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USGS2020

Using NASA Earth observations and Google Earth Engine to map winter cover crop conservation performance in the Chesapeake Bay watershed

Winter cover crops such as barley, rye, and wheat help to improve soil structure by increasing porosity, aggregate stability, and organic matter, while reducing the loss of agricultural nutrients and sediments into waterways. The environmental performance of cover crops is affected by choice of species, planting date, planting method, nutrient inputs, temperature, and precipitation. The Maryland Department of Agriculture (MDA) oversees an agricultural cost-share program that provides farmers with funding to cover costs associated with planting winter cover crops, and the U.S. Geological Survey (USGS) and the U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS) have partnered with the MDA to develop satellite remote sensing techniques for measuring cover crop performance. The MDA has developed the capacity to digitize field boundaries for all fields enrolled in their cover crop programs (>26,000 fields per year) to support a remote sensing performance analysis at a statewide scal,e and has requested assistance with the associated imagery processing from the National Aeronautics and Space Administration (NASA). Using the Google Earth Engine (GEE) cloud computing platform, scripts were developed to process Landsat 5/7/8 and Harmonized Sentinel-2 imagery to measure winter cover crop performance. We calibrated cover crop performance models using linear regression between satellite vegetation indices and USGS / USDA-ARS field sampling data collected on Maryland farms between 2006 and 2012 (1298 samples). Satellite-derived Normalized Difference Vegetation Index (NDVI) values showed significant correlation with the natural logarithm of cover crop biomass ( p ≤0.01, R 2 = 0.56) and with observed percent vegetative ground cover (p ≤0.01, R 2 = 0.68). The GEE scripts were used to composite seasonal maximum NDVI values for each enrolled cover crop field and calculate performance metrics for the winter and spring seasons of three enrollment years (2014–15, 2015–16, and 2017–18) for four Maryland counties. Results from winter 2017–18 demonstrate that rye and barley fields had higher biomass than wheat fields, and that early planting, along with planting methods that increase seed-soil contact, increased performance. The processing capabilities of GEE will support the MDA in scaling up remote sensing performance analysis statewide, providing information to evaluate the environmental outcomes associated with various agronomic management strategies. The tool can be modified for different seasonal cutoffs, utilize new sensors to capture phenology in winter and spring, and scale to larger regions for use in adaptive management of winter cover crops planted for environmental benefit.

Maryland↗

USGS2010

Change in avian abundance predicted from regional forest inventory data

An inability to predict population response to future habitat projections is a shortcoming in bird conservation planning. We sought to predict avian response to projections of future forest conditions that were developed from nationwide forest surveys within the Forest Inventory and Analysis (FIA) program. To accomplish this, we evaluated the historical relationship between silvicolous bird populations and FIA-derived forest conditions within 25 ecoregions that comprise the southeastern United States. We aggregated forest area by forest ownership, forest type, and tree size-class categories in county-based ecoregions for 5 time periods spanning 1963-2008. We assessed the relationship of forest data with contemporaneous indices of abundance for 24 silvicolous bird species that were obtained from Breeding Bird Surveys. Relationships between bird abundance and forest inventory data for 18 species were deemed sufficient as predictive models. We used these empirically derived relationships between regional forest conditions and bird populations to predict relative changes in abundance of these species within ecoregions that are anticipated to coincide with projected changes in forest variables through 2040. Predicted abundances of these 18 species are expected to remain relatively stable in over a quarter (27%) of the ecoregions. However, change in forest area and redistribution of forest types will likely result in changed abundance of some species within many ecosystems. For example, abundances of 11 species, including pine warbler (Dendroica pinus), brown-headed nuthatch (Sitta pusilla), and chuckwills- widow (Caprimulgus carolinensis), are projected to increase within more ecoregions than ecoregions where they will decrease. For 6 other species, such as blue-winged warbler (Vermivora pinus), Carolina wren (Thryothorus ludovicianus), and indigo bunting (Passerina cyanea), we projected abundances will decrease within more ecoregions than ecoregions where they will increase.

Forest Ecology and Management↗

USGS2013

Impacts of post-harvest slash and live-tree retention on biomass and nutrient stocks in Populus tremuloides Michx.-dominated forests, northern Minnesota, USA

Globally, there is widespread interest in using forest-derived biomass as a source of bioenergy. While conventional timber harvesting generally removes only merchantable tree boles, harvesting biomass feedstock can remove all forms of woody biomass (i.e., live and dead standing woody vegetation, downed woody debris, and stumps) resulting in a greater loss of biomass and nutrients as well as more severe habitat alteration. To investigate the potential impacts of this practice, this study examined the initial impacts (pre- and post-harvest) of various levels of slash and live-tree retention on biomass and nutrient stocks, including carbon (C), nitrogen (N), calcium (Ca), potassium (K), and phosphorus (P), in Populus tremuloides Michx.-dominated forests of northern Minnesota, USA. Treatments examined included three levels of slash retention, whole-tree harvest (WTH), 20% slash retention (20SR), and stem-only harvest (SOH), factored with three levels of green-tree retention, no trees retained (NONE), dispersed retention (DISP), and aggregate retention (AGR). Slash retention was the primary factor affecting post-harvest biomass and nutrient stocks, including woody debris pools. Compared to the unharvested control, stocks of biomass, carbon, and nutrients, including N, Ca, K, and P, in woody debris were higher in all treatments. Stem-only harvests typically contained greater biomass and nutrient stocks than WTH, although biomass and nutrients within 20SR, a level recommended by biomass harvesting guidelines in the US and worldwide, generally did not differ from WTH or SOH. Biomass in smaller-diameter slash material (typically 2.5-22.5 cm in diameter) dominated the woody debris pool following harvest regardless of slash retention level. Trends among treatments in this diameter range were generally similar to those in the total woody debris pool. Specifically, SOH contained significantly greater amounts of biomass than WTH while 20SR was not different from either WTH or SOH. Within P. tremuloides systems, we observed high stocks of smaller diameter slash material for all prescribed slash retention treatments. Most notably, WTH retains much more material than anticipated, up to 50% of available slash. These results reflect the high levels of breakage during winter harvest operations in these stands and, consequently, warrant consideration when anticipating the impacts of biomass harvesting on woody debris pools. Further investigation is necessary to understand how deliberate slash retention levels and season-of-harvest impact woody debris in other forest systems.

Minnesota↗

USGS2015

Assessing landscape change and processes of recurrence, replacement, and recovery in the Southeastern Coastal Plains, USA

The processes of landscape change are complex, exhibiting spatial variability as well as linear, cyclical, and reversible characteristics. To better understand the various processes that cause transformation, a data aggregation, validation, and attribution approach was developed and applied to an analysis of the Southeastern Coastal Plains (SECP). The approach integrates information from available national land-use, natural disturbance, and land-cover data to efficiently assess spatially-specific changes and causes. Between 2001 and 2006, the processes of change affected 7.8 % of the SECP but varied across small-scale ecoregions. Processes were placed into a simple conceptual framework to explicitly identify the type and direction of change based on three general characteristics: replacement, recurrence, and recovery. Replacement processes, whereby a land use or cover is supplanted by a new land use, including urbanization and agricultural expansion, accounted for approximately 15 % of the extent of change. Recurrent processes that contribute to cyclical changes in land cover, including forest harvest/replanting and fire, accounted for 83 %. Most forest cover changes were recurrent, while the extents of recurrent silviculture and forest replacement processes such as urbanization far exceeded forest recovery processes. The total extent of landscape recovery, from prior land use to natural or semi-natural vegetation cover, accounted for less than 3 % of change. In a region of complex change, increases in transitory grassland and shrubland covers were caused by large-scale intensive plantation silviculture and small-scale activities including mining reclamation. Explicit identification of the process types and dynamics presented here may improve the understanding of land-cover change and landscape trajectory.

Alabama, Georgia, Florida, Lousianna, Mississippi,↗

USGS2007

Relative abundance, site fidelity, and survival of adult lake trout in Lake Michigan from 1999 to 2001: Implications for future restoration strategies

We compared the relative abundance of lake trout Salvelinus namaycush spawners in gill nets during fall 1999–2001 in Lake Michigan at 19 stocked spawning sites with that at 25 unstocked sites to evaluate how effective site-specific stocking was in recolonizing historically important spawning reefs. The abundance of adult fish was higher at stocked onshore and offshore sites than at unstocked sites. This suggests that site-specific stocking is more effective at establishing spawning aggregations than relying on the ability of hatchery-reared lake trout to find spawning reefs, especially those offshore. Spawner densities were generally too low and too young at most sites to expect significant natural reproduction. However, densities were sufficiently high at some sites for reproduction to occur and therefore the lack of recruitment was attributable to other factors. Less than 3% of all spawners could have been wild fish, which indicates that little natural reproduction occurred in past years. Wounding by sea lamprey Petromyzon marinus was generally lower for Seneca Lake strain fish and highest for strains from Lake Superior. Fish captured at offshore sites in southern Lake Michigan had the lowest probability of wounding, while fish at onshore sites in northern Lake Michigan had the highest probability. The relative survival of the Seneca Lake strain was higher than that of the Lewis Lake or the Marquette strains for the older year-classes examined. Survival differences among strains were less evident for younger year-classes. Recaptures of coded-wire-tagged fish of five strains indicated that most fish returned to their stocking site or to a nearby site and that dispersal from stocking sites during spawning was about 100 km. Restoration strategies should rely on site-specific stocking of lake trout strains with good survival at selected historically important offshore spawning sites to increase egg deposition and the probability of natural reproduction in Lake Michigan.

North American Journal of Fisheries Management↗

USGS2011

Precipitation-runoff relations and water-quality characteristics at edge-of-field stations, Discovery Farms and Pioneer Farm, Wisconsin, 2003-8

A cooperative study between the U.S. Geological Survey, the University of Wisconsin (UW)-Madison Discovery Farms program (Discovery Farms), and the UW-Platteville Pioneer Farm program (Pioneer Farm) was developed to identify typical ranges and magnitudes, temporal distributions, and principal factors affecting concentrations and yields of sediment, nutrients, and other selected constituents in runoff from agricultural fields. Hydrologic and water-quality data were collected year-round at 23 edge-of-field monitoring stations on 5 privately owned Discovery Farms and on Pioneer Farm during water years 2003-8. The studied farms represented landscapes, soils, and farming systems typical of livestock farms throughout southern Wisconsin. Each farm employed a variety of soil, nutrient, and water-conservation practices to help minimize sediment and nutrient losses from fields and to improve crop productivity. This report summarizes the precipitation-runoff relations and water-quality characteristics measured in edge-of-field runoff for 26 "farm years" (aggregate years of averaged station data from all 6 farms for varying monitoring periods). A relatively wide range of constituents typically found in agricultural runoff were measured: suspended sediment, phosphorus (total, particulate, dissolved reactive, and total dissolved), and nitrogen (total, nitrate plus nitrite, organic, ammonium, total Kjeldahl and total Kjeldahl-dissolved), chloride, total solids, total suspended solids, total volatile suspended solids, and total dissolved solids. Mean annual precipitation was 32.8 inches for the study period, about 3 percent less than the 30-year mean. Overall mean annual runoff was 2.55 inches per year (about 8 percent of precipitation) and the distribution was nearly equal between periods of frozen ground (54 percent) and unfrozen ground (46 percent). Mean monthly runoff was highest during two periods: February to March and May to June. Ninety percent of annual runoff occurred between January and the end of June. Event mean concentrations of suspended sediment in runoff during unfrozen-ground periods were significantly higher (p<0.05) than those during frozen-ground periods. Mean annual suspended-sediment yields ranged from about 3 to nearly 5,000 pounds per acre (lb/acre), with a mean yield of 667 lb/acre. Ninety percent of suspended sediment was yielded in runoff during unfrozen-ground periods. May and June alone contributed more than 80 percent of the overall yield. Phosphorus concentrations and yields were also affected by the ground conditions at the time of runoff; however, unlike suspended sediment, phosphorus was usually available for transport in runoff regardless of ground condition. Mean annual total-phosphorus yields ranged from 0.03 to 7.0 lb/acre, with a mean yield of about 2.0 lb/acre. Nitrogen in runoff followed similar patterns to phosphorus in that concentrations were highest during unfrozen-ground periods, yields were highest during months of highest runoff, and speciation was affected by the ground conditions at the time of runoff. Mean annual total-nitrogen yields ranged from 0.11 to 19.2 lb/acre, and the mean was 7.2 lb/acre. Mean monthly total-nitrogen yields were strongly correlated with mean monthly total-phosphorus yields (r 2 = 0.92), indicating that the sources of nitrogen and phosphorus in runoff were likely similar. Analysis of runoff, concentration, and yield data on annual, monthly, and seasonal time scales, when combined with precipitation, soil moisture, soil temperature, and on-farm field-activity information, revealed conditions in which runoff was most likely. The analysis also revealed the effects that field conditions and the timing of field-management activities-most notably, manure applications and tillage-had on the quantity and quality of surface runoff from agricultural fields.

Scientific Investigations Report↗

USGS2025

Social composition of soft‐release groups is correlated with survival of translocated gopher tortoises

The social structure of translocated animal populations can have important effects on the survival and reproduction of translocated individuals for both solitary and social species. The gopher tortoise ( Gopherus polyphemus ) is a reptile of conservation concern that is currently experiencing high levels of mitigation translocation in Florida, USA. Individuals live in aggregations of burrows with frequent agonistic, courtship, and burrow-sharing interactions between residents. Given that exposure to many unfamiliar individuals may increase the frequency of aggressive interactions and social stress following translocation, we predicted that tortoises with greater numbers of familiar individuals co-translocated from the same origin site would have higher survival after translocation. To test this, we updated a recently published survival analysis of 2,822 translocated tortoises and 502 identified carcasses from a translocation site in the western Florida panhandle from 2006–2022. After controlling for simultaneous effects of soft-release enclosure identity, release season, release density, region of origin, sex, and size, adding the number of potentially familiar individuals improved model fit and showed increasing the number of familiars reduced the probability of being found dead. This effect was modulated by release density, being apparent only when density was high, suggesting a role for social interactions. This effect was also present only in the first few years after release, prior to the removal of soft-release enclosures preventing dispersal, and was similar in magnitude to previously identified effects of density, release season, and region of origin. We suggest that this effect may result from reduced aggressive interactions or social stress for tortoises with a greater number of familiar individuals in their release enclosures but cannot rule out the possibility of reduced novel pathogen exposure for individuals released with a greater number of individuals from the same source site or other factors that may be confounded with the size of translocated groups. Designing and implementing mitigation translocations to account for social composition of gopher tortoise groups could improve survival in release enclosures.

Florida↗

USGS2016

Benthic processes affecting contaminant transport in Upper Klamath Lake, Oregon

Executive Summary Multiple sampling trips during calendar years 2013 through 2015 were coordinated to provide measurements of interdependent benthic processes that potentially affect contaminant transport in Upper Klamath Lake (UKL), Oregon. The measurements were motivated by recognition that such internal processes (for example, solute benthic flux, bioturbation and solute efflux by benthic invertebrates, and physical groundwater-surface water interactions) were not integrated into existing management models for UKL. Up until 2013, all of the benthic-flux studies generally had been limited spatially to a number of sites in the northern part of UKL and limited temporally to 2–3 samplings per year. All of the benthic invertebrate studies also had been limited to the northern part of the lake; however, intensive temporal (weekly) studies had previously been completed independent of benthic-flux studies. Therefore, knowledge of both the spatial and temporal variability in benthic flux and benthic invertebrate distributions for the entire lake was lacking. To address these limitations, we completed a lakewide spatial study during 2013 and a coordinated temporal study with weekly sampling of benthic flux and benthic invertebrates during 2014. Field design of the spatially focused study in 2013 involved 21 sites sampled three times as the summer cyanobacterial bloom developed (that is, May 23 , June 13 , and July 3, 2013). Results of the 27-week, temporally focused study of one site in 2014 were summarized and partitioned into three periods (referred to herein as pre-bloom, bloom and post-bloom periods), each period involving 9 weeks of profiler deployments, water column and benthic sampling. Partitioning of the pre-bloom, bloom, and post-bloom periods were based on water-column chlorophyll concentrations and involved the following date intervals, respectively: April 15 through June 10 , June 17 through August 13 , and August 20 through October 16, 2014. To examine dissolved-solute (0.2-micrometer [μm] filtered) benthic flux, sets of nonmetallic pore-water profilers (U.S. Patent 8,051,727 B1) were deployed. In 2013, the deployment of profilers at 21 UKL sites occurred at the beginning of the annual cyanobacterial bloom of Aphanizomenon flos–aquae (AFA), in the middle of the bloom period, and at the peak of the bloom. Coordinated benthic invertebrate collections also were made. Based on results from 2013, weekly deployments of profilers and collection of benthic invertebrate samples from late spring to early autumn were used to estimate temporal trends in solute flux and benthic invertebrate densities. Estimates of nutrient efflux by benthic invertebrates were determined in the spring and autumn from 2011 through 2013 and three times (spring, summer, and autumn) in 2015. This work extends UKL studies that began in 2006 to quantify the importance of benthic solute sources in the lake. In 2015, piezometers and thermistor sets were deployed to quantify potential groundwater exchange with the lake water column. Analysis of the 2013 soluble reactive phosphorus (SRP) benthic flux indicated no effect of location (lake region), habitat, or sampling period, and the average lakewide flux values were consistent with earlier studies that had been confined to the northern region of UKL and adjacent wetlands. The 2014 study therefore focused on estimating temporal trends at a site within Ball Bay. During both 2013 and 2014 field studies, fluxes of macronutrients (soluble reactive phosphorus (SRP) and ammonia) and micronutrients (iron [Fe] and manganese [Mn]) were consistently positive and increased prior to the initial AFA bloom, varied or lagged with water-column chlorophyll during the summer bloom period, then decreased after the cyanobacterial blooms, only to rebound toward pre-bloom conditions in the final weeks of sampling. These four solutes exhibited benthic loads greater than maximum riverine loads estimated during the spring and early summers of 2013 and 2014. However, consistently detectable concentrations for all four solutes provide no evidence that they consistently serve as the limiting nutrient for primary production in the lake. In contrast to the four solutes (SRP, ammonia, Fe, and Mn), benthic fluxes of dissolved arsenic (As) were both negative and positive (that is, the lakebed currently serves as both a source and a sink for dissolved As, depending on season). In a further contrast with SRP, ammonia, dissolved Fe, and Mn, dissolved-As riverine loads to UKL were of similar magnitude to benthic loads. A negative relationship between dissolved-As flux and water-column As over the 2014 temporal study provides a potential advantage for the management of water-quality in contrast to solutes, like SRP or ammonia, with consistently positive flux. The mean total benthic invertebrate density during 2013 was 12,610 individuals per square meter (n=63). Although benthic invertebrate density did not change over the study period, it was higher in littoral habitats than open-lake or trench habitats and higher in the northern region compared to the central or southern regions of UKL. Mean total benthic invertebrate density during 2014 was 19,726 individuals m −2 (n=27). Density during the pre-bloom and bloom periods of April 15 to August 13, 2014 (the first two thirds of the 2014 sampling period), were similar to 2013. However, benthic invertebrate density more than doubled during the latter one-third of the study, that is, the post-bloom period between August 20 to October 16, 2014. Oligochaeta, Chironomidae and Hirudinea represented well over 90 percent of the benthic fauna; Oligochaeta were twice as abundant as Chironomidae or Hirudinea, the latter two of which were similar in density. Benthic invertebrates may enhance dissolved-nutrient (or toxicant) transport across the sediment-water interface by (1) modifying diffusion-layer thicknesses and permeability through bioturbation, (2) enhancing advective flow across the interface through bioirrigation, and (3) excreting or expelling dissolved or particulate solutes directly into the overlying water column (Boudreau and Jorgensen, 2001). We evaluated SRP efflux via excretion for approximately 15 different major taxa in UKL. Once these measures were scaled, it was evident that benthic invertebrates potentially contribute approximately 1.5 times the amount of SRP to the water column of Upper Klamath Lake as diffusive SRP flux alone, measured in profiler deployments. Sets of piezometers and temperature loggers were deployed in UKL to obtain estimates of vertical advective solute flux. The pressure transducer installations, within the piezometers, did not perform as designed, rendering the head gradient data unreliable. However, in terms of future research, this field work did demonstrate the feasibility of collecting vertical gradient data with piezometer deployments. Advective flux estimates herein are based solely on heat-flow modeling based on temperature data from four lake sites, without use of transducer data. Given the magnitudes (both positive or negative) of the heat-transfer fluxes for SRP, relative to diffusive-flux and macroinvertebrate efflux measurements (all positive but spanning the same orders of magnitude), further examination of solute advective flux is recommended as a potential transport process to integrate into existing water-quality (for example, Total Maximum Daily Load [TMDL]) models. As a complement to the biogeochemical focus of this study, initial analyses of suspended-particle (floc) characteristics and settling velocities from the water column were derived near the surface and lakebed at two UKL sites. To better understand changing particle characteristics during the AFA-bloom period, suspended particles were examined in 2015 using a LabSFLOC (LF), which is a Laboratory Spectral Flocculation Characteristics version of an In-Situ Settling Velocity instrument (INSSEV-LF). Particle characteristics and settling velocities were analyzed from the water column near the surface (sample dp_10 ) and lakebed (sample dp_90 ) at two lake sites (open-lake site ML and littoral site LS01). The term “floc” refers herein to suspended particles that may aggregate or disaggregate to change in size, composition, and settling velocity. During pre-bloom (May) conditions, where maximum suspended particulate matter concentration (SPMC) was 140 milligrams per liter (mg L −1 ) was now observed at site LS01 in close proximity to the bed, where D mean peaked at 305 μm, and the corresponding Ws mean was 3.9 millimeters per second (mm s −1 ). The high near-bed SPMC (828 mg L −1 ) experienced during post-bloom October 2015 at LS01 formed a benthic nepheloid layer (BNL) above the lake’s bed. Numerous low density, fast settling macrofloc-sized organic aggregates (D >160 μm) were observed (some up to 1 mm in size) near bed at LS01 both during the bloom and post-bloom conditions; many of these flocs displayed fibrous organic structures. In terms of mass settling fluxes, the post-bloom BNL produced a total MSF of 4,139 milligrams per square meter per second (mg m −2 s −1 ) (92.1 percent of MSF credited to the macrofloc-sized organic aggregates/cyanobacterial colonies); that was nearly three times the corresponding near-bed settling flux observed during the July 2015 bloom and 360 times greater than the pre-bloom conditions from May 2015 (98.8 percent and 14 percent of MSF credited to the macrofloc-sized fractions for those respective months). Such changes in the near-bed settling flux demonstrate the highly significant seasonal effects that the AFA bloom has on the floc depositional fluxes in UKL and highlights the importance of seasonal monitoring of these conditions in order to correctly parameterize the wide range in depositional characteristics and floc properties measured throughout UKL. Collectively, floc populations observed within UKL demonstrated a wide range in settling velocity (Ws) for a given particle size, D. Similarly, a given settling velocity was not associated with a specific particle size. This variability in particle characteristics and properties indicates the influence of varying floc effective density and its effect on mass and mass settling fluxes (MSF). The use of instruments, such as the INSSEV-LF, enables measuring the variability of settling velocity and its relation to particle density and size.

Oregon↗

USGS2020

Using advanced population genomics to better understand the relationship between offshore and spawning habitat use for Atlantic Sturgeon

Atlantic Sturgeon ( Acipenser oxyrinchus oxyrinchus ) are a large-bodied anadromous fish that historically supported important fisheries along the east coast of the United States. Following years of overharvest and habitat degradation, populations experienced severe declines. In 2012, the National Marine Fisheries Service listed Atlantic Sturgeon under the Endangered Species Act (ESA; 61 FR 4722). Their listing named five Distinct Population Segments (DPSs), predicated on genetic groups composed of geographically proximate populations. Federal management of Atlantic Sturgeon presents challenges, as sturgeon from each of the five DPSs mix extensively in coastal and marine habitats yet take and recovery progress must be evaluated separately for each unit. Genetic assignment testing based on mitochondrial and microsatellite markers allows individuals to be assigned back to their natal river and DPS. However, this approach is not perfect and some individuals may be incorrectly assigned. Recent advances in genomics offer the potential of a higher resolution approach to genetic assignment testing, and thus may reduce uncertainty associated with assignment testing. In addition, genomics allows a greater number of markers to be examined from across a broader portion of the sturgeon genome, thus may provide an enhanced perspective of population structure for the species, and potentially allow other previously intractable questions to be addressed (Bernatchez et al. 2017, Supple and Shapiro 2018). We used next-generation sequencing to develop a draft genome for Atlantic Sturgeon and identify single nucleotide polymorphisms (SNPs) that could be used to resolve the natal river and DPS of individual Atlantic Sturgeon. We identified 1,210 candidate SNPs within the nuclear genome as well as 49 SNPs within the mitochondrial genome. After filtering and review, we selected 161 nuclear SNPs and 39 mitochondrial SNPs for further testing and evaluation. We used genotyping-in-thousands by sequencing (GT-seq) to simultaneously sequence nuclear SNP loci, mitochondrial SNP loci, and the existing panel of twelve microsatellite loci. This effort required a pilot sequencing run on a single sturgeon sample to test marker amplification and refine primer strengths, followed by a series of sequencing runs to generate baseline data for 288 individuals representing nine populations of Atlantic Sturgeon in four DPSs. Using baseline data from the nine populations, we ran a series of genomic analyses to characterize diversity within and among populations, providing a benchmark for this species using the new SNP markers. Allelic richness was similar for all populations, although there was a general trend of more northern population containing greater levels of allelic richness. Interestingly, we observed linkage disequilibrium among many pairs of loci within many populations. This might be the result of physical linkage but could also suggest these populations are recovering from genetic bottlenecks and/or are effectively small, leading to specific haplotypes to be favored by chance. Pairwise differentiation among populations varied among the populations ( F ST range: 0.010-0.098) and was significantly correlated ( r = 0.771; P < 0.001) to pairwise F ST observed using microsatellite markers). Population clustering and ordination techniques using the new genomic data both support an overall population structure that is similar to the current DPS management units (which were developed primarily based on microsatellite genetic data). Overall, this suggests that existing microsatellite markers and the panel of SNP markers developed in this study provide similar information about the populations structure and ecology of Atlantic Sturgeon. Given the observed differences in allele frequencies among populations, our genomic baseline supports previous assertations that Atlantic Sturgeon show natal homing, despite mixing extensively in marine waters during non-breeding periods. Lower levels of differentiation between populations in the South Atlantic DPS suggest that populations in this region may have greater levels of gene flow relative to their more northerly conspecifics, which has also previously been suggested based on microsatellite data. The observed differentiation among populations provides the necessary foundation for determining the natal river and DPS of Atlantic Sturgeon using assignment testing. We tested the utility of our new genomic baseline for resolving the population and DPS of Atlantic Sturgeon. Our nuclear SNP markers showed utility for identifying the origin of unknown Atlantic Sturgeon samples, as 86.5% were assigned to the correct DPS and 66.3% were assigned to the correct natal river. However, since this study was funded the Conservation Genetics and Genomics Laboratory at Leetown Science Center has made significant improvements to their microsatellite genetic baseline, which now performs more effectively than our new genomic approach (the genetic baseline includes 12 populations and 5 DPSs, and correctly assigns 95.8% of individuals to DPS and 84.9% of individuals to their natal population using 12 microsatellite loci). We conducted an ad hoc exploration of how additional microsatellite or nuclear SNP loci may further improve the accuracy of assignment testing. We found that additional microsatellite markers are likely to result in greater improvements in assignment efficiency than additional nuclear SNPs. However, a much larger number of SNP loci (which if identified could be sequenced using other methods that are now available; e.g., the RAD-capture approach published by Ali et al. 2016) could produce assignment efficiencies that are greater than what is currently feasible using microsatellites. In the absence of further research and development of additional SNP markers for Atlantic Sturgeon (possibly using an approach other than GT-seq), the existing microsatellite loci are the most effective means available to determine the natal river and DPS of Atlantic Sturgeon encountered in offshore waters. Because our new genomic markers were less effective than the existing panel of 12 microsatellite markers, we chose to use the existing microsatellite markers to assign Atlantic Sturgeon captured in another BOEM-funded study (cooperative agreement M16AC00003; Monitoring endangered Atlantic Sturgeon and commercial finfish habitat use offshore New York) following consultation with our project officer. Using this approach, we genotyped and assigned 186 Atlantic Sturgeon captured in coastal waters off the Rockaway Peninsula, New York. The vast majority of these sturgeon were assigned to the New York Bight DPS (94.62%), and most appear to belong to the Hudson River population (87.10%) with smaller contributions from the Delaware River population (7.53%). Smaller contributions (2.15%) were observed from six other populations, including those from the James, York, Kennebec, Ogeechee, and Edisto rivers. Although most of the fish we assigned were assigned to the nearest spawning rivers (Hudson and Delaware), the contributions from distant rivers is consistent with the propensity of this species to move long distances and form mixed stock aggregations along the continental shelf. This finding indicates that spawning populations (and their corresponding DPS) from distant locations may potentially be impacted by offshore activities. In fact, activities in this region of the New York Bight could negatively impact Atlantic Sturgeon population from at least four different DPSs. Genetic or genomic assignment testing remains an essential tool to characterize potential impacts to Atlantic Sturgeon populations and should be applied more broadly to better characterize potential impacts of activities in other locations.

Atlantic Coast↗

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↗

USGS2010

Geohydrology of the stratified-drift aquifer system in the lower Sixmile Creek and Willseyville Creek trough, Tompkins County, New York

In 2002, the U.S. Geological Survey, in cooperation with the Tompkins County Planning Department began a series of studies of the stratified-drift aquifers in Tompkins County to provide geohydrologic data for planners to develop a strategy to manage and protect their water resources. This aquifer study in lower Sixmile Creek and Willseyville Creek trough is the second in a series of aquifer studies in Tompkins County. The study area is within the northern area of the Appalachian Plateau and extends about 9 miles from the boundary between Tompkins County and Tioga County in the south to just south of the City of Ithaca in the north. In lower Sixmile Creek and Willseyville Creek trough, confined sand and gravel aquifers comprise the major water-bearing units while less extensive unconfined units form minor aquifers. About 600 people who live in lower Sixmile Creek and Willseyville Creek trough rely on groundwater from the stratified-drift aquifer system. In addition, water is used by non-permanent residents such as staff at commercial facilities. The estimated total groundwater withdrawn for domestic use is about 45,000 gallons per day (gal/d) or 0.07 cubic foot per second (ft3/s) based on an average water use of 75 gal/d per person for self-supplied water systems in New York. Scouring of bedrock in the preglacial lower Sixmile Creek and Willseyville Creek valleys by glaciers and subglacial meltwaters truncated hillside spurs, formed U-shaped, transverse valley profiles, smoothed valley walls, and deepened the valleys by as much as 300 feet (ft), forming a continuous trough. The unconsolidated deposits in the study area consist mostly of glacial drift, both unstratified drift (till) and stratified drift (laminated lake, deltaic, and glaciofluvial sediments), as well as some post-glacial stratified sediments (lake-bottom sediments that were deposited in reservoirs, peat and muck that were deposited in wetlands, and alluvium deposited by streams). Multiple advances and retreats of the ice in the study area resulted in several sequences of various types of glacial deposits. A large moraine (Valley Heads Moraine) dominates the southern part of the study area, a large delta dominates the central part, and ground moraine (mostly till) dominates the northern part. Glacial sediments in the center of the lower Sixmile Creek and Willseyville Creek trough typically range from 150 to 200 ft but can be greater than 300 ft in some places. Where the sediments are composed of sand and gravel they form aquifers. In most parts of the lower Sixmile Creek and Willseyville Creek trough, there is an upper and a basal confined aquifer. However, underlying the central parts of the Brooktondale delta, there are as many as four confined aquifers, whereas in the northern part of the study area, only one extensive confined aquifer is present. The major sources of recharge to these confined aquifers are (1) direct infiltration of precipitation where confined aquifers crop out at land surface (mostly along the western trough wall in the southern and central parts of the study area and, to a lesser degree, along the eastern trough wall); (2) unchanneled surface and subsurface runoff from adjacent upland areas that seeps into the aquifer along the western trough walls; (3) subsurface flow from underlying till or bedrock at the lateral contacts at trough walls; (4) adjacent fine-grained stratified drift, especially when the aquifer is pumped; and (5) discharge from bedrock at the bottom and sides of the trough. In the central part of the study area, the surficial coarse-grained sediments (sand and gravel) comprise a delta near Brooktondale and form a small unconfined aquifer (0.3 square mile). Although much of the upper part of the delta has been removed by several aggregate mining operations, sufficient amounts of sand and gravel remain in most places to form a thin unconfined aquifer. The major sources of recharge to the unconfined aquifer are (1)

Scientific Investigations Report↗

USGS2015

Analysis of storm-tide impacts from Hurricane Sandy in New York

The hybrid cyclone-nor’easter known as Hurricane Sandy affected the mid-Atlantic and northeastern United States during October 28-30, 2012, causing extensive coastal flooding. Prior to storm landfall, the U.S. Geological Survey (USGS) deployed a temporary monitoring network from Virginia to Maine to record the storm tide and coastal flooding generated by Hurricane Sandy. This sensor network augmented USGS and National Oceanic and Atmospheric Administration (NOAA) networks of permanent monitoring sites that also documented storm surge. Continuous data from these networks were supplemented by an extensive post-storm high-water-mark (HWM) flagging and surveying campaign. The sensor deployment and HWM campaign were conducted under a directed mission assignment by the Federal Emergency Management Agency (FEMA). The need for hydrologic interpretation of monitoring data to assist in flood-damage analysis and future flood mitigation prompted the current analysis of Hurricane Sandy by the USGS under this FEMA mission assignment. The analysis of storm-tide impacts focused on three distinct but related aspects of coastal flooding from Hurricane Sandy, including flooding inland along the tidal reach of the Hudson River. These aspects are (1) comparisons of peak storm-tide elevations to those of historical storms and to annual exceedance probabilities, (2) assessments of storm-surge characteristics, and (3) comparisons of maps of inundation extent that were derived from differing amounts of available storm-tide data. Most peak storm-tide elevations from Hurricane Sandy were greater than about 9.5 feet (ft) above North American Vertical Datum of 1988. Peak storm-tide elevations from Hurricane Sandy were compared with data for the intense nor’easter of December 11–13, 1992, and Hurricane Irene (August 27–28, 2011), which weakened to a tropical storm before arriving in New York. Peak storm-tide elevations from Hurricane Sandy were higher than those from the December 1992 nor’easter at 24 of 27 sites; most differences were greater than about 0.7 ft or 9 percent (above the historical storm tide). Peak storm-tide elevations from Hurricane Sandy were higher than those from Tropical Storm Irene at all sites; most differences were greater than about 2.5 ft or 48 percent. Data from permanent and temporary monitoring sites and HWM sites were compared with corresponding FEMA flood elevations for the 10-, 2-, 1-, and 0.2-percent annual exceedance probabilities in New York. Peak storm-tide elevations from Hurricane Sandy had annual exceedance probabilities less than or equal to 1 percent and (or) greater than 0.2 percent at a plurality of sites—184 of 413. Peak storm-tide elevations greater than or equal to the 0.2-percent flood elevation accounted for 81 of 413 sites. Peak storm-tide elevations less than the 10-percent flood elevation accounted for only 10 of 413 sites. Data from selected permanent monitoring sites in the USGS and NOAA networks were used to assess storm-surge magnitude associated with the peak storm tide, and magnitude and timing of the peak storm surge. Most magnitudes of the peak storm surge were greater than about 8.3 ft, and most magnitudes of the storm surge component of the peak storm tide were greater than about 7.8 ft. Timing of peak storm surge arrival with respect to local phase of tide controlled where the most extreme peak storm-tide levels and coastal flooding occurred. This finding has bearing not only for locations impacted by the highest storm tides from Hurricane Sandy, but also for those that had the greatest storm surges yet were spared the worst flooding because of fortuitous timing during this storm. Results of FEMA Hazus Program (HAZUS) flood loss analyses performed for New York counties were compared for extents of storm-tide inundation from Hurricane Sandy mapped (1) pre-storm, (2) on November 11, 2012, and (3) on February 14, 2013. The resulting depictions of estimated total building stock losses document how differing amounts of available USGS data affect the resolution and accuracy of storm-tide inundation extents. Using the most accurate results from the final (February 14, 2013) inundation extent, estimated losses range from $380 million to $5.9 billion for individual New York counties; total estimated aggregate losses are about $23 billion for all New York counties. Quality of the inundation extents used in HAZUS analyses has a substantial effect on final results. These findings can be used to inform future post-storm reconstruction planning and estimation of insurance claims.

New York↗

USGS1976

Summary appraisals of the nation's ground-water resources – California region

Most people in the California Region live in a semiarid or arid climate, with precipitation less than the potential evapotranspiration- environments of perennial water deficiency. The deficiency becomes most onerous during the characteristically rainless summers and during recurrent droughts that may continue for 10--20 years. However, water from winter rain and snow can be stored for use during the dry summer months, and water stored during a wet climatic period can be used in a succeeding dry period; moreover, perennial deficiency can be overcome by bringing water from areas of perennial surplus. Ground-water reservoirs have especial significance in arid and semiarid regions as repositories where water is stored or can be stored with minimum loss by evaporation. Nearly all the ground-water reservoirs of the California Region are in alluvial sediments of valleys and plains that flank the mountain ranges. The largest, underlying the vast Central Valley, occupies 10 percent of the area of the region, has an estimated usable capacity exceeding 100 million acre-feet (125 cubic kilometres), and has an annual pumpage from wells of about 13 million acre-feet (16 cubic kilometres). Another 10 percent of the region is occupied by 55 developed ground-water reservoirs that are widely distributed; aggregate annual pumpage from them is about 3 1/2 million acre-feet (4 cubic kilometres). In the southeastern desert about 60 ground-water reservoirs occupy still another 10 percent of the region; these have been explored only enough to show that most have some usable water, but current use is negligible. In northeastern California and adjacent Oregon and Nevada, ground-water reservoirs are identified only in valleys and lowlands where wells are feasible, but basaltic rocks of the Cascade Range and Modoc Plateau are excellent aquifers distributed over an area constituting about 15 percent of the region. In sum, slightly less than half the California Region is underlain by ground-water reservoirs, either in valley fill or in volcanic rocks, which can yield significant quantities of water to wells. The rest of the California Region includes the mountains, canyons, slopes, and foothills of the Sierra Nevada, Coast Ranges, and Basin Ranges, whose consolidated rocks and products of their weathering may be permeable locally but are not generally so. Here, the prevailing method of ground-water development is still mostly trial and error, and while in many places a well can yield enough water for a family, some families might have to do without amenities such as flush toilets and automatic washers. For more than half a century the California Region has led all others in North America in pumping of ground water as well as in the area, variety, yield, and export of crops irrigated by water from wells. It has led in the development and use of deep-well turbine pumps for large yield and in the drilling of water wells to great depths. At the same time, such developments have resulted in the elimination of artesian pressures that produced thousands of flowing wells in the 19th century and led to the wide distribution of "falling water tables." Also, California was first to induce encroachment of seawater into wells (in 1906); first to recognize subsidence of land caused by pumping from wells (in 1933), generating news about land sinking in San Jose, Long Beach, and along the Delta-Mendota and Friant-Kern Canals; and first to experience pollution of ground-water reservoirs by brines, chemicals, industrial wastes, and petroleum byproducts including gasoline. The region has led in research in several fields leading to solution of many of these problems. Ground-water problems developed rapidly after World War II with booming population, agriculture, industry, and water demand during several years of regionwide drought. Water levels in wells trended downward almost everywhere as a natural effect of the drought and at accelerated rates in areas of pumping for new enterprises or to supplement subnormal surface-water supplies. The declines in many pumping areas exceeded 100 feet (30 metres), and in some confined aquifers the potentiometric surface was drawn down more than 330 feet (100 metres). The depletion of ground-water storage has had "permanent" side effects, including subsidence of the land exceeding 10 feet (3 metres) in extensive areas, and seawater intrusion that ended the useful lives of many wells along the coast and as much as 6 miles (10 kilometres) inland. Some problems have been solved, but these solutions have at times created other problems. Many ground-water reservoirs have gone through one or more stages - exploration for productive aquifers, exploitation and development for use of the water, restriction to the perennial supply or "safe" yield, importation of surface water, artificial recharge of ground water, conjunctive use of surface and ground water, protection of water quality, and integrated management of use and disposal of water. This evolutionary sequence is unique for each reservoir, and so generalizations become difficult in a regional appraisal; also, the changes with time are significant and varied, and knowledge of prior events is a prerequisite in an appraisal of the resource in a specific year. As of 1970, water levels in many wells had risen significantly from the minimum levels of record reached during the 1960's or earlier; only in areas of new development and in desert areas of long-continued "mining" of nonreplenished water was ground-water storage still being depleted. Land subsidence has continued at diminishing rates and practically has come to a halt in some areas; invading seawater has been stopped or nudged back in most places where problems were significant. The current, favorable situation has been helped by climatic variations, from drought in 1945-52 and exceedingly dry years in 1959 and 1961 to above-normal precipitation in 1969 and 1970; but most of the serious problems have been solved by human efforts, including especially the implementation of the California Water Plan, transporting water from areas of perennial surplus to areas where it is used in lieu of ground water or for ground-water replenishment. All major urban areas now import water to supplement or replace the water pumped from wells. Extensive agricultural areas that formerly were irrigated solely by ground water now obtain some of their water from surface reservoirs and canals, especially in the Central Valley. With surface water available as an alternative supply, well owners can view their ground water with complacency. But complacency can lead to neglect and carelessness and consequent deterioration of the ground-water resource by pollution. Claiming heritage from the English Common Law, the existing California law grants to the landowner (riparian) and private enterprise (appropriator) rights to the water stored in ground-water reservoirs or discharged from them, including the base flow of streams. Ground-water development has been by private and local enterprise, and the California legislature has protected and encouraged local responsibility, control, and management of ground water. As to surface water, a constitutional amendment in 1928 limited riparian rights to the quantities of water that were "reasonably required for the beneficial use to be served." The surpluses have become public waters which are collected, stored, transported, and delivered under various contracts by Federal, State, and other agencies. The agencies have not stored water underground because of uncertainty as to their rights, but some local agencies have been encouraged with favorable pricing schedules to undertake the artificial recharge and management of ground-water reservoirs. Thus, conjunctive use of surface and ground water has become a matter of interagency negotiation. Of all the constraints on effective use of ground-water reservoirs, the most formidable may be the attitudes of people. Assurance of water supply is vital in areas of water deficiency, and Government has assumed increasing responsibility for the welfare of people in these areas. Unfortunately, when Government provides this assurance, most beneficiaries demand continued subsidy to the exclusion of perhaps cheaper private development. Indeed, as the water resources are presently segregated-with private rights predominant in ground water and public interest dominant in surface water-ground-water development has suffered for lack of public concern. The region has the scientific and technologic capability for effective use of groundwater reservoirs, as shown by the achievements and programs of several districts, but many districts are not organized or staffed for such comprehensive management and will need assistance and scientific expertise available from State and Federal agencies. Those agencies, in turn, may not have the scientific data that are essential to prevent haphazard activities and to enable programs to be organized for the most effective and attractive utilization of the water resources. In these days of increasing concern over pollution, existing data are generally inadequate to assess the natural deterioration of ground waters as a basis for defining pollution.

California↗