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USGS2025

Environmental characteristics of select managed ponds in the Sacramento–San Joaquin Delta—Implications for native fish conservation and research

The use of wetlands to support native fish research and conservation efforts in the Sacramento–San Joaquin Delta (Delta) of California is a growing priority. The purpose of our study was to examine the physiochemical and biological characteristics of select managed ponds in the Delta to determine if they would be suitable habitats for research involving the conservation of delta smelt ( Hypomesus transpacificus ). We studied 10 managed ponds distributed across the central part of the Delta situated on Bacon Island and Bouldin Island in San Joaquin County, and Holland Tract and Webb Tract islands in Contra Costa County. The managed ponds had a diversity of physical habitat configurations and were not directly connected to waterways surrounding the islands and, therefore, not affected by tides. We studied the managed ponds from approximately November 2021 to December 2023 to assess water quality, zooplankton, fish, and pesticide metrics. Water levels in the managed ponds were managed to varying degrees and were mostly independent of climate-driven wet-dry seasonality. Water quality conditions varied among ponds and were independent of geographic location. Overall, mean monthly chlorophyll a concentration ranged from 15 to 57 (mean=30) micrograms per liter (μg/L), dissolved oxygen concentration ranged from 4 to 9 (mean=7) milligrams per liter (mg/L), pH was 8, salinity was 1 practical salinity units (PSU), specific conductance ranged from 1,202 to 1,839 (mean=1,471) microsiemens per centimeter (μS/cm), and turbidity ranged from 13 to 24 (mean=19) Formazin Nephelometric Units (FNU). Water temperature thresholds that contribute to stress (21 degrees Celsius [°C]) and mortality (28 °C) of delta smelt were often exceeded during summer and fall, though vertical stratification contributed to lower bottom temperatures in the deepest managed ponds, which could potentially provide thermal refugia for delta smelt so long as dissolved oxygen concentrations are suitable. Zooplankton populations were broadly similar among managed ponds and included calanoid and cyclopoid copepods that would be suitable prey for delta smelt. Overall average total zooplankton biomass, as measured with a Schindler-Patalas trap, was 0.6 μg/L (min=0, max=63.6) and peaked during spring at more than 4 μg/L. Fish populations highly varied among the managed ponds with potential predators of delta smelt such as largemouth bass ( Micropterus salmoides ) and black crappie ( Pomoxis nigromaculatus ) present in several of the managed ponds; predator distribution among ponds seemed to have been driven primarily by deliberate stocking to facilitate local fisheries. Measured pesticide concentrations were below U.S. Environmental Protection Agency Aquatic Life Benchmarks except for exceedances of three compounds (diuron [herbicide], clothianidin [insecticide], and deltamethrin [pyrethroid insecticide]) in samples collected from ponds on Bouldin Island and Webb Tract. Overall, most managed ponds seemed suitable to support delta smelt, though physical control of potential predators and summer temperature might be needed. The results provide guidance on how to engineer and manage new managed ponds to support research and conservation efforts for delta smelt and other native fishes.

California↗

USGS2001

Nature reserves: Do they capture the full range of America's biological diversity?

Less than 6% of the coterminous United States is in nature reserves. Assessment of the occurrence of nature reserves across ranges of elevation and soil productivity classes indicates that nature reserves are most frequently found at higher elevations and on less productive soils. The distribution of plants and animals suggests that the greatest number of species is found at lower elevations. A preliminary assessment of the occurrence of mapped land cover types indicates that ???60% of mapped cover types have <10% of their area in nature reserves Land ownership patterns show that areas of lower elevation and more productive soils are most often privately owned and already extensively converted to urban and agricultural uses. Thus any effort to establish a system of nature reserves that captures the full geographical and ecological range of cover types and species must fully engage the private sector.

Ecological Applications↗

USGS1998

Significance of nearshore trace-fossil assemblages of the cambro-ordovician deadwood formation and Aladdin Sandstone, South Dakota

The Cambro-Ordovician Deadwood Formation and Aladdin Sandstone represent intertidal and subtidal, nearshore deposystems that contain few well-preserved body fossils, but contain abundant trace fossils. The present study uses the much neglected trace-fossil fauna to describe the diverse paleoenvironments represented in the Deadwood-Aladdin deposystems, and to better understand the environmental conditions that controlled benthic life in the Early Paleozoic. The Deadwood-Aladdin ichnotaxa can be separated into three distinct assemblages based on the changing sedimentologic and hydrodynamic conditions that existed across the Cambro-Ordovician shelf. Trace-fossil assemblages and corresponding lithofacies characteristics indicate that the Deadwood-Aladdin deposystems formed within an intertidal-flat and subtidal-shelf environment. Based on the distribution and numbers of preserved ichnotaxa, the intertidal flat can be subdivided further into an ecologically stressful inner sand-flat environment, and a more normal marine outer sand-flat environment, both of which belong to a mixed, Skolithos-Cruziana softground ichnofacies. The inner sand flat is characterized by low diversity, low numbers, and a general lack of complexly constructed ichnotaxa. Trace fossils common to both assemblages tend to be smaller in the inner flat compared to the outer sand flat. Taphonomic effects, such as substrate type and sediment heterogeneity, also aid in differentiating between the inner and outer sand-flat assemblages. The subtidal shelf environment is categorized in the Cruziana Ichnofacies. Ichnological evidence of periodic tempestite deposition and hardground development within this subtidal regime is manifested by high diversity and low abundance of ichnogenera.

Annals of Carnegie Museum↗

USGS2024

Seabed maps showing topography, ruggedness, backscatter intensity, sediment mobility, and the distribution of geologic substrates in quadrangle 2 of the Stellwagen Bank National Marine Sanctuary region offshore of Boston, Massachusetts

The U.S. Geological Survey, in cooperation with the National Marine Sanctuary Program of the National Oceanic and Atmospheric Administration, has conducted seabed mapping and related research in the Stellwagen Bank National Marine Sanctuary (SBNMS) region since 1993. The area being mapped using geophysical and geological data includes the SBNMS and the surrounding region, which totals approximately 3,700 square kilometers (km 2 ) and is subdivided into 18 quadrangles. The seabed is a glaciated terrain that is topographically and texturally diverse. Quadrangle 2, the subject of this scientific investigations map, has a mapped area of 209 km 2 and has water depths that range from about 19 meters (m) on the Stellwagen Bank crest to about 68 m in the Stellwagen Basin. Seven map types, each at a scale of 1:25,000, depict seabed topography, ruggedness, backscatter intensity, distribution of geologic substrates, sediment mobility, distribution of fine- and coarse-grained sand, and substrate mud content. These maps show the distribution of geologic substrates across the southwestern part of Stellwagen Bank, in Stellwagen Basin to the west and southwest of the bank, and in Little Stellwagen Basin and the western part of Race Point Channel to the south of the bank. Interpretations of multibeam sonar bathymetric and seabed backscatter imagery, photographs, video imagery, and grain-size analyses were used to create the geology-based maps. Data from 733 stations were analyzed, including 656 sediment samples. The geologic substrate maps of quadrangle 2 show the distribution of 19 geologic substrates that represent a wide range of textures, such as rippled and immobile sand, immobile muddy sand and sandy mud, sand that partially veneers gravel, and a boulder ridge. Mapped substrates are characterized by sediment grain-size composition, surface morphology, substrate layering, the mobility or immobility of substrate surfaces, and water depth range. This scientific investigations map portrays the major geological elements (substrates, topographic features, and processes) of environments in quadrangle 2. It is intended to provide a foundation for research into present and past sediment transport processes in a complex terrain, provide insights into the ecological requirements of invertebrate and vertebrate species that utilize the various substrates, and support seabed management in the region.

Massachusetts↗

USGS2024

The dynamics of sea otter prey selection under population growth and expansion

Sea otters ( Enhydra lutris ) were extirpated from much of their range in the North Pacific by the early 1900s but have made a remarkable recovery in Southeast Alaska. Sea otter populations have been particularly successful in Glacier Bay, Alaska, a protected tidewater glacier fjord with a diverse and productive nearshore habitat. Collection of sea otter foraging observations in Glacier Bay began in 1993, along with high-resolution aerial surveys that provide estimates of sea otter abundance and distribution. We integrated these two data sources to investigate how sea otter diet changed in space and time as sea otters established and spread across Glacier Bay. Specifically, we developed a multilevel Bayesian model to capture how sea otter diet at a location (the number, type, and size of prey collected) changed as a function of local cumulative otter abundance and the year in which the location was first occupied. This framework enabled us to estimate the sequence of sea otter prey selection and switching as prey populations responded to sea otter foraging pressure. We found that local sea otter diet changed substantially as the population established, shifting away from large urchins, crabs, and clams to Modiolus mussels and small urchins, and lastly to small clams and Mytilus mussels. We also found that sea otter diet at newly occupied sites changed as otters spread over the main channel and into the arms of Glacier Bay. Further, by 2019, sea otters across the bay were primarily foraging on small prey, regardless of the local occupancy history. The absence of a spatial gradient in the size of prey captured late in the study suggests that feedbacks between the top-down effects of sea otter foraging, sea otter dispersal processes, and local variation in habitat productivity may have homogenized the size structure of available prey across Glacier Bay.

Alaska↗

USGS2009

Simulating the recovery of suspended sediment transport and river-bed stability in response to dam removal on the Elwha River, Washington

U.S. Department of the Interior is planning to remove two high dams (30 and 60 m) from the Elwha River, which will allow the river to erode sediment deposits in the reservoirs, and ultimately restore the river ecosystem. Fluvial sediment transport and deposition paradoxically represent ecological disturbance and restoration. A one-dimensional, movable boundary sediment-transport model was applied at a daily time step to simulate changes in river-bed elevations and particle-size distributions and concentrations of suspended sediment. The simulations included a three-year dam removal period and a four-year recovery period. Simulated concentrations of suspended sediment recover rapidly during the recovery period. Simulated bed elevation and particle-size distributions are stable for much of the river during the recovery period, but high flows periodically disturb the river bed, causing changes in river-bed elevation and particle-size distribution, especially during autumn, when summer/autumn chinook salmon are incubating in redds. Although the river bed will become increasingly stable after dam removal, episodic high flows will interrupt recovery trends. Productivity and diversity of the ecosystem may be lower because of excess sediment immediately after dam removal but should increase during recovery above current levels as the river. Monitoring of the recovery of the Elwha River ecosystem can target ecologically significant physical parameters indicating the transition from a sediment transport-limited state to a supply-limited state.

Ecological Engineering↗

USGS2011

Biology, status, and management of the yellowstone cutthroat trout

Yellowstone cutthroat trout Oncorhynchus clarkii bouvieri were historically distributed in the Yellowstone River drainage (Montana and Wyoming) and the Snake River drainage (Wyoming, Idaho, Utah, Nevada, and probably Washington). Individual populations evolved distinct life history characteristics in response to the diverse environments in which they were isolated after the last glaciation. Anthropogenic activities have resulted in a substantial decline (42% of the historical range is currently occupied; 28% is occupied by core [genetically unaltered] populations), but the number of extant populations, especially in headwater streams, has precluded listing of this taxon under the Endangered Species Act. Primary threats to persistence of Yellowstone cutthroat trout include (1) invasive species, resulting in hybridization, predation, disease, and interspecific competition; (2) habitat degradation from human activities such as agricultural practices, water diversions, grazing, dam construction, mineral extraction, grazing, timber harvest, and road construction; and (3) climate change, including an escalating risk of drought, wildfire, winter flooding, and rising temperatures. Extirpation of individual populations or assemblages has led to increasing isolation and fragmentation of remaining groups, which in turn raises susceptibility to the demographic influences of disturbance (both human and stochastic) and genetic factors. Primary conservation strategies include (1) preventing risks associated with invasive species by isolating populations of Yellowstone cutthroat trout and (2) connecting occupied habitats (where possible) to preserve metapopulation function and the expression of multiple life histories. Because persistence of isolated populations may be greater in the short term, current management is focused on isolating individual populations and restoring habitats; however, this approach implies that humans will act as dispersal agents if a population is extirpated because of stochastic events.

Idaho, Montana, Utah, Wyoming↗

USGS2024

High inter-population connectivity and occasional gene flow between subspecies improves recovery potential for the endangered Least Bell’s Vireo

Increasingly, genomic data are being used to supplement field-based ecological studies to help evaluate recovery status and trends in endangered species. We collected genomic data to address two related questions regarding the Least Bell’s Vireo ( Vireo bellii ), an endangered migratory songbird restricted to southern California riparian habitat for breeding. First, we sought to delineate the range limits and potential overlap between Least Bell’s Vireo and its sister subspecies, the Arizona Bell’s Vireo, by analyzing samples from the deserts of eastern California, southwestern Nevada, Utah and Arizona. Second, we evaluated genetic structure among Least Bell’s Vireo populations in coastal California and estimated effective population size. Clustering analyses based on 10,571 single nucleotide polymorphisms (SNPs) from 317 samples supported two major groups that aligned closely to the previously defined subspecies ranges. The first cluster included birds in the Central Valley, all coastal drainages, and westernmost deserts of California, with no further sub-structuring among coastal drainages. Almost all birds from the Amargosa River in eastern California and eastward assigned to the second cluster; however, low levels of gene flow were detected across the subspecies groups, with greater rates of gene flow from Arizona Bell’s Vireo to Least Bell’s Vireo than the reverse. Admixed individuals occurred in the California deserts; and although smaller than coastal populations, desert populations may be important for maintaining and replenishing genetic diversity and facilitating the movement of potentially adaptive genes between subspecies. Within Least Bell’s Vireo, local populations in coastal drainages comprised a single genetic population, with some evidence of close relatives distributed across drainages, suggesting these could function as a well-connected metapopulation. These results are consistent with previous Least Bell’s Vireo banding studies that reported high rates of dispersal among drainages. Effective population size for both subspecies was high, suggesting that adaptive potential has been maintained despite previous declines.

Ornithological Applications↗

USGS2013

Genetic relationships among some subspecies of the Peregrine Falcon ( Falco peregrinus L.), inferred from mitochondrial DNA control-region sequences

The ability to successfully colonize and persist in diverse environments likely requires broad morphological and behavioral plasticity and adaptability, and this may partly explain why the Peregrine Falcon ( Falco peregrinus ) exhibits a large range of morphological characteristics across their global distribution. Regional and local differences within Peregrine Falcons were sufficiently variable that ∼75 subspecies have been described; many were subsumed, and currently 19 are generally recognized. We used sequence information from the control region of the mitochondrial genome to test for concordance between genetic structure and representatives of 12 current subspecies and from two areas where subspecies distributions overlap. Haplotypes were broadly shared among subspecies, and all geographic locales shared a widely distributed common haplotype (FalconCR2). Haplotypes were distributed in a star-like phylogeny, consistent with rapid expansion of a recently derived species, with observed genetic patterns congruent with incomplete lineage sorting and/or differential rates of evolution on morphology and neutral genetic characters. Hierarchical analyses of molecular variance did not uncover genetic partitioning at the continental level, despite strong population-level structure ( F ST = 0.228). Similar analyses found weak partitioning, albeit significant, among subspecies ( F CT = 0.138). All reconstructions placed the hierofalcons' (Gyrfalcon [ F. rusticolus ] and Saker Falcon [ F. cherrug ]) haplotypes in a well-supported clade either basal or unresolved with respect to the Peregrine Falcon. In addition, haplotypes representing Taita Falcon ( F. fasciinucha ) were placed within the Peregrine Falcon clade.

The Auk↗

USGS2016

Determining the spatial variability of wetland soil bulk density, organic matter, and the conversion factor between organic matter and organic carbon across coastal Louisiana, U.S.A.

Soil bulk density (BD), soil organic matter (SOM) content, and a conversion factor between SOM and soil organic carbon (SOC) are often used in estimating SOC sequestration and storage. Spatial variability in BD, SOM, and the SOM–SOC conversion factor affects the ability to accurately estimate SOC sequestration, storage, and the benefits ( e.g., land building area and vertical accretion) associated with wetland restoration efforts, such as marsh creation and sediment diversions. There are, however, only a few studies that have examined large-scale spatial variability in BD, SOM, and SOM–SOC conversion factors in coastal wetlands. In this study, soil cores, distributed across the entire coastal Louisiana (approximately 14,667 km 2 ) were used to examine the regional-scale spatial variability in BD, SOM, and the SOM–SOC conversion factor. Soil cores for BD and SOM analyses were collected during 2006–09 from 331 spatially well-distributed sites in the Coastwide Reference Monitoring System network. Soil cores for the SOM–SOC conversion factor analysis were collected from 15 sites across coastal Louisiana during 2006–07. Results of a split-plot analysis of variance with incomplete block design indicated that BD and SOM varied significantly at a landscape level, defined by both hydrologic basins and vegetation types. Vertically, BD and SOM varied significantly among different vegetation types. The SOM–SOC conversion factor also varied significantly at the landscape level. This study provides critical information for the assessment of the role of coastal wetlands in large regional carbon budgets and the estimation of carbon credits from coastal restoration.

Louisiana↗

USGS2018

The potential of unmanned aerial systems for sea turtle research and conservation: a review and future directions

The use of satellite systems and manned aircraft surveys for remote data collection has been shown to be transformative for sea turtle conservation and research by enabling the collection of data on turtles and their habitats over larger areas than can be achieved by surveys on foot or by boat. Unmanned aerial vehicles (UAVs) or drones are increasingly being adopted to gather data, at previously unprecedented spatial and temporal resolutions in diverse geographic locations. This easily accessible, low-cost tool is improving existing research methods and enabling novel approaches in marine turtle ecology and conservation. Here we review the diverse ways in which incorporating inexpensive UAVs may reduce costs and field time while improving safety and data quality and quantity over existing methods for studies on turtle nesting, at-sea distribution and behaviour surveys, as well as expanding into new avenues such as surveillance against illegal take. Furthermore, we highlight the impact that high-quality aerial imagery captured by UAVs can have for public outreach and engagement. This technology does not come without challenges. We discuss the potential constraints of these systems within the ethical and legal frameworks which researchers must operate and the difficulties that can result with regard to storage and analysis of large amounts of imagery. We then suggest areas where technological development could further expand the utility of UAVs as data-gathering tools; for example, functioning as downloading nodes for data collected by sensors placed on turtles. Development of methods for the use of UAVs in sea turtle research will serve as case studies for use with other marine and terrestrial taxa.

Endangered Species Research↗

USGS2020

Small mammals and ungulates respond to and interact with revegetation processes following dam removal

Terrestrial wildlife communities are often overlooked as components of ecosystem restoration following dam removal. However, a diverse mammalian fauna colonizes habitat on dewatered reservoirs and may influence restoration processes. We studied mammalian colonization and ungulate herbivory from 2014 to 2018 following the removal of two large dams on the Elwha River in Washington, USA. Specifically, we examined (1) small mammal colonization and (2) Roosevelt elk ( Cervus elaphus roosevelti ) and Columbian black-tailed deer ( Odocoileus hemionus columbianus ) distribution and browsing pressure in association with revegetation efforts. We live-trapped small mammals on two former reservoir beds and monitored deer and elk use by conducting pellet group counts and quantifying ungulate herbivory at plots throughout the former reservoir beds and an adjacent reference site. We found that the proportion of deciduous riparian species on plots best predicted occupancy for mice, shrews, and voles. Small mammal species diversity was best explained by the proportion of logs and conifers on study plots. Roosevelt elk presence and browsing intensity on willows ( Salix spp.) and black cottonwood ( Populus balsamifera ssp. trichocarpa ) varied both spatially and temporally, affecting the stature and potentially the growth trajectories of these species. Early seral restoration of these terrestrial habitats has included the presence of a diversity of granivores, insectivores, and herbivores, with elk demonstrating the strongest influence over portions of the study area. Small mammal colonization complements revegetation succession and demonstrates restoration of ecological processes, while large ungulates may be playing a more substantial role in shaping revegetation.

Washington↗

USGS2014

Diverse juvenile life-history behaviours contribute to the spawning stock of an anadromous fish population

Habitat quality often varies substantially across space and time, producing a shifting mosaic of growth and mortality trade-offs across watersheds. Traditional studies of juvenile habitat use have emphasised the evolution of single optimal strategies that maximise recruitment to adulthood and eventual fitness. However, linking the distribution of individual behaviours that contribute to recruitment at the population level has been elusive, particularly for highly fecund aquatic organisms. We examined juvenile habitat use within a population of sockeye salmon (Oncorhynchus nerka) that spawn in a watershed consisting of two interconnected lakes and a marine lagoon. Otolith microchemical analysis revealed that the productive headwater lake accounted for about half of juvenile growth for those individuals surviving to spawn in a single river in the upper watershed. However, 47% of adults had achieved more than half of their juvenile growth in the downstream less productive lake, and 3% of individuals migrated to the estuarine environment during their first summer and returned to freshwater to overwinter before migrating back to sea. These results describe a diversity of viable habitat-use strategies by juvenile sockeye salmon that may buffer the population against poor conditions in any single rearing environment, reduce density-dependent mortality and have implications for the designation of critical habitat for conservation purposes. A network of accessible alternative habitats providing trade-offs in growth and survival may be important for long-term viability of populations.

Alaska↗

USGS2023

Relationships among rare plant communities and abiotic conditions in managed spring-fed arid wetlands

Spring-fed wetlands within arid and semiarid systems are hotspots for endemism and distribution of rare plants. Interactions among groundwater and the geomorphic and climatic features of the setting control the abiotic conditions, particularly soil salinity and moisture, that support these plants. However, water uncertainty and land use change challenge the persistence of conditions necessary to support rare plant communities. Wetland management can be implemented to sustain abiotic processes that support rare plant communities, but key information is needed to guide management practices. In this study, we evaluate the relationships of rare plants to abiotic conditions in a managed spring-fed arid wetland. Soil salinity and moisture conditions were monitored and related to the presence and abundance of rare plants within management units. Soil salinity and moisture variability were related to groundwater dynamics near springs, but wetland management influenced variability in seasonally flooded areas. Permanently saturated conditions and low soil salinities during the spring season supported higher plant diversity and the presence and greater abundance of rare plants. Rare plant presence and abundance were negatively related to low soil moisture, particularly in the summer. Results indicate that increases in soil salinity during the early establishment of plants may affect their distribution and abundance, an important management consideration in arid landscapes and hydrologically altered systems. Our findings inform the restoration and management of rare plant communities and contribute to the management of spring-fed arid wetlands.

New Mexico↗

USGS2024

Assessing spatial variability of nutrients, phytoplankton, and related water-quality constituents in the California Sacramento–San Joaquin Delta at the landscape scale—2018 high resolution mapping surveys

Executive Summary This study examined the abundance and distribution of nutrients and phytoplankton in the tidal aquatic environments of the Sacramento–San Joaquin Delta (Delta) and Suisun Bay, comprising three spatial surveys conducted in May, July, and October of 2018 that used continuous underway high frequency sampling and measurements onboard a high-speed boat to characterize spatial variation across the extent of the Delta. The method used involves simultaneously collecting information about the concentration and spatial distribution of all major nutrient forms with analogous information about the major classes of phytoplankton and associated water-quality conditions. The results showed substantial variation across space and time, providing an unprecedented snapshot of the dynamic environmental processes that shape the ways nutrients interact with and affect aquatic habitats in the Delta. The purposes of this study were to improve our understanding of how hydrodynamics, landscape features, and aquatic primary productivity interact to drive nutrient cycling and transport in the Delta and to provide insights into the underlying processes most directly responsible for the conditions at the time of this study, and thus into the range of conditions that may be expected following the wide array of prospective future changes to the Delta. One major anticipated change at the time of this study was the planned upgrade to the Sacramento Regional Wastewater Treatment Plant, but the study also informs our understanding of potential effects from other changes to the Delta, such as those caused by other nutrient-management actions, flow actions, large-scale wetland restoration, drought, flood, levee failure, and changes to water management. Nutrient loading is the primary driver of nutrient concentrations in the Delta, but several other major drivers interact to shape their distribution and effects: geomorphology, hydrodynamics, landscape features, and aquatic productivity. Hydrodynamics affect timescales of transport and dilution of nutrient loads in the Delta. During transit through the system, channel geometry, tidal mixing, and water exports affect hydrodynamics in diverse ways that influence water-residence and transport times, thereby markedly affecting the range of times during which natural internal cycling can alter nutrient concentrations and forms. Channel geometry and location shape tidal energy and river currents into these observed dynamics. Interactions with Delta aquatic landscapes such as herbaceous tidal marsh, submerged aquatic vegetation, and large expanses of intertidal or subtidal sediments (all highly productive landscapes) exert demand on available nutrient supplies but can also simultaneously transform and generate nutrients. Finally, while phytoplankton require nutrients to sustain production and thus are a potential nutrient sink, the amount and form of nutrients also can influence the occurrence of harmful algal blooms (HABs) that adversely affect aquatic organisms as well as affect the occurrence of beneficial algal blooms that result in production of algae that are favorable for imperiled Delta pelagic aquatic food webs. The surveys revealed a complex mosaic of spatial variation, with nutrient concentrations varying from near zero to well above concentrations considered eutrophic; nutrient concentrations were more often related to the extent of hydrologic transport and mixing than to specific geographic locations or to specific landscape features. Similarly, the surveys identified phytoplankton abundance ranging from near detection to the level of large phytoplankton blooms, with large variation in phytoplankton community composition. Although the study occurred during a period of low bloom activity, phytoplankton productivity appeared to be the strongest potential sink for inorganic nutrients in the Delta, indicating that it is a larger control on nutrient concentrations and distribution than previously understood. Cycling and transformation within the water column only appeared to substantially lower total nutrient concentrations at the longest estimated transport timescales. Contrary to expectations, we did not observe substantial nutrient depletion near landscape-scale features such as open-water habitats, submerged aquatic vegetation beds, extensive wetlands, or exposed sediments, indicating that these habitat types did not act as major sinks for nutrients in the Delta during these surveys. These results indicated that nutrient reduction efforts may have the greatest effect on pelagic phytoplankton productivity in the more productive reaches of the Delta and estuary, but these effects are unlikely to be magnified by changes to nutrient loss within the Delta over conceivable changes in flow conditions, Delta water management actions, or large-scale wetland restoration activities. Nevertheless, local processes were shown to cause substantial loss, and thus integrating of nutrient effects with other indicators of aquatic habitat conditions will help inform planning future actions at specific sites. Finally, we note that the primary contribution of this study was intended to be the survey data themselves. Aside from the results highlighted in this report, the surveys are a benchmark against which future environmental change may be evaluated, including changes to nutrient management or water exports, drought, large-scale wetland restoration, and climate change. Further, although we highlight some of the main findings from the surveys in this report, the necessarily limited scope precludes examination of many topics for which these surveys may be highly informative. To facilitate the utility of these data to stakeholders, managers, and researchers, we have released the data online (Bergamaschi and others, 2020) and created an online data exploration portal ( https://ca.water.usgs.gov/bay-delta/2018-delta-wide-mapping-surveys.html ) where users may query the surveys in a variety of ways to test hypotheses, examine relationships, assess spatial trends, and download data. The data exploration portal is intended to be an immersive experience that allows users to gain greater understanding of the complex interactions that shape Delta aquatic environments. This report is intended as a companion to the portal, allowing the reader to challenge and further explore the highlighted findings. This study was a collaboration between the U.S. Geological Survey and the Delta Regional Monitoring Program, with additional funding provided from U.S. Geological Survey Cooperative Matching Funds Program.

California↗

USGS1985

Carboniferous paleogeographic, phytogeographic, and paleoclimatic reconstructions

Two revised paleogeographic reconstructions of the Visean and Westphalian C-D stages are presented based on recent paleomagnetic, phytogeographic, stratigraphic, and tectonic data. These data change the positions of some continental blocks, and allow the definition of several new ones. The most important modifications that have been incorporated in these reconstructions are: (1) a proposed isthmus linking North America and Siberia across the Bering Strait; and (2) the separation of China and Southeast Asia in six major blocks, including South China, North China, Shan Thai-Malaya, Indochina, Qangtang, and Tarim blocks. Evidence is presented that suggests that at least the South China, Shan Thai-Malaya, and Qangtang blocks were derived from the northern margin of Gondwana. Multivariate statistical analysis of phytogeographic data from the middle and late Paleozoic allow definition of a number of different phytogeographic units for four time intervals: (1) the Early Devonian, (2) Tournaisian—early Visean, (3) Visean, and (4) late Visean—early Namurian A. Pre-late Visean—early Namurian A floral assemblages from South China show affinities with northern Gondwana floras suggesting a southerly position and provides additional support for our reconstruction of South China against the northern margin of Gondwana. There is a marked decrease in the diversity of phytogeographic units in the Namurian and younger Carboniferous. This correlates closely with the time of assembly of most of Pangaea. The general pattern of Carboniferous phytogeographic units corresponds well with global distribution of continents shown on our paleogeographic reconstructions. In addition, we have constructed paleoclimatic maps for the two Carboniferous time intervals. These maps stress the distribution of rainfall, as this should be strongly correlated with the floras. There is marked change in the rainfall patterns between the Visean and Westphalian C-D. This change corresponds with the closing of the Appalachian-Ouachita ocean between Laurussia and Gondwana, and reflects the removal of a low-latitude moisture source that probably gave rise to monsoonal conditions along the northern margin of Gondwana in the Visean and earlier times. As well, the presence of a substantial heat source at high elevation in the Late Carboniferous significantly influenced the distribution of climatic belts.

International Journal of Coal Geology↗

USGS2010

Hydraulic modeling of mussel habitat at a bridge-replacement site, Allegheny River, Pennsylvania, USA

The Allegheny River in Pennsylvania supports a large and diverse freshwater-mussel community, including two federally listed endangered species, Pleurobema clava (Clubshell) and Epioblasma torulosa rangiana (Northern Riffleshell). It is recognized that river hydraulics and morphology play important roles in mussel distribution. To assess the hydraulic influences of bridge replacement on mussel habitat, metrics such as depth, velocity, and their derivatives (shear stress, Froude number) were collected or computed. The objectives of the project were to evaluate mussel and hydraulic data at a reference site and to compare those findings to a bridge-replacement site. The findings were used to support a statistical analysis, which establishes correlations between mussel count and hydraulics, and a numerical model to forecast habitat based on the statistics. ArcGIS was selected to manage the data and generate a grid to compute area statistics for 3319, 4.9-m × 4.9-m cells (cell) for total mussel count, depth, velocity, shear stress, and Froude number. The Wilcoxon Rank Sum test indicated no statistical significance between the total mussel count and the hydraulic variables; however, trellis graphs were used to account for the spatial variability in the data set. For the flow conditions measured, the total mussel count per cell is greatest at sections where (1) velocities range from 0.061 to 0.21 m/s, (2) shear stresses range from 0.48 to 3.8 dyne/cm 2 , and (3) Froude numbers range from 0.006 to 0.04. Based on the statistical targets established, the hydraulic model results suggest that an additional 2428 m 2 or a 30-percent increase in suitable mussel habitat could be generated at the replacement-bridge site when compared to the baseline condition associated with the existing bridge at that same location. The study did not address the influences of substrate, acid mine drainage, sediment loads from tributaries, and surface-water/ground-water exchange on mussel habitat. Future studies could include methods for quantifying (1) channel–substrate composition and distribution using tools such as hydroacoustic echosounders specifically designed and calibrated to identify bed composition and mussel populations, (2) surface-water and ground-water interactions, and (3) a high-streamflow event.

Pennsylvania↗

USGS2014

Reconnaissance study of erosion and deposition produced by the flood of August 1955 in Connecticut

A large area in the valley bottoms in Connecticut was inundated by the flood of August 1955. Relative to the total area flooded that part permanently modified by the flow was surprisingly small. Although great in some places, the distribution of these permanent modifications of channel and flood plain was spotty. Erosion of the channel and valley bottom appears to have been most severe in narrow, steep valleys. Environments of deposition were diverse. They appeared to be related to rate and direction of flow, quantity and size of sediments locally available, and in some cases to the presence of vegetation. Most of the coarse sediment deposited in the valley appears to have been derived from local sources such as valley walls and terraces composed of glacial outwash and till and flood plains containing considerable gravel. Fine sand predominated in most of the sediment deposited. Considering the magnitude of the runoff, the quantity of fine sediment transported or deposited by the flood was small. The maximum observed concentration was 473 parts per million in Scantic River at Broad Brook. Newly deposited fine sediments are thin or absent on the flood plains of many valleys which were beneath 20 ft of slow‐moving flood waters. The paucity of deposition in such ideal depositional environments also indicates that the flow did not have a high concentration of fine sediments. A number of boulders five to seven feet in diameter were moved by flood waters in reaches in which smaller gravels were undisturbed. Severe erosion in the uplands was minor. In this reconnaissance we saw little evidence of newly formed gullies and no areas of severe sheet erosion. This was the case in both woodland and pasture land. Large amounts of subsurface flow and relatively unerodible ground are presumed to be responsible for the absence of erosion.

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