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USGS2008

Uncertainty and sensitivity issues in process-based models of carbon and nitrogen cycles in terrestrial ecosystems

Many process-based models of carbon (C) and nitrogen (N) cycles have been developed for northern forest ecosystems. These models are widely used to evaluate the long-term decisions in forest management dealing with effects like particulate pollution, productivity and climate change. Regarding climate change, one of the key questions that have sensitive political implications is whether northern forests will sequester atmospheric C or not. Whilst many process-based models have been tested for accuracy by evaluating or validating against observed data, few have dealt with the complexity of the incorporated procedures to estimate uncertainties associated with model predictions or the sensitivity of these predictions to input factors in a systematic, inter-model comparison fashion. In general, models differ in their underlying attempts to match natural complexities with assumed or imposed model structure and process formulations to estimate model parameters, to gather data and to address issues on scope, scale and natural variations. Uncertainties may originate from model structure, estimation of model parameters, data input, representation of natural variation and scaling exercises. Model structure relates to the mathematical representation of the processes modelled and the type of state variables that a model contains. The modelling of partitioning among above- and below-ground C and N pools and the interdependence among these pools remain a major source of uncertainty in model structure and error propagation. For example, most soil C models use at least three state variables to represent the different types of soil organic matter (SOM). This approach results in creating three artificial SOM pools, assuming that each one contains C compounds with the same turnover rate. In reality, SOM consists of many different types of C compounds with widely different turnover rates. Uncertainty in data and parameter estimates are closely linked. Data uncertainties are associated with high variations in estimating forest biomass, productivity and soil organic matter and their estimates may be incomplete for model initialisation, calibration, validation and sensitivity analysis of generalised predictor models. The scale at which a model is being used also affects the level of uncertainty, as the errors in the prediction of the C and N dynamics differ from site to landscape levels and across climatic regions. If the spatial or temporal scale of a model application is changed, additional uncertainty arises from neglecting natural variability in system variables in time and space. Uncertainty issues are also intimately related to model validation and sensitivity analysis. The estimation of uncertainties is needed to inform decision processes in order to detect the possible corridor of development. Uncertainty in this context is an essential measure of quality for stakeholder and decision makers.

Book chapter↗

USGS2008

Characterization of estuary use by Nisqually Hatchery Chinook based on Otolith analysis

INTRODUCTION The Nisqually Fall Chinook population is one of 27 stocks in the Puget Sound evolutionarily significant unit listed as threatened under the federal Endangered Species Act (ESA). Preservation and extensive restoration of the Nisqually delta ecosystem are planned to assist in recovery of the stock. A pre-restoration baseline including life history types, estuary residence time, growth rates, and habitat use are needed to evaluate the potential response of hatchery and wild Chinook salmon to restoration. Otolith analysis has been selected as a means to examine Chinook salmon life history, growth, and residence in the Nisqually estuary. Over time, the information from the otolith analyses will be used to: 1) determine if estuary restoration actions cause changes to the population structure (i.e. frequency of the different life history trajectories) for Nisqually River Chinook, 2) compare pre- and post- restoration residence times and growth rates, 3) suggest whether estuary restoration yields substantial benefits for Chinook salmon through (1) and (2), and 4) compare differences in habitat use between hatchery and wild Chinook to further protect ESA listed stock. Otoliths are calcium carbonate structures in the inner ear that grow in proportion to the overall growth of the fish. Daily growth increments can be measured so date and fish size at various habitat transitions can be back-calculated. Careful analysis of otolith microstructure can be used to determine the number of days that a fish resided in the estuary as a juvenile (increment counts), size at entrance to the estuary, size at egress, and the amount that the fish grew while in the estuary. Juvenile hatchery Chinook salmon are generally released as smolts that move quickly through the delta with much shorter residence times than for many wild fish and are not dependent on the delta as nursery habitat (Myers and Horton 1982; Mace 1983; Levings et al. 1986). The purpose of this study is to use and evaluate otolith microstructure analysis as a tool for assessing the role of the estuary in the life history of hatchery Chinook salmon in the Nisqually River before and after restoration efforts at the Nisqually National Wildlife Refuge (Nisqually NWR). This tool is used to quantify changes in rate of growth, length of residence and habitat use to help predict restoration benefits to the federally threatened Nisqually River hatchery and wild Chinook salmon populations. Analysis of otolith microstructure typically is superior to the alternative of traditional mark-recapture methods. The latter are extremely expensive or inadequate in estuary habitats, typically are biased and substantially underestimate use, and do not directly reveal the importance or contribution to adult recruitment (i.e., they do not account for any differential survival afterward in Puget Sound or the ocean). Analysis of otolith microstructure for these purposes is proving successful for the Nisqually wild Chinook stock as well as a similar study that USGS and partners are conducting in the Skagit River estuary system located in northern Puget Sound. This work is based on research by Neilson et al. (1985). We expect to use the Skagit River as a reference for the before/after restoration comparison in the Nisqually River.

Open-File Report↗

USGS2009

Pre-Restoration Habitat Use by Chinook Salmon in the Nisqually Estuary Using Otolith Analysis: An Additional Year

The Nisqually Fall Chinook population is one of 27 stocks in the Puget Sound evolutionarily significant unit listed as threatened under the Federal Endangered Species Act (ESA). Preservation and extensive restoration of the Nisqually delta ecosystem is currently taking place to assist in recovery of the stock as juvenile Fall Chinook salmon are dependent upon the estuary. A pre-restoration baseline that includes characterization of life history types, estuary residence times, growth rates, and habitat use is needed to evaluate the potential response of hatchery and natural origin Chinook salmon to restoration efforts and determine restoration success. Otolith analysis was selected to examine Chinook salmon life history, growth, and residence in the Nisqually Estuary. Previously funded work on wild samples collected in 2004 established the growth rate and length of residence associated with various habitats. The purpose of the current study is to build on the previous work by incorporating otolith microstructure analysis from 2005 (second sampling year), to verify findings from 2004, and to evaluate between-year variation in otolith microstructure. Our results from this second year of analysis indicated no inter-annual variation in the appearance of the tidal delta check (TDCK) and delta-flats check (DFCK). However, a new life history type (fry migrant) was observed on samples collected in 2005. Fish caught in the tidal delta regardless of capture date spent an average of 17 days in the tidal delta. There was a corresponding increase in growth rate as the fish migrated from freshwater (FW) to tidal delta to nearshore (NS) habitats. Fish grew 33 percent faster in the tidal delta than in FW habitat and slightly faster (14 percent) in the delta flats (DF) habitat compared to the tidal delta.

Open-File Report↗

USGS2011

Validation of a freshwater Otolith microstructure pattern for Nisqually Chinook Salmon (Oncorhynchus tshawytscha)

The Nisqually Fall Chinook salmon (Oncorhynchus tshawytscha) population is one of 27 stocks in the Puget Sound (Washington) evolutionarily significant unit listed as threatened under the federal Endangered Species Act (ESA). Extensive restoration of the Nisqually River delta ecosystem has taken place to assist in recovery of the stock since estuary habitat is a critical transition zone for juvenile fall Chinook salmon. A pre-restoration baseline that includes the characterization of life history strategies, estuary residence times, growth rates and habitat use is needed to evaluate the potential response of hatchery and natural origin Chinook salmon to restoration efforts and to determine restoration success. Otolith microstructure analysis was selected as a tool to examine Chinook salmon life history, growth and residence in the Nisqually River estuary. The purpose of the current study is to incorporate microstructural analysis from the otoliths of juvenile Nisqually Chinook salmon collected at the downstream migrant trap within true freshwater (FW) habitat of the Nisqually River. The results from this analysis confirmed the previously documented Nisqually-specific FW microstructure pattern and revealed a Nisqually-specific microstructure pattern early in development (“developmental pattern”). No inter-annual variation in the microstructure pattern was visually observed when compared to samples from previous years. Furthermore, the Nisqually-specific “developmental pattern” and the FW microstructure pattern used in combination during analysis will allow us to recognize and separate with further confidence future unmarked Chinook salmon otolith collections into Nisqually-origin (natural or unmarked hatchery) and non-Nisqually origin categories. Freshwater mean increment width, growth rate and residence time were also calculated.

Washington↗

USGS2002

Test of salt marsh as a site of production and export of fish biomass with implications for impoundment management and restoration

Salt marshes are among the most productive ecosystems in the world, and although they are thought to enhance the productivity of open estuarine waters, the mechanism by which energy transfer occurs has been debated for decades. One possible mechanism is the transfer of saltmarsh production to estuarine waters by vagile fishes and invertebrates. Saltmarsh impoundments in the Indian River Lagoon, Florida, that have been reconnected to the estuary by culverts provide unique opportunities for studying marsh systems with respect to aquatic communities. The boundaries between salt marshes and the estuary are clearly defined by a system of dikes that confine fishes into a known area, and the exchange of aquatic organisms are restricted to culverts where they may be easily sampled. A multi-gear approach was used monthly to estimate fish standing stock, fish ingress/egress, and predation. Changes in saltmarsh fish abundance, and exchange with the estuary reflected the seasonal pattern of marsh flooding in the xv northern Indian River Lagoon system. During a six month period of marsh flooding, saltmarsh fishes had continuous access to marsh food resources. Piscivorous fishes regularly entered the marsh via creeks and ditches to prey upon marsh fishes, and piscivorous birds aggregated following major fish migrations to the marsh surface or to deep habitats. As water levels receded in winter, saltmarsh fishes concentrated into deep habitats and migration to the estuary ensued. The monthly estimates of fish standing stock, net fish ingress, and predation were used to develop a biomass budget to estimate annual production of fishes and the relative yield to predatory fish, birds, and direct migration to the estuary. Annual production of saltmarsh fishes was estimated to be 17.7 g·m-2 salt marsh, which falls within the range of previously reported values for estuarine fish communities. The relative yields were at least 21% to piscivorous fishes, 14% to piscivorous birds, and 32% to export. Annual export of fish biomass was 5.6 g fish·m-2 salt marsh, representing about 2% of saltmarsh primary production. Saltmarsh fishes convert marsh production to high quality vagile biomass (fishes concentrate energy, protein, and nutrients as body mass) and move this readily useable production to the estuary, providing an efficient link between salt marshes and estuarine predators.

Thesis↗

USGS2020

Bug flows: Don’t count your midges until they hatch

Usually when people hear about a “bug problem” it’s due to an undesirable overabundance of insects (think plague of locusts). In the Colorado River in Grand Canyon, however, we are faced with the opposite predicament: the river is essentially devoid of bugs. Aquatic insects are a fundamental component of a healthy river ecosystem. Most aquatic insects spend their juvenile life stages (egg, larva, pupa) in the river and their winged adult life stage flying along the riparian corridor. Throughout these metamorphoses one thing is for certain: aquatic insects are prey for fish, birds, bats, lizards, and even other invertebrates. In Grand Canyon, food web studies conducted by the US Geological Survey (USGS) have demonstrated that populations of both native and sport fish are food limited (Cross et al. 2013, Kennedy et al. 2013). In other words, fish in Grand Canyon are consistently facing a calorie deficit. Indeed, the US Fish and Wildlife Service has cited the inadequate and unreliable food supply as the single greatest problem facing endangered Humpback Chub populations in the Grand Canyon (USFWS 2019).

Boatman's Quarterly Review↗

USGS2006

Dealing with uncertainty and sensitivity issues in process-based models of carbon and nitrogen cycles in northern forest ecosystems

Many process-based models on carbon (C) and nitrogen (N) cycles have been developed for northern forest ecosystems. These models are widely used to evaluate the long-term decisions in forest management dealing with effects like particulate pollution, productivity and climate change. Regarding climate change, one of the key questions that have sensitive political implications is whether northern forests will sequester atmospheric C or not. Whilst many process-based models have been tested for accuracy by evaluating or validating against observed data, few have dealt with the complexity of the incorporated procedures to estimate uncertainties associated with model predictions or the sensitivity of these predictions to input factors in a systematic, inter-model comparison fashion. In general, models differ in their underlying attempts to match natural complexities with assumed or imposed model structure and process formulations to estimate model parameters, to gather data and to address issues on scope, scale and natural variations. Uncertainties may originate from model structure, estimation of model parameters, data input, representation of natural variation and scaling exercises. Model structure relates to the mathematical representation of the processes modelled and the type of state variables that a model contains. The modelling of partitioning among above- and below-ground C and N pools and the interdependence among these pools remain a major source of uncertainty in model structure and error propagation. Most soil C models use at least three state variables to represent the different types of soil organic matter (SOM). This approach results in creating three artificial SOM pools, assuming that each one contains C compounds with same turnover rate. In reality, SOM consists of many different types of C compounds with widely different turnover rates. Uncertainty in data and parameter estimates are closely linked. Data uncertainties are associated with high variations in estimating forest biomass, productivity and soil organic matter and may be incomplete for model initialization, calibration, validation and sensitivity analysis of generalized predictor models. The scale at which a model is being used also affects the level of uncertainty, as the errors in the prediction of the C and N dynamics differ from the site to the landscape levels and across climatic regions. If the spatial or temporal scale of a model application is changed, additional uncertainty arises from neglecting natural variability in system variables in time and space. Uncertainty issues are also intimately related to model validation and sensitivity analysis. The estimation of uncertainties is needed to inform decision process, in order to detect the possible corridor of development. Uncertainty in this context is an essential measure of quality for stakeholder and decision makers.

Conference Paper↗

USGS2006

Multimodeling: new approaches for linking ecological models

The Everglades region of South Florida presents one of the major natural system management challenges facing the United States. With its assortment of alligators, crocodiles, manatees, panthers, large mixed flocks of wading birds, highly diverse subtropical flora, and sea of sawgrass, the ecosystem is unique in this country (Davis and Ogden 1994). The region is also perhaps the largest human-controlled system on the planet in that the major environmental factor influencing the region is water, and water flows are managed on a daily basis--subject to the vagaries of rainfall--by a massive system of locks, pumps, canals, and levees constructed over the past century. The changes brought about by such control have led to extensive modifications of historical patterns and magnitudes of flow, causing large declines in many native species, extensive changes in nutrient cycling and vegetation across south Florida, and great increases in pollutants such as mercury. Constrained by the conflicting demands of agriculture, urban human populations, and wildlife for control of water resources, and the varying agendas of hosts of government agencies and nongovernmental organizations, there is now an ongoing effort to plan for major changes to the system with expenditure estimates of eight billion dollars or more over the next several decades (USACOE 1999). Carrying out such planning, particularly as it impacts the natural systems of the region, provides one of the major challenges to the new field of computational ecology.

Florida↗

USGS2026

Investigation of fish communities in natural channel sections of the Mohawk River, New York

Little is known about the natural resources in the natural channel sections of the Mohawk River between Rome and Frankfort, New York, where the river channel runs separately from and parallel to the Erie Canal. This river section runs through multiple locations that are listed as active remediation sites under New York’s Inactive Hazardous Waste Disposal Site Program and has negligible public or commercial access. As a result, there is minimal recreational usage of this river section, and efforts to conduct biological sampling have been limited. To better understand the composition of fish communities and contaminant concentrations in the natural channel of the Mohawk River, the U.S. Geological Survey, in cooperation with the New York State Department of Environmental Conservation, sampled resident fish in the 34-kilometer section from the mouth of Oriskany Creek downstream to Frankfort. Fish communities were sampled using boat electrofishing during 2021, 2023, and 2024 across multiple reaches within this section. These data were used to estimate species richness (number of species), relative abundance and biomass (catch rates), population size structure (distribution of lengths), and fish condition (a proxy for health). Some gamefish specimens were also analyzed to determine contaminant concentrations in fish tissue. A total of 1,531 individual fish and 38 fish species were captured across all surveys. Seventeen of the 38 (45 percent) species were classified as native to the Mohawk River watershed, whereas 21 of the 38 (55 percent) species were classified as nonnative. Some popular gamefish species such as largemouth bass ( Micropterus salmoides ) and smallmouth bass ( Micropterus dolomieu ) were abundant in most reaches, whereas others such as walleye ( Sander vitreus ) and northern pike ( Esox lucius ) were found sporadically. Only one round goby ( Neogobius melanostomus ) was captured, indicating that this high-profile invasive species remains uncommon in this habitat. A backwater reach had the greatest relative abundance and condition of many species. This indicates connected lentic habitats such as oxbows and backwaters may be important nursery and refuge areas in the aquatic ecosystem. Polychlorinated biphenyl (PCB) concentrations in fish tissue were highly elevated relative to the New York State Department of Health (NYSDOH) fish consumption “don’t eat” advisory guideline. Some specimens exceeded the guideline by an order of magnitude or more, particularly those from a localized area downstream from the Utica Harbor Dam. Concentrations of perfluorooctanesulfonic acid (PFOS) often approached the NYSDOH “don’t eat” consumption guideline but only one sample exceeded the guideline. Concentrations of other contaminants such as mercury and pesticides were consistently measured at less than the “don’t eat” consumption guidelines. These data indicate PCBs remain the primary contaminant of concern in the natural channel of the Mohawk River and are readily bioaccumulating in aquatic organisms despite prior remediation measures. Taken together, the findings in this report are intended to inform future decisions related to fisheries management, public access, recreational usage, and fish consumption advisories.

New York↗

USGS2009

Sediment losses and gains across a gradient of livestock grazing and plant invasion in a cool, semi-arid grassland, Colorado Plateau, USA

Large sediment fluxes can have significant impacts on ecosystems. We measured incoming and outgoing sediment across a gradient of soil disturbance (livestock grazing, plowing) and annual plant invasion for 9 years. Our sites included two currently ungrazed sites: one never grazed by livestock and dominated by perennial grasses/well-developed biocrusts and one not grazed since 1974 and dominated by annual weeds with little biocrusts. We used two currently grazed sites: one dominated by annual weeds and the other dominated by perennial plants, both with little biocrusts. Precipitation was highly variable, with years of average, above-average, and extremely low precipitation. During years with average and above-average precipitation, the disturbed sites consistently produced 2.8 times more sediment than the currently undisturbed sites. The never grazed site always produced the least sediment of all the sites. During the drought years, we observed a 5600-fold increase in sediment production from the most disturbed site (dominated by annual grasses, plowed about 50 years previously and currently grazed by livestock) relative to the never grazed site dominated by perennial grasses and well-developed biocrusts, indicating a non-linear, synergistic response to increasing disturbance types and levels. Comparing sediment losses among the sites, biocrusts were most important in predicting site stability, followed by perennial plant cover. Incoming sediment was similar among the sites, and while inputs were up to 9-fold higher at the most heavily disturbed site during drought years compared to average years, the change during the drought conditions was small relative to the large change seen in the sediment outputs. ?? 2009 Elsevier B.V. All rights reserved.

Aeolian Research↗

USGS2023

Revealing the extent of sea otter impacts on bivalve prey through multi-trophic monitoring and mechanistic models

Sea otters are apex predators that can exert considerable influence over the nearshore communities they occupy. Since facing near extinction in the early 1900s, sea otters are making a remarkable recovery in Southeast Alaska, particularly in Glacier Bay, the largest protected tidewater glacier fjord in the world. The expansion of sea otters across Glacier Bay offers both a challenge to monitoring and stewardship and an unprecedented opportunity to study the top-down effect of a novel apex predator across a diverse and productive ecosystem. Our goal was to integrate monitoring data across trophic levels, space, and time to quantify and map the predator–prey interaction between sea otters and butter clams Saxidomus gigantea , one of the dominant large bivalves in Glacier Bay and a favoured prey of sea otters. We developed a spatially-referenced mechanistic differential equation model of butter clam dynamics that combined both environmental drivers of local population growth and estimates of otter abundance from aerial survey data. We embedded this model in a Bayesian statistical framework and fit it to clam survey data from 43 intertidal and subtidal sites across Glacier Bay. Prior to substantial sea otter expansion, we found that butter clam density was structured by an environmental gradient driven by distance from glacier (represented by latitude) and a quadratic effect of current speed. Estimates of sea otter attack rate revealed spatial heterogeneity in sea otter impacts and a negative relationship with local shoreline complexity. Sea otter exploitation of productive butter clam habitat substantially reduced the abundance and altered the distribution of butter clams across Glacier Bay, with potential cascading consequences for nearshore community structure and function. Spatial variation in estimated sea otter predation processes further suggests that community context and local environmental conditions mediate the top-down influence of sea otters on a given prey. Overall, our framework provides high-resolution insights about the interaction among components of this food web and could be applied to a variety of other systems involving invasive species, epidemiology or migration.

Journal of Animal Ecology↗

USGS2001

GRA prospectus: optimizing design and management of protected areas

Protected areas comprise one major type of global conservation effort that has been in the form of parks, easements, or conservation concessions. Though protected areas are increasing in number and size throughout tropical ecosystems, there is no systematic method for optimally targeting specific local areas for protection, designing the protected area, and monitoring it, or for guiding follow-up actions to manage it or its surroundings over the long run. Without such a system, conservation projects often cost more than necessary and/or risk protecting ecosystems and biodiversity less efficiently than desired. Correcting these failures requires tools and strategies for improving the placement, design, and long-term management of protected areas. The objective of this project is to develop a set of spatially based analytical tools to improve the selection, design, and management of protected areas. In this project, several conservation concessions will be compared using an economic optimization technique. The forest land use portfolio model is an integrated assessment that measures investment in different land uses in a forest. The case studies of individual tropical ecosystems are developed as forest (land) use and preservation portfolios in a geographic information system (GIS). Conservation concessions involve a private organization purchasing development and resource access rights in a certain area and retiring them. Forests are put into conservation, and those people who would otherwise have benefited from extracting resources or selling the right to do so are compensated. Concessions are legal agreements wherein the exact amount and nature of the compensation result from a negotiated agreement between an agent of the conservation community and the local community. Funds are placed in a trust fund, and annual payments are made to local communities and regional/national governments. The payments are made pending third-party verification that the forest expanse and quality have been maintained.

Open-File Report↗

USGS2010

Otolith analysis of pre-restoration habitat use by Chinook salmon in the delta-flats and nearshore regions of the Nisqually River Estuary

The Nisqually Fall Chinook population is one of 27 salmon stocks in the Puget Sound (Washington) evolutionarily significant unit listed as threatened under the federal Endangered Species Act (ESA). Extensive restoration of the Nisqually River delta ecosystem is currently taking place to assist in recovery of the stock as juvenile Fall Chinook salmon are dependent on the estuary. A pre-restoration baseline that includes the characterization of life history strategies, estuary residence times, growth rates, and habitat use is needed to evaluate the potential response of hatchery and natural origin Chinook salmon to restoration efforts and to determine restoration success. Otolith analysis was selected as a tool to examine Chinook salmon life history, growth, and residence in the Nisqually River estuary. Previously funded work on samples collected in 2004 (marked and unmarked) and 2005 (unmarked only) partially established a juvenile baseline on growth rates and length of residence associated with various habitats (freshwater, forested riverine tidal, emergent forested transition, estuarine emergent marsh, delta-flats and nearshore). However, residence times and growth rates for the delta-flats (DF) and nearshore (NS) habitats have been minimally documented due to small sample sizes. The purpose of the current study is to incorporate otolith microstructural analysis using otoliths from fish collected within the DF and NS habitats during sampling years 2004-08 to increase sample size and further evaluate between-year variation in otolith microstructure. Our results from this analysis indicated the delta-flats check (DFCK) on unmarked and marked Chinook samples in 2005-08 varied slightly in appearance from that seen on samples previously analyzed only from 2004. A fry migrant life history was observed on otoliths of unmarked Chinook collected in 2005, 2007, and 2008. Generally, freshwater mean increment width of unmarked fish, on average, was smaller compared to marked Chinook followed by tidal delta and DF/NS portions respectively. On average, the complete tidal delta growth rate was higher for marked Chinook compared to unmarked Chinook. The DF/NS growth rate was highest for unmarked and marked Chinook during 2008 compared to all other sampling years. The average DF/NS growth rate on unmarked Chinook was consistently lower than marked Chinook during all years; however, sample sizes were small during some years. Unmarked Chinook, on average, spent longer in the tidal delta compared to marked Chinook. Our results from this report suggest that otolith microstructural analysis can be a valuable tool in establishing baseline information on the utilization of Nisqually River estuary habitats by juvenile Chinook salmon prior to the newly funded restoration efforts.

Open-File Report↗

USGS2016

Ecoregions of California

Ecoregions denote areas of general similarity in ecosystems and in the type, quality, and quantity of environmental resources. They are designed to serve as a spatial framework for the research, assessment, management, and monitoring of ecosystems and ecosystem components. By recognizing the spatial differences in the capacities and potentials of ecosystems, ecoregions stratify the environment by its probable response to disturbance (Bryce and others, 1999). These general purpose regions are critical for structuring and implementing ecosystem management strategies across Federal agencies, State agencies, and nongovernment organizations that are responsible for different types of resources in the same geographical areas (Omernik and others, 2000). The approach used to compile this map is based on the premise that ecological regions are hierarchical and can be identified through the analysis of the spatial patterns and the composition of biotic and abiotic phenomena that affect or reflect differences in ecosystem quality and integrity (Wiken, 1986; Omernik, 1987, 1995). These phenomena include geology, physiography, vegetation, climate, soils, land use, wildlife, and hydrology. The relative importance of each characteristic varies from one ecological region to another regardless of the hierarchical level. A Roman numeral hierarchical scheme has been adopted for different levels of ecological regions. Level I is the coarsest level, dividing North America into 15 ecological regions. Level II divides the continent into 50 regions (Commission for Environmental Cooperation Working Group, 1997, map revised 2006). At level III, the continental United States contains 105 ecoregions and the conterminous United States has 85 ecoregions (U.S. Environmental Protection Agency, 2013). Level IV, depicted here for California, is a further refinement of level III ecoregions. Explanations of the methods used to define these ecoregions are given in Omernik (1995), Omernik and others (2000), and Omernik and Griffith (2014). California has great ecological and biological diversity. The State contains offshore islands and coastal lowlands, large alluvial valleys, forested mountain ranges, deserts, and various aquatic habitats. There are 13 level III ecoregions and 177 level IV ecoregions in California and most continue into ecologically similar parts of adjacent States of the United States or Mexico (Bryce and others, 2003; Thorson and others, 2003; Griffith and others, 2014). The California ecoregion map was compiled at a scale of 1:250,000. It revises and subdivides an earlier national ecoregion map that was originally compiled at a smaller scale (Omernik, 1987; U.S. Environmental Protection Agency, 2013). This poster is the result of a collaborative project primarily between U.S. Environmental Protection Agency (USEPA) Region IX, USEPA National Health and Environmental Effects Research Laboratory (Corvallis, Oregon), California Department of Fish and Wildlife (DFW), U.S. Department of Agriculture (USDA)–Natural Resources Conservation Service (NRCS), U.S. Department of the Interior–Geological Survey (USGS), and other State of California agencies and universities. The project is associated with interagency efforts to develop a common framework of ecological regions (McMahon and others, 2001). Reaching that objective requires recognition of the differences in the conceptual approaches and mapping methodologies applied to develop the most common ecoregion-type frameworks, including those developed by the USDA–Forest Service (Bailey and others, 1994; Miles and Goudy, 1997; Cleland and others, 2007), the USEPA (Omernik 1987, 1995), and the NRCS (U.S. Department of Agriculture–Soil Conservation Service, 1981; U.S. Department of Agriculture–Natural Resources Conservation Service, 2006). As each of these frameworks is further refined, their differences are becoming less discernible. Regional collaborative projects such as this one in California, where some agreement has been reached among multiple resource-management agencies, are a step toward attaining consensus and consistency in ecoregion frameworks for the entire nation.

California↗

USGS2008

Davis Pond freshwater prediversion biomonitoring study: freshwater fisheries and eagles

In January 2001, the construction of the Davis Pond freshwater diversion structure was completed by the U.S. Army Corps of Engineers. The diversion of freshwater from the Mississippi River is intended to mitigate saltwater intrusion from the Gulf of Mexico and to lessen the concomitant loss of wetland areas. In addition to the freshwater inflow, Barataria Bay basin would receive nutrients, increased flows of sediments, and water-borne and sediment-bound compounds. The purpose of this biomonitoring study was, therefore, to serve as a baseline for prediversion concentrations of selected contaminants in bald eagle ( Haliaeetus leucocephalus ) nestlings (hereafter referred to as eaglets), representative freshwater fish, and bivalves. Samples were collected from January through June 2001. Two similarly designed postdiversion studies, as described in the biological monitoring program, are planned. Active bald eagle nests targeted for sampling eaglet blood (n = 6) were generally located southwest and south of the diversion structure. The designated sites for aquatic animal sampling were at Lake Salvador, at Lake Cataouatche, at Bayou Couba, and along the Mississippi River. Aquatic animals representative of eagle prey were collected. Fish were from three different trophic levels and have varying feeding strategies and life histories. These included herbivorous striped mullet ( Mugil cephalus ), omnivorous blue catfish ( Ictalurus furcatus ), and carnivorous largemouth bass ( Micropterus salmoides ). Three individuals per species were collected at each of the four sampling sites. Freshwater Atlantic rangia clams ( Rangia cuneata ) were collected at the downstream marsh sites, and zebra mussels ( Dreissena spp.) were collected on the Mississippi River. The U.S. Geological Survey (USGS) Biomonitoring of Environmental Status and Trends (BEST) protocols served as guides for fish sampling and health assessments. Fish are useful for monitoring aquatic ecosystems because they accumulate pesticides and other contaminants. Biomarker data on individual fish, generated at the USGS National Wetlands Research Center (Lafayette, La.), included percent white blood cells in whole blood, spleen weight to body weight ratio, liver weight to body weight ratio, condition factor, splenic macrophage aggregates, and liver microsomal 7-ethoxyresorufin-o-deethylase (EROD) activity. Fish age was estimated by comparing total lengths with values from the same species in the Southeast United States as determined from the literature. Contaminant analyses were coordinated by the U.S. Fish and Wildlife Service (USFWS) Analytical Control Facility (Laurel, Md.), where residues of organochlorine (OC) pesticides, total polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), aliphatic hydrocarbons (AHs), and trace elements were determined. The organic contaminant data were generated at the Mississippi State University Chemical Lab (Mississippi State, Miss.), and the inorganic contaminant data were generated by the Texas A&M University Geochemical and Environmental Research Group (College Station, Tex.). Statistical tests were performed to assess relationships among contaminants, fish age, fish species, and collection sites. Trends in interspecific differences among fish in concentrations of contaminants were noted. Striped mullet (hereafter mullet) frequently displayed the highest chemical concentrations. Levels of contaminants were generally higher in samples obtained from the Mississippi River than in those collected from the diversion area and were higher in mussels and clams (hereafter bivalves) than in fish. Because the Mississippi River sampling site for mullet and largemouth bass was downriver of the structure and south of New Orleans and the catfish site was upriver, the downriver data may not be directly reflective of the results from the receiving waters at the Davis Pond structure. Compared to the Caernarvon freshwater prediversion study in 1990 that assessed possible influx of contaminants with the freshwater diversion, contaminant levels in fishes and bivalves in this study were generally lower, yet three nontoxic inorganic elements in Davis Pond fish samples exhibited ranges of concentrations that were more than two times higher than did those from Caernarvon. Levels in bivalves were different between diversions but about equal in the numbers of trace elements showing high levels per location. Contaminant values were compared to those listed in various literature and agency sources, both regional and national, including the National Contaminant Biomonitoring Program (NCBP), in which the 85th percentile and above represents what is considered to be an elevated contaminant concentration and cause for concern. Generally, bivalves were at the high end of their ranges for both organic and inorganic contaminants. In this study, OCs were detectable in 67 percent of fish from the Mississippi River site, ranging from 0.15 to 1.09 μg/g wet weight (ww) or fresh weight (fw), and in 11 percent of the fish from the marsh sites, ranging from 0.06 to 0.612 μg/g ww. Bivalves from the Mississippi River had OC levels of 0.096 μg/g ww, whereas none were detectable in bivalves at the marsh sites. In this study, p,p ’-dichlorodiphenyldichloroethylene ( p,p’ -DDE) (a biodegradation product of DDT [dichlorodiphenyl trichloroethane]) and total PCBs were the most frequently detected OCs and were primarily from the Mississippi River. For total OC content, using adjusted least squares means, some significant interactions were noted between fish species and sites. PAHs were detected in aquatic animals at all sites (range of 0.017–17.534 μg/g ww), as were AHs (range of 0.423–4.549 μg/g ww); the highest levels of PAHs and AHs were found in bivalves from the Mississippi River. When analysis of variance (α = 0.05) was performed with data from aquatic animals, there were only two significant relationships between PAHs, AHs, and OCs between species, site, and age or the interaction among these variables. There was an interaction between fish species and n-decane (an AH) in that mullet and largemouth bass had significantly higher levels than did catfish ( P = 0.0175). When general linear means were used to investigate associations of inorganic contaminants among fish species, site, and age or any interactions among these variables, no significant results were noted for arsenic, cadmium, lead, beryllium, boron, molybdenum, or nickel. The range of mercury in fish in this study was 0.04–0.14 μg/g ww (0.14– 0.48 μg/g dry weight [dw]), with the most elevated levels detected in predatory largemouth bass at the sampling point farthest downstream from the structure and within the marsh area. Mercury was positively correlated with fish age ( P = 0.0152), where levels were estimated to increase 0.0253 parts per million (ppm) dw per year. In the Mississippi River, catfish showed significantly higher levels of mercury than did mullet or largemouth bass ( P = 0.00167). Among fish species, mullet displayed the highest levels in fish of aluminum, barium, manganese, and iron, all considered to have low toxicity in hydrologic systems. An interaction between fish and site was seen with aluminum ( P = 0.0031), where concentrations in mullet were significantly higher in the Mississippi River than at the other sites, as was also seen with barium ( P = 0.0009), chromium ( P = <0.0001), manganese ( P = 0.0004), strontium ( P = 0.0074), vanadium ( P = 0.0156), and zinc ( P = 0.0059). For iron ( P = 0.0.0001), mullet and largemouth bass at both the Mississippi River and Lake Salvador showed higher levels than did catfish, and these two species showed higher levels at two of the four sites. An interaction between fish and site was also seen with chromium ( P = <0.0001) in that concentrations in mullet were significantly higher in the Mississippi River than at the other sites, as was also seen with strontium ( P = 0.0074), vanadium ( P = 0.0156), and zinc ( P = 0.0059), metals for which deleterious effects have been demonstrated in other ecosystems. The NCBP program lists the 85th percentile for zinc at 34.2 μg/g fw (117.9 μg/g dw). In the Davis Pond prediversion biomonitoring study (hereafter the current study), one fish (MUL31RIVER, fish ID 8) showed values higher than that (125.4 μg/g dw or 37.54 μg/g ww), and the Mississippi River bivalve sample (MUSSRIVER) had a value of 140 μg/g dw (41.2 μg/g ww). In the current study, approximately 86 percent of the fish had measurable selenium levels, yet none reached the 85th percentile. The 85th percentile for selenium from the NCBP was 0.73 μg/g ww. Significantly higher levels of selenium were seen in mullet than in largemouth bass and catfish ( P = 0.0023). The NCBP 85th percentile for lead is 0.22 μg/g ww (0.76 μg/g dw). In the current study, the range of concentrations of lead was as much as 18.3 ppm dw (MUL31RIVER, fish ID 8), with the three most elevated values (range of 3.46–5.31 μg/g ww) coming from mullet from the Mississippi River. Biomarker data are measurable and directly reflect the condition of the animal, and measuring more than one biomarker in an individual increases confidence in health assessments. In the current study, biomarkers included macrophage aggregates (MAs), liver (hepatosomatic index [HSI]) and spleen (splenosomatic index [SSI]) weight to body weight ratios, percent white blood cells (WBCs) in whole blood, and condition factor. Few significant differences were noted with any of the biomarkers between sites, and there were no relationships between species and sites. For improved use of biomarker assessments, an increase in fish sample size would be useful for postdiversion sampling, as would comparisons of fish of the same sex and reproductive condition. During the current study, success for eagle nests in the diversion area and reference sites was similar as determined by numbers of nestlings fledged. When temperatures were below average during winter 2000, nests in both regions similarly failed. At each nest, the primary evidence of food items was small mammals. Eaglets (n = 6) generally appeared healthy, and whole blood concentrations of organic contaminants exceeded detection limits with three incidences of p,p’ -DDE (0.002–0.006 μg/L ww) and one incidence of oxychlordane (0.002 μg/L ww). The levels of p,p’ -DDE were well below those that have been inversely correlated with productivity and success rates of nesting bald eagles on a regional scale. The low values found in the whole blood samples for OC pesticides and PCBs were even lower when corrected for plasma volume. Aluminum values were 3.66 and 5.75 μg/L in two samples, zinc ranged from 5.21 to 6.77 μg/L ww in six samples, and silicon ranged from 1.7 to 4.6 μg/L in four samples. Selenium was detectable in each bird with the range at 0.332–0.566 μg/L ww, and strontium ranged from 0.0581 to 0.0975 μg/L ww. Mercury was detectable in blood samples from each bird and ranged from 0.0254 to 0.0845 μg/L ww, whereas lead was detectable in four samples and ranged from 0.0042 to 0.0136 μg/L ww. Although no detectable levels of total PCBs were found (also correlated with decreased reproductive productivity), 70 percent of the aquatic animals from the Mississippi River contained total PCBs (range 0.13–0.79 μg/L), whereas only about 7 percent of the aquatic animals sampled from the marsh area contained PCBs. Suggestions for postdiversion sampling include lowering the analytical detection limit for some metals, sampling aquatic animals over the course of a single season, obtaining a higher sample number of mature fish of one species (for example, blue catfish) within a range of total lengths for biomarker analyses, obtaining otoliths for estimating fish ages, assessing dioxins in eaglet blood, examining triazines in water, and obtaining all Mississippi River fish samples as close to the Davis Pond structure intake as possible. Because contaminants found in blood of eaglets reflect their prey species and because of the contaminant levels found in fish in the current study, eaglets may not be consuming primarily these species; therefore, obtaining juvenile nutria ( Myocastor coypus ) or turtle species for contaminant analyses might be considered, as well as collecting greater blood volume and using plasma to measure OCs and PCBs. Data obtained postdiversion will be compared with prediversion data to monitor changes.

Louisiana↗

USGS2014

Global research priorities to mitigate plastic pollution impacts on marine wildlife

Marine wildlife faces a growing number of threats across the globe, and the survival of many species and populations will be dependent on conservation action. One threat in particular that has emerged over the last 4 decades is the pollution of oceanic and coastal habitats with plastic debris. The increased occurrence of plastics in marine ecosystems mirrors the increased prevalence of plastics in society, and reflects the high durability and persistence of plastics in the environment. In an effort to guide future research and assist mitigation approaches to marine conservation, we have generated a list of 16 priority research questions based on the expert opinions of 26 researchers from around the world, whose research expertise spans several disciplines, and covers each of the world’s oceans and the taxa most at risk from plastic pollution. This paper highlights a growing concern related to threats posed to marine wildlife from microplastics and fragmented debris, the need for data at scales relevant to management, and the urgent need to develop interdisciplinary research and management partnerships to limit the release of plastics into the environment and curb the future impacts of plastic pollution.

Endangered Species Research↗

USGS2012

Impacts of climate change on biodiversity, ecosystems, and ecosystem services: technical input to the 2013 National Climate Assessment

Ecosystems, and the biodiversity and services they support, are intrinsically dependent on climate. During the twentieth century, climate change has had documented impacts on ecological systems, and impacts are expected to increase as climate change continues and perhaps even accelerates. This technical input to the National Climate Assessment synthesizes our scientific understanding of the way climate change is affecting biodiversity, ecosystems, ecosystem services, and what strategies might be employed to decrease current and future risks. Building on past assessments of how climate change and other stressors are affecting ecosystems in the United States and around the world, we approach the subject from several different perspectives. First, we review the observed and projected impacts on biodiversity, with a focus on genes, species, and assemblages of species. Next, we examine how climate change is affecting ecosystem structural elements—such as biomass, architecture, and heterogeneity—and functions—specifically, as related to the fluxes of energy and matter. People experience climate change impacts on biodiversity and ecosystems as changes in ecosystem services; people depend on ecosystems for resources that are harvested, their role in regulating the movement of materials and disturbances, and their recreational, cultural, and aesthetic value. Thus, we review newly emerging research to determine how human activities and a changing climate are likely to alter the delivery of these ecosystem services. This technical input also examines two cross-cutting topics. First, we recognize that climate change is happening against the backdrop of a wide range of other environmental and anthropogenic stressors, many of which have caused dramatic ecosystem degradation already. This broader range of stressors interacts with climate change, and complicates our abilities to predict and manage the impacts on biodiversity, ecosystems, and the services they support. The second cross-cutting topic is the rapidly advancing field of climate adaptation, where there has been significant progress in developing the conceptual framework, planning approaches, and strategies for safeguarding biodiversity and other ecological resources. At the same time, ecosystem-based adaptation is becoming more prominent as a way to utilize ecosystem services to help human systems adapt to climate change. In this summary, we present key findings of the technical input, focusing on themes that can be found throughout the report. Thus, this summary takes a more integrated look at the question of how climate change is affecting our ecological resources, the implications for humans, and possible response strategies. This integrated approach better reflects the impacts of climate in the real world, where changes in ecosystem structure or function will alter the viability of different species and the efficacy of ecosystem services. Likewise, adaptation to climate change will simultaneously address a range of conservation goals. Case studies are used to illustrate this complete picture throughout the report; a snapshot of one case study, 2011 Las Conchas, New Mexico Fire , is included in this summary.

Report↗

USGS2025

Integrating sea level rise scenarios into Everglades restoration planning

One of the largest and most expensive restoration efforts in the world is occurring in the Everglades, a sub-tropical freshwater wetland system located in southern Florida. This unique ecosystem supports several endangered species, provides flood control for Florida’s large urban population, and provides water for both agriculture and drinking supply within the state. The Comprehensive Everglades Restoration Plan (CERP), authorized by Congress in 2000, guides federal, state, and local efforts to build the infrastructure necessary to bring more water into the Everglades and restore its ecological integrity, while balancing other water-related needs such as water supply and flood protection in the human environment. The Everglades encompasses the southern coast of Florida and restoration efforts are likely to be impacted by climate-induced sea level rise. However, currently, many project planning studies do not formally incorporate the potential impacts of sea level rise when evaluating restoration plan outcomes. Resource managers and project planners require methods and tools to confidently incorporate scenarios of sea level rise into their evaluations. The U.S. Geological Survey (USGS) and partners from the University of Florida worked with project planners from multiple agencies to identify restoration questions for consideration when addressing sea level rise. In addition, our project team sought to understand the types of sea level rise decision-support tools that would be of interest, and then worked with Everglades restoration managers and project planners to develop those tools. The tools developed by this project can be used by project planners to inform their decision-making abilities when considering multiple restoration plans across the Everglades landscape. Specifically, the novel ways to visualize output information from ecological models that came of this project can help project planners compare alternative restoration plans that include potential sea level rise impacts. This effort demonstrates how incorporating sea level rise scenarios into Everglades restoration project planning can help managers decide whether projects will maintain or improve ecological integrity and evaluate water availability for wildlife and humans.

Final Report↗