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USGS2020

Combining genetic and demographic monitoring better informs conservation of an endangered urban snake

Conversion and fragmentation of wildlife habitat often leads to smaller and isolated populations and can reduce a species’ ability to disperse across the landscape. As a consequence, genetic drift can quickly lower genetic variation and increase vulnerability to extirpation. For species of conservation concern, quantification of population size and connectivity can clarify the influence of genetic drift in local populations and provides important information for conservation management and recovery strategies. Here, we used genome-wide single nucleotide polymorphism (SNP) data and capture-mark-recapture methods to evaluate the genetic diversity and demography within seven focal sites of the endangered San Francisco gartersnake ( Thamnophis sirtalis tetrataenia ), a species affected by alteration and isolation of wetland habitats throughout its distribution. The primary goals were to determine the population structure and degree of genetic isolation among T . s . tetrataenia populations and estimate effective size and population abundance within sites to better understand the present and future importance of genetic drift. We also used temporally sampled datasets to examine the magnitude of genetic change over time. We found moderate population genetic structure throughout the San Francisco Peninsula that partitions sites into northern and southern regional clusters. Point estimates of both effective size and population abundance were generally small (≤ 100) for a majority of the sites, and estimates were particularly low in the northern populations. Genetic analyses of temporal datasets indicated an increase in genetic differentiation, especially for the most geographically isolated sites, and decreased genetic diversity over time in at least one site (Pacifica). Our results suggest that drift-mediated processes as a function of small population size and reduced connectivity from neighboring populations may decrease diversity and increase differentiation. Improving genetic diversity and connectivity among T . s . tetrataenia populations could promote persistence of this endangered snake.

California↗

USGS2005

Genetics of Central Valley, O. mykiss, populations: Drainage and watershed scale analyses

Genetic variation at 11 microsatellite loci described population genetic structure for Oncorhynchus mykiss in the Central Valley, California. Spatial and temporal variation was examined as well as relationships between hatchery and putative natural spawning anadromous stocks. Genetic diversity was analyzed at two distinct spatial scales: fine-scale within drainage for five populations on Clear Creek; between and among drainage diversity for 23 populations. Significant regional spatial structure was apparent, both within Clear Creek and among rainbow trout populations throughout the Central Valley. Significant differences in allelic frequencies were found among most river or drainage systems. Less than 1% of the molecular variance could be attributed to differences found between drainages. Hatchery populations were shown to carry similar genetic diversity to geographically proximate wild populations. Central Valley M = 0.626 (below the M < 0.68 threshold) supported recent population reductions within the Central Valley. However, average estimated effective population size was relatively high (Ne = 5066). Significant allelic differences were found in rainbow trout collected above and below impassable dams on the American, Yuba, Stanislaus and Tuolumne rivers. Rainbow trout sampled in Spring Creek were extremely bottlenecked with allelic variation at only two loci and an estimated effective population size of 62, suggesting some local freshwater O. mykiss stocks may be declining rapidly. These data support significant genetic population structure for steelhead and rainbow trout populations within the Central Valley across multiple scales. Careful consideration of this genetic diversity and its distribution across the landscape should be part of future conservation and restoration efforts.

California↗

USGS2024

Bird habitat value and management priorities of the California Winter Rice Habitat Incentive Program

Flooding rice ( Oryza sativa ) agricultural fields during winter to facilitate rice straw decomposition has mitigated the loss of some of the natural wetlands in California’s Central Valley. We conducted bird surveys in 253 rice checks (2,158 ha) within 177 rice fields in the Sacramento Valley during the fall and winter of 2021-2022 and 2022-2023 to evaluate factors influencing bird use of winter-flooded, post-harvest rice fields enrolled in the California Winter Rice Habitat Incentive Program. We counted 143,932 birds from 57 species, including dabbling ducks (86.4%), geese (8.0%), shorebirds (0.9%), wading birds (0.7%), and other birds (4.0%). Extrapolating from the lowest densities observed in rice fields during the 70-day mandatory flooding period, we estimated that properties enrolled in this public-private partnership provided habitat for at least 271,312 birds day-1 (16,248 ha; 2021-2022) and 147,315 birds day-1 (8,448 ha; 2022-2023), totaling >10 million bird-use-days each winter. Water depth had the greatest influence on bird abundance and diversity. Relatively shallow water depths (≤13 cm) had greater abundance of shorebirds, wading birds, and geese, and higher diversity, whereas intermediate depths (~23 cm) resulted in the greatest dabbling duck abundance. Duck, goose, and wading bird abundances were greatest and species richness and family diversity were highest 8 days after the onset of flooding in rice fields (typically late October), followed by a decline in bird use until 65-87 days post flooding, after which bird use increased slightly. Bird abundance and species diversity were lowest in rice fields with the greatest hunting intensity (≥3 days week-1). We identified several habitat variables that could be managed and prioritized by landowner incentive programs to increase bird use of winter-flooded rice, including water depth, variation in emergent vegetation height, mudflat habitat availability, rice check shape, hunting intensity, and post-harvest treatment of residual rice straw.

California↗

USGS2002

Genetic characterization of infectious hematopoietic necrosis virus of coastal salmonid stocks in Washington State

Infectious hematopoietic necrosis virus (IHNV) is a pathogen that infects many Pacific salmonid stocks from the watersheds of North America. Previous studies have thoroughly characterized the genetic diversity of IHNV isolates from Alaska and the Hagerman Valley in Idaho. To enhance understanding of the evolution and viral transmission patterns of IHNV within the Pacific Northwest geographic range, we analyzed the G gene of IHNV isolates from the coastal watersheds of Washington State by ribonuclease protection assay (RPA) and nucleotide sequencing. The RPA analysis of 23 isolates indicated that the Skagit basin IHNV isolates were relatively homogeneous as a result of the dominance of one G gene haplotype (S). Sequence analysis of 303 bases in the middle of the G gene (midG region) of 61 isolates confirmed the high frequency of a Skagit River basin sequence and identified another sequence commonly found in isolates from the Lake Washington basin. Overall, both the RPA and sequence analysis showed that the Washington coastal IHNV isolates are genetically homogeneous and have little genetic diversity. This is similar to the genetic diversity pattern of IHNV from Alaska and contrasts sharply with the high genetic diversity demonstrated for IHNV isolates from fish farms along the Snake River in Idaho. The high degree of sequence and haplotype similarity between the Washington coastal IHNV isolates and those from Alaska and British Columbia suggests that they have a common viral ancestor. Phylogenetic analyses of the isolates we studied and those from different regions throughout the virus's geographic range confirms a conserved pattern of evolution of the virus in salmonid stocks north of the Columbia River, which forms Washington's southern border.

Washington↗

USGS2011

Spatial variation in fish species richness of the upper Mississippi River system

Important natural environmental gradients, including the connectivity of off-channel aquatic habitats to the main-stem river, have been lost in many reaches of the upper Mississippi River system, and an understanding of the consequences of this isolation is lacking in regard to native fish communities. The objectives of this study were to describe patterns of fish species richness, evenness, and diversity among representative habitats and river reaches and to examine the relationship between fish species richness and habitat diversity. Each year (1994-1999) fish communities of main-channel borders (MCB), side channel borders (SCB), and contiguous backwater shorelines (BWS) were sampled using boat-mounted electrofishing, mini-fyke-nets, tyke nets, hoop nets, and seines at a standardized number of sites. A total of 0.65 million fish were collected, representing 106 species from upper Mississippi River Pools 4, 8, 13, and 26; the open (unimpounded) river reach; and the La Grange Reach of the Illinois River. Within pools, species richness based on rarefaction differed significantly among habitats and was highest in BWS and lowest in MCB (P < 0.0001). At the reach scale, Pools 4, 8, and 13 consistently had the highest species richness and Pool 26, the open-river reach, and the La Grange Reach were significantly lower (P < 0.0001). Species evenness and diversity indices showed similar trends. The relationship between native fish species richness and habitat diversity was highly significant (r(2) = 0.85; P = 0.0091). These results support efforts aimed at the conservation and enhancement of connected side channels and backwaters. Although constrained by dams, pools with high native species richness could serve as a relative reference. The remnants of natural riverine dynamics that remain in these reaches should be preserved and enhanced; conditions could be used to guide restoration activities in more degraded reaches.

Illinois, Iowa, Minnesota, Missouri, Wisconsin↗

USGS2017

Short-term vegetation response following mechanical control of saltcedar ( Tamarix spp.) on the Virgin River, Nevada, USA

Tamarisk (a.k.a. saltcedar, Tamarix spp.) is an invasive plant species that occurs throughout western riparian and wetland ecosystems. It is implicated in alterations of ecosystem structure and function and is the subject of many local control projects, including removal using heavy equipment. We evaluated short-term vegetation responses to mechanical Tamarix spp. removal at sites ranging from 2 to 5 yr post-treatment along the Virgin River in Nevada, USA. Treatments resulted in lower density and cover (but not eradication) of Tamarix spp., increased cover of the native shrub Pluchea sericia (arrow weed), decreased density and cover of all woody species combined, increased density of both native annual forbs and the nonnative annual Salsola tragus (prickly Russian-thistle), and lower density of nonnative annual grasses. The treated plots had lower mean woody species richness, but greater herbaceous species richness and diversity. Among herbaceous species, native taxa increased in richness whereas nonnative species increased in both species richness and diversity. Thus, efforts to remove Tamarix,/i> spp. at the Virgin River reduced vegetative cover contributing to fuel loads and probability of fire, and resulted in positive effects for native plant diversity, with mixed effects on other nonnative species. However, absolute abundances of native species and species diversity were very low, suggesting that targets of restoring vegetation to pre-invasion conditions were not met. Longer evaluation periods are needed to adequately evaluate how short-term post-treatment patterns translate to long-term patterns of plant community dynamics.

Nevada↗

USGS2016

A comparison of three macroinvertebrate sampling devices for use in conducting rapid-assessment procedures of Delmarva Peninsula wetlands

Three types of macroinvertebrate collecting devices, Gerking box traps, D-shaped sweep nets, and activity traps, have commonly been used to sample macroinvertebrates when conducting rapid biological assessments of North American wetlands. We compared collections of macroinvertebrates identified to the family level made with these devices in 6 constructed and 2 natural wetlands on the Delmarva Peninsula of Maryland. We also assessed their potential efficacy in comparisons among wetlands using several proportional and richness attributes. Differences in median diversity among samples from the 3 devices were significant; the sweep-net samples had the greatest diversity and the activity-trap samples had the least diversity. Differences in median abundance were not significant between the Gerking box-trap samples and sweep-net samples, but median abundance among activity-trap samples was significantly lower than among samples of the other 2 devices. Within samples, the proportions of median diversity composed of major class and order groupings were similar among the 3 devices. However the proportions of median abundance composed of the major class and order groupings within activity-trap samples were not similar to those of the other 2 devices. There was a slight but significant increase in the total number of families captured when we combined activity-trap samples with Gerking box-trap samples or with sweep-net samples, and the per-sample median numbers of families of the combined activity-trap and sweep-net samples was significantly higher than that of the combined activity-trap and Gerking box-trap samples. We detected significant differences among wetlands for 4 macroinvertebrate attributes with the Gerking box-trap data, 6 attributes with sweep-net data, and 5 attributes with the activity-trap data. A small, but significant increase in the number of attributes showing differences among wetlands occurred when we combined activity-trap samples with those of the Gerking boxtrap or sweep net.

Delaware, Maryland↗

USGS2010

Red imported fire ant impacts on upland arthropods in Southern Mississippi

Red imported fire ants (Solenopsis invicta) have negative impacts on a broad array of invertebrate species. We investigated the impacts of fire ants on the upland arthropod community on 20???40 ha study sites in southern Mississippi. Study sites were sampled from 19972000 before, during, and after fire ant bait treatments to reduce fire ant populations. Fire ant abundance was assessed with bait transects on all sites, and fire ant population indices were estimated on a subset of study sites. Species richness and diversity of other ant species was also assessed from bait transects. Insect biomass and diversity was determined from light trap samples. Following treatments, fire ant abundance and population indices were significantly reduced, and ant species diversity and richness were greater on treated sites. Arthropod biomass, species diversity and species richness estimated from light trap samples were negatively correlated with fire ant abundance, but there were no observable treatment effects. Solenopsis invicta has the potential to negatively impact native arthropod communities resulting in a potential loss of both species and function.

American Midland Naturalist↗

USGS2015

Waterbird use of catfish ponds and migratory bird habitat initiative wetlands in Mississippi

Aquaculture can provide important surrogate habitats for waterbirds. In response to the 2010 Deepwater Horizon oil spill, the National Resource Conservation Service enacted the Migratory Bird Habitat Initiative through which incentivized landowners provided wetland habitats for migrating waterbirds. Diversity and abundance of waterbirds in six production and four idled aquaculture facilities in the Mississippi Alluvial Valley were estimated during the winters of 2011–2013. Wintering waterbirds exhibited similar densities on production (i.e., &sim;22 birds/ha) and idled (i.e., &sim;20 birds/ha) sites. A total of 42 species were found using both types of aquaculture wetlands combined, but there was considerable departure in bird guilds occupying the two wetland types. The primary users of production ponds were diving and dabbling ducks and American coots. However, idled ponds, with varying water depths (e.g., mudflats to 20 cm) and diverse emergent vegetation-water interspersion, attracted over 30 species of waterbirds and, on average, had more species of waterbirds from fall through early spring than catfish production ponds. Conservation through the Migratory Bird Habitat Initiative was likely responsible for this difference. Our results suggest production and idled Migratory Bird Habitat Initiative aquaculture impoundments produced suitable conditions for various waterbird species and highlight the importance of conservation programs on private lands that promote diversity in vegetation structure and water depths to enhance waterbird diversity.

Mississippi↗

USGS1997

Gradients, vegetation and climate: spatial and temporal dynamics in the Olympic Mountains, USA

The steep environmental gradients of mountains result in the juxtaposition of diverse vegetation associations with narrow ecotones because life zones are compressed. Variation in geologic substrate, landforms, and soils, in combination with steep environmental gradients, create habitat diversity across spatial scales from 10 6 ha to <10 m 2 . This leads to higher biodiversity in a smaller space than in landscapes with less topographic variation. Mountains are often considered to be refuges for biological diversity at the regional scale, although variation in landscape features creates refuges at a fine scale as well. Mountains should also be considered a source of biological diversity, because they provide the germplasm for migration into lowland areas following glacial recession. Many taxa are distributed over a broad range of elevations and habitats, which maximizes the potential to respond to environmental perturbations. Reorganization of species distribution and abundance as a result of climatic change may be impacted considerably by human-caused fragmentation of landscape features, especially at lower elevations. This paper uses palaeoecological and biogeographical data to investigate the spatial and temporal vegetation dynamics of a steep maritime range, the Olympic Mountains (USA). The role of resource management in protecting vegetation in a fragmented landscape is discussed, with emphasis on how to address uncertainties such as climatic change.

Washington↗

USGS2015

Landscape pattern of seed banks and anthropogenic impacts in forested wetlands of the northern Mississippi River Alluvial Valley

Agricultural development on floodplains contributes to hydrologic alteration and forest fragmentation, which may alter landscape-level processes. These changes may be related to shifts in the seed bank composition of floodplain wetlands. We examined the patterns of seed bank composition across a floodplain watershed by looking at the number of seeds germinating per m2 by species in 60 farmed and intact forested wetlands along the Cache River watershed in Illinois. The seed bank composition was compared above and below a water diversion (position), which artificially subdivides the watershed. Position of these wetlands represented the most variability of Axis I in a Nonmetric Multidimensional Scaling (NMS) analysis of site environmental variables and their relationship to seed bank composition (coefficient of determination for Axis 1: r2 = 0.376; Pearson correlation of position to Axis 1: r = 0.223). The 3 primary axes were also represented by other site environmental variables, including farming status (farmed or unfarmed), distance from the mouth of the river, latitude, and longitude. Spatial analysis based on Mantel correlograms showed that both water-dispersed and wind/water-dispersed seed assemblages had strong spatial structure in the upper Cache (above the water diversion), bur the spatial structure of water-dispersed seed assemblage was diminished in the lower Cache (below the water diversion), which lost floodpulsing. Bearing analysis also Suggested that water-dispersal process had a stronger influence on the overall spatial pattern of seed assemblage in the upper Cache, while wind/water-dispersal process had a stronger influence in the lower Cache. An analysis of the landscapes along the river showed that the mid-lower Cache (below the water diversion) had undergone greater land cover changes associated with agriculture than did the upper Cache watershed. Thus, the combination of forest fragmentation and hydrologic changes in the surrounding landscape may have had an influence on the seed bank composition and spatial distribution of the seed banks of the Cache River watershed. Our study suggests that the spatial pattern of seed bank composition may be influenced by landscape-level factors and processes.

Écoscience↗

USGS2005

Beringia: Intercontinental exchange and diversification of high latitude mammals and their parasites during the Pliocene and Quaternary

Beringia is the region spanning eastern Asia and northwestern North America that remained ice-free during the full glacial events of the Pleistocene. Numerous questions persist regarding the importance of this region in the evolution of northern faunas. Beringia has been implicated as both a high latitude refugium and as the crossroads (Bering Land Bridge) of the northern continents for boreal mammals. The Beringian Coevolution Project (BCP) is an international collaboration that has provided material to assess the pattern and timing of faunal exchange across the crossroads of the northern continents and the potential impact of past climatic events on differentiation. Mammals and associated parasite specimens have been collected and preserved from more than 200 field sites in eastern Russia, Alaska and northwestern Canada since 1999. Previously, fossils and taxonomic comparisons between Asia and North America mammals have shed light on these events. Molecular phylogenetics based on BCP specimens is now being used to trace the history of faunal exchange and diversification. We have found substantial phylogeographic structure in the Arctic and in Beringia in mustelid carnivores, arvicoline rodents, arctic hares and soricine shrews, including spatially concordant clades and contact zones across taxa that correspond to the edges of Beringia. Among the tapeworms of these mammalian hosts, new perspectives on diversity have also been developed. Arostrilepis horrida (Hymenolepididae) was considered to represent a single widespread and morphologically variable species occurring in a diversity of voles and lemmings in eastern and western Beringia and more broadly across the Holarctic region. The BCP has demonstrated a complex of at least 10 species that are poorly differentiated morphologically. The diversity of Paranoplocephala spp. and Anolocephaloides spp. (Anoplocephalidae) in Beringia included relatively few widespread and morphologically variable species in arvicolines. BCP collections have changed this perspective, allowing the recognition of a series of highly endemic species of Paranoplocephala that demonstrate very narrow host specificity, and additional species complexes among arvicolines. Thus, extensive, previously unrecognized, diversity for tapeworms of 2 major families characterizes the Beringian fauna. By elucidating evolutionary relationships and phylogeographic variation among populations, species and assemblages, refined views of the sequence and timing of biotic expansion, geographic colonization and impact of episodic climate change have been developed for Beringia. Ultimately, Beringia was a determining factor in the structure and biogeography of terrestrial faunas across the Nearctic and Neotropical regions during the Pliocene and Quaternary.

Berengia↗

USGS2012

Stream ecosystems change with urban development

The healthy condition of the physical living space in a natural stream—defined by unaltered hydrology (streamflow), high diversity of habitat features, and natural water chemistry—supports diverse biological communities with aquatic species that are sensitive to disturbances. In a highly degraded urban stream, the poor condition of the physical living space—streambank and tree root damage from altered hydrology, low diversity of habitat, and inputs of chemical contaminants—contributes to biological communities with low diversity and high tolerance to disturbance.

General Information Product↗

USGS2004

Simulated Water-Management Alternatives Using the Modular Modeling System for the Methow River Basin, Washington

A precipitation-runoff model for the Methow River Basin was used to simulate six alternatives: (1) baseline of current flow, (2) line irrigation canals to limit seepage losses, (3) increase surface-water diversions through unlined canals for aquifer recharge, (4) convert from surface-water to ground-water resources to supply water for irrigation, and (5) reduce tree density in forested headwater catchments, and (6) natural flow. Daily streamflow from October 1, 1959, to September 30, 2001 (water years 1960?2001) was simulated. Lining irrigation canals (alternative 2) increased flows in the Chewuch, Twisp, and the Methow (upstream and at Twisp) Rivers during September because of lower diversion rates, but not in the Methow River near Pateros. Increasing diversions for aquifer recharge (alternative 3) increased streamflow from September into January, but reduced streamflow earlier in the summer. Conversion of surface-water diversions to ground-water wells (alternative 4) resulted in the largest increase in September streamflow of any alternative, but also marginally lower January flows (at most -8 percent in the 90-percent exceedence value). Forest-cover reduction (alternative 5) produced large increases in streamflow during high-flow periods in May and June and earlier onset of high flows and small increases in January streamflows. September streamflows were largely unaffected by alternative 5. Natural streamflow (alternative 6) was higher in September and lower in January than the baseline alternative.

Open-File Report↗

USGS2012

Dissolved oxygen analysis, TMDL model comparison, and particulate matter shunting—Preliminary results from three model scenarios for the Klamath River upstream of Keno Dam, Oregon

Efforts are underway to identify actions that would improve water quality in the Link River to Keno Dam reach of the Upper Klamath River in south-central Oregon. To provide further insight into water-quality improvement options, three scenarios were developed, run, and analyzed using previously calibrated CE-QUAL-W2 hydrodynamic and water-quality models. Additional scenarios are under development as part of this ongoing study. Most of these scenarios evaluate changes relative to a "current conditions" model, but in some cases a "natural conditions" model was used that simulated the reach without the effect of point and nonpoint sources and set Upper Klamath Lake at its Total Maximum Daily Load (TMDL) targets. These scenarios were simulated using a model developed by the U.S. Geological Survey (USGS) and Watercourse Engineering, Inc. for the years 2006–09, referred to here as the "USGS model." Another model of the reach was developed by Tetra Tech, Inc. for years 2000 and 2002 to support the Klamath River TMDL process; that model is referred to here as the "TMDL model." The three scenarios described in this report included (1) an analysis of whether this reach of the Upper Klamath River would be in compliance with dissolved oxygen standards if sources met TMDL allocations, (2) an application of more recent datasets to the TMDL model with comparison to results from the USGS model, and (3) an examination of the effect on dissolved oxygen in the Klamath River if particulate material were stopped from entering Klamath Project diversion canals. Updates and modifications to the USGS model are in progress, so in the future these scenarios will be reanalyzed with the updated model and the interim results presented here will be superseded. Significant findings from this phase of the investigation include: * The TMDL analysis used depth-averaged dissolved oxygen concentrations from model output for comparison with dissolved oxygen standards. The Oregon dissolved oxygen standards do not specify whether the numeric criteria are based on depth-averaged dissolved oxygen concentration; this was an interpretation of the standards rule by the Oregon Department of Environmental Quality (ODEQ). In this study, both depth-averaged and volume-averaged dissolved oxygen concentrations were calculated from model output. Results showed that modeled depth-averaged concentrations typically were lower than volume-averaged dissolved oxygen concentrations because depth-averaging gives a higher weight to small volume areas near the channel bottom that often have lower dissolved oxygen concentrations. Results from model scenarios in this study are reported using volume-averaged dissolved oxygen concentrations. * Under all scenarios analyzed, violations of the dissolved oxygen standard occurred most often in summer. Of the three dissolved oxygen criteria that must be met, the 30-day standard was violated most frequently. Under the base case (current conditions), fewer violations occurred in the upstream part of the reach. More violations occurred in the down-stream direction, due in part to oxygen demand from the decay of algae and organic matter from Link River and other inflows. * A condition in which Upper Klamath Lake and its Link River outflow achieved Upper Klamath Lake TMDL water-quality targets was most effective in reducing the number of violations of the dissolved oxygen standard in the Link River to Keno Dam reach of the Klamath River. The condition in which point and nonpoint sources within the Link River to Keno Dam reach met Klamath River TMDL allocations had no effect on dissolved oxygen compliance in some locations and a small effect in others under current conditions. On the other hand, meeting TMDL allocations for nonpoint and point sources was predicted to be important in meeting dissolved oxygen criteria when Upper Klamath Lake and Link River also met Upper Klamath TMDL water-quality targets. * The location of greatest dissolved oxygen improvement from nutrient and organic matter reductions was downstream from point and nonpoint source inflows because time and distance are required for decay to occur and for oxygen demand to be exerted. * After assessing compliance with dissolved oxygen standards at all 102 model segments in the Link River to Keno Dam reach, it was determined that the seven locations used by ODEQ appear to be a representative subset of the reach for dissolved oxygen analysis. * The USGS and TMDL models were qualitatively compared by running both models for the 2006–09 period but preserving the essential characteristics of each, such as organic matter partitioning, bathymetric representation, and parameter rates. The analysis revealed that some constituents were not greatly affected by the differing algorithms, rates, and assumptions in the two models. Conversely, other constituents, especially organic matter, were simulated differently by the two models. Organic matter in this river system is best represented by a mixture of relatively labile particulate material and a substantial concentration of refractory dissolved material. In addition, the use of a first-order sediment oxygen demand, as in the USGS model, helps to capture the seasonal and dynamic effect of settled organic and algal material. * Simulation of shunting (diverting) particulate material away from the intake of four Klamath Project diversion canals, so that the material stayed in the river and out of the Project area, caused higher concentrations of particulate material to occur in the river. In all cases modeled, the increase in in-river particulate material also produced decreased dissolved oxygen concentrations and an increase in the number of days when dissolved oxygen standards were violated. * If particulate material were shunted back into the river at the Klamath Project diversion canals, less organic matter and nutrients would be taken into the Klamath Project area and the Lost River basin, resulting in return flows to the Klamath River via Lost River Diversion Channel that may have reduced nutrient concentrations. Model scenarios bracketing potential end-member nutrient concentrations showed that the composition of the return flows had little to no effect on dissolved oxygen compliance under simulated conditions.

Oregon↗

USGS2012

Hydrological information products for the Off-Project Water Program of the Klamath Basin Restoration Agreement

The Klamath Basin Restoration Agreement (KBRA) was developed by a diverse group of stakeholders, Federal and State resource management agencies, Tribal representatives, and interest groups to provide a comprehensive solution to ecological and water-supply issues in the Klamath Basin. The Off-Project Water Program (OPWP), one component of the KBRA, has as one of its purposes to permanently provide an additional 30,000 acre-feet of water per year on an average annual basis to Upper Klamath Lake through "voluntary retirement of water rights or water uses or other means as agreed to by the Klamath Tribes, to improve fisheries habitat and also provide for stability of irrigation water deliveries." The geographic area where the water rights could be retired encompasses approximately 1,900 square miles. The OPWP area is defined as including the Sprague River drainage, the Sycan River drainage downstream of Sycan Marsh, the Wood River drainage, and the Williamson River drainage from Kirk Reef at the southern end of Klamath Marsh downstream to the confluence with the Sprague River. Extensive, broad, flat, poorly drained uplands, valleys, and wetlands characterize much of the study area. Irrigation is almost entirely used for pasture. To assist parties involved with decisionmaking and implementation of the OPWP, the U.S. Geological Survey (USGS), in cooperation with the Klamath Tribes and other stakeholders, created five hydrological information products. These products include GIS digital maps and datasets containing spatial information on evapotranspiration, subirrigation indicators, water rights, subbasin streamflow statistics, and return-flow indicators. The evapotranspiration (ET) datasets were created under contract for this study by Evapotranspiration, Plus, LLC, of Twin Falls, Idaho. A high-resolution remote sensing technique known as Mapping Evapotranspiration at High Resolution and Internalized Calibration (METRIC) was used to create estimates of the spatial distribution of ET. The METRIC technique uses thermal infrared Landsat imagery to quantify actual evapotranspiration at a 30-meter resolution that can be related to individual irrigated fields. Because evaporation uses heat energy, ground surfaces with large ET rates are left cooler as a result of ET than ground surfaces that have less ET. As a consequence, irrigated fields appear in the Landsat images as cooler than nonirrigated fields. Products produced from this study include total seasonal and total monthly (April-October) actual evapotranspiration maps for 2004 (a dry year) and 2006 (a wet year). Maps showing indicators of natural subirrigation were also provided by this study. "Subirrigation" as used here is the evapotranspiration of shallow groundwater by plants with roots that penetrate to or near the water table. Subirrigation often occurs at locations where the water table is at or above the plant rooting depth. Natural consumptive use by plants diminishes the benefit of retiring water rights in subirrigated areas. Some agricultural production may be possible, however, on subirrigated lands for which water rights are retired. Because of the difficulty in precisely mapping and quantifying subirrigation, this study presents several sources of spatially mapped data that can be used as indicators of higher subirrigation probability. These include the floodplain boundaries defined by stream geomorphology, water-table depth defined in Natural Resources Conservation Service (NRCS) soil surveys, and soil rooting depth defined in NRCS soil surveys. The two water-rights mapping products created in the study were "points of diversion" (POD) and "place of use" (POU) for surface-water irrigation rights. To create these maps, all surface-water rights data, decrees, certificates, permits, and unadjudicated claims within the entire 1,900 square mile study area were aggregated into a common GIS geodatabase. Surface-water irrigation rights within a 5-mile buffer of the study area were then selected and identified. The POU area was then totaled by water right for primary and supplemental water rights. The maximum annual volume (acre-feet) allowed under each water right also was calculated using the POU area and duty (allowable annual irrigation application in feet). In cases where a water right has more than one designated POD, the total volume for the water right was equally distributed to each POD listed for the water right. Because of this, mapped distribution of diversion rates for some rights may differ from actual practice. Water-right information in the map products was from digital datasets obtained from the Oregon Water Resources Department and was, at the time acquired, the best available compilation of water-right information available. Because the completeness and accuracy of the water-right data could not be verified, users are encouraged to check directly with the Oregon Water Resources Department where specific information on individual rights or locations is essential. A dataset containing streamflow statistics for 72 subbasins in the study area was created for the study area. The statistics include annual flow durations (5-, 10-, 25-, 50-, and 95-percent exceedances) and 7-day, 10-year (7Q10) and 7-day, 2-year (7Q2) low flows, and were computed using regional regression equations based on measured streamflow records in the region. Daily streamflow records used were adjusted as needed for crop consumptive use; therefore the statistics represent streamflow under more natural conditions as though irrigation diversions did not exist. Statistics are provided for flow rates resulting from streamflow originating from within the entire drainage area upstream of the subbasin pour point (referring to the outlet of the contributing drainage basin). The statistics were computed for the purpose of providing decision makers with the ability to estimate streamflow that would be expected after water conservation techniques have been implemented or a water right has been retired. A final product from the study are datasets of indicators of the potential for subsurface return flow of irrigation water from agricultural areas to nearby streams. The datasets contain information on factors such as proximity to surface-water features, geomorphic floodplain characteristics, and depth to water. The digital data, metadata, and example illustrations for the datasets described in this report are available on-line from the USGS Water Resources National Spatial Data Infrastructure (NSDI) Node Website http://water.usgs.gov/lookup/getgislist or from the U.S. Government website DATA.gov at http://www.data.gov with links provided in a Microsoft® Excel® workbook in appendix A.

California;Oregon↗

USGS2013

Geomorphic and vegetation processes of the Willamette River floodplain, Oregon: current understanding and unanswered science questions

This report summarizes the current understanding of floodplain processes and landforms for the Willamette River and its major tributaries. The area of focus encompasses the main stem Willamette River above Newberg and the portions of the Coast Fork Willamette, Middle Fork Willamette, McKenzie, and North, South and main stem Santiam Rivers downstream of U.S. Army Corps of Engineers dams. These reaches constitute a large portion of the alluvial, salmon-bearing rivers in the Willamette Basin. The geomorphic, or historical, floodplain of these rivers has two zones - the active channel where coarse sediment is mobilized and transported during annual flooding and overbank areas where fine sediment is deposited during higher magnitude floods. Historically, characteristics of the rivers and geomorphic floodplain (including longitudinal patterns in channel complexity and the abundance of side channels, islands and gravel bars) were controlled by the interactions between floods and the transport of coarse sediment and large wood. Local channel responses to these interactions were then shaped by geologic features like bedrock outcrops and variations in channel slope. Over the last 150 years, floods and the transport of coarse sediment and large wood have been substantially reduced in the basin. With dam regulation, nearly all peak flows are now confined to the main channels. Large floods (greater than 10-year recurrence interval prior to basinwide flow regulation) have been largely eliminated. Also, the magnitude and frequency of small floods (events that formerly recurred every 2–10 years) have decreased substantially. The large dams trap an estimated 50–60 percent of bed-material sediment—the building block of active channel habitats—that historically entered the Willamette River. They also trap more than 80 percent of the estimated bed material in the lower South Santiam River and Middle and Coast Forks of the Willamette River. Downstream, revetments further decrease bed-material supply by an unknown amount because they limit bank erosion and entrainment of stored sediment. The rivers, geomorphic floodplain, and vegetation within the study area have changed noticeably in response to the alterations in floods and coarse sediment and wood transport. Widespread decreases have occurred in the rates of meander migration and avulsions and the number and diversity of landforms such as gravel bars, islands, and side channels. Dynamic and, in some cases, multi-thread river segments have become stable, single-thread channels. Preliminary observations suggest that forest area has increased within the active channel, further reducing the area of unvegetated gravel bars. Alterations to floods and sediment transport and ongoing channel, floodplain, and vegetation responses result in a modern Willamette River Basin. Here, the floodplain influenced by the modern flow and sediment regimes, or the functional floodplain, is narrower and inset with the broader and older geomorphic floodplain. The functional floodplain is flanked by higher elevation relict floodplain features that are no longer inundated by modern floods. The corridor of present- day active channel surfaces is narrower, enabling riparian vegetation to establish on formerly active gravel bar surfaces. The modern Willamette River Basin with its fundamental changes in the flood, sediment transport, and large wood regimes has implications for future habitat conditions. System-wide future trends probably include narrower floodplains and a lower diversity of landforms and habitats along the Willamette River and its major tributaries compared to historical patterns and today. Furthermore, specific conditions and future trends will probably vary between geologically stable, anthropogenically stable, and dynamic reaches. The middle and lower segments of the Willamette River are geologically stable, whereas the South Santiam and Middle Fork Willamette Rivers were historically dynamic, but are now largely stable in response to flow regulation and revetment construction. The upper Willamette and North Santiam Rivers retain some dynamic characteristics, and provide the greatest diversity of aquatic and riparian habitats under the current flow and sediment regime. The McKenzie River has some areas that are more dynamic, whereas other sections are stable due to geology or revetments. Historical reductions in channel dynamism also have implications for ongoing and future recruitment and succession of floodplain forests. For instance, the succession of native plants like black cottonwood is currently limited by (1) fewer low-elevation gravel bars for stand initiation; (2) altered streamflow during seed release, germination, and stand initiation; (3) competition from introduced plant species; and (4) frequent erosion of young vegetation in some locations because scouring flows are concentrated within a narrow channel corridor. Despite past alterations, the Willamette River Basin has many of the physical and ecological building blocks necessary for highly functioning rivers. Management strategies, including environmental flow programs, river and floodplain restoration, revetment modifications, and reclamation of gravel mines, are underway to mitigate some historical changes. However, there are some substantial gaps in the scientific understanding of the modern Willamette basin that is needed to efficiently integrate these blocks and to establish realistic objectives for future conditions. Unanswered questions include: 1. What is the distribution and diversity of landforms and habitats along the Willamette River and its tributaries? 2. What is the extent of today’s functional floodplain—the part of the river corridor actively formed and modified by fluvial processes? 3. How are landforms and habitats in the Willamette River Basin created and sustained by present-day flow and sediment conditions? 4. How is the succession of native floodplain vegetation shaped by present-day flow and sediment conditions? Answering these questions will produce baseline data on the current distributions of landforms and habitats (question 1), the extent of the functional floodplain (question 2), and the effects of modern flow and sediment regimes on future floodplain landforms, habitats, and vegetation succession (questions 3 and 4). Addressing questions 1 and 2 is a logical next step because they underlie questions 3 and 4. Addressing these four questions would better characterize the modern Willamette Basin and help in implementing and setting realistic targets for ongoing management strategies, demonstrating their effectiveness at the site and basin scales, and anticipating future trends and conditions.

Oregon↗

USGS2015

Evaluating potential overlap between pack stock and Sierra Nevada bighorn sheep ( Ovis canadensis sierrae ) in Sequoia and Kings Canyon National Parks, California

Pack stock (horses, mules, burros, llamas, and goats) are frequently assumed to have negative effects on public lands, but there is a general lack of data to be able to quantify the degree to which this is actually the case. Sequoia and Kings Canyon National Parks have received complaints that pack stock may affect Sierra Nevada bighorn sheep ( Ovis canadensis sierrae ; SNBS), a federally endangered subspecies that occurs in largely disjunct herds in the Sierra Nevada Range of California. The potential effects are thought to be displacement of SNBS from meadows on their summer range (altered habitat use) or, more indirectly, through changes in SNBS habitat or forage quality. Our goals were to conduct an association analysis to quantify the degree of potential spatial overlap in meadow use between SNBS and pack stock and to compare differences in vegetation community composition, structure, and diversity among meadows with different levels of use by bighorn sheep and pack stock. For the association analysis, we used two approaches: (1) we quantified the proportion of meadows that were within the herd home ranges of bighorn sheep and were potentially open to pack stock, and, (2) we used Monte Carlo simulations and use-availability analyses to compare the proportion of meadows used by bighorn sheep relative to the proportional occurrence or area of meadows available to bighorn sheep that were used by pack stock. To evaluate potential effects of pack stock on meadow plant communities and SNBS forage, we sampled vegetation in 2011 and 2012 at 100 plots to generate data that allowed us to compare: 1. Herbaceous plant species composition, structure, and diversity in plots with different combinations of use by pack stock and SNBS; 2. Cover of bare ground in plots with different combinations of use by pack stock and SNBS; and, 3. Total cover, diversity, and species composition of SNBS forage species in plots with different combinations of use by pack stock and SNBS. The association analyses indicated the potential for overlap between pack stock and SNBS was minimal; only 1 percent of the potential meadow area in the SNBS herd home ranges overlapped that of pack stock meadows. There were no systematic differences in overall vegetation structure or composition, or in diversity, cover, or composition of forage species, that indicated pack stock were altering SNBS habitat or affecting their nutrition. Variation in plant species composition was influenced primarily by random differences among meadows and environmental gradients, and there was little evidence that pack stock use contributed in meaningful ways to this variation. The few differences among meadows with different levels of use by bighorn sheep and pack stock either were minor or were not in a direction consistent with negative effects of pack stock on SNBS. We conclude that the current plan for managing pack stock grazing has been successful in minimizing significant negative effects on Sierra Nevada bighorn sheep at Sequoia and Kings Canyon National Parks.

California↗