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USGS2005

Coral disease and health workshop: Coral histopathology II, July 12-14, 2005

The health and continued existence of coral reef ecosystems are threatened by an increasing array of environmental and anthropogenic impacts. Coral disease is one of the prominent causes of increased mortality among reefs globally, particularly in the Caribbean. Although over 40 different coral diseases and syndromes have been reported worldwide, only a few etiological agents have been confirmed; most pathogens remain unknown and the dynamics of disease transmission, pathogenicity and mortality are not understood. Causal relationships have been documented for only a few of the coral diseases, while new syndromes continue to emerge. Extensive field observations by coral biologists have provided substantial documentation of a plethora of new pathologies, but our understanding, however, has been limited to descriptions of gross lesions with names reflecting these observations (e.g., black band, white band, dark spot). To determine etiology, we must equip coral diseases scientists with basic biomedical knowledge and specialized training in areas such as histology, cell biology and pathology. Only through combining descriptive science with mechanistic science and employing the synthesis epizootiology provides will we be able to gain insight into causation and become equipped to handle the pending crisis. One of the critical challenges faced by coral disease researchers is to establish a framework to systematically study coral pathologies drawing from the field of diagnostic medicine and pathology and using generally accepted nomenclature. This process began in April 2004, with a workshop titled Coral Disease and Health Workshop: Developing Diagnostic Criteria co-convened by the Coral Disease and Health Consortium (CDHC), a working group organized under the auspices of the U.S. Coral Reef Task Force, and the International Registry for Coral Pathology (IRCP). The workshop was hosted by the U.S. Geological Survey, National Wildlife Health Center (NWHC) in Madison, Wisconsin and was focused on gross morphology and disease signs observed in the field. A resounding recommendation from the histopathologists participating in the workshop was the urgent need to develop diagnostic criteria that are suitable to move from gross observations to morphological diagnoses based on evaluation of microscopic anatomy. As a continuation of building the foundation and framework for coral disease diagnostics, the CDHC convened the Coral Disease and Health Workshop: Coral Histopathology II in Charleston, South Carolina, July 11-14, 2005. The workshop was hosted by the Department of Pathology and Laboratory Medicine at the Medical University of South Carolina, Charleston, SC which provided expertise, facilities and equipment in support of the workshop. All of the histological slides and related photographs used in the discussions were prepared and supplied by the IRCP. This workshop brought together 15 experts in veterinary and medical pathology and coral biology from national and international research institutes and government laboratories. The mission was to devise a standardized approach to examining microscopic anatomy and pathology of corals and a standardized nomenclature to facilitate accurate descriptions of the microscopic morphology of corals and enhance communication among specialists investigating causes of coral death. 2 The participants of this workshop deliberated for 3 days to refine the nomenclature for gross and microscopic anatomy of corals and systematically described microscopic changes associated with selected coral diseases. The findings and recommendations from the deliberations will be submitted to the research community for peer review. The standardized nomenclature and descriptions produced at this workshop will ultimately be made available to the scientific community through a variety of media including the World Wide Web. An exciting highlight of this meeting was provided by Professor Robert Ogilvie (MUSC Department of Cell Biology and Anatomy) when he introduced participants to a new digital technology that is revolutionizing histology and histopathology in the medical field. The Virtual Slide technology creates digital images of histological tissue sections by computer scanning actual slides in high definition and storing the images for retrieval and viewing. Virtual slides now allow any investigator with access to a computer and the web to view, search, annotate and comment on the same tissue sections in real time. Medical and veterinary slide libraries across the country are being converted into virtual slides to enhance biomedical education, research and diagnosis. The coral health and disease researchers at this workshop deem virtual slides as a significant way to increase capabilities in coral histology and a means for pathology consultations on coral disease cases on a global scale.

NOAA Technical Memorandum↗

USGS2004

Pattern detection in stream networks: Quantifying spatial variability in fish distribution

Biological and physical properties of rivers and streams are inherently difficult to sample and visualize at the resolution and extent necessary to detect fine-scale distributional patterns over large areas. Satellite imagery and broad-scale fish survey methods are effective for quantifying spatial variability in biological and physical variables over a range of scales in marine environments but are often too coarse in resolution to address conservation needs in inland fisheries management. We present methods for sampling and analyzing multiscale, spatially continuous patterns of stream fishes and physical habitat in small- to medium-size watersheds (500–1000 hectares). Geospatial tools, including geographic information system (GIS) software such as ArcInfo dynamic segmentation and ArcScene 3D analyst modules, were used to display complex biological and physical datasets. These tools also provided spatial referencing information (e.g. Cartesian and route-measure coordinates) necessary for conducting geostatistical analyses of spatial patterns (empirical semivariograms and wavelet analysis) in linear stream networks. Graphical depiction of fish distribution along a one-dimensional longitudinal profile and throughout the stream network (superimposed on a 10-metre digital elevation model) provided the spatial context necessary for describing and interpreting the relationship between landscape pattern and the distribution of coastal cutthroat trout ( Oncorhynchus clarki clarki ) in western Oregon, U.S.A. The distribution of coastal cutthroat trout was highly autocorrelated and exhibited a spherical semivariogram with a defined nugget, sill, and range. Wavelet analysis of the main-stem longitudinal profile revealed periodicity in trout distribution at three nested spatial scales corresponding ostensibly to landscape disturbances and the spacing of tributary junctions.

Oregon↗

USGS2005

Forestry practices and aquatic biodiversity: Fish

In the Pacific Northwest, fish communities are found in a diverse array of aquatic habitats ranging from the large coastal rivers of the temperate rainforests, to the fragmented and sometimes ephemeral streams of the xeric interior basins, and high-elevation streams and lakes in the mountainous areas (Rieman et al. 2003). Only high-elevation lakes and streams isolated above barriers to fish passage remained historically devoid of fish because they were never invaded following Pleistocene glaciation (Smith 1981). Despite this widespread distribution and once great population abundances, taxonomic diversity of fishes in these forested systems is naturally lower than in aquatic habitats in the eastern U.S. (Reeves, Bisson, and Dambacher 1998). Interactions among factors that influence species richness in aquatic systems (e.g., basin size, long-term stability of habitat, and barriers to colonization; Smith 1981) continue to influence the occurrence and persistence of fishes in these systems today. Consequently, the larger low-elevation rivers and estuaries support the greatest variety of fish species. In the high-elevation tributary streams, fish communities are less complex because these aquatic systems were less climatically and geologically stable, and fish populations were smaller and more prone to local extirpation. Furthermore, barriers to fish passage inhibited dispersal and colonization (Smith 1981). Streams in forested landscapes generally support salmon and trout, Oncorhynchus spp., whitefish Prosopium spp., sculpins Cottus spp., suckers Catostomus spp., and minnows (Cyprinidae), but in some of the colder streams, chars (e.g., Salvelinus confluentus and Salvelinus malma ) and lampreys (Petromyzontidae)may also occur (Rieman et al. 2003). Although biodiversity defined in terms of fish species richness is low in the Pacific Northwest, intraspecific variability is high, and polytypic fish species are common in the diverse aquatic habitats of the region. For example, the salmonids in the coastal rivers and streams, and the larger interconnected streams, rivers, and lakes of the interior exhibit a variety of ecotypes and migratory life histories (Healey 1986; Trotter 1989; Larson and McIntire 1993; Northcote 1997). This life-history variation appears to be associated with adaptation to spatial and temporal variation in environment (e.g., Schaffer and Elson 1975; Carl and Healey 1984; Beacham and Murray 1987), and there is some evidence of the genetic heritability of life-history traits (Carl and Healey 1984; Gharrett and Smoker 1993; Hankin, Nicholas, and Downey 1993). Persistence of any level of biological organization (e.g., life-history type, population, metapopulation, subspecies, species, community) is related to the interaction of environmental and biological components, and intraspecific diversity is a means of spreading risk ( sensu den Boer 1968) of extirpation in dynamic environments (Gresswell 1999). Unfortunately, despite the broad distribution and extensive intraspecific diversity, persistence of native fishes is uncertain in the Pacific Northwest. Many populations of anadromous salmonids, once synonymous with vigorous biological communities throughout the region, are threatened with extinction (Nehlsen, Williams, and Lichatowich 1991; Frissell 1993; Thurow, Lee, and Rieman 1997). Furthermore, over half of the native taxa in the Columbia River Basin are either listed under the Endangered Species Act, are being considered for listing, or are deemed sensitive by the management agencies (Lee et al. 1997; Thurow, Lee, and Rieman 1997). Potamodromous species like bull trout Salvelinus confluentus are estimated to occur as strong populations in less than 5% of their potential range (Rieman, Lee, and Thurow 1997). Although not currently listed under the endangered species list, the coastal cutthroat trout Oncorhynchus clarki is managed as a sensitive species in Oregon and California (Hall, Bisson, and Gresswell 1997). Native non-game fishes have rarely been monitored, but populations of species such as large-scale suckers ( Catostomus macrocheilus ), squawfish ( Ptychocheilus umpquae ), and Pacific lamprey ( Lampetra tridentata ) also are declining in some drainages (Oregon Department of Fish and Wildlife, unpublished data).

Pacific Northwest↗

USGS2000

Nutrient pollution of coastal rivers, bays, and seas

Over the past 40 years, antipollution laws have greatly reduced discharges of toxic substances into our coastal waters. This effort, however, has focused largely on point-source pollution of industrial and municipal effluent. No comparable effort has been made to restrict the input of nitrogen (N) from municipal effluent, nor to control the flows of N and phosphorus (P) that enter waterways from dispersed or nonpoint sources such as agricultural and urban runoff or as airborne pollutants. As a result, inputs of nonpoint pollutants, particularly N, have increased dramatically. Nonpoint pollution from N and P now represents the largest pollution problem facing the vital coastal waters of the United States. Nutrient pollution is the common thread that links an array of problems along the nations coastline, including eutrophication, harmful algal blooms, dead zones, fish kills, some shellfish poisonings, loss of seagrass and kelp beds, some coral reef destruction, and even some marine mammal and seabird deaths. More than 60 percent of our coastal rivers and bays in every coastal state of the continental United States are moderately to severely degraded by nutrient pollution. This degradation is particularly severe in the mid Atlantic states, in the southeast, and in the Gulf of Mexico. A recent report from the National Research Council entitled Clean Coastal Waters: Understanding and Reduc- ing the Effects of Nutrient Pollution concludes that: Nutrient over-enrichment of coastal ecosystems generally triggers ecological changes that decrease the biologi- cal diversity of bays and estuaries. While moderate N enrichment of some coastal waters may increase fish production, over-enrichment generally degrades the marine food web that supports commercially valuable fish. The marked increase in nutrient pollution of coastal waters has been accompanied by an increase in harmful algal blooms, and in at least some cases, pollution has triggered these blooms. High nutrient levels and the changes they cause in water quality and the makeup of the algal community are detrimental to the health of coral reefs and the diversity of animal life supported by seagrass and kelp communi- ties. Research during the past decade confirms that N is the chief culprit in eutrophication and other impacts of nutrient over-enrichment in temperate coastal waters, while P is most problematic in eutrophication of freshwa- ter lakes. Human conversion of atmospheric N into biologically useable forms, principally synthetic inorganic fertilizers, now matches the natural rate of biological N fixation from all the land surfaces of the earth. Both agriculture and the burning of fossil fuels contribute significantly to nonpoint flows of N to coastal waters, either as direct runoff or airborne pollutants. N from animal wastes that leaks directly to surface waters or is volatilized to the atmosphere as ammonia may be the largest single source of N that moves from agricultural operations into coastal waters. The National Research Council report recommended that, as a minimum goal, the nation should work to reverse nutrient should be taken to assure that the 40 percent of coastal areas now ranked as healthy do not develop symptoms of nutrient pollution in 10 percent of its degraded coastal systems by 2010 and 25 percent of them by 2020. Also, action should be taken to assure that the 40 percent of coastal areas now ranked as healthy do not develop symptoms of nutrient pollution. Meeting these goals will require an array of strategies and approaches tailored to specific regions and coastal ecosystems. There is an urgent need for development and testing of techniques that can reliably pinpoint the sources of N pollutants to an estuary. For some coastal systems, N removal during treatment of human sewage may be sufficient to reverse nutrient pollution. For most coastal systems, however, the solutions will be more complex and may involve controls on N compounds emitted during fossil fuel combustion as well as incentives to reduce over-fertilization of agricul- tural fields and nutrient pollution from animal wastes in livestock feedlot operations.

Alabama, California, Connecticut, Delaware, Florid↗

USGS1994

San Francisco Bay/delta regional monitoring program plankton and water quality pilot study, 1993, in 1993 Annual Report, San Francisco Estuary Regional Monitoring Program for Trace Substances: San Francisco Estuary Institute

The pilot program described here is motivated by a fundamental principle of the Regional Monitoring Strategy, namely “...the development of data that will provide information on status and trends in the Estuary.” As pointed out in the Strategy, knowledge of status and trends serves two primary purposes: (1) to become aware of or anticipate deleterious conditions in the Estuary, and (2) to assess the effectiveness of management actions. This program addresses these two purposes by focusing on aquatic resources, one of the five key management issues identified by the Comprehensive Conservation and Management Plan and central to the Regional Monitoring Strategy. It also bears on at least two of the other management issues - pollutants and water use. A regional monitoring program must cover many types of resources, including pelagic and benthic channel habitat, shoal habitat, wetlands, river channels, sloughs, and small bays and harbors. This particular program centers on the pelagic channel habitat. However, because of the intimate connection between channel habitat and many or most of these other habitats, channel measurements reflect to some extent the status of and trends in other resource types as well. A primary aim of this program is to provide a high-resolution description of critical aspects of habitat quality, which can be used along with other information (1) to determine the suitability of habitat for aquatic resources; (2) to monitor responsiveness of the habitat to freshwater flow variability; and (3) to provide a context for understanding pollutant distributions. In a single transect, measurements are made throughout the water column at up to 37 stations to define physical (salinity, temperature, suspended particulate matter, and light penetration), chemical (dissolved oxygen) and biological (chlorophyll a ) characteristics that influence both chemical and biological reactions. A second aim of the program is to investigate planktonic indicators of ecosystem structure and function. Phytoplankton production is the major single source of energy for the San Francisco Bay food web. Our measurements of chlorophyll and light penetration can be used to provide an estimate of this production, and therefore the availability of food for organisms at higher trophic levels. Phytoplankton community composition at the species level, which can be a sensitive indicator of habitat change, is also a standard component of this program. Community composition data enable detection of species known to be responsible for harmful or nuisance algal blooms. In 1993, two other indicators were also evaluated, photosynthetic parameters and water column respiration . Photosynthetic parameters partially characterize the physiological state of the phytoplankton and may provide indirect evidence of nutrient deficiency or the effects of pollutants. Water column respiration serves as a simple integrated measure of organic matter metabolism by the plankton, including bacteria, phytoplankton, and microzooplankton. It therefore reflects the total supply of organic matter, whether from photosynthesis, tidal marsh efflux, point sources, or upstream in the Delta. These biological indicators therefore contain much information about the flow of energy into the food web.

California↗

USGS1997

Introduced species: A significant component of human-caused global change

Biological invasions are a widespread and significant component of human-caused global environmental change. The extent of invasions of oceanic islands, and their consequences for native biological diversity, have long been recognized. However, invasions of continental regions also are substantial. For example, more than 2,000 species of alien plants are established in the continental United States. These invasions represent a human-caused breakdown of the regional distinctiveness of Earth's flora and fauna—a substantial global change in and of itself. Moreover, there are well- documented examples of invading species that degrade human health and wealth, alter the structure and functioning of otherwise undisturbed ecosystems, and/or threaten native biological diversity. Invasions also interact synergistically with other components of global change. notably land use change. People and institutions working to understand, prevent, and control invasions are carrying out some of the most important—and potentially most effective—work on global environmental change.

New Zealand Journal of Ecology↗

USGS2016

Response of fish assemblages to decreasing acid deposition in Adirondack Mountain lakes

The CAA and other federal regulations have clearly reduced emissions of NOx and SOx, acidic deposition, and the acidity and toxicity of waters in the ALTM lakes, but these changes have not triggered widespread recovery of brook trout populations or fish communities. The lack of detectable biological recovery appears to result from relatively recent chemical recovery and an insufficient period for species populations to take advantage of improved water quality. Recovery of extirpated species’ populations may simply require more time for individuals to migrate to and repopulate formerly occupied lakes. Supplemental stocking of selected species may be required in some lakes with no remnant (or nearby) populations or with physical barriers between the recovered lake and source populations. The lack of detectable biological recovery could also be related to our inability to calculate measures of uncertainty or error and, thus, examine temporal changes or differences in populations and community metrics in more depth (e.g., within individual lakes) using existing datasets. Indeed, recovery of brook trout populations and partial recovery of fish communities are documented in several lakes of the region, both with and without human intervention. Multiple fish surveys (annually or within the same year) or the use of mark and recapture methods within individual lakes would help alleviate the issue (provide measures of error for key fishery metrics) within the context of a more focused sampling strategy. Efforts to evaluate and detect recovery in fish assemblages from streams may be more effective than in lakes because various life stages, species’ populations, and entire assemblages are easier to quantify, with known levels of error, in streams than in lakes. Such long-term monitoring efforts could increase our ability to detect and quantify biological recovery in recovering (neutralizing) surface waters throughout the Adirondack Region.

New York↗

USGS2019

Supporting the development and use of native plant materials for restoration on the Colorado Plateau (Fiscal Year 18 Report)

Introduction A primary focus of the Colorado Plateau Native Plant Program (CPNPP) is to identify and develop appropriate native plant materials (NPMs) for current and future restoration projects. Multiple efforts have characterized the myriad challenges inherent in providing appropriate seed resources to enable effective, widespread restoration and identified a broad suite of research activities to provide the information necessary to overcome those challenges (e.g., Plant Conservation Alliance 2015; Breed et al. 2018). Many of the most complex information needs relate to identifying the appropriate plant species and populations that can successfully establish in dryland environments, like the Colorado Plateau, where low and highly variable precipitation is standard. Providing this information requires synergistic research efforts in which results from earlier investigations inform the design of subsequent investigations. Southwest Biological Science Center’s (SBSC’s) research activities in FY18 followed the FY18 Statement of Work (“Research supporting native plant materials development for the Colorado Plateau Native Plant Program, FY18”) to support a research framework that is continually adapting based on the needs of the restoration community and results from previous investigations; the long-term research framework is now outlined in the 2019-2023 5-Year Research Strategy (discussed below; hereafter referred to as the 5-Year Research Strategy). This research framework provides support for the National Seed Strategy for Rehabilitation and Restoration (Plant Conservation Alliance, 2015), Department of Interior Secretarial Order #3347 (Conservation Stewardship and Outdoor Recreation), and Bureau of Land Management Leadership Priority #1 (Create a conservation stewardship legacy second only to Teddy Roosevelt). The overall focus of activities in FY18 centered on landscape genetics and planning for common garden and other research projects. These activities were supported by two biological technicians that were hired and trained by Dr. Rob Massatti and Dr. Daniel Winkler. Many of the field-related activities, including plant trait measurement and seed/tissue collecting, were assigned to these technicians, which freed Dr. Massatti to work on other research objectives, including the time-consuming activities of processing and analyzing genetic data. A major challenge to field work in FY18 was the drought conditions that pervaded the Plateau during the spring field season. Due to low winter and spring precipitation, many plant communities did not green up in the spring, which prevented the biological technicians from collecting plant trait data, tissues samples, and seeds in many areas. To cope with the dry conditions, the technicians searched sites across a wider range of environmental space and considered a broader suite of species from which to collect data (i.e., species that may be included in research projects in future years). Monsoonal precipitation starting in July supported a late summer/fall field season and allowed the technicians to follow a more normal work plan. While Dr. Massatti was the only scientist supported by the SBSC-CPNPP agreement in FY18, other scientists, including Drs. John Bradford, Seth Munson, Mike Duniway, Sasha Reed, Daniel Winkler, and Jayne Belnap, spent a considerable amount of time discussing individual projects and the newly developed 5-Year Research Strategy. Some of these discussions resulted in a publication by Dr. Winkler, in addition to a large group of researchers, practitioners, and others who work on the Colorado Plateau, concerning the restoration challenges facing the Plateau into the future and the types of efforts that may support successful restoration (Winkler et al., 2018).

Colorado↗

USGS2017

Assessing the risk of non-native marine species in the Bering Sea

Invasive species are one of the leading global conservation concerns, which can have strong, negative impacts on ecosystems, vulnerable species, and valuable natural resources. Arctic regions have experienced a relatively low number of biological introductions to date. Their geographical remoteness, cold waters, and presence of sea ice present challenging conditions for both non-native organisms and the vessels that transport them, presumably leading to low rates of introduction and establishment. However, observed increases in water temperatures reductions in sea ice, and projected increases in shipping traffic are expected to render arctic marine regions more susceptible to the arrival and colonization of marine invasives. Risk assessments for these Arctic regions are important to inform management and monitoring priorities by determining which species pose the greatest risk. To this end, we developed a ranking system for non-native marine species and used this system to assess the risk of non-native species to the Bering Sea. Using species’ published physiological tolerances, we mapped habitat suitability under current and future climate scenarios to identify geographic areas of current and future concern. In addition, we described shipping traffic from commercial and fishing vessels to identify ports of entry for non-native species. Collectively, these analyses identify which marine species have the greatest risk for invasion, where in the Bering Sea invasion risk and species establishment is greatest, and which ports are most likely to serve as an entry point for marine invasives into Alaska’s Bering Sea. The ranking system we developed for non-native marine species consists of 33 questions grouped into five categories. The first four categories evaluate a species’ ability to arrive and establish in the Bering Sea, its reliance on humans for introductions, its biology, and its impacts on ecological and human systems. The fifth category is not included in the total ranking score, but provides information on management considerations. The ranking system has methods to account for data deficiencies and calculates these deficiencies to allow readers to weigh the lack of knowledge with the ranking score. We prioritized non-native species for ranking based on their geographic proximity to the Bering Sea. We evaluated 46 species and ranking scores ranged from 29.1 to 74.3 (out of a possible 100), with highest scores indicating greatest risk. Taxonomy at the level of phylum did not explain variation in ranking values, likely due to the substantial biological variation relative to our ranking criteria among members of the same phylum. To investigate where non-native species may survive and persist in the Bering Sea, we compared species’ temperature and salinity thresholds to environmental conditions of the Bering Sea. Environmental conditions were obtained from three Regional Ocean Modeling Systems (ROMS) and investigated under two time periods: current (2003-2012) and mid-century (2030-2039). We identified potential habitat for survival for 42 species, and potential habitat for reproduction for 29 species. Under current conditions, all species had temperature and salinity thresholds that would allow survival in the Bering Sea for at least part of the year, and most species (79% to 83%) had thresholds that would allow for survival year-round. For species with temperature and salinity thresholds unsuitable for survival in the Bering Sea, winter temperatures appear to be the limiting factor. Most species had six to nine weeks of suitable conditions for reproduction. Future increases in water temperatures are expected to open more habitat for marine invasives. Two of the three ROMs project an increase in the number of non-native species that would be able to survive year-round by mid-century. Moreover, models project between 37% and 60% of the Bering Sea shelf habitat to become more suitable under mid-century climate condition.

Alaska↗

USGS2021

Sedex hydrothermal systems triggered upheavals to marine chemistry and mass extinctions: Applications for ore genesis research and mineral exploration

New USGS research reveals that the discharge of metal-rich brine that formed sedex deposits on ancient seafloors had profound effects on global ocean chemistry and biologic evolution. For example, brine expulsion caused short-duration positive excursions (“spikes”) in the global marine Sr isotope record. While these spikes are unexplained by conventional oceanic models, our chronostratigraphic correlations of major sedex events, combined with mass balance evidence and oceanographic modeling, confirm that the flux of radiogenic Sr from sedex brines during ore formation was sufficient to cause these once enigmatic 87Sr/86Sr spikes. Recognition that the timing of peak 87 Sr/ 86 Sr spikes correlates exactly with global δ 13 C (and δ 18 O) spikes, climate change, deposition of metal-rich black shales and ironstones, metal-induced malformation (teratology) of marine organisms, and mass extinctions, establishes a causal relationship between sedex deposits and these dramatic events in earth history. The relationships among these features are not fully understood. However, our new model demonstrates that the flux of key biolimiting nutrients and metals contained in sedex brines exceeds that of the total modern riverine flux to the ocean. Undoubtably, these immense nutrient fluxes spurred ocean eutrophication, which, ultimately, through a series of positive feedback mechanisms, may be a previously unrecognized trigger of global ocean anoxic events (OAEs) that produced these chemical and biological perturbations. A derivative result from this integrative research is the recognition that OAEs resulted in the formation of “bathtub rim” deposits at redox boundaries along continental margins that concentrated various redox sensitive critical minerals. For example, we have identified midcontinent phosphorite deposits that contains heavy REE grades and tonnages that rival any REE deposit in the world. The recognition that sedex-forming fluid expulsion events are recorded in the global marine isotopic, geologic, and biological records, defines a new approach to the study of and exploration for sedex deposits. Traditional ore genesis research, coupled with chronostratigraphic correlation and high-resolution 87 Sr/ 86 Sr isotope chemostratigraphy can be used to answer long-standing questions about geologic processes responsible for formation of these extraordinary deposits. This approach allows us to constrain, for the first time, the age, duration, and fluxes of fluids and metals vented into the ocean by these giant hydrothermal systems. Accordingly, the fact that large mineralizing events are recorded in the marine sedimentary record opens the tantalizing prospect that we have the ability to conduct effective resource assessments and define prospective basins anywhere in the world. This innovative approach allows for identification of favorable stratigraphic ages and basins and remote evaluation of the size (and, thus, the mineral potential) of undiscovered mineral deposits. This methodology could be applied on regional basin-wide assessments, to evaluate sedimentary basin prospectivity, resource favorability of specific horizons therein, and to the evaluation of the potential of early-stage prospects.

Geological Society of Nevada Newsletter↗

USGS2020

Cascadia Margin cold seeps: Subduction zone fluids, gas hydrates, and chemosynthetic habitats

Priority Geographic Area: The outer continental shelf and upper continental slope from Canada/U.S. border offshore Washington State to the Mendocino Fracture Zone (Northern California), entirely within the U.S. Exclusive Economic Zone (EEZ), from the outermost shelf to at least 2000 m water depth (Figure 1). Description of Priority Area: Since 2015, over a thousand water column gas plumes originating at seafloor gas seeps have been discovered landward of the Cascadia deformation front (e.g., Embley et al., 2016; Johnson et al., 2015, 2019; Merle and Embley, 2016; NA-95 Cruise Report, 2018; Riedel et al., 2018), adding to those that had long been known on Hydrate Ridge (e.g., Heeschen et al., 2003; Tréhu et al., 2004). The recently-discovered seeps stretch from offshore Vancouver Island to the Mendocino Fracture Zone and from the outer shelf to ~2000 m water depth, occurring both landward and seaward of the nominal limit for gas hydrate stability zone on the upper continental slope (Figure 1). Hundreds of seeps likely remain undiscovered. Water column imaging is incomplete both within the target geographic area and farther seaward, between the 2000 m isobath and the deformation front, which is the subject of an imaging study described in a white paper by Watt et al. The recently-discovered Cascadia Margin cold seeps partially overlap an important active margin gas hydrate province (Spence et al., 2001; Tréhu et al., 2003, 2004), as well as an area where sediments on the North American plate are folded and faulted and affected by fluids generated in the subduction complex beneath the Cascadia forearc (e.g., Saffer and Tobin, 2011). Several Ocean Drilling Program expeditions have focused on hydrate systems offshore Vancouver and Oregon (e.g., Riedel et al., 2009; Tréhu et al., 2004) and on the connection between the shallow and deep hydrogeologic systems. Cabled observatories now continuously monitor physical, chemical, and venting processes on south Hydrate Ridge (OOI; e.g., Philip et al., 2016a) and offshore Vancouver Island (NEPTUNE; e.g. Römer et al., 2016). Outside of these well-studied gas hydrate areas, a subset of the recently-discovered Cascadia seeps, including some that we visited with R/V Falkor in 2019 (e.g., https://schmidtocean.org/cruise/methane-seeps-at-edge-of-hydrate-stability/), also likely emit methane associated with shallow subseafloor gas hydrate systems. Other seeps are delivering not only methane, but also deep-derived gases (Baumberger et al., 2018, 2020) to the seafloor. Many Cascadia Margin seeps have also been recognized at water depths too shallow (e.g., 175 m) to be connected to gas hydrate dynamics. These seeps are postulated to be emitting gas and fluids that originated deep in accretionary wedge before migrating up normal faults generated during forearc extension associated with large earthquakes (Johnson et al., 2019). Only a small fraction of the recently discovered U.S. Cascadia Margin water column gas plumes has so far been verified by ROVs (Hercules from E/V Nautilus in 2016 and 2018; SuBastian from R/V Falkor in 2018 and 2019) to correspond to seafloor seeps. Careful scientific mapping, investigation, and sampling at the seeps have also been limited (e.g., Baumberger et al., 2018, 2020; Merle and Embley, 2016; Seabrook et al., 2018; Greinert et al. 2019). This white paper focuses on expanding exploration of already-identified U.S. Cascadia Margin cold seeps through a multipronged and multidisciplinary discovery program that could be accomplished with a variety of NOAA assets. The goals of the proposed exploration activities are to develop high-resolution maps of seep fields from deep ocean vehicles; to verify (and sample) seafloor gas emissions at the locations of water column plumes for compositional and isotopic studies; to map, sample, and conduct analyses on chemosynthetic communities and deep-sea coral habitats near seep sites to document species distributions and habitats as a function of depth and latitude along the margin; to collect seep geologic samples that can constrain the timing of methane emissions through geochronology; and to record environmental data (e.g., CTD) near the seafloor and in the water column above the seeps. Seafloor mapping using shipboard systems (multibeam/backscatter) would be needed to characterize seafloor features near seep sites. Water column imaging (EK60/80 and/or multibeam WCD data) conducted before and after seafloor explorations would capture active methane plumes and constrain temporal variations in seep emissions (e.g., Kannberg et al., 2013; Philip et al., 2016a, 2016b), which are known to vary on time scales as rapid as tidal cycles on this margin (e.g., Römer et al., 2016). What are the characterization and data needs in this area? Check all that apply: __x_ Biology, Geology, Physical Oceanography, Chemistry ___ Marine Archaeology ___ Other Provide a list or brief description of the data needed within this area, from your perspective: 1. Water column backscatter to image active gas plumes 2. High-resolution multibeam bathymetry, seafloor backscatter, and shallow sub-bottom imaging 3. Visual characterization and ground truthing of potential seeps, including high-resolution mapping and photography from near-seafloor vehicles; collection of seep-associated species, corals, sediments, authigenic carbonates, gases, and seawater Describe relevance to national security, conservation, and/or the economy: The Cascadia margin seeps provide significant ecosystem services, including habitat for commercially important fishes and support for diversity along the continental margin. Methane seeps are also biological hotspots for krill, plankton, and crustaceans, which in turn sustain higher trophic levels (e.g., whales). Methane-derived authigenic carbonates serve as a hard substrate for deep-sea corals and sponges on millennial time scales. The studies proposed here will elucidate the relationship among seep environments, deep-sea corals, sponges, fisheries, and other organisms and provide new insight into subduction zone and hydrate-associated fluids in this important seismogenic zone. The studies address fishery management concerns and inform future conservation of sensitive species (e.g., deep-sea corals) and benthic habitats. From your perspective, what makes this area unique? The Cascadia Margin seeps are a critical component of the leaky margin that stretches from Baja California to the Aleutian Arc along the Pacific coastline of North America. Cold seeps have been intensely studied on the Gulf of Mexico and U.S. Atlantic passive margins with a focus on chemosynthetic communities, deep-sea corals, and leakage of microbially-generated and/or thermogenic hydrocarbons; however, the recently-discovered Cascadia Margin seeps, as well as active margin seep systems in general, remain more poorly characterized. Such seeps not only contribute to the ocean carbon cycle (e.g., Pohlman et al., 2011), thereby fueling the base of the food chain in these settings, but also emit subduction zone fluids that provide clues about processes within the seismogenic zone and the accretionary complex. The Cascadia seeps area allows both biological (e.g., benthic habitats, coral distributions) and physical processes (e.g., generation of subduction zone fluids) to be studied along both depth (perpendicular to the deformation front) and latitudinal gradients.

California, Oregon, Washington↗

USGS2024

Ten quick tips to get you started with Bayesian statistics

Bayesian statistics is a framework in which our knowledge about unknown quantities of interest (especially parameters) is updated with the information in observed data, though it can also be viewed as simply another method to fit a statistical model. It has become popular in many branches of biology. For context, five of the ten most cited papers in Web of Science with keywords 'Bayesian statistics' are related to biology (as of August 19, 2024). Bayesian statistics is particularly valuable for biology because it allows researchers to incorporate prior knowledge, handle complex systems, and work effectively with limited or messy data. However, most biologists are trained in frequentist techniques, and the learning curve to become fluent in Bayesian statistics may be perceived as too time-consuming to undertake, or the prospect of adopting an unfamiliar statistical framework can simply appear too daunting. We provide a list of 10 tips to help you get started with Bayesian statistics. You can also refer to the Glossary for definitions of the technical terms. This paper isn’t just for newcomers; even those with some experience in Bayesian methods may find it a useful roadmap to design, conduct, and publish Bayesian analyses. We’ve drawn mainly on our experience teaching and working with ecologists, but we hope these tips will be relevant to a broader audience of biologists. For those seeking to deepen their understanding, we point to more comprehensive resources that offer in-depth exploration of Bayesian statistics.

HAL Open Science↗

USGS2025

Ecosystems

The Fifth National Climate Assessment updates the evidence regarding how climate change influences ecosystems, biological diversity, and the implications for changes to critical ecosystem services—as noted in the key messages above (McElwee et al., 2023). Large-scale transformational changes to ecosystems are occurring, including—but not limited to—land-use conversion, hydrological alteration, and fire regimes. Implications of such transformational change include ecosystem capacity to maintain biological diversity and ecosystem services, impacting recreational opportunities (e.g., hunting and fishing, birding, ecotourism) and agriculture production (McElwee et al., 2023). A central tenet of the Fifth National Climate Assessment regarding ecosystems was the shifts to alternative states and how the Resist-Accept-Direct (RAD) framework may guide the adaptive management of ecosystems moving forward (Lynch et al., 2022). Nebraska is in the northern Great Plains, where extremes in climate and resulting ecosystem processes are experienced (Knapp et al., 2023). Pressures on ecosystems to provide essential services, including healthy soil and water to benefit humans and animals, will inevitably impact economic development, urban and rural communities, and fish and wildlife populations as climate change continues (Knapp et al., 2023). All ecosystems will be impacted in Nebraska, but aquatic systems—wetlands, aquifers, lakes, streams, and rivers—may be most impacted, given the scarcity of water as human demand (i.e., agriculture and a growing population) persists and increases (Bathke et al., 2014). Major knowledge gaps remain regarding how fish and wildlife populations will persist in changing environments. Past changes, including large-scale land conversion, water delivery systems, and water storage (construction of reservoirs), suggest that some species can adapt to novel environments and shift distributions. However, many more species may be maladapted to the expected changes in climate. Species may be unable to move to suitable habitats, and biological constraints under rapidly changing conditions may impede adaptation— resulting in extirpation and potential extinction. Further, changing conditions open multiple pathways for invasive species and novel diseases, impacting native fish populations, wildlife populations, and human health.

Nebraska↗

USGS2008

GAP Analysis Bulletin Number 15

The Mission of the Gap Analysis Project (GAP) <http://gapanalysis.nbii.gov> is to promote conservation by providing broad geographic information on biological diversity to resource managers, planners, and policy makers who can use the information to make informed decisions. As part of the National Biological Information Infrastructure (NBII) <http://www.nbii.gov>?a collaborative program to provide increased access to data and information on the nation?s biological resources--GAP data and analytical tools have been used in hundreds of applications: from basic research to comprehensive state wildlife plans; from educational projects in schools to ecoregional assessments of biodiversity. The challenge: keeping common species common means protecting them BEFORE they become threatened. To do this on a state or regional basis requires key information such as land cover descriptions, predicted distribution maps for native animals, and an assessment of the level of protection currently given to those plants and animals. GAP works cooperatively with Federal, state, and local natural resource professionals and academics to provide this kind of information. GAP activities focus on the creation of state and regional databases and maps that depict patterns of land management, land cover, and biodiversity. These data can be used to identify ?gaps? in conservation--instances where an animal or plant community is not adequately represented on the existing network of conservation lands. GAP is administered through the U.S. Geological Survey. Through building partnerships among disparate groups, GAP hopes to foster the kind of collaboration that is needed to address conservation issues on a broad scale. For more information, contact: John Mosesso National GAP Director 703-648-4079 Kevin Gergely National GAP Operations Manager 208-885-3565

GAP Bulletin↗

USGS2003

Challenges to reestablishment of free-ranging populations of black-footed ferrets

The black-footed ferret ( Mustela nigripes ) of North America is critically endangered due in part to its extreme specialization on formerly stable and abundant prairie dogs ( Cynomys ). Its close relative, the Siberian polecat ( M. eversmannii ) seems to have been subjected to a varying environment that was not conducive to specialization. One source of environmental variation in Asian steppes was plague (caused by Yersina pestis ), which was absent from North America. Introduction of plague to North America presents serious challenges to ferret recovery. Partial solutions to other biological and political problems have been found, resulting in improved production in captivity, increased survival post-release, and thriving populations in plague-free South Dakota.

Comptes Rendus - Biologies↗

USGS2001

Landscape determinants of nonindigenous fish invasions

Much has been written about the influence of exotic or nonindigenous species on natural habitats and communities of organisms, but little is known of the physical or biological conditions that lead to successful invasion of native habitats and communities by exotics. We studied invasivity factors in headwater streams of the Susquehanna River West Branch, which drains portions of the northern Appalachian Plateau. A replicated (two major tributaries) 3 × 3 factorial design was used to determine landscape effects of size (stream order) and quality (land use) on abiotic (physical and chemical) and biotic (fish community structure and function) stream attributes. Seven (21%) of thirty-four fish species (brown trout, common carp, mimic shiner, bluegill, smallmouth bass, fantail darter, and banded darter) collected in the eighteen streams sampled were nonindigenous to the basin. Watershed size (stream orders 1, 3, and 5) significantly affected stream geomorphologic and habitat variables (gradient, width, depth, current velocity, diel water temperature, bank overhang, canopy cover, and woody debris density) but not water-quality variables, while land use in watersheds (conservation, mining, and agriculture) significantly affected measured water-quality variables (alkalinity and concentrations of manganese, calcium, chloride, nitrate, and total dissolved solids) but not stream physical or habitat quality. Both watershed size and land use affected fish-community variables such as presence of particular species, species density, species diversity, tolerance diversity, and mean fish size, but in both cases the effect was transparent to native-origin status of fish species. No relationships were found between occurrence of nonindigenous species in watersheds and trophic structure or functional diversity. Therefore, the hypothesis that reduced species diversity increases vulnerability to nonindigenous species was not supported. However, the spatial variation associated with both water-quality and habitat-quality factors was greater in streams with mixed (those with nonindigenous species) than with exclusively native assemblages. These findings suggest that the mechanism for successful invasion by nonindigenous or exotic species is through change in water or habitat quality associated with human or natural disturbances, such as agriculture and mining activities in watersheds. Biotic factors appear to play no or a lesser role in the invasibility of northern Appalachian lotic systems.

Biological Invasions↗

USGS2015

Non-native and native organisms moving into high elevation and high latitude ecosystems in an era of climate change: new challenges for ecology and conservation

Cold environments at high elevation and high latitude are often viewed as resistant to biological invasions. However, climate warming, land use change and associated increased connectivity all increase the risk of biological invasions in these environments. Here we present a summary of the key discussions of the workshop ‘Biosecurity in Mountains and Northern Ecosystems: Current Status and Future Challenges’ (Flen, Sweden, 1–3 June 2015). The aims of the workshop were to (1) increase awareness about the growing importance of species expansion—both non-native and native—at high elevation and high latitude with climate change, (2) review existing knowledge about invasion risks in these areas, and (3) encourage more research on how species will move and interact in cold environments, the consequences for biodiversity, and animal and human health and wellbeing. The diversity of potential and actual invaders reported at the workshop and the likely interactions between them create major challenges for managers of cold environments. However, since these cold environments have experienced fewer invasions when compared with many warmer, more populated environments, prevention has a real chance of success, especially if it is coupled with prioritisation schemes for targeting invaders likely to have greatest impact. Communication and co-operation between cold environment regions will facilitate rapid response, and maximise the use of limited research and management resources.

Biological Invasions↗

USGS2018

Influences of the invasive tamarisk leaf beetle (Diorhabda carinulata) on avian diets along the Dolores River in Southwestern Colorado USA

The tamarisk leaf beetle ( Diorhabda carinulata ), introduced from Eurasia in 2001 as a biological control agent for the invasive plant Tamarix ramosissima , has spread widely throughout the western USA. With D. carinulata now very abundant, scientists and restoration managers have questioned what influence this introduced arthropod might have upon the avian component of riparian ecosystems. From 2009 through 2012 we studied the consequences of biological invasions of the introduced tamarisk shrub and tamarisk leaf beetles on the diets of native birds along the Dolores River in southwestern Colorado, USA. We examined avian foraging behavior, sampled the arthropod community, documented bird diets and the use of invasive tamarisk shrubs and tamarisk leaf beetles by birds. We documented D. carinulata abundance, on what plants the beetles occurred, and to what degree they were consumed by birds as compared to other arthropods. We hypothesized that if D. carinulata is an important new avian food source, birds should consume beetles at least in proportion to their abundance. We also hypothesized that birds should forage more in tamarisk in the late summer when tamarisk leaf beetle larvae are more abundant than in early summer, and that birds should select beetle-damaged tamarisk shrubs. We found that D. carinulata composed 24.0 percent (± 19.9–27.4%) and 35.4% biomass of all collected arthropods. From the gut contents of 188 birds (25 passerine species), only four species ( n = 11 birds) contained tamarisk leaf beetle parts. Although D. carinulata comprised one-quarter of total insect abundance, frequency of occurrence in bird gut contents was only 2.1% by abundance and 3.4% biomass. Birds used tamarisk shrubs for foraging in proportion to their availability, but foraging frequency did not increase during the late summer when more tamarisk leaf beetles were present and birds avoided beetle-damaged tamarisk shrubs. Despite D. carinulata being the most abundant arthropod in the environment, these invasive beetles were not frequently consumed by birds and seem not to provide a significant contribution to avian diets.

Colorado↗