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USGS2017

Storage filters upland suspended sediment signals delivered from watersheds

Climate change, tectonics, and humans create long- and short-term temporal variations in the supply of suspended sediment to rivers. These signals, generated in upland erosional areas, are filtered by alluvial storage before reaching the basin outlet. We quantified this filter using a random walk model driven by sediment budget data, a power-law distributed probability density function (PDF) to determine how long sediment remains stored, and a constant downstream drift velocity during transport of 157 km/yr. For 25 km of transport, few particles are stored, and the median travel time is 0.2 yr. For 1000 km of transport, nearly all particles are stored, and the median travel time is 2.5 m.y. Both travel-time distributions are power laws. The 1000 km travel-time distribution was then used to filter sinusoidal input signals with periods of 10 yr and 10 4 yr. The 10 yr signal is delayed by 12.5 times its input period, damped by a factor of 380, and is output as a power law. The 10 4 yr signal is delayed by 0.15 times its input period, damped by a factor of 3, and the output signal retains its sinusoidal input form (but with a power-law “tail”). Delivery time scales for these two signals are controlled by storage; in-channel transport time is insignificant, and low-frequency signals are transmitted with greater fidelity than high-frequency signals. These signal modifications are essential to consider when evaluating watershed restoration schemes designed to control sediment loading, and where source-area geomorphic processes are inferred from the geologic record.

Geology↗

USGS2007

Incremental assembly and prolonged consolidation of Cordilleran magma chambers--Evidence from the Southern Rocky Mountain volcanic field

Recent inference that Mesozoic Cordilleran plutons grew incrementally during >10 6 yr intervals, without the presence of voluminous eruptible magma at any stage, minimizes close associations with large ignimbrite calderas. Alternatively, Tertiary ignimbrites in the Rocky Mountains and elsewhere, with volumes of 1–5 × 10 3 km 3 , record multistage histories of magma accumulation, fractionation, and solidification in upper parts of large subvolcanic plutons that were sufficiently liquid to erupt. Individual calderas, up to 75 km across with 2–5 km subsidence, are direct evidence for shallow magma bodies comparable to the largest granitic plutons. As exemplified by the composite Southern Rocky Mountain volcanic field (here summarized comprehensively for the first time), which is comparable in areal extent, magma composition, eruptive volume, and duration to continental-margin volcanism of the central Andes, nested calderas that erupted compositionally diverse tuffs document deep composite subsidence and rapid evolution in subvolcanic magma bodies. Spacing of Tertiary calderas at distances of tens to hundreds of kilometers is comparable to Mesozoic Cordilleran pluton spacing. Downwind ash in eastern Cordilleran sediments records large-scale explosive volcanism concurrent with Mesozoic batholith growth. Mineral fabrics and gradients indicate unified flow-age of many pluton interiors before complete solidification, and some plutons contain ring dikes or other textural evidence for roof subsidence. Geophysical data show that low-density upper-crustal rocks, inferred to be plutons, are 10 km or more thick beneath many calderas. Most ignimbrites are more evolved than associated plutons; evidence that the subcaldera chambers retained voluminous residua from fractionation. Initial incremental pluton growth in the upper crust was likely recorded by modest eruptions from central volcanoes; preparation for caldera-scale ignimbrite eruption involved recurrent magma input and homogenization high in the chamber. Some eroded calderas expose shallow granites of similar age and composition to tuffs, recording sustained postcaldera magmatism. Plutons thus provide an integrated record of prolonged magmatic evolution, while volcanism offers snapshots of conditions at early stages. Growth of subvolcanic batholiths involved sustained multistage open-system processes. These commonly involved ignimbrite eruptions at times of peak power input, but assembly and consolidation processes continued at diminishing rates long after peak volcanism. Some evidence cited for early incremental pluton assembly more likely records late events during or after volcanism. Contrasts between relatively primitive arc systems dominated by andesitic compositions and small upper-crustal plutons versus more silicic volcanic fields and associated batholiths probably reflect intertwined contrasts in crustal thickness and magmatic power input. Lower power input would lead to a Cascade- or Aleutian-type arc system, where intermediate-composition magma erupts directly from middle- and lower-crustal storage without development of large shallow plutons. Andean and southern Rocky Mountain–type systems begin similarly with intermediate-composition volcanism, but increasing magma production, perhaps triggered by abrupt changes in plate boundaries, leads to development of larger upper-crustal reservoirs, more silicic compositions, large ignimbrites, and batholiths. Lack of geophysical evidence for voluminous eruptible magma beneath young calderas suggests that near-solidus plutons can be rejuvenated rapidly by high-temperature mafic recharge, potentially causing large explosive eruptions with only brief precursors.

Southern Rocky Mountains↗

USGS1987

Snowpack ion accumulation and loss in a basin draining to Lake Superior

The objective of this study was to relate winter precipitation ionic inputs, snowpack retention, and change in first-order stream chemistry with spring snowpack melt. During winter 1982–83, measurement of precipitation inputs, snowpack concentration and loading, and streamwater concentration and discharge of Ca2+, K+, H+, NO3−, and SO42− from a 176-ha watershed reveals that only H+ might be lost from the snowpack before first thaw. Above-freezing soil temperature beneath the snowpack may be a factor in H+ loss. An initial 1-d thaw resulted in loss of over one third (6 eq∙ha−1) of the snowpack Ca2+. Over one half the snowpack load of K+, H+, NO3−, and SO42−, was lost in a subsequent midwinter freeze–thaw period. Snowpack loading of ionic species was reduced by 70–90% before peak spring melting and stream discharge. Ecosystem H+ retention and biological uptake of NO3− further mitigate ionic "pulses" in streamwater. Sulfate discharge exceeds bulk inputs, which suggests significant dry deposition input and little forest soil retention of this anion. The snowpack was relatively small, which limits wider application of these results to the region.

Lake Superior↗

USGS1990

Pattern of solute movement from snow into an upper Michigan stream

Precipitation, snowpack, snowmelt, and streamwater samples were collected in a small gauged watershed draining into Lake Superior during winter 1987–88 to assess the importance of snowmelt pattern and meltwater pathways in the occurrence of solute pulses in streamwater. The snowpack along the south shore of Lake Superior can contain 50% of annual precipitation inputs and 38% of annual ionic inputs including moderate levels of strong acids. Throughout winter, thawed surface soils and small but steady snowpack moisture release promoted movement of snowpack solutes to surface mineral soils. Preferential elution of K + , NH4 + , and H + from the snowpack occurred with the initial thaw. Most ions exhibited pulses in snowmelt. Transport of snowpack solutes to the stream during snowmelt was through near-surface soil macropores and overland flow. For those ions with concentrations higher in the snowpack than in the premelt streamwater, K + , NH 4 + , and H + , the earliest snowmelt pulses had the greatest influence on streamwater chemistry. Unlike other portions of the region with resistant bedrock, the widespread presence of alkaline glacial till provides excess stream acid neutralization capacity (ANC) to buffer acidic inputs. Peak winter streamwater ANC reduction was caused principally by spring melt dilution of base cations and associated alkalinity, constant high SO 4 2- levels, and an increase in NO 3 - . The maximum reduction in stream ANC was concurrent with overland flow. Relative to its snowmelt concentration, NO 3 - was highest in streamwater with some stream input likely the result of nitrification and N mineralization.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2008

Families of miocene monterey crude oil, seep, and tarball samples, coastal California

Biomarker and stable carbon isotope ratios were used to infer the age, lithology, organic matter input, and depositional environment of the source rocks for 388 samples of produced crude oil, seep oil, and tarballs to better assess their origins and distributions in coastal California. These samples were used to construct a chemometric (multivariate statistical) decision tree to classify 288 additional samples. The results identify three tribes of 13C-rich oil samples inferred to originate from thermally mature equivalents of the clayey-siliceous, carbonaceous marl and lower calcareous-siliceous members of the Monterey Formation at Naples Beach near Santa Barbara. An attempt to correlate these families to rock extracts from these members in the nearby COST (continental offshore stratigraphic test) (OCS-Cal 78-164) well failed, at least in part because the rocks are thermally immature. Geochemical similarities among the oil tribes and their widespread distribution support the prograding margin model or the banktop-slope-basin model instead of the ridge-and-basin model for the deposition of the Monterey Formation. Tribe 1 contains four oil families having geochemical traits of clay-rich marine shale source rock deposited under suboxic conditions with substantial higher plant input. Tribe 2 contains four oil families with traits intermediate between tribes 1 and 3, except for abundant 28,30-bisnorhopane, indicating suboxic to anoxic marine marl source rock with hemipelagic input. Tribe 3 contains five oil families with traits of distal marine carbonate source rock deposited under anoxic conditions with pelagic but little or no higher plant input. Tribes 1 and 2 occur mainly south of Point Conception in paleogeographic settings where deep burial of the Monterey source rock favored petroleum generation from all three members or their equivalents. In this area, oil from the clayey-siliceous and carbonaceous marl members (tribes 1 and 2) may overwhelm that from the lower calcareous-siliceous member (tribe 3) because the latter is thinner and less oil-prone than the overlying members. Tribe 3 occurs mainly north of Point Conception where shallow burial caused preferential generation from the underlying lower calcareous-siliceous member or another unit with similar characteristics. In a test of the decision tree, 10 tarball samples collected from beaches in Monterey and San Mateo counties in early 2007 were found to originate from natural seeps representing different organofacies of Monterey Formation source rock instead from one anthropogenic pollution event. The seeps apparently became more active because of increased storm activity. Copyright ?? 2008. The American Association of Petroleum Geologists. All rights reserved.

American Association of Petroleum Geologists Bulle↗

USGS2017

Evaluating the role of land cover and climate uncertainties in computing gross primary production in Hawaiian Island ecosystems

Gross primary production (GPP) is the Earth’s largest carbon flux into the terrestrial biosphere and plays a critical role in regulating atmospheric chemistry and global climate. The Moderate Resolution Imaging Spectrometer (MODIS)-MOD17 data product is a widely used remote sensing-based model that provides global estimates of spatiotemporal trends in GPP. When the MOD17 algorithm is applied to regional scale heterogeneous landscapes, input data from coarse resolution land cover and climate products may increase uncertainty in GPP estimates, especially in high productivity tropical ecosystems. We examined the influence of using locally specific land cover and high-resolution local climate input data on MOD17 estimates of GPP for the State of Hawaii, a heterogeneous and discontinuous tropical landscape. Replacing the global land cover data input product (MOD12Q1) with Hawaii-specific land cover data reduced statewide GPP estimates by ~8%, primarily because the Hawaii-specific land cover map had less vegetated land area compared to the global land cover product. Replacing coarse resolution GMAO climate data with Hawaii-specific high-resolution climate data also reduced statewide GPP estimates by ~8% because of the higher spatial variability of photosynthetically active radiation (PAR) in the Hawaii-specific climate data. The combined use of both Hawaii-specific land cover and high-resolution Hawaii climate data inputs reduced statewide GPP by ~16%, suggesting equal and independent influence on MOD17 GPP estimates. Our sensitivity analyses within a heterogeneous tropical landscape suggest that refined global land cover and climate data sets may contribute to an enhanced MOD17 product at a variety of spatial scales.

Hawaii↗

USGS2011

Epistemic uncertainty in California-wide synthetic seismicity simulations

The generation of seismicity catalogs on synthetic fault networks holds the promise of providing key inputs into probabilistic seismic-hazard analysis, for example, the coefficient of variation, mean recurrence time as a function of magnitude, the probability of fault-to-fault ruptures, and conditional probabilities for foreshock–mainshock triggering. I employ a seismicity simulator that includes the following ingredients: static stress transfer, viscoelastic relaxation of the lower crust and mantle, and vertical stratification of elastic and viscoelastic material properties. A cascade mechanism combined with a simple Coulomb failure criterion is used to determine the initiation, propagation, and termination of synthetic ruptures. It is employed on a 3D fault network provided by Steve Ward (unpublished data, 2009) for the Southern California Earthquake Center (SCEC) Earthquake Simulators Group. This all-California fault network, initially consisting of 8000 patches, each of ∼12 square kilometers in size, has been rediscretized into Graphic patches, each of ∼1 square kilometer in size, in order to simulate the evolution of California seismicity and crustal stress at magnitude M∼5–8. Resulting synthetic seismicity catalogs spanning 30,000 yr and about one-half million events are evaluated with magnitude-frequency and magnitude-area statistics. For a priori choices of fault-slip rates and mean stress drops, I explore the sensitivity of various constructs on input parameters, particularly mantle viscosity. Slip maps obtained for the southern San Andreas fault show that the ability of segment boundaries to inhibit slip across the boundaries (e.g., to prevent multisegment ruptures) is systematically affected by mantle viscosity.

California↗

USGS2005

Tree mortality, canopy turnover, and woody detritus in old cove forests of the southern Appalachians

A long-term study of tree mortality, canopy turnover, and coarse woody detritus inputs was conducted in cove forests of the Great Smoky Mountains, Tennessee, USA. Seven old-growth stands were studied over a 10-yr period using 0.6–1.0 ha plots. Annual mortality of trees >10 cm dbh was 0.5–1.4% among stands (mean 0.7%). The highest mortality rate among canopy trees was exhibited by trees >80 cm dbh. An increase in mortality rate with canopy tree size was evident for two (Tsuga canadensis and Acer saccharum) of the three most abundant species in the forest. The increase in mortality with tree size had implications for canopy turnover and detritus input. Gap disturbance frequency was estimated at 0.008–0.019 forest area/yr, giving a return interval of ∼130 yr or less. Standing death was the most common mode of mortality (59%). Annual rates of snag formation were 1.4 snags/ha for trees >10 cm dbh and 0.4 snags/ha for trees >50 cm dbh. The density of large snags (>50 cm dbh) was 5 snags/ha. Snags accounted for 8% of the total standing tree basal area and 23% of the coarse woody detritus mass (total of 48 Mg/ ha). The mean annual rate of coarse woody detritus input was 3.0 Mg/ha. A decay rate constant was estimated at 0.07, yielding a detritus half-life of 10 yr. Although mean mortality rates and canopy turnover in old cove forests were moderate in comparison with other old forests of eastern North America, input and accumulation of coarse woody detritus were high for the region. This resulted, in part, from the relatively large sizes attained by canopy trees and the fact that larger trees tended to suffer higher mortality. In comparison to forests worldwide, rates of mortality, canopy gap formation, and decay of coarse woody detritus were intermediate.

Tennessee↗

USGS2010

Diet shift of lentic dragonfly larvae in response to reduced terrestrial prey subsidies

Inputs of terrestrial plant detritus and nutrients play an important role in aquatic food webs, but the importance of terrestrial prey inputs in determining aquatic predator distribution and abundance has been appreciated only recently. I examined the numerical, biomass, and diet responses of a common predator, dragonfly larvae, to experimental reduction of terrestrial arthropod input into ponds. I distributed paired enclosures ( n = 7), one with a screen between the land and water (reduced subsidy) and one without a screen (ambient subsidy), near the shoreline of 2 small fishless ponds and sampled each month during the growing season in the southern Appalachian Mountains, Virginia (USA). Screens between water and land reduced the number of terrestrial arthropods that fell into screened enclosures relative to the number that fell into unscreened enclosures and open reference plots by 36%. The δ 13 C isotopic signatures of dragonfly larvae shifted towards those of aquatic prey in reduced-subsidy enclosures, a result suggesting that dragonflies consumed fewer terrestrial prey when fewer were available (ambient subsidy: 30%, reduced subsidy: 19% of diet). Overall abundance and biomass of dragonfly larvae did not change in response to reduced terrestrial arthropod inputs, despite the fact that enclosures permitted immigration/emigration. These results suggest that terrestrial arthropods can provide resources to aquatic predators in lentic systems, but that their effects on abundance and distribution might be subtle and confounded by in situ factors.

Journal of the North American Benthological Societ↗

USGS2013

SPARROW models used to understand nutrient sources in the Mississippi/Atchafalaya River Basin

Nitrogen (N) and phosphorus (P) loading from the Mississippi/Atchafalaya River Basin (MARB) has been linked to hypoxia in the Gulf of Mexico. To describe where and from what sources those loads originate, SPAtially Referenced Regression On Watershed attributes (SPARROW) models were constructed for the MARB using geospatial datasets for 2002, including inputs from wastewater treatment plants (WWTPs), and calibration sites throughout the MARB. Previous studies found that highest N and P yields were from the north-central part of the MARB (Corn Belt). Based on the MARB SPARROW models, highest N yields were still from the Corn Belt but centered over Iowa and Indiana, and highest P yields were widely distributed throughout the center of the MARB. Similar to that found in other studies, agricultural inputs were found to be the largest N and P sources throughout most of the MARB: farm fertilizers were the largest N source, whereas farm fertilizers, manure, and urban inputs were dominant P sources. The MARB models enable individual N and P sources to be defined at scales ranging from SPARROW catchments (∼50 km 2 ) to the entire area of the MARB. Inputs of P from WWTPs and urban areas were more important than found in most other studies. Information from this study will help to reduce nutrient loading from the MARB by providing managers with a description of where each of the sources of N and P are most important, thus providing a basis for prioritizing management actions and ultimately reducing the extent of Gulf hypoxia.

Mississippi/atchafalaya River Basin↗

USGS1992

Sources of nitrogen and phosphorous to northern San Francisco Bay

We studied nutrient sources to the Sacramento River and Suisun Bay (northern San Francisco Bay) and the influence which these sources have on the distributions of dissolved inorganic nitrogen (DIN) and dissolved reactive phosphorus (DRP) in the river and bay. We found that agricultural return flow drains and a municipal wastewater treatment plant were the largest sources of nutrients to the river during low river flow. The Sutter and Colusa agricultural drains contributed about 70% of the transport of DIN and DRP by the river above Sacramento (about 20% of the total transport by the river) between August 8 and September 26, 1985. Further downstream, the Sacramento Regional Wastewater Treatment Plant discharged DIN and DRP at rates that were roughly 70% of total DIN and DRP transport by the river at that time. Concentrations at Rio Vista on the tidal river below the Sacramento plant and at the head of the estuary were related to the reciprocals of the river flows, indicating the importance of dilution of the Sacramento waste by river flows. During very dry years, elevated DIN and DRP concentrations were observed in Suisun Bay. We used a steady-state, one-dimensional, single-compartment box model of the bay, incorporating terms for advection, exchange, and waste input, to calculate a residual rate for all processes not included in the model. We found that the residual for DIN was related to concentrations of chlorophylla (Chla). The residual for DRP was also related to Chla at high concentrations of Chla, but showed significant losses of DRP at low Chla concentrations. These losses were typically equivalent to about 80% of the wastewater input rate.

Estuaries and Coasts↗

USGS1997

A geologic history of the north-central Appalachians, part 2: The Appalachian basin from the Silurian through the Carboniferous

The north-central Appalachians occupy a critical position within the 3000+ km-long Appalachian orogen, lying southwest of the boundary between the central and northern Appalachians (CNAB). The one-billion-year-long history of tectonic activity in the north-central Appalachians includes the assembly and breakup of a late Proterozoic supercontinent, the creation and evolution of the Appalachian orogen during the Paleozoic, and the Mesozoic transformation of the active orogen into a passive margin during Pangea's disassembly. An important part of the Middle and Late Paleozoic history is the formation and growth of the Appalachian basin, an enormous, elongate continental basin lying cratonward of the active Appalachian internides along Laurentia's eastern margin. The Appalachian basin developed out of the Taconic orogeny, the second of the four orogenies that formed and modified the character of the Appalachian orogen. Prior to the Taconic orogeny, the eastern margin of Laurentia consisted of a broad carbonate shelf facing the Theic Ocean. The Taconic orogeny obduced various Theic components, including microcontinents, magmatic arcs, and accretionary prisms, onto the carbonate shelf. The resulting Taconic highlands formed a topographic barrier between Theia and the craton's interior. Because tectonic activity in the internides continued more or less throughout the remainder of the Paleozoic, the Appalachian basin never had a direct connection with Theia. The coarse-grained molasse from the newly uplifted Taconic highland spread westward over most of the basin during the Early Silurian. Carbonate deposition gradually encroached eastward over the basin as the siliciclastic input from the southeast waned. A resurgence in the earliest Late Silurian, perhaps related to orogenesis in Newfoundland and the Maritimes, expanded the clastic wedge somewhat. Before long, however, carbonate deposition once again dominated most of the north-central basin for the remainder of the Silurian and into the Early Devonian. The Early-to-Middle Devonian Acadian orogeny began introducing siliciclastic material into the eastern part of the Appalachian basin, thereby ending the largely paralic environment that persisted from the Late Silurian. A number of deltas formed around local sediment-input centers during the Middle Devonian. Continued uplift and/or orogenesis must have continued into the Late Devonian because a vast amount of terrigenous sediment was introduced into the Appalachian basin to form the vast Upper Devonian Catskill delta. Although the principal tectonic activity appears to have centered in New England, the large volume of sediment input suggests that orogenesis may have extended southward to the north-central Appalachians. However, direct evidence of actual Acadian deformation and metamorphism is lacking at this latitude. The north-central Appalachian basin underwent a significant change during the Carboniferous. Prior to this time, the shoreline shifted laterally through transgressions and regressions largely as a function of sediment input and regional subsidence. In the Carboniferous, vertical movements in the basin became more important. During the Early Carboniferous, much of the Mauch Chunk delta was eroded in the central and western parts of the basin. At the end of the Early Carboniferous, an unconformity truncated progressively older rocks to the north toward New York. New sediment transport patterns and depositional environments within the basin during the Late Carboniferous probably reflect significant topographic and tectonic changes, not only in the hinterland, but in the basin itself, perhaps in conjunction with climatic changes. Extensive interfluvial swamps on a lower delta plain accumulated thick organic deposits which would become coal. This delta plain graded southwestward into tidal and marine environments. The Alleghany orogeny in the Early Permian interrupted deposition in much of the north-central Appalachian basin and profoundly altered its structure.

American Journal of Science↗

USGS2011

Chemical ecology of red mangroves, Rhizophora mangle, in the Hawaiian Islands

The coastal red mangrove, Rhizophora mangle L., was introduced to the Hawaiian Islands from Florida 100 yr ago and has spread to cover many shallow intertidal shorelines that once were unvegetated mudflats. We used a field survey approach to test whether mangroves at the land-ocean interface could indicate watershed inputs, especially whether measurements of leaf chemistry could identify coasts with high nutrient inputs and high mangrove productivities. During 2001-2002, we sampled mangroves on dry leeward coasts of southern Moloka'i and O'ahu for 14 leaf variables including stable carbon and nitrogen isotopes (delta 13 C, delta 15 N), macronutrients (C, N, P), trace elements (B, Mn, Fe, Cu, Zn), and cations (Na, Mg, K, Ca). A new modeling approach using leaf Na, N, P, and delta 13 C indicated two times higher productivity for mangroves in urban versus rural settings, with rural mangroves more limited by low N and P nutrients and high-nutrient urban mangroves more limited by freshwater inputs and salt stress. Leaf chemistry also helped identify other aspects of mangrove dynamics: especially leaf delta 15 N values helped identify groundwater N inputs, and a combination of strongly correlated variables (C, N, P, B, Cu, Mg, K, Ca) tracked the mangrove growth response to nutrient loading. Overall, the chemical marker approach is an efficient way to survey watershed forcing of mangrove forest dynamics.

Hawai'i↗

USGS2000

MODFLOW-2000, the U.S. Geological Survey modular ground-water model; user guide to the observation, sensitivity, and parameter-estimation processes and three post-processing programs

This report documents the Observation, Sensitivity, and Parameter-Estimation Processes of the ground-water modeling computer program MODFLOW-2000. The Observation Process generates model-calculated values for comparison with measured, or observed, quantities. A variety of statistics is calculated to quantify this comparison, including a weighted least-squares objective function. In addition, a number of files are produced that can be used to compare the values graphically. The Sensitivity Process calculates the sensitivity of hydraulic heads throughout the model with respect to specified parameters using the accurate sensitivity-equation method. These are called grid sensitivities. If the Observation Process is active, it uses the grid sensitivities to calculate sensitivities for the simulated values associated with the observations. These are called observation sensitivities. Observation sensitivities are used to calculate a number of statistics that can be used (1) to diagnose inadequate data, (2) to identify parameters that probably cannot be estimated by regression using the available observations, and (3) to evaluate the utility of proposed new data. The Parameter-Estimation Process uses a modified Gauss-Newton method to adjust values of user-selected input parameters in an iterative procedure to minimize the value of the weighted least-squares objective function. Statistics produced by the Parameter-Estimation Process can be used to evaluate estimated parameter values; statistics produced by the Observation Process and post-processing program RESAN-2000 can be used to evaluate how accurately the model represents the actual processes; statistics produced by post-processing program YCINT-2000 can be used to quantify the uncertainty of model simulated values. Parameters are defined in the Ground-Water Flow Process input files and can be used to calculate most model inputs, such as: for explicitly defined model layers, horizontal hydraulic conductivity, horizontal anisotropy, vertical hydraulic conductivity or vertical anisotropy, specific storage, and specific yield; and, for implicitly represented layers, vertical hydraulic conductivity. In addition, parameters can be defined to calculate the hydraulic conductance of the River, General-Head Boundary, and Drain Packages; areal recharge rates of the Recharge Package; maximum evapotranspiration of the Evapotranspiration Package; pumpage or the rate of flow at defined-flux boundaries of the Well Package; and the hydraulic head at constant-head boundaries. The spatial variation of model inputs produced using defined parameters is very flexible, including interpolated distributions that require the summation of contributions from different parameters. Observations can include measured hydraulic heads or temporal changes in hydraulic heads, measured gains and losses along head-dependent boundaries (such as streams), flows through constant-head boundaries, and advective transport through the system, which generally would be inferred from measured concentrations. MODFLOW-2000 is intended for use on any computer operating system. The program consists of algorithms programmed in Fortran 90, which efficiently performs numerical calculations and is fully compatible with the newer Fortran 95. The code is easily modified to be compatible with FORTRAN 77. Coordination for multiple processors is accommodated using Message Passing Interface (MPI) commands. The program is designed in a modular fashion that is intended to support inclusion of new capabilities.

Open-File Report↗

USGS2008

User's Guide to Handlens - A Computer Program that Calculates the Chemistry of Minerals in Mixtures

HandLens is a computer program, written in Excel macro language, that calculates the chemistry of minerals in mineral mixtures (for example, in rocks, soils and sediments) for related samples from inputs of quantitative mineralogy and chemistry. For best results, the related samples should contain minerals having the same chemical compositions; that is, the samples should differ only in the proportions of minerals present. This manual describes how to use the program, discusses the theory behind its operation, and presents test results of the program's accuracy. Required input for HandLens includes quantitative mineralogical data, obtained, for example, by RockJock analysis of X-ray diffraction (XRD) patterns, and quantitative chemical data, obtained, for example, by X-ray florescence (XRF) analysis of the same samples. Other quantitative data, such as sample depth, temperature, surface area, also can be entered. The minerals present in the samples are selected from a list, and the program is started. The results of the calculation include: (1) a table of linear coefficients of determination (r2's) which relate pairs of input data (for example, Si versus quartz weight percents); (2) a utility for plotting all input data, either as pairs of variables, or as sums of up to eight variables; (3) a table that presents the calculated chemical formulae for minerals in the samples; (4) a table that lists the calculated concentrations of major, minor, and trace elements in the various minerals; and (5) a table that presents chemical formulae for the minerals that have been corrected for possible systematic errors in the mineralogical and/or chemical analyses. In addition, the program contains a method for testing the assumption of constant chemistry of the minerals within a sample set.

Open-File Report↗

USGS2009

Natural offshore oil seepage and related tarball accumulation on the California coastline — Santa Barbara Channel and the southern Santa Maria Basin; source identification and inventory

Oil spillage from natural sources is very common in the waters of southern California. Active oil extraction and shipping is occurring concurrently within the region and it is of great interest to resource managers to be able to distinguish between natural seepage and anthropogenic oil spillage. The major goal of this study was to establish the geologic setting, sources, and ultimate dispersal of natural oil seeps in the offshore southern Santa Maria Basin and Santa Barbara Basins. Our surveys focused on likely areas of hydrocarbon seepage that are known to occur between Point Arguello and Ventura, California. Our approach was to 1) document the locations and geochemically fingerprint natural seep oils or tar; 2) geochemically fingerprint coastal tar residues and potential tar sources in this region, both onshore and offshore; 3) establish chemical correlations between offshore active seeps and coastal residues thus linking seep sources to oil residues; 4) measure the rate of natural seepage of individual seeps and attempt to assess regional natural oil and gas seepage rates; and 5) interpret the petroleum system history for the natural seeps. To document the location of sub-sea oil seeps, we first looked into previous studies within and near our survey area. We measured the concentration of methane gas in the water column in areas of reported seepage and found numerous gas plumes and measured high concentrations of methane in the water column. The result of this work showed that the seeps were widely distributed between Point Conception east to the vicinity of Coal Oil Point, and that they by in large occur within the 3-mile limit of California State waters. Subsequent cruises used sidescan and high resolution seismic to map the seafloor, from just south of Point Arguello, east to near Gaviota, California. The results of the methane survey guided the exploration of the area west of Point Conception east to Gaviota using a combination of seismic instruments. The seafloor was mapped by sidescan sonar, and numerous lines of high -resolution seismic surveys were conducted over areas of interest. Biomarker and stable carbon isotope ratios were used to infer the age, lithology, organic matter input, and depositional environment of the source rocks for 388 samples of produced crude oil, seep oil, and tarballs mainly from coastal California. These samples were used to construct a chemometric fingerprint (multivariate statistics) decision tree to classify 288 additional samples, including tarballs of unknown origin collected from Monterey and San Mateo County beaches after a storm in early 2007. A subset of 9 of 23 active offshore platform oils and one inactive platform oil representing a few oil reservoirs from the western Santa Barbara Channel were used in this analysis, and thus this model is not comprehensive and the findings are not conclusive. The platform oils included in this study are from west to east: Irene, Hildago, Harvest, Hermosa, Heritage, Harmony, Hondo, Holly, Platform A, and Hilda (now removed). The results identify three “tribes” of 13 C-rich oil samples inferred to originate from thermally mature equivalents of the clayey-siliceous, carbonaceous marl, and lower calcareous-siliceous members of the Monterey Formation. Tribe 1 contains four oil families having geochemical traits of clay-rich marine shale source rock deposited under suboxic conditions with substantial higher-plant input. Tribe 2 contains four oil families with intermediate traits, except for abundant 28,30-bisnorhopane, indicating suboxic to anoxic marine marl source rock with hemipelagic input. Tribe 3 contains five oil families with traits of distal marine carbonate source rock deposited under anoxic conditions with pelagic but little or no higher-plant input. Tribes 1 and 2 occur mainly south of Point Conception in paleogeographic settings where deep burial of the Monterey Formation source rock favored generation from all three members or their equivalents. In this area, oil from the clayey-siliceous and carbonaceous marl members (Tribes 1 and 2) may overwhelm that from the lower calcareous-siliceous member (Tribe 3) because the latter is thinner and less oil-prone than the overlying members. Tribe 3 occurs mainly north of Point Conception, where shallow burial caused preferential generation from the underlying lower calcareous-siliceous member or another unit with similar characteristics. It is very desirable to be able to clearly distinguish the naturally occurring seep oils from the anthropogenically derived platform oils. Within the “training set” of oils and tars (388 samples), the biomarker parameters are sometimes sufficient to allow unique discrimination of individual platform oils. More often however, platform samples and seep samples with sources geographically close to each other are too similar to each other, with respect to the biomarker parameters, to definitively differentiate them on that basis alone. In some cases other parameters can be helpful. These other parameters are related to the degree of biogeochemical degradation or weathering that the oils or tars have experienced. These components include the typical oil distribution of n-alkane hydrocarbons and isoprenoids pristane and phytane. All of the platform oils in our sample set contain these components. On the other hand, the seep oils or tars have been exposed to significant biodegradation while in the near subsurface. The majority, but not all of seep oils or tars have been biodegraded up to or beyond the loss of n-alkanes and isoprenoids. Seep oils found in the vicinity of Coal Oil Point or Arroyo Burro are apparently the least weathered and are particularly likely to retain significant n-alkanes and isoprenoids. Therefore the combination of chemometric fingerprinting and the presence or absence of n-alkanes and isoprenoids help to differentiate anthropogenic production oils versus natural seeps oils and tars. The differentiation is not always definitive because of the close chemical similarity of some samples and the variability in the biodegradation progression. This is the case near Coal Oil Point, and near Platform A (Dos Cuadros Field) where seep oils and Platform Holly and Platform A oils are genetically very similar and cannot be definitively distinguished after a period of a few days of weathering. In contrast, oils from the Point Conception platforms can be distinguished on the basis of chemometric fingerprinting alone. In the middle of this spectrum are oils from Platforms Harmony, Heritage, and Hondo, where it is expected that oil weathering would take on the order of two weeks to a month to produce tarballs similar to those seen near Point Conception. In this case there is a much greater degree of weathering needed to proceed from produced oil to the biodegraded tar characteristic of tarball stranded on the beach. Tar deposition on beaches was monitored as part of cooperative with the County of Santa Barbara Energy Division and the U.S. Geological Survey during 2001-2003. We found tar deposition varies on a seasonal basis. In general, tarballs accumulate at a faster rate or remain longer on all beaches during the summer and fall months. The reasons for this are unclear based on our limited observations, however we speculate that factors such as prevailing winds and currents combined with more quiescent wave conditions favors the accumulation and preservation of tarballs on the beach during the summer and fall months. In contrast, winter storms, with much greater wave action remove beach sand and other materials, and stormy seas tend to break up oil that might weather into tarballs. Natural seepage is affected by the spring/neap tidal cycle; however, the link to tar deposition is unclear. Longer periods of monitoring are needed to address the variability in the data and provide a more robust statistical analysis.

California↗

USGS2016

Construction, calibration, and validation of the RBM10 water temperature model for the Trinity River, northern California

We constructed a one-dimensional daily averaged water-temperature model to simulate Trinity River temperatures for 1980–2013. The purpose of this model is to assess effects of water-management actions on water temperature and to provide water temperature inputs for a salmon population dynamics model. Simulated meteorological data, observed streamflow data, and observed water temperatures were used as model inputs to simulate a continuous 34-year time series of historical daily mean water temperature at eight locations along 112.2 river miles from Lewiston Dam near Weaverville, California, downstream to the Klamath River confluence. To demonstrate the utility of the model to inform management actions, we simulated three management alternatives to assess the effects of bypass flow augmentation in a drought year, 1994, and compared those results to the simulated historical baseline, referred to as the “No Action” alternative scenario. Augmentation flows from the Lewiston Dam bypass consist of temperature-controlled releases capable of cooling downstream water temperatures in hot times of the year, which can reduce the probability of disease outbreaks in fish populations. Outputs from the Trinity River water-temperature model were then used as inputs to an existing water-temperature model of the Klamath River to evaluate the effect of augmentation flow releases on water temperatures in the lower Klamath River. We structured the Trinity River water-temperature model in River Basin Model-10 (RBM10), which uses a simple equilibrium flow model, assuming discharge in each river segment on each day is transmitted downstream instantaneously. The model uses a heat-budget formulation to quantify heat flux at the air-water interface. Inputs for the heat budget are calculated from daily mean meteorological data, including net shortwave solar radiation, net longwave atmospheric radiation, air temperature, wind speed, vapor pressure, and a psychrometric constant needed to calculate the Bowen ratio. The modeling domain was divided into eight reaches ranging in length from 8.8 to 20.6 miles, which were calibrated and validated separately with observed water temperature data collected irregularly from 1980 to 2013. Root mean square errors of observed and simulated water temperatures for the eight reaches ranged from 0.25 to 1.12 degrees Celsius (°C). Mean absolute errors ranged from 0.18 to 0.89 °C. For model validation, a k -fold cross-validation technique was used. Validation root mean square error and mean absolute error for the eight reaches ranged from 0.24 to 1.11 °C and from 0.18 to 0.89 °C, respectively. Augmentation scenarios were based on historical hydrological and meteorological data, combined with prescribed flow and temperature releases from Lewiston Dam provided by the Bureau of Reclamation. Water releases were scheduled to achieve targeted flows of 2,500, 2,800, and 3,200 cubic feet per second in the lower Klamath River from mid-August through late September, coinciding with the upstream migration of adult fall-run Chinook salmon ( Oncorhynchus tshawytscha ). Water temperatures simulated at river mile 5.7 on the Klamath River showed a 5 °C decrease from the No Action historical baseline, which was near or greater than 23 °C when augmentation began in mid-August. Thereafter, an approximate 1 °C difference among augmentation scenarios emerged, with the decrease in water temperature commensurate to the level of augmentation. All augmentation scenarios simulated water temperatures equal to or less than 21 °C from mid-August through late September. Water temperatures equal to or greater than 23 °C are of particular interest because of a thermal threshold known to inhibit upstream migration of salmon. When temperatures exceed this approximate 23 °C threshold, Chinook salmon are known to congregate in high densities in thermal refugias and show extended residence times, which can potentially trigger epizootic outbreaks such as of Ichthyophthirius multifiliis (“Ich”) and Flavobacterium columnare (“Columnaris”) that were the causative factors of the Klamath River fish kill in 2002. A model with the ability to simulate water temperatures in response to management actions at the basin scale is a valuable asset for water managers who must make decisions about how best to use limited water resources, which directly affect the state of fisheries in the Klamath Basin.

California↗

USGS2021

Oyster model inventory: Identifying critical data and modeling approaches to support restoration of oyster reefs in coastal U.S. Gulf of Mexico waters

Executive Summary Along the coast of the U.S. Gulf of Mexico, the eastern oyster ( Crassostrea virginica ) plays important ecological and economic roles. Commercial landings from this region account for more than 50 percent of all U.S. landings; these oyster reefs also provide varied ecosystem services, including nursery habitat for many fish and macroinvertebrate species, shoreline protection, and water-quality maintenance. Declining trends in both total oyster production and functional reef area across this region have spurred investment in restoration of oyster resources, with specific calls for restoration projects to develop a network of reefs and identify broodstock and sanctuary reef restoration sites. Decision making related to restoration and establishment of a network of oyster reefs in the Gulf of Mexico requires information on both the environment and the effects of the environment on the oyster life cycle (including larval movement, survival, oyster recruitment, reproduction, growth, and mortality). Here, we examined the current state of data and model development in this region with the goal of providing an overview of oyster modeling approaches and an inventory of available data and existing oyster models. This report is meant to provide an overview to managers for understanding existing efforts and identify a path forward to most efficiently inform oyster resource management and restoration planning in moving from a single reef management approach to a reef network management approach. Numerous models related to some aspect of the oyster life cycle have been built, calibrated, and validated for various Gulf of Mexico estuaries over the last few decades (over 30 models identified). These models, which could inform site restoration, can be classified into four approaches: (1) oyster Habitat Suitability Index (HSI) models; (2) larval transport models; (3) on-reef oyster models that may include oyster growth, mortality and reproduction, and substrate persistence; and (4) coupled larval transport on-reef metapopulation models that simulate the entire oyster life cycle. The data requirements, model complexity and assumptions, and transferability vary by approach. Specifically, some approaches may offer greater accessibility, flexibility, and transferability spatially or temporally, with minimal data input, but only provide broad information to support site selection. In contrast, other approaches may require significant site-specific data for their construction and validation but may provide more accurate and location-specific data to support site selection for broodstock reefs. Regardless of modeling approach used, data on environmental drivers, such as salinity, water temperature, or water flow impacting oyster metabolism and movement, are required at appropriate spatial and temporal scales. While numerous data collection platforms, environmental models, and research products exist within Gulf of Mexico estuaries to provide important environmental data to use as drivers in the oyster models, significant variability in temporal and spatial coverage of the data, and variation in the availability of future condition models, exists across estuaries. This variation influences the spatial and temporal scales at which oyster models may be developed and impacts the calibration and validation of the oyster models within a given estuary, affecting its potential ability to address specific management or restoration questions. While multiple modeling approaches exist for informing site selection of broodstock or sanctuary oyster reefs, the development, calibration, and validation of a single modeling platform presents the most efficient, transferable, and useful tool for managers across the Gulf of Mexico. The development of a single modeling platform would involve using standardized input variables, governing equations, and assumptions for the modeled oyster processes and outputs, and for standardized calibration and validation procedures that could be applied within each estuary. The differences among estuary applications would require substituting only estuary-specific environmental data, and calibrating and validating the modeling approach with local oyster data. Two modeling approaches likely to be useful include (1) development of a general geospatial HSI modeling framework that could be applied consistently across estuaries and (2) a mechanistic coupled larval transport on-reef metapopulation model requiring only estuarine specific calibration and hydrodynamic models. Both approaches benefit from existing work across multiple Gulf of Mexico estuaries and could provide valuable support for oyster restoration, but may differ in their ability to address specific questions related to oyster restoration. HSI models specifically guide restoration practitioners in determining suitable habitat based on available data. The HSI approach, while currently more widely used and accessible, requires more development of larval suitability and larval input and output components in order to inform reef connectivity. A metapopulation approach considering the full oyster life cycle that simulates both on-reef oyster growth, mortality, reproduction, substrate persistence, and larval transport (ideally with larval growth and mortality) would provide the greatest detail and level of understanding but requires significant up-front investment. The larval oyster model and on-reef oyster model are usually developed independently for systems, although the two approaches can be coupled to represent the entire oyster life cycle in order to characterize and assess a reef metapopulation. This approach may be less accessible and much more data-intensive, however, and it requires some expertise to run and apply to inform oyster resource management. Ultimately, the development of single modeling platforms for each of these approaches would provide flexible tools applicable across all Gulf of Mexico oyster supporting estuaries. By using a single platform for model development, testing, calibrating and validating, and evaluation of modeled future scenarios, oyster restoration scientists and managers would not only be able to examine different scenario outcomes within a single estuary, but could also have comparable modeled results to evaluate potential outcomes, across estuaries and regions, that are not confounded by varying modeled data inputs, governing equations, assumptions, or user judgement.

Alabama, Florida, Louisiana, Mississippi, Texas↗