completed vegetation classification and mapping of CUVA. Mappers, ecologists, and botanists collaborated to identify and describe vegetation types within the National Vegetation Classification Standard (NVCS) and to determine how best to map them by using aerial imagery. The team collected data from 221 vegetation plots within CUVA to develop detailed descriptions of vegetation types. Data from 50 verification sites were also collected to test both the key to vegetation types and the application of vegetation types to a sample set of map polygons. Furthermore, data from 647 accuracy assessment (AA) sites were collected (of which 643 were used to test accuracy of the vegetation map layer). These data sets led to the identification of 45 vegetation types at the association level in the NVCS at CUVA. A total of 44 map classes were developed to map the vegetation and general land cover of CUVA, including the following: 29 map classes represent natural/semi-natural vegetation types in the NVCS, 12 map classes represent cultural vegetation (agricultural and developed) in the NVCS, and 3 map classes represent non-vegetation features (open-water bodies). Features were interpreted from viewing color-infrared digital aerial imagery dated October 2010 (during peak leaf-phenology change of trees) via digital onscreen three-dimensional stereoscopic workflow systems in geographic information systems (GIS). The interpreted data were digitally and spatially referenced, thus making the spatial database layers usable in GIS. Polygon units were mapped to either a 0.5 ha or 0.25 ha minimum mapping unit, depending on vegetation type. A geodatabase containing various feature-class layers and tables shows the locations of vegetation types and general land cover (vegetation map), vegetation plot samples, verification sites, AA sites, project boundary extent, and aerial photographic centers. The feature-class layer and relate tables for the CUVA vegetation map provides 4,640 polygons of detailed attribute data covering 13,288.4 ha, with an average polygon size of 2.9 ha. Summary reports generated from the vegetation map layer show map classes representing natural/semi-natural types in the NVCS apply to 4,151 polygons (89.4% of polygons) and cover 11,225.0 ha (84.5%) of the map extent. Of these polygons, the map layer shows CUVA to be 74.4% forest (9,888.8 ha), 2.5% shrubland (329.7 ha), and 7.6% herbaceous vegetation cover (1,006.5 ha). Map classes representing cultural types in the NVCS apply to 435 polygons (9.4% of polygons) and cover 1,825.7 ha (13.7%) of the map extent. Map classes representing non-NVCS units (open water) apply to 54 polygons (1.2% of polygons) and cover 237.7 ha (1.8%) of the map extent. A thematic AA study was conducted of map classes representing natural/semi-natural types in the NVCS. Results present an overall accuracy of 80.7% (kappa index of 79.5%) based on data from 643 of the 647 AA sites. Most individual map-class themes exceed the NPS VIP standard of 80% with a 90% confidence interval. The CUVA vegetation mapping project delivers many geospatial and vegetation data products in hardcopy and/or digital formats. These products consist of an in-depth project report discussing methods and results, which include descriptions and a dichotomous key to vegetation types, map classification and map-class descriptions, and a contingency table showing AA results. The suite of products also includes a database of vegetation plots, verification sites, and AA sites; digital pictures of field sites; field data sheets; aerial photographic imagery; hardcopy and digital maps; and a geodatabase of vegetation types and land cover (map layer), fieldwork locations (vegetation plots, verification sites, and AA sites), aerial photographic index, project boundary, and metadata. All geospatial products are projected in Universal Transverse Mercator, Zone 17, by using the North American Datum of 1983. Information on the NPS VIP and completed park mapping projects are located on the Internet at <http://science.nature.nps.gov/im/inventory/veg> and <http://www.usgs.gov/core_science_systems/csas/vip/index.html>.

Natural Resource Technical Report↗

USGS2012

Future scenarios of land-use and land-cover change in the United States--the Marine West Coast Forests Ecoregion

Detecting, quantifying, and projecting historical and future changes in land use and land cover (LULC) has emerged as a core research area for the U.S. Geological Survey (USGS). Changes in LULC are important drivers of changes to biogeochemical cycles, the exchange of energy between the Earth’s surface and atmosphere, biodiversity, water quality, and climate change. To quantify the rates of recent historical LULC change, the USGS Land Cover Trends project recently completed a unique ecoregion-based assessment of late 20th century LULC change for the western United States. To characterize present LULC, the USGS and partners have created the National Land Cover Database (NLCD) for the years 1992, 2001, and 2006. Both Land Cover Trends and NLCD projects continue to evolve in an effort to better characterize historical and present LULC conditions and are the foundation of the data presented in this report. Projecting future changes in LULC requires an understanding of the rates and patterns of change, the major driving forces, and the socioeconomic and biophysical determinants and capacities of regions. The data presented in this report is the result of an effort by USGS scientists to downscale the Intergovernmental Panel on Climate Change (IPCC) Special Report on Emission Scenarios (SRES) to ecoregions of the conterminous United States as part of the USGS Biological Carbon Sequestration Assessment. The USGS biological carbon assessment was mandated by Section 712 of the Energy Independence and Security Act of 2007. As part of the legislative mandate, the USGS is required to publish a methodology describing, in detail, the approach to be used for the assessment. The development of future LULC scenarios is described in chapter 3.2 and appendix A. Spatial modeling is described in chapter 3.3.2 and appendix B and in Sohl and others (2011). In this report, we briefly summarize the major components and methods used to downscale IPCC-SRES scenarios to ecoregions of the conterminous United States, followed by a description of the Marine West Coast Forests Ecoregion, and lastly a description of the data being published as part of this report.

California;Oregon;Washington↗

USGS2005

Landscape level reforestation priorities for forest breeding landbirds in the Mississippi Alluvial Valley

Thousands of ha of cleared wetlands are being reforested annually in the Mississippi Alluvial Valley (MAV). Despite the expansive and long-term impacts of reforestation on the biological communities of the MAV, there is generally a lack of landscape level planning in its implementation. To address this deficiency we used raster-based digital data to assess the value of forest restoration to migratory landbirds for each ha within the MAV. Raster themes were developed that reflected distance from 3 existing forest cover parameters: (1) extant forest, (2) contiguous forest patches between 1,012 and 40,000 ha, and (3) forest cores with contiguous area <5,200 ha. Forest core habitat was any forest habitat >1 km from an agricultural, urban, or pastoral edge. Two additional raster themes were developed that combined information on the proportion of forest cover and average size of forest patches, respectively, within landscapes of 50,000, 100,000, 150,000, and 200,000 ha. Data from these 5 themes were amalgamated into a single raster using a weighting system that gave increased emphasis to existing forest cores, larger forest patches, and moderately forested landscapes while deemphasizing reforestation near small or isolated forest fragments and within largely agricultural landscapes. This amalgamated raster was then modified by the geographic location of historical forest cover and the current extent of public land ownership to assign a reforestation priority score to each ha in the MAV. However, because reforestation is not required on areas with extant forest cover and because restoration is unlikely on areas of open water and urban communities, these lands were not assigned a reforestation priority score. These spatially explicit reforestation priority scores were used to simulate reforestation of 368,000 ha (5%) of the highest priority lands in the MAV. Targeting restoration to these high priority areas resulted in a 54% increase in forest core - an area of forest core that exceeded the area of simulated reforestation. Bird Conservation Regions, developed within the framework of the Partners in Flight: Mississippi Alluvial Valley Bird Conservation Plan, encompassed a large proportion (circa 70%) of the area with highest priority for reforestation. Similarly, lands with high reforestation priority often were enrolled in the Wetland Reserve Program.

Book chapter↗

USGS2008

Biological communities and geomorphology of patch reefs in Biscayne National Park, Florida, U.S.A.

Coral reef ecosystem management benefits from continual, quantitative assessment of the resources being managed, plus assessment of factors that affect distribution patterns of organisms in the ecosystem. In this study, we investigated the relationships among physical, benthic, and fish variables in effort to help explain the distribution patterns of ecologically and economically important species on twelve patch reefs within Biscayne National Park (BNP), Florida, U.S.A. We visited 196 randomly-located sampling stations across twelve shallow (< 10m) patch reefs, using SCUBA to conduct our surveys. We measured physical variables (e.g., substratum type), estimated the percent cover of benthic community members (e.g., coral, algae), and counted and estimated mean size for each fish species observed. We also used high-density bathymetric data collected remotely via airborne laser surveying (Experimental Advanced Airborne Research Lidar (EAARL)) to calculate rugosity (bumpiness) of the reef habitat. Here we present our findings visually by graphing our quantitative community and physical structure data simultaneously in a GIS map format. You will see that biological organisms arrange themselves on each patch reef in a non-random manner. For example, many species of fish prefer to locate themselves in areas of the reef where the rugosity index is high. Rugose parts of the reef provide them with good hiding places from predators. These maps (and the data used to create them) are permanent records of the status of reef resources found on these twelve patch reefs in BNP as of September, 2003. The survey data found in the shapefile located on this CD product includes benthic percent cover data for algae, coral, encrusting invertebrates, and substratum type, in addition to gorgonian abundance and volume, total fish abundance and species richness, and specific counts for Acanthurids (surgeonfish), Scarids (parrotfish), Lutjanids (snappers), Haemulids (grunts), Serranids (groupers), and Pomacentrids (damselfish).

Florida↗

USGS2002

Ecological evaluation of the abundance and effects of elk herbivory in Rocky Mountain National Park, Colorado, 1994-1999

Several National Park Service units in the Intermountain region possess a number of closely related management needs relative to the abundance of wild ungulates and their herbivory effects on plants and ecosystem processes. In 1993, the then National Biological Service (NBS) - now U.S. Geological Survey, Biological Resources Discipline (USGS, BRD) initiated a series of research studies in four park units in the Intermountain West., into the abundance and effects of ungulates on park ecosystems. Each of these parks received a number of similar research study elements including: (a) a number of new ungulate grazing exclosures (n = 12-21 exclosures per park); (b) aerial survey sightability models to estimate population sizes of ungulates; (e) measures of biomass production and consumption rates near the exclosures and across the landscape; (d) studies of the effects of the grazing on plant abundance, species diversity, and ecosystem effects; and (e) computer model simulations (SAVANNA) of the effects on the ecosystem and plant resources of different ungulate management scenarios. One park unit, Rocky Mountain National Park, Colorado, received funding from the U.S. Geological Survey (USGS, BRD) and parallel funding from NPS for an intensive research study of the effects of elk on the park ecosystems.

Colorado↗

USGS2017

The Wetland and Aquatic Research Center strategic science plan

Introduction The U.S. Geological Survey (USGS) Wetland and Aquatic Research Center (WARC) has two primary locations (Gainesville, Florida, and Lafayette, Louisiana) and field stations throughout the southeastern United States and Caribbean. WARC’s roots are in U.S. Fish and Wildlife Service (USFWS) and National Park Service research units that were brought into the USGS as the Biological Research Division in 1996. Founded in 2015, WARC was created from the merger of two long-standing USGS biology science Centers—the Southeast Ecological Science Center and the National Wetlands Research Center—to bring together expertise in biology, ecology, landscape science, geospatial applications, and decision support in order to address issues nationally and internationally. WARC scientists apply their expertise to a variety of wetland and aquatic research and monitoring issues that require coordinated, integrated efforts to better understand natural environments. By increasing basic understanding of the biology of important species and broader ecological and physiological processes, this research provides information to policymakers and aids managers in their stewardship of natural resources and in regulatory functions. This strategic science plan (SSP) was developed to guide WARC research during the next 5–10 years in support of Department of the Interior (DOI) partnering bureaus such as the USFWS, the National Park Service, and the Bureau of Ocean Energy Management, as well as other Federal, State, and local natural resource management agencies. The SSP demonstrates the alignment of the WARC goals with the USGS mission areas, associated programs, and other DOI initiatives. The SSP is necessary for workforce planning and, as such, will be used as a guide for future needs for personnel. The SSP also will be instrumental in developing internal funding priorities and in promoting WARC’s capabilities to both external cooperators and other groups within the USGS.

Open-File Report↗

USGS2012

Simulated effects of dam removal on water temperatures along the Klamath River, Oregon and California, using 2010 Biological Opinion flow requirements

Computer model simulations were run to determine the effects of dam removal on water temperatures along the Klamath River, located in south-central Oregon and northern California, using flow requirements defined in the 2010 Biological Opinion of the National Marine Fisheries Service. A one-dimensional, daily averaged water temperature model (River Basin Model-10) developed by the U.S. Environmental Protection Agency Region 10, Seattle, Washington, was used in the analysis. This model had earlier been configured and calibrated for the Klamath River by the U.S. Geological Survey for the U.S. Department of the Interior, Klamath Secretarial Determination to simulate the effects of dam removal on water temperatures for current (2011) and future climate change scenarios. The analysis for this report was performed outside of the scope of the Klamath Secretarial Determination process at the request of the Bureau of Reclamation Technical Services Office, Denver, Colorado.  For this analysis, two dam scenarios were simulated: “dams in” and “dams out.” In the “dams in” scenario, existing dams in the Klamath River were kept in place. In the “dams out” scenario, the river was modeled as a natural stream, without the J.C. Boyle, Copco1, Copco2, and Iron Gate Dams, for the entire simulation period. Output from the two dam scenario simulations included daily water temperatures simulated at 29 locations for a 50-year period along the Klamath River between river mile 253 (downstream of Link River Dam) and the Pacific Ocean. Both simulations used identical flow requirements, formulated in the 2010 Biological Opinion, and identical climate conditions based on the period 1961–2009.  Simulated water temperatures from January through June at almost all locations between J.C. Boyle Reservoir and the Pacific Ocean were higher for the “dams out” scenario than for the “dams in” scenario. The simulated mean monthly water temperature increase was highest [1.7–2.2 degrees Celsius (°C)] in May downstream of Iron Gate Dam. However, from August to December, dam removal generally cooled water temperatures. During these months, water temperatures decreased 1°C or more between Copco Lake and locations 50 miles or more downstream. The greatest mean monthly temperature decrease was 4°C in October just downstream of Iron Gate Dam. Near the ocean, the effects of dam removal were small (less than 0.2°C) for most months. However, the mean November temperature near the ocean was almost 0.5°C cooler with dam removal.

Open-File Report↗

USGS2015

Southern Salish Sea Habitat Map Series: Admiralty Inlet

In 2010 the Environmental Protection Agency, Region 10 initiated the Puget Sound Scientific Studies and Technical Investigations Assistance Program, designed to support research in support of implementing the Puget Sound Action Agenda. The Action Agenda was created in response to Puget Sound having been designated as one of 28 estuaries of national significance under section 320 of the U.S. Clean Water Act, and its overall goal is to restore the Puget Sound Estuary's environment by 2020. The Southern Salish Sea Mapping Project was funded by the Assistance Program request for proposals process, which also supports a large number of coastal-zone- and ocean-management issues. The issues include the recommendations of the Marine Protected Areas Work Group to the Washington State Legislature (Van Cleve and others, 2009), which endorses a Puget Sound and coast-wide marine conservation needs assessment, gap analysis of existing Marine Protected Areas (MPA) and recommendations for action. This publication is the first of four U.S. Geological Survey Scientific Investigation Maps that make up the Southern Salish Sea Mapping Project. The remaining three map blocks to be published in the future, located south of Admiralty Inlet, are shown in figure 1. Puget Sound is a deep, fjord-type estuary covering an area of 2,330 km 2 in the Pacific Northwest region of the United States (fig. 1). It is connected to the ocean by the Strait of Juan de Fuca, a turbulent passage approximately 160 km in length and 22 km wide at its west end, expanding to over 40 km wide at its east end (Thomson, 1994). During the Pleistocene, the area was occupied several times by lobes of continental ice, resulting in a complex basin-fill of glacial and interglacial deposits that are locally as thick as 1100 m (Johnson and others, 2001). The last glaciation, called the Fraser glaciation, began after 28,800±740 14 C yr B.P. when ice started a slow expansion (Clague, 1981). At peak advance the westward Juan de Fuca lobe reached the edge of the continental shelf through the Juan de Fuca Strait shortly before 14,460±200 14 C yr B.P. (Herzer and Bornhold, 1982). The southward Puget lobe advanced to its terminal position in Puget Sound by around 14,150 14 C yr B.P. (Porter and Swanson, 1998). Ice retreated from its maximum to northern Whidbey Island by 13,650±350 14 C yr B.P. (Dethier and others, 1995). Retreating glaciers resulted in a thick sequence of ice-contact, glacial-marine sediment, and early post-glacial sediments (Linden and Schurrer, 1988). These deposits have experienced the effects of a marine transgression followed by regression, resulting in a sea-level several tens of meters lower than the present day (Linden and Schurrer, 1988). A second transgression brought sea level to about the present level by around 5,470±120 14 C yr B.P. (Clague and others, 1982) establishing the present oceanographic and geologic environment Puget Sound is separated into four interconnected basins; Whidbey, Central (Main), Hood Canal, and South (Thomson, 1994). The Whidbey, Central, and Hood Canal basins are the three main branches of the Puget Sound estuary and are separated from the Strait of Juan de Fuca by a double sill at Admiralty Inlet. The Admiralty Inlet map area includes the Inlet and a portion of the Whidbey Basin (fig. 1). The shallower South Basin is separated by a sill at Tacoma Narrows and is highly branched with numerous finger inlets. Flow within Puget Sound is dominated by tidal currents of as much as 1 m/s at Admiralty Inlet, reducing to approximately 0.5 m/s in the Central Basin (Lavelle and others, 1988). The lack of silt and clay-sized sediments in the Admiralty Inlet map area is likely a result of the strong currents (see Ground-Truth Studies for the Admiralty Inlet Map Area, sheet 3). The subtidal component of flow reaches approximately 0.1 m/s and is driven by density gradients arising from the contrast in salty ocean water at the entrance and freshwater inputs from stream flow (Lavelle and others, 1988). The total freshwater input to Puget Sound is approximately 3.4 x 10 6 m 3 /day, primarily from the Skagit River (Cannon, 1983). The subtidal circulation mostly consists of a two-layered flow in the basins with fresher water exiting at the surface and saltier water entering at depth (Ebbesmeyer and Cannon, 2001). In general, surface waters flow north and deeper waters flow south; variations arise from wind effects that can drive a surface current in the same direction as the wind, and a baroclinic response in the lower layer to about 100-m depth (Matsuura and Cannon, 1997). Oceanographic properties are influenced by temporal forcing parameters such as reduced stream flow during the 2000-01 drought that increased surface salinity and decreased differences between surface and bottom waters (Newton and others, 2003). On offshore seismic-reflection profiles, Pleistocene strata (excluding latest Pleistocene glacial and post-glacial deposits) form a distinct seismic unit, bounded below by pre-Tertiary or Tertiary basement and above by typically flat-lying latest Pleistocene to Holocene deposits that fill in erosional or depositional relief (Johnson and others, 2001). Cores from central Puget Sound have accumulation rates that range from 85 to 1200 mg/cm 2 /yr, or 0.12 to 2.4 cm/yr; the highest accumulation rates are near the southern end of central Puget Sound (Carpenter and others, 1985). Carpenter and others (1985) un-weighted arithmetic mean of accumulation rates for central Puget Sound deeper stations is 480±340 (± one standard deviation) mg/cm 2 /yr. Lavelle and others (1985) also found rates as high as 1200 mg/cm 2 /yr over the past approximately 70 years in cores in the Central Basin off of and north and south of Elliott Bay. Puget Sound basin rates are comparable to rates in midshelf silt deposits on the Washington coast north of the Columbia River (Nittrouer and others, 1979). The deep subtidal (in other words, below SCUBA depths) habitats of Puget Sound are relatively poorly known. A few subtidal surveys exist for several habitat types from the 1960s and 1970s (reviewed in Dethier, 1990), using grab and box core data. The Dethier (1990) review divides habitat up into Coast and Marine Ecological Classification Standard (CMECS) substrate, water column energy, and depth zones but does not attempt to map these habitats, rather it is an inventory of habitats found in the area and the flora and fauna associated with each habitat. The approach of the Southern Salish Sea Mapping project is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar data (the undersea equivalent of satellite remote-sensing data in terrestrial mapping), acoustic backscatter, seafloor video, seafloor photography, and bottom-sediment sampling data. This approach is based in part on methods presented and data collection and product needs identified at the Washington State Seafloor Mapping Workshop (Washington State Seafloor Mapping Workshop Steering Committee, 2008), attended by coastal and marine managers and scientists. The map products display seafloor geomorphology and substrate, and identify potential marine benthic habitats. It is emphasized that the more interpretive habitat and geology maps rely on the integration of multiple, new high-resolution datasets and that mapping at small scales would not be possible without such data. Oceanographic current and wave data is not included in this analysis, however, the accompanying geographic information system (GIS) data set is designed and intended to be combined with oceanographic and biologic data sets assembled by others in the future and some of the GIS data has already been incorporated in the unpublished Nature Conservancy Benthic Habitats of Puget Sound database. This publication includes four map sheets, explanatory text, and a descriptive pamphlet. Each map sheet is published as a portable document format (PDF) file. ESRI ArcGIS compatible geotiffs (for example, bathymetry) and shapefiles (for example video observation points) will be available for download in the data catalog associated with this publication (Cochrane, 2015). An ArcGIS Project File with the symbology used to generate the map sheets is also provided. For those who do not own the full suite of ESRI GIS and mapping software, the data can be read using ESRI ArcReader, a free viewer that is available at http://www.esri.com/software/arcgis/arcreader/index.html .

Washington↗

USGS2016

California State Waters Map Series — Offshore of Santa Cruz, California

Introduction In 2007, the California Ocean Protection Council initiated the California Seafloor Mapping Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, marine benthic habitats, and geology within the limit of California’s State Waters. The CSMP approach is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar data, acoustic backscatter, seafloor video, seafloor photography, high-resolution seismic-reflection profiles, and bottom-sediment sampling data. The map products display seafloor morphology and character, identify potential marine benthic habitats, and illustrate both the surficial seafloor geology and shallow subsurface geology. The Offshore of Santa Cruz map area is located in central California, on the Pacific Coast about 98 km south of San Francisco. The city of Santa Cruz (population, about 63,000), the largest incorporated city in the map area and the county seat of Santa Cruz County, lies on uplifted marine terraces between the shoreline and the northwest-trending Santa Cruz Mountains, part of California’s Coast Ranges. All of California’s State Waters in the map area is part of the Monterey Bay National Marine Sanctuary. The map area is cut by an offshore section of the San Gregorio Fault Zone, and it lies about 20 kilometers southwest of the San Andreas Fault Zone. Regional folding and uplift along the coast has been attributed to a westward bend in the San Andreas Fault Zone and to right-lateral movement along the San Gregorio Fault Zone. Most of the coastal zone is characterized by low, rocky cliffs and sparse, small pocket beaches backed by low, terraced hills. Point Santa Cruz, which forms the north edge of Monterey Bay, provides protection for the beaches in the easternmost part of the map area by sheltering them from the predominantly northwesterly waves. The shelf in the map area is underlain by variable amounts (0 to 25 m) of upper Quaternary shelf, estuarine, and fluvial sediments deposited as sea level fluctuated in the late Pleistocene. The inner shelf is characterized by bedrock outcrops that have local thin sediment cover, the result of regional uplift, high wave energy, and limited sediment supply. The midshelf occupies part of an extensive, shore-parallel mud belt. The thickest sediment deposits, inferred to consist mainly of lowstand nearshore deposits, are found in the southeastern and northwestern parts of the map area. Coastal sediment transport in the map area is characterized by northwest-to-southeast littoral transport of sediment that is derived mainly from ephemeral streams in the Santa Cruz Mountains and also from local coastal-bluff erosion. During the last approximately 300 years, as much as 18 million cubic yards (14 million cubic meters) of sand-sized sediment has been eroded from the area between Año Nuevo Island and Point Año Nuevo and transported south; this mass of eroded sand is now enriching beaches in the map area. Sediment transport is within the Santa Cruz littoral cell, which terminates in the submarine Monterey Canyon. Benthic species observed in the Offshore of Santa Cruz map area are natives of the cold-temperate biogeographic zone that is called either the “Oregonian province” or the “northern California ecoregion.” This biogeographic province is maintained by the long-term stability of the southward-flowing California Current, the eastern limb of the North Pacific subtropical gyre that flows from southern British Columbia to Baja California. At its midpoint off central California, the California Current transports subarctic surface (0–500 m deep) waters southward, about 150 to 1,300 km from shore. Seasonal northwesterly winds that are, in part, responsible for the California Current, generate coastal upwelling. The south end of the Oregonian province is at Point Conception (about 300 km south of the map area), although its associated phylogeographic group of marine fauna may extend beyond to the area offshore of Los Angeles in southern California. The ocean off of central California has experienced a warming over the last 50 years that is driving an ecosystem shift away from the productive subarctic regime towards a depopulated subtropical environment. Biological productivity resulting from coastal upwelling supports populations of Sooty Shearwater, Western Gull, Common Murre, Cassin’s Auklet, and many other less populous bird species. In addition, an observable recovery of Humpback and Blue Whales has occurred in the area; both species are dependent on coastal upwelling to provide nutrients. The large extent of exposed inner shelf bedrock supports large forests of “bull kelp,” which is well adapted for high-wave-energy environments. The kelp beds are the northernmost known habitat for the population of southern sea otters. Common fish species found in the kelp beds and rocky reefs include lingcod and various species of rockfish and greenling.

California↗

USGS2019

Contaminant baselines and sediment provenance along the Puget Sound Energy Transport Corridor, 2015

The transport of coal and oil can result in contaminated soil, water, and organisms from unintended releases. Trains carrying coal and crude oil regularly pass through Puget Sound, Washington, and an increase in the number of coal and oil trains is expected in the future. This study characterized levels of potentially toxic contaminants in sediment in September 2015: arsenic, metals, and polycyclic aromatic hydrocarbons (PAHs) at four sites with fine-grained sediment (Chuckanut Bay, Padilla Bay, Snohomish River Delta, Nisqually River Delta) adjacent to the Burlington Northern Santa Fe (BNSF) rail line in the Puget Sound region. Arsenic (As) and metals levels were compared to those measured at a fifth site, urban Saltwater State Park, which was expected to show contaminants associated with urbanization but not rail transport of coal and oil because it is not adjacent to the BNSF rail line. Knowledge about current properties of soil and sediment is essential for quantifying impacts of spills and other releases, and for setting remediation or restoration targets. For the sampling effort and timing of this study, all five sites had fine sediment contents of cadmium (Cd), mercury (Hg), lead (Pb), and zinc (Zn) below minimal effects levels. Pb and Zn appeared to be urban sourced. Median As, chromium (Cr), copper (Cu), and nickel (Ni) levels were in the range where adverse biological effects would possibly occur; however, Cr and Ni were geologically sourced and unlikely to be bioavailable to organisms. As, Cu, and antimony (Sb) levels were highly correlated, an association that is characteristic of legacy smelting operations; however, total sediment contents of these three elements, along with Hg and As/Sb ratios, were near natural levels and could indicate river-borne inputs. Median total PAH concentrations were highest at Snohomish River Delta, but were below minimal effects levels at all sites. Diagnostic PAH ratios were indicative of PAHs sourced from petroleum combustion and coal/biomass burning, rather than from spilled petroleum or coal. Rare earth element patterns were distinct among watersheds with Cascade volcanoes, granitic rocks, or non-volcanic sediments, making them promising sediment provenance indicators. Knowledge about sediment sources and contaminant distributions could provide unique insights about sediment-bound contaminant sourcing, delivery, and dispersal in nearshore regions.

Washington↗

USGS2010

Biological, Physical and Chemical Data From Gulf of Mexico Gravity and Box Core MRD05-04

This paper presents the benthic foraminiferal census data, magnetic susceptibility measurements, vanadium and organic geochemistry (carbon isotope, sterols, and total organic carbon) data from the MRD05-04 gravity and box cores. The MRD05-04 cores were obtained from the Louisiana continental shelf in an on-going initiative to examine the geographic and temporal extent of hypoxia, low-oxygen bottom-water content, and geochemical transport. The development of low-oxygen bottom water conditions in coastal waters is dependent upon a new source of bio-available nutrients introduced into a well-stratified water column. A number of studies have concluded that the development of the current seasonal hypoxia (dissolved oxygen < 2 mg L-1) in subsurface waters of the northern Gulf of Mexico is related to increased transport of nutrients (primarily nitrogen, but possibly also phosphorous) by the Mississippi River. However, the development of earlier episodes of seasonal low-oxygen subsurface water on the Louisiana shelf may be related to Mississippi River discharge.

Open-File Report↗

USGS2008

USGS Workshop on Scientific Aspects of a Long-Term Experimental Plan for Glen Canyon Dam, April 10-11, 2007, Flagstaff, Arizona

Executive Summary Glen Canyon Dam is located in the lower reaches of Glen Canyon National Recreation Area on the Colorado River, approximately 15 miles upriver from Grand Canyon National Park (fig. 1). In 1992, Congress passed and the President signed into law the Grand Canyon Protection Act (GCPA; title XVIII, sec. 1801?1809, of Public Law 102-575), which seeks ?to protect, mitigate adverse impacts to, and improve the values for which Grand Canyon National Park and Glen Canyon National Recreation Area were established.? The Glen Canyon Dam Adaptive Management Program (GCDAMP) was implemented as a result of the 1996 Record of Decision on the Operation of Glen Canyon Dam Final Environmental Impact Statement to ensure that the primary mandate of the GCPA is met through advances in information and resources management (U.S. Department of the Interior, 1995). On November 3, 2006, the Bureau of Reclamation (Reclamation) announced it would develop a long-term experimental plan environmental impact statement (LTEP EIS) for operational activities at Glen Canyon Dam and other management actions on the Colorado River. The purpose of the long-term experimental plan is twofold: (1) to increase the scientific understanding of the ecosystem and (2) to improve and protect important downstream resources. The proposed plan would implement a structured, longterm program of experimentation to include dam operations, potential modifications to Glen Canyon Dam intake structures, and other management actions such as removal of nonnative fish species. The development of the long-term experimental plan continues efforts begun by the GCDAMP to protect resources downstream of Glen Canyon Dam, including Grand Canyon, through adaptive management and scientific experimentation. The LTEP EIS will rely on the extensive scientific studies that have been undertaken as part of the adaptive management program by the U.S. Geological Survey?s (USGS) Grand Canyon Monitoring and Research Center (GCMRC), one of the four research stations within the USGS Southwest Biological Science Center. On April 10 and 11, 2007, at the behest of Reclamation, the GCMRC convened a workshop with scientific experts to identify one or more scientifically credible, long-term experimental options for Reclamation to consider for the LTEP EIS that would be consistent with the purpose and need for the plan. Workshop participants included government, academic, and private scientists with broad experience in the Colorado River in Grand Canyon and regulated rivers around the world. Resource managers and GCDAMP participants were also present on the second day of the workshop. In advance of the workshop, Reclamation and LTEP EIS cooperating agencies identified 14 core scientific questions. Workshop participants were asked to consider how proposed options would address these questions, which fall primarily into four areas: (1) conservation of endangered humpback chub (Gila cypha) and other high-priority biological resources, (2) conservation of sediment resources, (3) enhancement of recreational resources, and (4) preservation of cultural resources. A secondary objective of the workshop was the evaluation of four long-term experimental options developed by the GCDAMP Science Planning Group (SPG) (appendix B). The flow and nonflow treatments called for in the four experimental options were an important starting point for workshop discussions. At the beginning of the workshop, participants were provided with the final LTEP EIS scoping report prepared by Reclamation. Participants were also advised that Reclamation had committed to ?make every effortEto ensure that a new population of humpback chub is established in the mainstem or one or more of the tributaries within Grand Canyon? in the 1995 Operation of Glen Canyon Dam Final Environmental Impact Statement (U.S. Department of the Interior, 1995). This decision was consistent with the U.S. Fish and Wildlife Service?s 1995 bi

Open-File Report↗

USGS1987

Reconnaissance of hydrology, land use, ground-water chemistry, and effects of land use on ground-water chemistry in the Albuquerque-Belen basin, New Mexico

In 1984, the U.S. Geological Survey began regional assessments of groundwater contamination in 14 areas, one of which was the Albuquerque-Belen basin. Groundwater recharge occurs along the basin margins. Groundwater discharge occurs as evapotranspiration in the Rio Grande valley, pumpage, and groundwater flow to the Socorro basin. Open-space land use, which primarily is used for grazing livestock, occupies the majority of the basin. In the Rio Grande valley, agricultural and residential land uses are predominant; in the area near Albuquerque, the land also is used for commercial, institutional , and industrial purposes. The Albuquerque-Belen basin was divided into seven zones on the basis of water chemistry. These water-chemistry zones indicate that large variations in water chemistry exist in the basin as the result of natural processes. Groundwater in the majority of the Albuquerque-Belen basin has a relatively low susceptibility to contamination because the depth to water is > 100 ft and there is virtually no natural mechanism for recharge to the groundwater system. Groundwater in the Rio Grande valley has a relatively high susceptibility to contamination because the depth to water is generally < 30 ft and there are many types of recharge to the groundwater system. Changes in land use may cause changes in the chemical composition of recharge to the groundwater system. The relatively large concentrations of dissolved iron in the Rio Grande valley near Albuquerque may result from the change from agricultural land use to residential land use. Recharge associated with agricultural land use is relatively oxidized because the water is in equilibrium with the atmosphere, whereas recharge associated with residential land use (onsite waste-disposal effluent) is relatively reduced and has larger concentrations of organic carbon, biological oxygen demand, and chemical oxygen demand. The constituents in the onsite waste-disposal effluent could cause reducing conditions in the aquifer and the subsequent dissolution of iron and manganese oxides. Trace metals adsorbed to these iron and manganese oxides could be remobilized in groundwater after dissolution of the oxides.

New Mexico↗

USGS2011

Mechanisms influencing changes in lake area in Alaskan boreal forest

During the past &sim;50 years, the number and area of lakes have declined in several regions in boreal forests. However, there has been substantial finer-scale heterogeneity; some lakes decreased in area, some showed no trend, and others increased. The objective of this study was to identify the primary mechanisms underlying heterogeneous trends in closed-basin lake area. Eight lake characteristics ( δ 18 O, electrical conductivity, surface : volume index, bank slope, floating mat width, peat depth, thaw depth at shoreline, and thaw depth at the forest boundary) were compared for 15 lake pairs in Alaskan boreal forest where one lake had decreased in area since &sim;1950, and the other had not. Mean differences in characteristics between paired lakes were used to identify the most likely of nine mechanistic scenarios that combined three potential mechanisms for decreasing lake area (talik drainage, surface water evaporation, and terrestrialization) with three potential mechanisms for nondecreasing lake area (subpermafrost groundwater recharge through an open talik, stable permafrost, and thermokarst). A priori expectations of the direction of mean differences between decreasing and nondecreasing paired lakes were generated for each scenario. Decreasing lakes had significantly greater electrical conductivity, greater surface : volume indices, shallower bank slopes, wider floating mats, greater peat depths, and shallower thaw depths at the forest boundary. These results indicated that the most likely scenario was terrestrialization as the mechanism for lake area reduction combined with thermokarst as the mechanism for nondecreasing lake area. Terrestrialization and thermokarst may have been enhanced by recent warming which has both accelerated permafrost thawing and lengthened the growing season, thereby increasing plant growth, floating mat encroachment, transpiration rates, and the accumulation of organic matter in lake basins. The transition to peatlands associated with terrestrialization may provide a transient increase in carbon storage enhancing the role of northern ecosystems as major stores of global carbon.

Alaska↗