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Forecasting species distributions: Correlation does not equal causation

Aim Identifying the mechanisms influencing species' distributions is critical for accurate climate change forecasts. However, current approaches are limited by correlative models that cannot distinguish between direct and indirect effects. Location New Hampshire and Vermont, USA. Methods Using causal and correlational models and new theory on range limits, we compared current (2014–2019) and future (2080s) distributions of ecologically important mammalian carnivores and competitors along range limits in the northeastern US under two global climate models (GCMs) and a high-emission scenario (RCP8.5) of projected snow and forest biomass change. Results Our hypothesis that causal models of climate-mediated competition would result in different distribution predictions than correlational models, both in the current and future periods, was well-supported by our results; however, these patterns were prominent only for species pairs that exhibited strong interactions. The causal model predicted the current distribution of Canada lynx ( Lynx canadensis ) more accurately, likely because it incorporated the influence of competitive interactions mediated by snow with the closely related bobcat ( Lynx rufus ). Both modeling frameworks predicted an overall decline in lynx occurrence in the central high-elevation regions and increased occurrence in the northeastern region in the 2080s due to changes in land use that provided optimal habitat. However, these losses and gains were less substantial in the causal model due to the inclusion of an indirect buffering effect of snow on lynx. Main conclusions Our comparative analysis indicates that a causal framework, steeped in ecological theory, can be used to generate spatially explicit predictions of species distributions. This approach can be used to disentangle correlated predictors that have previously hampered understanding of range limits and species' response to climate change.

New Hampshire, Vermont↗

Level II scour analysis for Bridge 14 (CLARTH00010014) on Town Highway 1, crossing Cold River, Clarendon, Vermont

This report provides the results of a detailed Level II analysis of scour potential at structure CLARTH00010014 on town highway 1 crossing the Cold River, Clarendon, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). A Level I study is included in Appendix E of this report. A Level I study provides a qualitative geomorphic characterization of the study site. Information on the bridge available from VTAOT files was compiled prior to conducting Level I and Level II analyses and can be found in Appendix D. The site is in the Taconic Section of the New England physiographic province in westcentral Vermont in the town of Clarendon. The 36.2-mi 2 drainage area is in a predominantly rural basin. In the vicinity of the study site, the surface cover is primarily pasture, except for the right bank upstream which is forested. In the study area, the Cold River has a sinuous channel with a slope of approximately 0.02 ft/ft, an average channel top width of 104 ft and an average channel depth of 3 ft. The predominant channel bed material is cobble with a median grain size (D 50 ) of 103 mm (0.339 ft). The geomorphic assessment at the time of the Level I and Level II site visit on April 27, 1995, indicated that the reach was laterally unstable. This assessment was due to the cut-banks and the local anabranching occurring upstream of the bridge. The town highway 1 crossing of the Cold River is a 80-ft-long, two-lane bridge consisting of one 77-foot span (Vermont Agency of Transportation, written communication, March 13, 1995). The bridge is supported by vertical, concrete abutments with wingwalls. The left abutment and upstream wingwalls are protected by type-2 stone fill (less than 36 inches diameter). The channel is skewed approximately 10 degrees to the opening while the opening-skew-to-roadway is 15 degrees. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1993). Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for modelled flows ranged from 0.0 to 0.6 ft. Abutment scour ranged from 17.4 to 23.3 ft. The worst-case contraction and abutment scour occurred at the 500- year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1993, p. 48). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Vermont↗

Economic analysis of the proposed rule to prevent arrival of new genetic strains of the rust fungus Puccinia psidii in Hawai'i.

Since its first documented introduction to Hawai‘i in 2005, the rust fungus P. psidii has already severely damaged Syzygium jambos (Indian rose apple) trees and the federally endangered Eugenia koolauensis (nioi). Fortunately, the particular strain has yet to cause serious damage to ‘ōhi‘a, which comprises roughly 80% of the state’s native forests and covers 400,000 ha. Although the rust has affected less than 5% of Hawaii’s ‘ōhi‘a trees thus far, the introduction of more virulent strains and the genetic evolution of the current strain are still possible. Since the primary pathway of introduction is Myrtaceae plant material imported from outside the state, potential damage to ‘ohi‘a can be minimized by regulating those high-risk imports. We discuss the economic impact on the state’s florist, nursery, landscaping, and forest plantation industries of a proposed rule that would ban the import of non-seed Myrtaceae plant material and require a one-year quarantine of seeds. Our analysis suggests that the benefits to the forest plantation industry of a complete ban on non-seed material would likely outweigh the costs to other affected sectors, even without considering the reduction in risk to ‘ōhi‘a. Incorporating the value of ‘ōhi‘a protection would further increase the benefit-cost ratio in favor of an import ban.

Hawaii↗

Climatic controls on the global distribution, abundance, and species richness of mangrove forests

Mangrove forests are highly productive tidal saline wetland ecosystems found along sheltered tropical and subtropical coasts. Ecologists have long assumed that climatic drivers (i.e., temperature and rainfall regimes) govern the global distribution, structure, and function of mangrove forests. However, data constraints have hindered the quantification of direct climate-mangrove linkages in many parts of the world. Recently, the quality and availability of global-scale climate and mangrove data have been improving. Here, we used these data to better understand the influence of air temperature and rainfall regimes upon the distribution, abundance, and species richness of mangrove forests. Although our analyses identify global-scale relationships and thresholds, we show that the influence of climatic drivers is best characterized via regional range limit-specific analyses. We quantified climatic controls across targeted gradients in temperature and/or rainfall within 14 mangrove distributional range limits. Climatic thresholds for mangrove presence, abundance, and species richness differed among the 14 studied range limits. We identified minimum temperature-based thresholds for range limits in eastern North America, eastern Australia, New Zealand, eastern Asia, eastern South America, and southeast Africa. We identified rainfall-based thresholds for range limits in western North America, western Gulf of Mexico, western South America, western Australia, Middle East, northwest Africa, east central Africa, and west central Africa. Our results show that in certain range limits (e.g., eastern North America, western Gulf of Mexico, eastern Asia), winter air temperature extremes play an especially important role. We conclude that rainfall and temperature regimes are both important in western North America, western Gulf of Mexico, and western Australia. With climate change, alterations in temperature and rainfall regimes will affect the global distribution, abundance, and diversity of mangrove forests. In general, warmer winter temperatures are expected to allow mangroves to expand poleward at the expense of salt marshes. However, dispersal and habitat availability constraints may hinder expansion near certain range limits. Along arid and semi-arid coasts, decreases or increases in rainfall are expected to lead to mangrove contraction or expansion, respectively. Collectively, our analyses quantify climate-mangrove linkages and improve our understanding of the expected global- and regional-scale effects of climate change upon mangrove forests.

Ecological Monographs↗

Geologic map of Scoggins Dam, Henry Hagg Lake, and Scoggins Valley, Washington County, Oregon

New geologic mapping (Wells and others, 2020b) and geophysical mapping (Blakely and others, 2000; McPhee and others, 2014; Wells and others, 2020a) document kilometers of Cenozoic right-lateral offset along the Gales Creek Fault Zone, a major, northwest-striking fault zone forming the boundary between the Tualatin Valley and the Coast Range. The Bureau of Reclamation’s (Reclamation) Scoggins Dam (fig. 1), in the Coast Range foothills west of Forest Grove, Oregon, lies within the Gales Creek Fault Zone as mapped by Wells and others (2020a, 2020b; fig. 2). Active faults of the Gales Creek Fault Zone defined by paleoseismic trenching (Redwine and others, 2017, 2019b, Horst and others, 2018, 2019, 2021, and Wells and others, 2020a) are presently mapped as projecting through the existing dam. The Pacific Northwest Region of Reclamation requested assistance with geologic studies around Scoggins Dam to provide better understanding of fault locations and their activity, which are needed to design a modification of the dam (Maguire, 2019a, b). The scope of this project includes detailed geology of the existing Scoggins Dam site, Henry Hagg Lake, the reservoir behind the dam, and Scoggins Valley downstream of the existing dam, particularly around a potential new dam site, where Scoggins Creek cuts through a narrow gap formed by a resistant felsic tuff bed that crosses the valley.

Oregon↗

Alpine glacier reveals ecosystem impacts of Europe's prosperity and peril over the last millennium

Information about past ecosystem dynamics and human activities is stored in the ice of Colle Gnifetti glacier in the Swiss Alps. Adverse climatic intervals incurred crop failures and famines and triggered reestablishment of forest vegetation but also societal resilience through innovation. Historical documents and lake sediments record these changes at local—regional scales but often struggle to comprehensively document continental-scale impacts on ecosystems. Here, we provide unique multiproxy evidence of broad-scale ecosystem, land use, and climate dynamics over the past millennium from a Colle Gnifetti microfossil and oxygen isotope record. Microfossil data indicate that before 1750 CE forests and fallow land rapidly replaced crop cultivation during historically documented societal crises caused by climate shifts and epidemics. Subsequently, with technology and the introduction of more resilient crops, European societies adapted to the Little Ice Age cold period, but resource overexploitation and industrialization led to new regional to global-scale environmental challenges.

Geophysical Research Letters↗

Statistical facilitation in environmental science: Integrating results from complementary statistical analyses can improve ecological interpretations

Professionals working in biological conservation seek to understand, manage, and restore populations of native organisms using many techniques. A common approach for this discipline is using long-term data collections to inform decision making. However, several quantitative issues complicate statistical analysis of monitoring datasets and can reduce the utility of results for conservation decision making. Integrating results from multiple analyses applied to the same dataset (i.e., approaching the same biological problem using different techniques) is one way to address concerns related to field data that violate statistical assumptions. This process allows data analysts, researchers, and managers to assemble insights based on the weight of evidence. Here we tested whether three different statistical techniques [(1) multiple logistic regression on original data, (2) multiple logistic regression on standardized data (i.e., mean of 0 and standard deviation of 1), and (3) random forest analysis] identified a similar hierarchy for selecting natural and anthropogenic habitat regressors. Our examination of how environmental variables affected Plains Minnow ( Hybognathus placitus ), a state-threatened fish, is relevant to other taxa and locations. We gained useful information from redundancies (i.e., agreements across analyses). New directions also emerged by addressing ambiguities (i.e., disagreements among results across analyses). When multiple analyses were integrated into one ecological story, a clearer interpretation emerged. Viewing different statistical tests as facilitators that provide mutual advantages can advance the understanding and application of statistical analyses applied to non-experimental field datasets.

Kansas↗

Rosaceous Chamaebatiaria-like foliage from the Paleogene of western North America

Chamaebatiaria and Chamaebatia, two characteristic genera of the Californian floristic province, are traditionally placed in different subfamilies of Rosaceae, Spiraeoideae and Rosoideae, respectively. Analysis of the foliar and reproductive characters of the extant species of these genera indicates that the two genera could be closely related and the assignment of Chamaebatia to Rosoideae invalid. Fossil leaves of lineages of both genera occur in the Paleogene montane floras of the Rocky Mountain region and provide evidence that the two lineages diverged from a common ancestor in the Eocene. The common ancestor probably was adapted to sunny habitats in mesic coniferous forest, and, during the post-Eocene, the two lineages were able to adapt to progressively drier climates. A third extant genus, the east Asian Sorbaria, also appears to be closely related to the California genera and to have been derived from the same common ancestor. New taxa and combinations proposed are: St onebergia columbiana. n. gen. and n. sp.; Salmonensea prefoliolosa (R. W. Br.), n. gen. and n. comb.; Stockeya creedensis (R. W. Br.), n. gen. and n. comb.; Stockeya montana, n. sp.; and Sorbaria wahrhaftigii, n. sp.

Aliso↗

The response of streams to changes in atmospheric deposition of sulfur and nitrogen in the Adirondack Mountains

Acidic deposition is the result of upwind sulfur (S) and nitrogen (N) emissions into the atmosphere from human activities. Environmental impacts from acidic deposition across forested landscapes include acidification of soil and drainage water, depletion of available soil nutrient bases, and impacts to and changes in forest and aquatic species composition and biodiversity. Acidic deposition can mobilize aluminum (Al) from soil-to-soil solution and subsequently to drainage water in forms that can be toxic to aquatic life. When exposed to decreasing levels of acidic deposition, which has been occurring in New York since the late 1970s, some soils and drainage waters have become gradually less acidic. Remaining questions relate to effects on stream resources, anticipated resource recovery under increasingly lower levels of deposition, and the levels of deposition (target loads, TLs) needed to reach a range of stream ecosystem recovery targets. Environmental scientists commonly estimate thresholds of air pollutant emissions and resulting atmospheric deposition at which adverse ecological effects are manifested. This analysis is often done using critical loads (CL) and/or TLs, using approaches that account for the spatial and temporal aspects of acidification and recovery. Exceedance represents the extent to which current levels of acidic deposition exceed the level expected to cause ecological harm. The research reported here is intended to help address S and N deposition TLs and ecosystem recovery of Adirondack streams, a resource that has been less thoroughly investigated than lakes. The overarching goal of this work is to highlight key considerations that will help inform decision-makers and ecosystem managers who are responsible for environmental policy in New York State and beyond. Salient aspects of stream TL modeling are discussed with an aim of informing not only scientists, but also policymakers, ecosystem managers, and nonscientists who are required to make decisions related to the effects of acidic deposition on natural ecosystems. Analyses reported herein quantify relations among chemical indicators and metrics of fish community health and biodiversity in streams of the Adirondack Park. This information is used to indicate levels of atmospheric deposition necessary to alleviate harmful effects on fish populations. Results of this investigation provide a framework that can be applied to better understand how modeled stream acid neutralizing capacity (ANC) values that are developed to support TL investigations can be adjusted to reflect high-flow ANC values that may be associated with toxic conditions. Since process models are often calibrated to a low-flow or average flow condition, the magnitude and spatial extent of TL exceedances increase substantially when episodic acidification is considered.

New York↗

Quantifying water requirements of riparian river red gum ( Eucalyptus camaldulensis ) in the Murray-Darling Basin, Australia: Implications for the management of environmental flows

Water resource development and drought have altered river flow regimes, increasing average flood return intervals across floodplains in the Murray-Darling Basin, Australia, causing health declines in riparian river red gum ( Eucalyptus camaldulensis ) forests and woodlands. Environmental flow allocations helped to alleviate water stress during the recent Millennium Drought (1997–2010), however, quantification of the flood frequency required to support healthy E. camaldulensis communities is still needed. We quantified water requirements of E. camaldulensis for two years across a flood gradient (trees inundated at frequencies of 1:2, 1:5 and 1:10 years) at Yanga National Park, New South Wales to help inform management decision-making and design of environmental flows. Sap flow, evaporative losses and soil moisture measurements were used to determine transpiration, evapotranspiration and plant-available soil water before and after flooding. A formula was developed using plant-available soil water post-flooding and average annual rainfall, to estimate maintenance time of soil water reserves in each flood frequency zone. Results indicated that soil water reserves could sustain 1:2 and 1:5 trees for 15 months and six years, respectively. Trees regulated their transpiration rates, allowing them to persist within their flood frequency zone, and showed reduction in active sapwood area and transpiration rates when flood frequencies exceeded 1:2 years. A leaf area index of 0.5 was identified as a potential threshold indicator of severe drought stress. Our results suggest environmental water managers may have greater flexibility to adaptively manage floodplains in order to sustain E. camaldulensis forests and woodlands than has been appreciated hitherto.

New South Wales↗

Botanical prospecting for uranium on La Ventana Mesa, Sandoval County, New Mexico

A botanical sampling program has been completed by the U.S. Geological Survey on La Ventana Mesa, Sandoval County, N. Mex. A uranium-bearing coal in the Allison-Gibson members of the Cretaceous Mesaverde formation crops out in erosional remnants of the mesa.The coal is capped by a well-fractured 65-foot sandstone bed through which roots of a pinyon-juniper forest penetrate. Samples of several hundred branches of trees growing on top of the mesa were collected and analyzed for uranium. The assays ranged from 0.1 part per million to 2.3 ppm uranium in the wood ash. Dead branches, which were found to contain more uranium in the ash than live branches, were sampled where possible. The results have been contoured to indicated probable areas of mineralized coal. Parts of the north butte are recommended as favorable for physical exploration.

New Mexico↗

The United States National Climate Assessment - Alaska Technical Regional Report

The Alaskan landscape is changing, both in terms of effects of human activities as a consequence of increased population, social and economic development and their effects on the local and broad landscape; and those effects that accompany naturally occurring hazards such as volcanic eruptions, earthquakes, and tsunamis. Some of the most prevalent changes, however, are those resulting from a changing climate, with both near term and potential upcoming effects expected to continue into the future. Alaska's average annual statewide temperatures have increased by nearly 4°F from 1949 to 2005, with significant spatial variability due to the large latitudinal and longitudinal expanse of the State. Increases in mean annual temperature have been greatest in the interior region, and smallest in the State's southwest coastal regions. In general, however, trends point toward increases in both minimum temperatures, and in fewer extreme cold days. Trends in precipitation are somewhat similar to those in temperature, but with more variability. On the whole, Alaska saw a 10-percent increase in precipitation from 1949 to 2005, with the greatest increases recorded in winter. The National Climate Assessment has designated two well-established scenarios developed by the Intergovernmental Panel on Climate Change (Nakicenovic and others, 2001) as a minimum set that technical and author teams considered as context in preparing portions of this assessment. These two scenarios are referred to as the Special Report on Emissions Scenarios A2 and B1 scenarios, which assume either a continuation of recent trends in fossil fuel use (A2) or a vigorous global effort to reduce fossil fuel use (B1). Temperature increases from 4 to 22°F are predicted (to 2070-2099) depending on which emissions scenario (A2 or B1) is used with the least warming in southeast Alaska and the greatest in the northwest. Concomitant with temperature changes, by the end of the 21st century the growing season is expected to lengthen by 15-25 days in some areas of Alaska, with much of that corresponding with earlier spring snow melt. Future projections of precipitation (30-80 years) over Alaska show an increase across the State, with the largest changes in the northwest and smallest in the southeast. Because of increasing temperatures and growing season length, however, increased precipitation may not correspond with increased water availability, due to temperature related increased evapotranspiration. The extent of snow cover in the Northern Hemisphere has decreased by about 10 percent since the late 1960s, with stronger trends noted since the late 1980s. Alaska has experienced similar trends, with a strong decrease in snow cover extent occurring in May. When averaged across the State, the disappearance of snow in the spring has occurred from 4 to 6 days earlier per decade, and snow return in fall has occurred approximately 2 days later per decade. This change appears to be driven by climate warming rather than a decrease in winter precipitation, with average winter temperatures also increasing by about 2.5°F. The extent of sea ice has been declining, as has been widely published in both national and scientific media outlets, and is projected to continue to decline during this century. The observed decline in annual sea ice minimum extent (September) has occurred more rapidly than was predicted by climate models and has been accompanied by decreases in ice thickness and in the presence of multi-year ice. This decrease was first documented by satellite imagery in the late 1970s for the Bering and Chukchi Seas, and is projected to continue, with the potential for the disappearance of summer sea ice by mid- to late century. A new phenomenon that was not reported in previous assessments is ocean acidification. Uptake of carbon dioxide (CO2) by oceans has a significant effect on marine biogeochemistry by reducing seawater pH. Ocean acidification is of particular concern in Alaska, because cold sea water absorbs CO2 more rapidly than warm water, and a decrease in sea ice extent has allowed increased sea surface exposure and more uptake of CO2 into these northern waters. Ocean acidification will likely affect the ability of organisms to produce and maintain shell material, such as aragonite or calcite (calcium carbonate minerals structured from carbonate ions), required by many shelled organism, from mollusks to corals to microscopic organisms at the base of the food chain. Direct biological effects in Alaska further along the food chain have yet to be studied and may vary among organisms. Some of the potentially most significant changes to Alaska that could result from a changing climate are the effects on the terrestrial cryosphere - particularly glaciers and permafrost. Alaskan glaciers are changing at a rapid rate, the primary driver appearing to be temperature. Statewide, glaciers lost 13 cubic miles of ice annually from the 1950s to the 1990s, and that rate doubled in the 2000s. However, like temperature and precipitation, glacier ice loss is not spatially uniform; most glaciers are losing mass, yet some are growing (for example Hubbard Glacier in southeast Alaska). Alaska glaciers with the most rapid loss are those terminating in sea water or lakes. With this increasing rate of melt, the contribution of surplus fresh water entering into the oceans from Alaska's glaciers, as well as those in neighboring British Columbia, Canada, is approximately 20 percent of that contributed by the Greenland Ice Sheet. Permafrost degradation (that is, the thawing of ice-rich soils) is currently (2012) impacting infrastructure and surface-water availability in areas of both discontinuous and continuous ground ice. Over most of the State, the permafrost is warming, with increasing temperatures broadly consistent with increasing air temperatures. On the Arctic coastal plain of Alaska, permafrost temperatures showed some cooling in the 1950s and 1960s but have been followed by a roughly 5°F increase since the 1980s. Many areas in the continuous permafrost zone have seen increases in temperature in the seasonally active layer and a decrease in re-freezing rates. Changes in the discontinuous permafrost zone are initially much more observable due to the resulting thermokarst terrain (land surface formed as ice rich permafrost thaws), most notable in boreal forested areas. Climate warming in Alaska has potentially broad implications for human health and food security, especially in rural areas, as well as increased risk for injury with changing winter ice conditions. Additionally, such warming poses the potential for increasing damage to existing water and sanitation facilities and challenges for development of new facilities, especially in areas underlain by permafrost. Non-infectious and infectious diseases also are becoming an increasing concern. For example, from 1999 to 2006 there was a statistically significant increase in medical claims for insectbite reactions in five of six regions of Alaska, with the largest percentage increase occurring in the most northern areas. The availability and quality of subsistence foods, normally considered to be very healthy, may change due to changing access, changing habitats, and spoilage of meat in food storage cellars. These and other trends and potential outcomes resulting from a changing climate are further described in this report. In addition, we describe new science leadership activities that have been initiated to address and provide guidance toward conducting research aimed at making available information for policy makers and land management agencies to better understand, address, and plan for changes to the local and regional environment. This report cites data in both metric and standard units due to the contributions by numerous authors and the direct reference of their data.

Alaska↗

Examining patterns of bat activity in Bandelier National Monument, New Mexico, using walking point transects

We conducted a preliminary study using small field crews, a single Anabat II detector coupled with a laptop computer, and point transects to examine patterns of bat activity at a scale of interest to local resource managers. The study was conducted during summers of 1996–1998 in Bandelier National Monument in the Jemez Mountains of northern New Mexico, a landscape with distinct vegetation zones and high species richness of bats. We developed simple models that described general patterns of acoustic activity within 4 vegetation zones based primarily on nightly variation and a qualitative index of habitat complexity. Bat acoustic activity (number of bat passes&sol point) did not vary dramatically among a limited sample of transects within a vegetation zone during 1996. In 1997 and 1998, single transects within each vegetation zone were established, and bat activity did not vary annually within these zones. Acoustic activity differed among the 4 vegetation zones of interest, with the greatest activity occurring in riparian canyon bottomland, intermediate activity in coniferous forest and a 1977 burned zone, and lowest activity in piñon-juniper woodlands. We identified 68.5% of 2,529 bat passes recorded during point-transect surveys to species using an echolocation call reference library we established for the area and qualitative characteristics of bat calls. Bat species richness and composition differed among vegetation zones. Results of these efforts were consistent with general knowledge of where different bat species typically forage and with the natural history of bats of New Mexico, suggesting such a method might have value for drawing inferences about bat activity in different vegetation zones.

Southwestern Naturalist↗

Crims Island-Restoration and monitoring of juvenile salmon rearing habitat in the Columbia River Estuary, Oregon, 2004-10

Under the 2004 Biological Opinion for operation of the Federal Columbia River Power System released by the National Marine Fisheries Service, the U.S. Army Corps of Engineers (USACE), the Bonneville Power Administration (BPA), and the Bureau of Reclamation (Reclamation) were directed to restore more than 4,047 hectares (10,000 acres) of tidal marsh in the Columbia River estuary by 2010. Restoration of Crims Island near Longview, Washington, restored 38.1 hectares of marsh and swamp in the tidal freshwater portion of the lower Columbia River. The goal of the restoration was to improve habitat for juveniles of Endangered Species Act (ESA)-listed salmon stocks and ESA-listed Columbian white-tailed deer. The U.S. Geological Survey (USGS) monitored and evaluated the fisheries and aquatic resources at Crims Island in 2004 prior to restoration (pre-restoration), which began in August 2004, and then post-restoration from 2006 to 2009. This report summarizes pre- and post-restoration monitoring data used by the USGS to evaluate project success. We evaluated project success by examining the interaction between juvenile salmon and a suite of broader ecological measures including sediments, plants, and invertebrates and their response to large-scale habitat alteration. The restoration action at Crims Island from August 2004 to September 2005 was to excavate a 0.6-meter layer of soil and dig channels in the interior of the island to remove reed canary grass and increase habitat area and tidal exchange. The excavation created 34.4 hectares of tidal emergent marsh where none previously existed and 3.7 hectares of intertidal and subtidal channels. Cattle that had grazed the island for more than 50 years were relocated. Soil excavated from the site was deposited in upland areas next to the tidal marsh to establish an upland forest. Excavation deepened and widened an existing T-shaped channel to increase tidal flow to the interior of the island. The western arm of the existing 'T-channel' was extended westward and connected to Bradbury Slough to create a second outlet to the main river. New intertidal channels were constructed from the existing 'T-channel' and tidal mudflats became inundated at high tide to increase rearing habitat for juvenile salmonids. The restoration action resulted in a 95-percent increase in available juvenile salmon rearing habitat. We collected juvenile salmon and other fishes at Crims Island and a nearby reference site using beach seines and fyke nets annually from March through August during all years. Benthic invertebrates were collected with sediment corers and drift invertebrates were collected with neuston nets. Juvenile salmon stomach contents were sampled using lavage. Vegetation and sediments characteristics were surveyed and we conducted a topographic/bathymetric survey using a RTK (real time kinematic) GPS (global positioning system). The fish assemblage at Crims Island, composed primarily of threespine stickleback (Gasterosteus aculeatus), non-native banded killifish (Fundulus diaphanus), peamouth chub (Mylocheilus caurinus), subyearling Chinook salmon (Oncorhynchus tshawytscha) (hereinafter referred to as subyearlings), and small numbers of juvenile chum salmon (Oncorhynchus keta), did not differ appreciably pre- and post-restoration. Subyearlings were the primary salmonid collected and were seasonally abundant from April through May during all years. The abundance of juvenile salmon declined seasonally as water temperature exceeded 20 degrees C in the Reference site by mid-June; however, subyearlings persisted at the Mainstem site and in subtidal channels of the Restoration site through the summer in water temperatures exceeding 22 degrees C. Residence times of subyearlings in Crims Island backwaters generally were short consisting of one or two tidal cycles. Median residence time was longer in the Restoration site than in the Reference site pre- and post-restoration. Small (mean = 55.7 millimeters) subyea

Scientific Investigations Report↗

Advancing dendrochronological studies of fire in the United States

Dendroecology is the science that dates tree rings to their exact calendar year of formation to study processes that influence forest ecology (e.g., Speer 2010 , Amoroso et al., 2017 ). Reconstruction of past fire regimes is a core application of dendroecology, linking fire history to population dynamics and climate effects on tree growth and survivorship. Since the early 20th century when dendrochronologists recognized that tree rings retained fire scars (e.g., Figure 1) , and hence a record of past fires, they have conducted studies worldwide to reconstruct the historical range and variability of fire regimes (e.g., frequency, severity, seasonality, spatial extent), the influence of fire regimes on forest structure and ecosystem dynamics, and the top-down (e.g., climate) and bottom-up (e.g., fuels, topography) drivers of fire that operate at a range of temporal and spatial scales. As in other scientific fields, continued application of dendrochronological techniques to study fires has shaped new trajectories for the science. Here we highlight some important current directions in the United States (US) and call on our international colleagues to continue the conversation with perspectives from other countries.

Fire↗

Optimizing an inner-continental shelf geologic framework investigation through data repurposing and machine learning

The U.S. Geological Survey (USGS) and the National Oceanic Atmospheric Administration (NOAA) have collected approximately 5,400 km2 of geophysical and hydrographic data on the Atlantic continental shelf between Delaware and Virginia over the past decade and a half. Although originally acquired for different objectives, the comprehensive coverage and variety of data (bathymetry, backscatter, imagery and physical samples) presents an opportunity to merge collections and create high-resolution, broad-scale geologic maps of the seafloor. This compilation of data repurposes hydrographic data, expands the area of geologic investigation, highlights the versatility of mapping data, and creates new geologic products that would not have been independently possible. The data are classified using a variety of machine learning algorithms, including unsupervised and supervised methods. Four unique classes were targeted for classification, and source data include bathymetry, backscatter, slope, curvature, and shaded-relief. A random forest classifier used on all five source data layers was found to be the most accurate method for these data. Geomorphologic and sediment texture maps are derived from the classified acoustic data using over 200 groundtruth samples. The geologic data products can be used to identify sediment sources, inform resource management, link seafloor environments to sediment texture, improve our understanding of seafloor structure and sediment pathways, and demonstrate how ocean mapping resources can be useful beyond their original intent to maximize the footprint and scientific impact of a study.

Delaware, Maryland, Virginia↗

Elk monitoring in Lewis and Clark National Historical Park: 2008-2012 synthesis report

Maintaining elk (Cervus elaphus roosevelti) herds that frequent Lewis and Clark National Historical Park (NHP) is central to the park’s purpose of preserving the historic, cultural, scenic, and natural resources associated with the winter encampment of the Lewis and Clark expedition. Elk were critically important to the Lewis and Clark expedition in providing food and hides that sustained the expedition during the winter of 1805-06 and supplied them for their return east during 1806. Today, elk remain a key component of interpreting the Lewis and Clark story to over 200,000 park visitors each year at the Fort Clatsop visitor center. In 2008, the US Geological Survey (USGS) began collaborating with Lewis and Clark NHP and the NPS North Coast and Cascades Network to develop a protocol for monitoring long-term changes in the magnitude and spatial patterns of elk use within and adjacent to Lewis and Clark NHP (Griffin et al. 2011). Specific objectives of the monitoring program were to measure trends in (1) relative use of the Fort Clatsop unit by elk during winter; (2) the proportion of areas where elk sign is present in the Fort Clatsop unit in winter; and (3) the frequency of elk sightings from roads in and around the Fort Clatsop unit. This report synthesizes the results of the first four years of monitoring elk distribution and use in Lewis and Clark NHP from 2008-2012. We also present data from FY2012 (Appendix 1), in lieu of an annual report for that year. We used fecal pellet group surveys as the cornerstone for monitoring trends in both relative use of the Fort Clatsop Unit by elk and the proportion of areas where elk sign was present at the end of winter. We estimated pellet group density based on data collected from a network of fecal pellet plots distributed systematically throughout the unit. We developed a double observer sampling scheme that enabled us to estimate detection biases and improve the accuracy of pellet group density estimates. We computed the estimated detection probability for any pellet group observed; this probability was a function of the pellet group size and stage of decay, as well as lighting and vegetation conditions, and the number of observers (one or two) searching for pellets in that subplot. We then used these estimated detection probabilities to adjust the raw counts of the detected pellet groups to account for groups that likely went undetected under similar pellet and environmental conditions (each observed pellet group was weighted by the inverse of its estimated detection probability). We also used results from the late winter fecal pellet surveys to quantify the proportion of areas where elk pellets occurred (PAO), which was based on the presence of fecal pellet groups and estimation of detection biases (i.e., accounting for pellet groups that likely went undetected by both observers). In this synthesis, we report temporal trends in both pellet group density and PAO from 2008-2012, based on weighted linear regression analyses as well as spatial variation of pellet group densities over time. We completed late winter fecal pellet surveys at 61-66 plots annually, depending on yearly variation in access. We cleared fecal pellets at survey points in late October / early November each year and returned in late February / early March to count pellet groups left by elk over the winter. The estimated probability that a pellet group was detected by any one observer during late winter was affected most by the pellet group size and was less affected by decay class and lighting conditions. Per-observer detection probabilities ranged from as low as ~10-15% for single pellets to ~85-90% for pellet groups with 50 pellets. Average pellet group density in the Fort Clatsop unit ranged annually from 0.58 (+/- 1.43 standard error [SE]) to 0.93 (+/- 2.25 SE) pellet groups per 3-m radius subplot. Pellet group density declined over time, at approximately 8.8% per year (+/- 2.5% SE), but that slope was not statistically distinguishable from zero (2- tailed P=0.16). Following correction for detection biases, the proportion of surveyed points used by elk (i.e., PAO) ranged from 0.44 (+/- 0.07 SE) to 0.53 (+/- 0.07 SE) during the 4 winters. The estimated proportion of areas where elk pellets occurred (PAO) declined at a rate of 2.6% per year (+/- 1.2% per year SE), but that trend also was not statistically distinguishable from zero (2- tailed P=0.17). Statistical significance of a measure’s trend depends on both the magnitude (i.e., slope) of the observed trend and the number of years the trend continues in the same increasing or decreasing direction. Through simulation modeling we determined how many additional years of surveys would be required to reveal a statistically significant trend, based on the same trends in pellet group density and PAO, and associated variation, observed from 2009-2012. Assuming the same trends persist in the future, simulations indicated that there is a 70% probability that a statistically significant trend would be detected after two more years of conducting pellet group surveys. Relative use by elk during winter, as indexed by elk pellet group density, was generally greatest in the southeast region of the Fort Clatsop unit in or near the large freshwater marsh at the mouth of Colewort Creek and adjacent upland areas. Pellet group density was also higher than average in the north-central forested area, not far from a privately-owned pasture north of the park boundary. This spatial pattern in pellet group densities across the Fort Clatsop unit was consistent across all four years, although specific pellet group densities varied from year to year. Pellet group density declined significantly over time at two points in the southeast of the Fort Clatsop unit, even though pellet group density at those points remained higher than the unit average. Pellet group density increased significantly over time at one point in the north-central region, and at one point in the south-central region of the unit, indicating a slight shift in the distribution of elk use within the Fort Clatsop Unit over the four years. As an index of visitors’ opportunities to see elk in and around the Fort Clatsop Unit, we conducted replicated roadside elk surveys 3-5 times monthly during February, April, June, August, October and December 2008-2012. During each morning of survey, we searched for elk along four routes that totaled 32 km. We examined bimonthly trends in the numbers of elk groups seen, the total number of elk seen, and the observed composition ratios for those six months of the year. The average number of elk groups seen per survey ranged from 0.75 (+/- 0.32 SE) during February to a peak of 1.95 (+/- 0.36 SE) during June. Despite this seasonal variation in numbers of elk groups seen, the average total number of elk seen per morning was less variable. The average ratios of antlered elk to antlerless adult elk (i.e., bulls:cows) and calves to antlerless adult elk (i.e. calves:cows) varied seasonally, with the highest of both average ratios observed in August. We detected no significant trends in the average number of elk groups and total numbers of elk seen per survey from 2008-2012. Similarly, ratios of calves and antlered elk per antlerless elk did not differ over time. Elk groups were frequently seen from January to August in the southeast region of the Fort Clatsop unit, in the vicinity of Colewort Creek. Outside of NPS lands, we observed elk most frequently in open areas near the Astoria regional airport, in the pastures and forests immediately north of the Fort Clatsop unit and, prior to the construction of a residential development, in a pasture northwest of the Fort Clatsop unit. Elk monitoring at Lewis and Clark NHP is still in its initial years and additional monitoring will be required to verify trends that appear to be emerging. For example, the initial monitoring suggested incipient declining trends in both pellet group density and proportion of plots with pellets present, as well as, potentially, a small shift in elk distribution away from a new trail that was recently constructed in the southeast portion of the Fort Clatsop unit. Continued monitoring will aid in determining whether this local change in distribution persists (or, alternatively, resulted from short-term random variation), and whether there will be any positive or negative effect in the northern portion of the unit where a new trail has been constructed. High variability in road counts prevented our ability to find any clear trend in numbers or composition of elk observed in and near Fort Clatsop, but changes in the patterns of observations of elk from roadways suggest that residential development outside the park has reduced the available habitat for elk in some of the areas surveyed, and may have affected spatial use patterns of elk adjacent to some areas of the park. In addition to monitoring future effects of land use changes outside the park, continued monitoring may also prove useful for assessing elk responses to natural succession in forests disturbed by windthrow in December 2007 and to NPS vegetation management activities such as variable density thinning in the forest, trail development, and restoration at Otter Point tidal area and Colewort Creek Slough.

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Organic Compounds and Trace Elements in Fish Tissue and Bed Sediment in the Delaware River Basin, New Jersey, Pennsylvania, New York, and Delaware, 1998-2000

As part of the National Water-Quality Assessment (NAWQA) program activities in the Delaware River Basin (DELR), samples of fish tissue from 21 sites and samples of bed sediment from 35 sites were analyzed for a suite of organic compounds and trace elements. The sampling sites, within subbasins ranging in size from 11 to 600 square miles, were selected to represent 5 main land-use categories in the DELR -forest, low-agricultural, agricultural, urban, and mixed use. Samples of both fish tissue and bed sediment were also collected from 4 'large-river' sites that represented drainage areas ranging from 1,300 to 6,800 square miles, areas in which the land is used for a variety of purposes. One or more of the organochlorine compounds-DDT and chlordane metabolites, polychlorinated biphenyls (total PCBs), and dieldrin- were detected frequently in samples collected over a wide geographic area. One or more of these compounds were detected in fish-tissue samples from 92 percent of the sites and in bed-sediment samples from 82 percent of the sites. Concentrations of total DDT, total chlordanes, total PCBs, and dieldrin in whole white suckers and in bed sediment were significantly related to urban/industrial basin characteristics, such as percentage of urban land use and population density. Semi-volatile organic compounds (SVOCs)-total polycyclic aromatic hydrocarbons (PAHs), total phthalates, and phenols- were detected frequently in bed-sediment samples. All three types of SVOCs were detected in samples from at least one site in each land-use category. The highest detection rates and concentrations typically were in samples from sites in the urban and mixed land-use categories, as well as from the large-river sites. Concentrations of total PAHs and total phthalates in bed-sediment samples were found to be statistically related to percentages of urban land use and to population density in the drainage areas represented by the sampling sites. The samples of fish tissue and bed sediment collected throughout the DELR were analyzed for a large suite of trace elements, but results of the analyses for eight elements-arsenic, cadmium, chromium, copper, lead, nickel, mercury, and zinc- that are considered contaminants of concern are described in this report. One or more of the eight trace elements were detected in samples from every fish tissue and bed-sediment sampling site, and all of the trace elements were detected in samples from 97 percent of the bed-sediment sites. The concentrations of organic compounds and trace elements in the DELR samples were compared to applicable guidelines for the protection of wildlife and other biological organisms. Concentrations of total DDT, total chlordanes, total PCBs, and dieldrin in fish-tissue samples from 14 sites exceeded one or more of the Wildlife Protective Guidelines established by the New York State Department of Environmental Conservation. Concentrations of one or more organic compounds in samples from 16 bed-sediment sites exceeded the Threshold Effects Concentrations (TEC) of the Canadian Sediment Quality Guidelines, and concentrations of one or more of the eight trace elements in samples from 38 bed-sediment sites exceeded the TEC. (The TEC is the concentration below which adverse biological effects in freshwater ecosystems are expected to be rare.) Concentrations of organic compounds in samples from some bed-sediment sites exceeded the Canadian Probable Effects Concentrations (PEC), and concentrations of trace elements in samples from 18 sites exceeded the PEC. (The PEC is the concentration above which adverse effects to biological organisms are expected to occur frequently). Concentrations of organic compounds and trace elements in samples from the DELR were compared to similar data from other NAWQA study units in the northeastern United States and also data from the Mobile River (Alabama) Basin and the Northern Rockies Intermontane Basin study units. Median concentrations of to

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