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USGS2025

Incidence of pollution, bioaccumulation, biomagnification, and toxic effects of per- and polyfluoroalkyl substances (PFAS) in aquatic ecosystems: A review

Per- and polyfluoroalkyl substances (PFAS) are persistently accumulated in both environmental media and biological systems, leading to significant toxicological effects. Although research on PFAS has expanded in recent years, systematic reviews on its concentration distribution in aquatic environments and biota, as well as its toxicological effects, remain scarce. Moreover, existing literature lacks systematic analyses of diverse aquatic environments and organisms. This review investigates the contamination levels of PFAS in aquatic environments. It also provides a systematic analysis of bioaccumulation in planktonic, swimming, and benthic organisms, including bioaccumulation factors (BAF), biomagnification factors (BMF), trophic magnification factors (TMF), and biota-sediment accumulation factors (BSAF), and evaluates the potential toxic effects on aquatic ecosystems. This study aims to provide theoretical support for the environmental regulation and management of PFAS. Additionally, it seeks to offer data references and potential research directions for future studies, thereby promoting the advancement of PFAS-related research and policy development.

Aquatic Toxicology↗

USGS1982

Habitat Suitability Index Models: Brook trout

The habitat use information and Habitat Suitability Index (HSI) models presented in this document are an aid for impact assessment and habitat management activities. Literature concerning a species' habitat requirements and preferences is reviewed and then synthesized into HSI models, which are scaled to produce an index between 0 (unsuitable habitat) and 1 (optimal habitat). Assumptions used to transform habitat use information into these mathematical models are noted, and guidelines for model application are described. Any models found in the literature which may also be used to calculate an HSI are cited, and simplified HSI models, based on what the authors believe to be the most important habitat characteristics for this species, are presented.

FWS/OBS↗

USGS2018

United States bat species of concern: A synthesis

In 1994 the federal government designated 24 species or subspecies of bats in the United States (U.S.) and its territories as Category 2 candidates for listing as Endangered or Threatened under the U.S. Endangered Species Act. Category 2 was eliminated in 1996, but taxa previously receiving this designation were informally considered “species of concern”. Various state and federal agencies and conservation organizations assigned bat species of concern to more formal conservation categories. Some of the original 24 taxa designated as Category 2 candidates in 1994 were later listed as Endangered, whereas others were subject to refinements in knowledge of their taxonomy and distribution. The remaining 20 species of bats have the subjects of increased research efforts over the past two decades, and are the focus of this review. Two species occur in the U.S. Territories. All of the 18 mainland species ranges include areas west of the Mississippi River (15 are found primarily in western states), and 13 occur in California (72% of the 18 mainland species). In this review, we provide a comprehensive summary of the literature pertinent to the conservation designations, systematics, distribution, habitats, relative abundance, foraging, diet, roosting ecology, population ecology, and management of each of these 20 species. The species of concern are distributed among four families of bats. The Samoan flying fox (Pteropus samoensis) belong to the old-world family Pteropodidae. The California leaf-nosed bat (Macrotus californicus), red fruit bat (Stenoderma rufum), and Mexican long-tongued bat (Choeronycteris mexicana) are members of the new-world family Phyllostomidae. Three species belong to the cosmopolitan family Molossidae: the greater bonneted bat (Eumops perotis californicus), Underwood’s bonneted bat (Eumops underwoodi), and the big free-tailed bat (Nyctinomops macrotis). Most bat species of concern are in the globally distributed family Vespertilionidae: Townsend’s big-eared bat (Corynorhinus townsendii), Rafinesque’s big-eared bat (C. rafinesquii), spotted bat (Euderma maculatum), Allen’s big-eared bat (Idionycteris phyllotis), southeastern myotis (M. austroriparius), western small-footed myotis (Myotis ciliolabrum), long-eared myotis (M. evotis), eastern small-footed myotis (M. leibii), Arizona myotis (M. occultus), fringed myotis (M. thysanodes), cave myotis (M. velifer), long-legged myotis (M. volans), and Yuma myotis (M. yumanensis). An impressive amount of knowledge has accumulated about these species since their informal designation as species of concern, but this knowledge is unevenly distributed. Comparatively little research has been conducted on the Samoan flying fox and the red fruit bat over the past decade in tropical territories, nor on the Mexican long-tongued bat and Underwood’s mastiff bat in the southwestern U.S. Within temperate regions of the U.S., habitat use of two eastern species that roost in hollow trees or caves (southeastern myotis and Rafinesque’s big-eared bat) has been the focus of much research, as have aspects of the biology of cave-roosting and tree-roosting western species, particularly where information about management of forests, caves and abandoned mines can be used to benefit bat conservation. Comparatively less information has accrued about species that roost in rock crevices and high on cliff faces. Other major gaps in information are also identified. We anticipate that this review will help guide future research and conservation efforts directed at the bat species of concern.

Proceedings of the California Academy of Sciences,↗

USGS2026

dMODELS, a MATLAB software package for modeling crustal deformation near volcanic centers and active faults using Global Navigation Satellite System data—User guide

dMODELS is a MATLAB software package that implements the most common analytical models used to interpret deformation measurements near faults and active volcanic centers. This manual focuses on inversion of deformation data from the Global Navigation Satellite System (GNSS). The included case studies emphasize the GNSS inversion component of the software. Source models include pressurized spherical, spheroidal, and horizontal sill (penny-crack) magma reservoirs in a homogeneous, elastic, isotropic, flat half-space. A topography correction is available for the spherical source. Dikes and faults are described following the mathematical notation for the rectangular dislocations in a homogeneous, elastic, flat half-space. Equations have been reviewed for typographical errors present in the original literature and verified against finite-element method numerical models. GNSS data from the 2006 eruption at Augustine Volcano, Alaska; the 1998–2000 unrest at Taal Volcano, Philippines; and the 2009 earthquake in L’Aquila, Italy, are used to demonstrate the application of the software package.

Techniques and Methods↗

USGS2000

The bellerophont controversy revisited

An old controversy reestablished itself in the late 1970s and early 1980s that focused on the systematic placement of the enigmatic Bellerophontoidea (informally, "bellerophonts"), a group of planispirally coiled, wholly fossil molluscs. The controversy embraced three fundamental concepts that are based on different philosophical interpretations of shell form, muscle scar patterns, and other preserved shell features: 1) all bellerophonts were monoplacophorans; 2) all bellerophonts were gastropods; and 3) some bellerophonts were monoplacophorans and some were gastropods. A review of the main issues appearing in the literature since the early 1980s indicates that these three philosophical divisions still exist and, indeed, have become entrenched. An examination of the relevant anatomical and shell features of recent gastropods and monoplacophorans, and comparison with preserved features in enigmatic fossil forms, convinces us that the bellerophontoideans and the coiled and high-domed "monoplacophorans" (Cyclomya) were gastropods. Only the flattened, spoon-and cap-shaped monoplacophorans (Tergomya) were true monoplacophorans. We present a hypothetical scheme for the morphological diversification of gastropods from early monoplacophorans that could account for Cyclomya, Bellerophontoidea, Patellogastropoda, and Prosobranchia.

American Malacological Bulletin↗

USGS2011

Arsenic in Chinese coals: Distribution, modes of occurrence, and environmental effects

Arsenic, one of the most hazardous elements occurring in coals, can be released to the environment during coal processing and combustion. Based on the available literature and published results obtained in our laboratory, the content, distribution and the modes of occurrence of As in Chinese coals, and its environmental and impacts are reviewed in this article. With the 4763 sets of data (from the literature) rearranged, the arithmetic mean As concentration of each province and weighted mean As concentration of the entire country (using the expected coal reserves as the weighting factor) were calculated. The weighted mean As concentration in Chinese coals is 3.18 mg/kg, with As concentration increasing from northern China to southern China. The As concentration in coal varies with coal-forming ages and coal ranks. Arsenic has several modes of occurrence in coals. According to results obtained by other studies and our own experiments, As is mainly associated with mineral matter (such as pyrite and other sulfide minerals) in coals, although a significant amount of arsenic is associated with organic matter. The accumulation of As in coal is controlled by many geological factors during coal-forming processes, including plant decomposition, sedimentary environments, and epigenetic hydrothermal activity. During the combustion of coal, As is released to the air, water, and soil, causing serious environmental pollution. More than 45% of the coal consumed in China is utilized by power plants, and it is estimated that nearly 522 tonnes, 21 tonnes and 252 tonnes of As are emitted into the atmosphere by industries, residential buildings and coal-fired power plants, respectively, every year.

Article↗

USGS2020

Freshwater neurotoxins and concerns for human, animal, and ecosystemhealth: A review of anatoxin-a and saxitoxin

Toxic cyanobacteria are a concern worldwide because they can adversely affect humans, animals, and ecosystems. However, neurotoxins produced by freshwater cyanobacteria are understudied relative to microcystin. Thus, the objective of this critical review was to provide a comprehensive examination of the modes of action, production, fate, and occurrence of the freshwater neurotoxins anatoxin-a and saxitoxin as they relate to human, animal, and ecosystem health. Literature on freshwater anatoxin-a and saxitoxin was obtained and reviewed for both laboratory and field studies. Current (2020) research identifies as many as 41 anatoxin-a producing species and 15 saxitoxin-producing species of freshwater cyanobacteria. Field studies indicate that anatoxin-a and saxitoxin have widespread distribution, and examples are given from every continent except Antarctica. Human and animal health concerns can range from acute to chronic. However, few researchers studied chronic or sublethal effects of freshwater exposures to anatoxin-a or saxitoxin. Ecosystemhealth also is a concern, as the effects of toxicity may be far reaching and include consequences throughout the food web. Several gaps in knowledgewere identified for anatoxin-a and saxitoxin, including triggers of production and release, environmental fate and degradation, primary and secondary exposure routes, diel variation, food web effects, effects of cyanotoxin mixtures, and sublethal health effects on individual organisms and populations. Despite the gaps, this critical review facilitates our current understanding of freshwater neurotoxins and thus can serve to guide future research on anatoxin-a, saxitoxin, and other cyanotoxins.

Science of the Total Environment↗

USGS2020

Do empirical observations support commonly-held climate change range shift hypotheses? A systematic review protocol

Background Among the most widely anticipated climate-related impacts to biodiversity are geographic range shifts, whereby species shift their spatial distribution in response to changing climate conditions. In particular, a series of commonly articulated hypotheses have emerged: species are expected to shift their distributions to higher latitudes, greater elevations, and deeper depths in response to climate change, reflecting an underlying hypothesis that species will move to cooler locations to track spatial changes in the temperature of their current range. Yet, many species are not demonstrating range shifts consistent with these hypotheses. Resolving this discrepancy and providing effective explanations for the observed variability in species’ range shifts is urgently needed to help support a range of natural resource management decisions. Here, we propose a protocol to review the body of evidence for commonly-held climate change range shift hypotheses at the species level focusing on observed latitudinal, longitudinal, elevational, and depth shifts in response to temperature and precipitation changes. We aim to answer the question: what is the impact of anthropogenic climate change (specifically changes in temperature and precipitation) on species ranges? Methods In this review protocol, we propose to conduct a systematic search of literature from internet databases and search engines in English. Articles will be screened in a two-stage process (title/abstract and full text) to evaluate whether they meet a list of eligibility criteria (e.g., presents species-level data, compares >1 time period). Initial data coding and extraction will be completed by four reviewers and checked by a secondary reviewer from among our co-authors. We will perform a formal meta-analysis to document estimated effect size using the subset of available range-shift data expressed in distance per time (e.g., km/decade). We will also use multinomial logistic regression models to assess the probability that species are shifting in a direction that supports our hypotheses (i.e. towards higher latitudes, greater elevations, and deeper depths). We will account for study methodology as a potential source of variation.

Environmental Evidence↗

USGS2025

A synthesis of freshwater forested wetland soil organic carbon storage

Freshwater forested wetlands account for ~76% (918 M ha) of the total global wetland extent. However, freshwater forested wetlands are difficult to distinguish from upland forest due to canopy coverage, the abundance of wetland-nonwetland mosaics, seasonal hydropatterns, and fewer readily observable connections to large surface water bodies relative to marshes and other emergent habitats. Therefore, freshwater forested wetland ecosystems are often misclassified as upland forests in carbon accounting models, underestimating soil organic carbon (SOC) storage. This study highlights freshwater forested wetland SOC accounting challenges and presents SOC densities/stocks from a global literature synthesis across different freshwater forested wetland types. We reviewed 374 forested wetland articles, compiling and calculating carbon densities by depth from 90 freshwater forested wetland studies to construct a database of 334 study sites including nine countries. The median (± median absolute deviation) SOC stock was 91.2 ± 46.4 Mg C ha −1 and 235.3 ± 125.6 Mg C ha −1 in the top 30 cm and 100 cm of soil, respectively. The tidal freshwater forested wetland had highest SOC stock (341.6 ± 98.4 Mg C ha −1 ) in the upper 100 cm soil profile followed by rainforest (285.6 ± 75.8 Mg C ha −1 ), non-tidal swamps (229.3 ± 120.4 Mg C ha −1 ), and floodplain forested wetlands (176.6 ± 84 Mg C ha −1 ). Within the conterminous United States forest type groups, the Tsuga / Picea group had the highest median SOC stocks (353.6 ± 82.9 Mg ha −1 ) in the top 100 cm of soil followed by Quercus/Pinus (246.6 ± 82.3 Mg ha −1 ) and Quercus/Liquidambar/Taxodium (207.9 ± 87.7 Mg ha −1 ) groups, likely driven by variability in litter degradability, wetland hydroperiod, geomorphic positions, and regional climatic factors. This literature synthesis highlights SOC accounting in freshwater forested wetland carbon pools when estimating carbon stocks and fluxes. Results can be used to improve carbon modeling outcomes, as well as inform regional, national, and global management of wetland carbon resources.

Frontiers in Forests and Global Change↗

USGS1982

Habitat Suitability Index Models: Northern pike

The habitat use information and Habitat Suitability Index (HSI) models presented in this document are intended for use in impact assessment and habitat management activities. Literature concerning the habitat requirements and preferences of northern pike is reviewed and then synthesized into HSI models, which are scaled to produce an index between 0 (unsuitable habitat) and 1 (optimal habitat). Assumptions used to transform habitat use information into these quantitative models are noted, and guidelines for model application are described. Other models found in the literature which may also be used to calculate an HSI are cited.

FWS/OBS↗

USGS2014

Editors are editors, not oracles

Farji-Brener and Kitzberger (2014; hereafter FBK) resurrect the issues of Farji-Brener (2007) concerning manuscripts that are submitted to journals but that are not sent out for peer review: a process we call “reject following editorial review” (RFER). We thank FBK for reviving discussion about this important topic as new challenges, including new publication outlets, peer-review models, and an increasingly complex and voluminous scientific literature, are emerging across the publication landscape. While we disagree with FBK's perspective and conclusions, we recognize that this discussion can help to improve editorial and publication processes, and we welcome the opportunity to inform the ecological community about the current status of editorial practice at ESA journals.

Bulletin of the Ecological Society of America↗

USGS2007

Environmental effects of off-highway vehicles on Bureau of Land Management lands: A literature synthesis, annotated bibliographies, extensive bibliographies, and internet resources

This report and its associated appendixes compile and synthesize the results of a comprehensive literature and Internet search conducted in May 2006. The literature search was undertaken to uncover information regarding the effects of off-highway vehicle (OHV) use on land health, or “natural resource attributes,” and included databases archiving information from before OHVs came into existence to May 2006. Information pertaining to socioeconomic implications of OHV activities is included as well. The literature and Internet searches yielded approximately 700 peer-reviewed papers, magazine articles, agency and non-governmental reports, and internet websites regarding effects of OHV use as they relate to the Bureau of Land Management’s (BLM) standards of land health. Discussions regarding OHV effects are followed by brief syntheses of potential indicators of OHV effects, as well as OHV-effects mitigation, site-restoration techniques, and research needs.

Open-File Report↗

USGS2011

An inventory and monitoring plan for a Sonoran Desert ecosystem; Barry M. Goldwater Range-West

Marine Corps Air Station Yuma manages the Barry M. Goldwater Range-West, which encompasses approximately 2,800 square kilometers of Sonoran Desert habitat in southwestern Arizona. The Barry M. Goldwater Range is a major U.S. military installation designed as an air combat training location for the U.S. Marine Corps and U.S. Air Force, but it also includes some of the most pristine desert habitat in the United States. In an effort to ensure the long-term viability of this unique natural resource, the U.S. Geological Survey (USGS) has developed an Integrated Natural Resources Management Plan and Inventory and Monitoring Plan to guide natural resource management of the Barry M. Goldwater Range-West. This Inventory and Monitoring Plan provides a framework for long-term ecosystem monitoring on Barry M. Goldwater Range-West lands by identifying existing and potential threats to ecosystem function, prioritizing resources for monitoring, and providing information and protocols necessary to initiate a long-term ecosystem monitoring program. The Inventory and Monitoring Plan and related protocols were developed through extensive review of existing Sonoran Desert monitoring programs and monitoring literature and through a 2-day workshop with resource managers, monitoring experts, and other stakeholders. The Barry M. Goldwater Range-West Inventory and Monitoring Plan stresses the importance of regional monitoring partnerships and protocol standardization for understanding landscape-scale ecosystem changes in the Sonoran Desert; information and protocols contained within the plan may also be of interest to land managers engaged in large-scale ecosystem monitoring and adaptive management of other arid regions.

Open-File Report↗

USGS1987

Synopsis of wetland functions and values: bottomland hardwoods with special emphasis on eastern Texas and Oklahoma

Bottomland hardwood wetlands are the natural cover type of many floodplain ecosystems in the southeastern United States. They are dynamic, productive systems that depend on intermittent flooding and moving water for maintenance of structure and function. Many of the diverse functions performed by bottomland hardwoods (e.g., flood control, sediment trapping, fish and wildlife habitat) are directly or indirectly valued by humans. Balanced decisions regarding bottomland hardwoods are often hindered by a limited ability to accurately specify the functions being performed by these systems and, furthermore, by an inability to evaluate these functions in economic terms. This report addresses these informational needs. It focuses on the bottomland hardwoods of eastern Texas and Oklahoma, serving as an introduction and entry to the literature. It is not intended to serve as a substitute for reference to the original literature. The first section of the report is a review of the major functions of bottomland hardwoods, grouped under the headings of hydrology, water quality, productivity, detritus, nutrients, and habitat. Although the hydrology of these areas is diverse and complex, especially with respect to groundwater, water storage at high flows can clearly function to attenuate peak flows, with possible reductions in downstream flooding damage. Water moving through a bottomland hardwood system carries with it various organic and inorganic constituents, including sediment, organic matter, nutrients, and pollutants. When waterborne materials are introduced to bottomland hardwoods (from river flooding or upland runoff), they may be retained, transformed, or transported. As a result, water quality may be significantly altered and improved. The fluctuating and flowing water regime of bottomland hardwoods is associated with generally high net primary productivity and rapid fluxes of organic matter and nutrients. These, in turn, support secondary productivity in the bottomland hardwoods and downstream through detrital export. A large number of studies detail the extensive utilization of bottomland hardwoods by animals. Several basic habitat components contribute to this support function, including: 1. Fluctuating water levels and permanent bodies of water, 2. Hard mast (e.g., acorns), 3. Dens and cavities, 4. High soil fertility, 5. Diversity of food and cover, 6. Predominance of woody plant communities, 7. Close proximity of diverse structural features, and 8. Linear features providing movement corridors. The second section of the report focuses on the bottomlands of eastern Texas and Oklahoma, including topics such as climate, soils, water resources, historical perspective, vegetation, and fauna. Considerable attention is given to structural characteristics in this section, in order to provide contrasts with bottomland hardwood ecosystems in other areas. In general, the bottomland hardwoods of eastern Texas and Oklahoma are very similar to those elsewhere in the southeastern United States. Differences include the occurrence and relative importance of some community types and plant species and the greater importance of reservoir construction as a source of bottomland hardwoods loss in eastern Texas and Oklahoma. Again, information on faunal utilization is extensive relative to the information available concerning other functions.

Oklahoma;Texas↗

USGS1988

The past, present, and future of manatees in the southeastern United States: realities, misunderstandings and enigmas

A review of the historical and recent (1970s-1980s) literature on the distribution, abundance, and mortality of West Indian manatees ( Trichechus manatus ) in the southern United States is presented. Recent unpublished data on mortality, Florida boat registrations, size of certain manatee wintering populations, and records outside of Florida are also given. Manatees never regularly occurred outside of Florida, except during the summer in Georgia. Current distribution is also limited largely to Florida and coastal Georgia in summer, with extralimital records in other southeastern states. In winter the range contracts and is centered around warm water sources in Florida. The historical record on past abundance is inconclusive, but does not provide any compelling evidence to claim that manatees ever nearly became extinct. There are no satisfactory means to estimate manatee population size. However, within Florida, manatees have become more widespread and possibly more abundant during the past 30 years due to protection, greater availability of warm water in winter, and in some areas, increased exotic vegetation. Deliberate killing for food was long a historical pressure on manatee populations in Florida, but is not almost non-existent. Nevertheless, recent increasing trends in accidental mortality caused by boats, coupled with an understanding of manatee population dynamics, suggests that the future for manatees is not secure. Ample justification exists for continued manatee conservation efforts.

Book↗

USGS1983

Inbreeding in fish populations used for aquaculture

The theoretical causes of inbreeding depression are reviewed. Studies to measure depression at a series of inbreeding levels in rainbow trout populations using the method of inbred-outbred half-sib families are discussed. While the actual depression estimates varied widely between populations and inbreeding levels, significant levels of depression were found in many hatchery, field, and brood stock performance traits after only one generation of brother-sister mating. Especially susceptible to inbreeding depression, were measures of growth based upon attained fish weight at a given age in each test situation examined: 147 day weight (0.0 to 19.1%), 364 day weight (6.2 to 62.8%), weight after 6 months in fishing pond (−4.6 to 25.4%), weight after 12 months in fishing pond (13.0 to 29.1%), 2-year male weight (11.3 to 55.3%), and 2-year female weight (10.2 to 57.0%). Other hatchery performance traits that showed inbreeding depression were: egg hatch-ability (−0.2 to 53.1%), fry survival (0.4 to 8.2%), feed conversion efficiency (5.0 to 9.0%), fish length at 2-years of age (4.7 to 36.9%), and egg mass produced at 2-years (12.1 to 57.0%). Field performance traits that yielded inbreeding depression were percent recovery of fish stocked (−2.5 to 41.1%) and biomass index (16.2 to 47.7%). Literature on the effects of inbreeding in fish populations is reviewed and the breeding approaches for controlling the rate of inbreeding accumulation in brood stock populations are outlined and discussed.

Aquaculture↗

USGS2024

Imperiled Great Basin terminal lakes: Synthesizing ecological and hydrological science gaps and research needs for waterbird conservation

Terminal lakes are declining globally because of human water demands, drought, and climate change. Through literature synthesis and feedback from the resource and conservation community, we review the state of research for terminal lakes in the Great Basin of the United States, which support millions of waterbirds annually, to prioritize ecological and hydrologic information needs. From an ecological perspective, research priorities include measuring the underlying differences in waterbird resource selection and distribution, migratory connectivity, abiotic factors that interact with prey densities to affect prey availability, and waterbird fitness or demography. Integrated links between water availability, water quality, and food webs are lacking in the literature. Scarce water availability data hinder the current knowledge of water extraction and evapotranspiration rates. Research that can address these priorities would help advance our understanding of how the Great Basin terminal lakes function as an interrelated system and support conservation efforts to reverse the decline of these critical lakes.

California, Nevada, Oregon, Utah↗

USGS2013

Exploration Review

This summary of international mineral exploration activities for 2012 draws upon information from industry sources, published literature and U.S. Geological Survey (USGS) specialists. The summary provides data on exploration budgets by region and mineral commodity, identifies significant mineral discoveries and areas of mineral exploration, discusses government programs affecting the mineral exploration industry and presents analyses of exploration activities performed by the mineral industry. Three sources of information are reported and analyzed in this annual review of international exploration for 2012: 1) budgetary statistics expressed in U.S. nominal dollars provided by SNL Metals Economics Group (MEG) of Halifax, Nova Scotia; 2) regional and site-specific exploration activities that took place in 2012 as compiled by the USGS and 3) regional events including economic, social and political conditions that affected exploration activities, which were derived from published sources and unpublished discussions with USGS and industry specialists.

Mining Engineering↗