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USGS2007

Analysis of the sea otter ( Enhydra lutris ) reproductive tract: A methods manual

Reproduction in the female sea otter, Enhydra lutris, was relatively unstudied until Sinha et al. (1966) examined 140 reproductive tracts collected 1955-62 and used their findings to describe sea otter reproductive anatomy and biology. Two years later Sinha and Conaway (1968) published a more detailed paper on the ovary of the sea otter. These descriptive papers have been used as the basis for all subsequent studies of sea otter reproductive tracts. During biological collections of sea otters in the 1960s and 70s a large number of female carcasses became available to wildlife biologists. Using Sinha’s research, Schneider (1973) analyzed 1,482 female reproductive tracts to determine the timing of reproduction, gestation period, age of sexual maturity, fetal sex ratio and growth rate of otters in the Aleutian Islands. A similar study was conducted by Bodkin et al. (1993) on a sample of 177 females collected after the 1989 Exxon Valdez oil spill. Recently (von Biela 2007) examined 134 reproductive tracts obtained from beachcast and harvested otters across the three Alaskan population stocks as part of a Master’s thesis. As with most life history data, comparisons among and within populations that differ in status relative to equilibrium densities provide useful data with which to test hypotheses about the cause and effects of changes in demographic rates such as reproductive rate. However, in order to make such comparisons, methods used in different periods must be comparable. The purpose of this manual is to explicitly describe how to collect and analyze sea otter reproductive tracts for the determination of reproductive rate, pregnancy rate, percentage of mature females, and timing of reproduction so that the data will be directly comparable to that collected in the past. The techniques presented in this manual have been used to study sea otter populations over the last 50 years, and maintaining such consistency is essential to comparisons in the future. This manual is based on the methods of previous researchers and draws heavily on the published and unpublished works of James Bodkin, Karl Kenyon, Calvin Lensink, Daniel Mulcahy, Karl Schneider, and Akhouri Sinha. Most invaluable to the production of this manual were the direct communications with Karl Schneider and Dan Mulcahy. In each instance, researchers have communicated with each other to attain comparable methods. Recognizing that researchers in the future may not have this luxury, this guide has been produced to preserve the technique. In addition to using this manual, researchers should consult with colleagues experienced in the analysis of mammalian reproductive tracts, preferably specific to sea otters. Individuals are encouraged to contact V. von Biela with any questions. Sea otter reproductive tracts have most commonly come from either intentional sampling through harvests (Sinah et al. 1966, Schneider 1975) or unintentional large scale mortalities (e.g. the 1989 Exxon Valdez oil spill) (Bodkin et al. 1993). Carcasses and reproductive tracts can also be obtained through the collection of fresh beach cast carcasses. Analysis of reproductive tracts should consider the source of carcasses as samples representing either the “living” or “dead” sea otter population, as they may differ in reproductive parameters. In most cases the reproductive tracts are fixed in formalin or frozen (minimum of –20˚C) immediately after collection; both methods are acceptable for later analysis of the tissue. Immediate fixation is preferred as it is a necessary step in analysis. Uteri and ovaries are then examined to determine the current and past reproductive history of each individual. This manual also includes an example datasheet (Appendix A) and glossary (Appendix B).

Technical Report↗

USGS2012

Summer-time use of west coast U. S. National Marine Sanctuaries by migrating sooty shearwaters ( Puffinus griseus )

Non-breeding sooty shearwaters are the most abundant seabird in the California Current Large Marine Ecosystem (CCLME) during boreal spring and summer months. This, combined with relatively great energy demands, reliance on patchy, shoaling prey (krill, squid, and forage fishes), and unconstrained mobility free from central-place-foraging demands—make shearwaters useful indicators of ecosystem variability. During 2008 and 2009, we used satellite telemetry to evaluate shearwater ranging patterns throughout the CCLME and specifically within the US Exclusive Economic Zone (EEZ) among birds captured at three locations: Columbia River Plume, WA; Monterey Bay, CA; and Santa Barbara Channel, CA. Shearwaters ranged throughout the entire CCLME from southeast Alaska to southern Baja California, Mexico. Within the EEZ during 2008 and 2009, shearwaters spent 68% and 46% of time over the shelf (<200 m), 27% and 43% of time over the slope (200–1000 m), and 5% and 11% of time over the continental rise and abyssal regions (>1000 m), respectively. In 2008 and 2009, shearwaters spent 22% and 25% of their time in the EEZ within the five west coast National Marine Sanctuaries, respectively; high utilization occurred in non-sanctuary waters of the EEZ. Shearwater utilization distribution (based on the Brownianbridge movement model) among sanctuaries was disproportionate according to sanctuary availability (based on area) within the EEZ. Shearwaters utilized the Monterey Bay sanctuary (2008, 2009) and the Channel Islands sanctuary (2009) disproportionately more than other sanctuaries. Although all five sanctuaries were used by shearwaters, waters outside sanctuary zones appeared significantly more important and likely supported large aggregations of shearwaters. Utilization distributions among individual birds from three discrete capture locations were variable and revealed greater similarity in space-use sharing within capture-location groupings and during 2008 when shearwaters were more aggregated than in 2009. We identified several regional ‘‘habitat hotspot’’ areas, including the Columbia River Plume, Cape Blanco, Monterey Bay, Estero/San Luis Obispo Bays, and the eastern Santa Barbara Channel through the inner Southern California Bight.

California;Washington↗

USGS2019

Potential interaction of groundwater and surface water including autonomous underwater vehicle reconnaissance at Nolin River Lake, Kentucky, 2016

The U.S. Geological Survey collaborated with the U.S. Army Corps of Engineers, Louisville District, on a synoptic study of water quality at Nolin River Lake during August 2016. The purpose of the study was to develop a better understanding of the potential for interaction between groundwater and surface water at Nolin River Lake, Kentucky. Groundwater can have properties that are measurably different from those in adjacent surface water, and inflows and outflows can be an important component of water quality and quantity. An improved understanding of potential interaction of groundwater and surface water at Nolin River Lake may be used to refine lake-management strategies. This study (1) compiled and interpreted existing information to characterize the hydrogeological setting and implications for potential interaction of groundwater and surface water in the Nolin River Lake watershed; (2) collected transects of onsite water-quality parameters using an autonomous underwater vehicle (AUV) in areas with potential for interaction of groundwater and surface water, including five sites on Nolin River Lake and one site on the Nolin River; and (3) collected discrete water-quality and phytoplankton community data at the same six sites. A review of existing hydrogeologic information did not indicate the presence of karst features adjacent to or beneath Nolin River Lake that would facilitate groundwater interaction with the reservoir. Observations leading to this conclusion include (1) limestone that is adjacent to the shoreline and perhaps beneath the lake, is overlain with siliciclastic rocks and fine-grained sediment that inhibits infiltration and development of karst features that encourage rapid groundwater flow; (2) the geologic deposits surrounding the reservoir are described as having limited or no potential for development of karst features, some exceptions may exist in tributary valleys; (3) very few karst features were mapped within 1 mile of the reservoir or in the area currently occupied by the reservoir; and (4) faults that intersect the reservoir but may not possess hydraulic properties that cause the faults to be conduits for groundwater flow. Groundwater interaction with reservoir tributaries is likely more common in areas of the watershed upstream from Nolin River Lake where karst hydrogeology is prevalent. Results of water-quality surveys using an AUV from August 15 to 19, 2016, did not identify areas of anomalous values that might indicate groundwater inflows through preferential flow zones. Spatial distributions of water-quality parameters were generally uniform within each constant-depth layer. The constant-depth layers were selected to be above, within, and below the thermocline and ranged from the water surface to 25 feet. Surveys near the bottom of the reservoir that might have been more sensitive to groundwater inflows were not done because presurvey data were not available to indicate locations of obstacles that could ensnare the AUV. Water-quality data collected with the AUV did identify water-quality anomalies where stream tributaries were discharging to the reservoir. The discrete water-quality samples indicated uniformity among the five reservoir sites. The riverine site that is immediately upstream from Nolin River Lake, however, had some unique water-quality characteristics relative to sites on the reservoir. The highest concentrations of nitrate plus nitrite as nitrogen (0.145 milligrams per liter [mg/L]), total phosphorous (0.07 mg/L), chlorophyll a (36.1 micrograms per liter), and pheophytin a (10.2 micrograms per liter) were measured at the Nolin River Lake riverine site (site 2NRR20034). The concentrations of nutrients and chlorophyll a at the riverine site did exceed the 25th percentile of median concentrations measured by the U.S. Environmental Protection Agency (EPA) at other lakes and reservoirs in EPA level IV ecoregion 71a. Concentrations of most nutrients and chlorophyll a at the five reservoir sites also exceeded the 25th percentile of median concentrations in EPA level IV ecoregion 72h. The exception was the concentrations of total phosphorus as phosphorus at the reservoir sites that were at or below the 25th percentile of median concentrations measured by EPA (0.03 mg/L). Concentrations of orthophosphate as phosphorus were less than the method detection limit of 0.004 mg/L at all sites. The phytoplankton community in Nolin River Lake was almost exclusively (greater than 90 percent of total phytoplankton abundance) cyanobacteria, also known as blue-green algae. A species of Cylindrospermopsis dominated the cyanobacterial community at the five reservoir sites, while Chroococcus microscopicus was most abundant at the riverine site. Cyanobacterial cell densities ranged from 10,000 to 198,067,460 cells per liter in five areas in the reservoir and from 4,800 to 73,751,253 cells per liter at the riverine site. Multiple potential sources of water to Nolin River Lake include direct precipitation, overland flow, interflow, groundwater, and surface water. Understanding the exact contribution of each of these components to the water budget at Nolin River Lake may help the U.S. Army Corps of Engineers manage the water quality, water quantity, and biological communities in the reservoir. Additional hydrogeologic and water-quality data that builds on the results of this study may refine the inferences of this study; for example, deeper AUV surveys that target the largest fault zones might further the understanding of the potential for groundwater flow through those features. A complete understanding of the reservoir hydrology, however, may require the use of scientific methods intended for water bodies as large as Nolin River Lake, such as aerial infrared photography and imagery; water mass, chemical, and isotopic balance studies; geophysical measurements; and numerical simulations.

Kentucky↗

USGS2023

Selenium hazards in the Salton Sea environment—Summary of current knowledge to inform future wetland management

Quaternary marine and continental shales in the western United States are sources of selenium that can be loaded into the aquatic environment through mining, agricultural, and energy production processes. The mobilization of selenium from shales through agricultural irrigation has been recognized since the 1930s; however, discovery of deformities in birds and other wildlife using agricultural habitats during the 1980s spurred studies to determine the extent and effects of the contamination. Through these early studies, researchers determined that biota in the Salton Sea drainage basin was at risk from legacy selenium contamination in the Colorado River watershed. The Salton Sea and its surrounding managed and unmanaged wetlands provide vital inland habitat and trophic support for diverse assemblages of resident and migratory wildlife, and understanding regional selenium hazards for these trust species is a priority for many Federal and State agencies. The modern Salton Sea is a shallow, landlocked saline lake in Riverside and Imperial Counties (not shown) of California that is sustained by irrigation return and perennial river inflow. Changes in water transfer agreements under the 2003 Quantification Settlement Agreement (QSA) have resulted in reduced irrigation flow, declining lake levels, and the evolution of unmanaged wetlands in areas where drains and rivers no longer reach the Salton Sea. These wetlands provide additional habitat for some species of concern, but their potential to increase selenium hazards for trust species is largely unknown. From the 1980s to 2020, efforts to document selenium contamination and effects throughout the region have resulted in a considerable amount of selenium data from the Salton Sea and its surrounding drainage basin; however, no long-term (greater than 20 years), consistent sampling program has been established, and all data have been collected by different entities using a variety of protocols and analytical techniques. This lack of coordination has been previously documented in regional management plans and has led to difficulty in reliably assessing selenium hazards in the Salton Sea environment. This report provides a summary of the available disparate selenium information collected from water, sediment, and biota in the Salton Sea region since the 1980s and to identify data gaps that need to be filled to understand the potential effects of selenium on species of concern, including federally endangered desert pupfish ( Cyprinodon macularius ) and Yuma Ridgway’s Rail ( Rallus obsoletus yumanensis; formerly Yuma Clapper Rail, Rallus longirostris yumanensis ). Available data from the Salton Sea drainage basin show that water from the Colorado River has the lowest selenium concentration of all surface water sources. All other surface water flowing into the Salton Sea has elevated selenium concentrations due to evaporation and evapotranspiration that occurs in agricultural fields and associated water delivery infrastructure or leaching of selenium from irrigated farmland soils. The Salton Sea has lower selenium concentrations because of various biogeochemical processes that recycle selenium into the sediment or volatilize it to the atmosphere; however, these mechanisms are not well defined, and it is not clear if selenium cycling will change in response to possible changes in the oxidation state of the Salton Sea bottom waters as water levels decline. Agricultural drains have the highest average selenium concentrations, but few drains have been sampled since changes in irrigation practices have occurred (due to the 2003 QSA). Groundwater selenium concentrations are variable; some wells south of the Salton Sea have selenium concentrations as high as 300 micrograms per liter (µg/L), whereas selenium concentrations are below detection in other wells. Groundwater and surface-water geothermal discharge zones around the margins of the Salton Sea and in unmanaged wetlands have not been studied in detail, and published selenium measurements are not available for these surface features. Selenium concentrations in the sediment of the Salton Sea drainage basin are highest in wetland particulate organic matter and the Salton Sea lakebed, indicating that removal of selenium from the water to the sediment has been a primary mechanism for keeping selenium concentrations low in the water column. Sediment selenium concentrations in wetlands are lower than in the Salton Sea but higher than inflowing drains and rivers, indicating the lentic wetland sites also may be important sinks for selenium because of biogeochemical processes. Sediment selenium data have not been collected in agricultural drains since changes in irrigation practices occurred (due to the 2003 QSA), and it is unknown if selenium sequestration from the water column has changed in these systems. We divided biological data into broad taxonomic categories, including primary producers, invertebrates, herpetofauna, mammals, fishes, and birds to facilitate evaluation of selenium concentrations and spatiotemporal trends observed in the Salton Sea. Overall, selenium concentrations were substantially greater in algae samples compared to all vascular plant samples combined. Median selenium concentrations in several invertebrate taxa (Chironomidae, Formicidae, Corixidae, Corbiculidae and Nereididae, and Decapoda) exceeded the maximum suggested dietary threshold of 3.0–4.0 micrograms per gram (µg/g) dry weight (dw) for predators consuming invertebrates in aquatic food webs. The greatest number of samples were collected from fish, and selenium distributions among species and locations showed that the range for most samples was lower than the U.S. Environmental Protection Agency selenium criterion for aquatic life (8.5 µg/g dw whole body, 11.3 µg/g dw fillets). The median selenium concentrations for whole body fish were below the selenium criterion in most locations, except for bairdiella ( Bairdiella icistia ) from the Salton Sea and irrigation drains, a few individual tilapia spp. (family Cichlidae, including genera Tilapia, Oreochromis , and their hybrids) from the river and river outlets, and several western mosquitofish ( Gambusia affinis ) and sailfin molly ( Poecilia latipinna ) from irrigation drain outlets. For avian samples combined among years and locations, median selenium concentrations in livers from all families except waders and Ibis (family Threskiornithidae) were higher than levels expected to cause selenium toxicosis (10–20 µg/g dw), and all median egg concentrations were above or near 6.0 μg/g dw, which is a conservative threshold value for reproductive impairment. Most knowledge gaps we identified for water, sediment, and biota were interrelated, and the use of integrated approaches to address knowledge gaps can provide greater insight into the drivers behind selenium hazards. Integrated water, sediment, and biota studies could help identify cost-effective management solutions that serve multiple purposes. A comprehensive analysis of the hydrology, biogeochemistry, and food-web processes in wetlands and other habitats can inform predictive models to identify drivers of selenium bioavailability, uptake from the environment and subsequent trophic transfer, ultimately forming the basis for experimental habitat management manipulations to minimize selenium hazards to wildlife. Furthermore, a comprehensive, long-term sampling and analytical laboratory plan would enable comparison of data among different entities that are sampling at the Salton Sea. Such efforts are well suited to help fill knowledge gaps that preclude understanding of selenium hazards and future management options for biota using Salton Sea habitats, including newly formed wetlands throughout the region. All data compiled for this report are available in two U.S. Geological Survey data releases: Groover and others (2022) for water and sediment samples and De La Cruz and others (2022) for biological samples. The data releases include all publicly available data for selenium concentrations in water, sediment, and biological samples collected in and around the Salton Sea, including the Coachella and Imperial Valleys. The data releases also include previously unpublished data.

California↗

USGS2024

Evaluating effectiveness of restoration to address current stressors to riverine fish

River restoration programmes with the goal of conserving and rehabilitating inland fishes have a multi-decadal history, but evaluation and synthesis of past restoration actions have been limited by a lack of monitoring and reporting. Given that calls for both monitoring and systematic reviews of restoration have increased, we were interested in the influence that restoration has had on improving conditions for riverine fishes resulting from long-standing and increasingly prominent stressors. Our objectives were to (1) identify which stressors were targeted in river restoration efforts, (2) determine the proportion of published studies that articulate restoration goals and develop comparative monitoring designs for assessing the effects of restoration on fishes, and (3) conduct a meta-analysis to synthesise fish responses to restoration projects. We assessed restoration effectiveness for increasing fish density and richness from peer-reviewed papers published over the past decade using a global systematic review and meta-analysis. We found that restoration actions addressed major stressors primarily by improving in-stream habitat (37%), increasing in-stream longitudinal connectivity (26%) and increasing lateral floodplain connections (9%). Although 81% of studies had comparative monitoring designs (i.e., before/after and control/impact) and stated restoration goals, only 40% of those studies reported sufficient data to be included in the meta-analysis. Projects which increased in-stream connectivity had the largest positive effect size on fish density and richness compared to in-stream habitat improvements and increasing floodplain connections. Time since restoration and restoration size (i.e., geographical footprint) were not strong predictors of fish response effect sizes. Restoration effectiveness was highly variable among project types. Authors of studies included in the meta-analysis often identified spatial or temporal scale of monitoring, overriding catchment conditions, and recolonisation potential as sources of variability and effectiveness in restoration outcomes. Systematic reporting of these and other covariates may help guide processes in restoration evaluation and provide valuable research insights. Despite increased emphasis on monitoring, incomplete data reporting limited the number of studies that could be included for quantitative meta-analysis. Persistent emphasis on setting specific criteria (e.g., measurable outcomes of fish response) for restoration goals, project monitoring, data reporting, information sharing and collaborative projects is likely to continue to improve understanding of restoration effectiveness transferable to future endeavours. Our results can be used to support river restoration practitioners with evidence-based information to evaluate the cost–benefit ratio of competing restoration priorities, and inform restoration planning and implementation for riverine fish.

Freshwater Biology↗

USGS2002

Effects of fire and post-fire salvage logging on avian communities in conifer-dominated forests of the western United States

Historically, fire was one of the most widespread natural disturbances in the western United States. More recently, however, significant anthropogenic activities, especially fire suppression and silvicultural practices, have altered fire regimes; as a result, landscapes and associated communities have changed as well. Herein, we review current knowledge of how fire and postfire salvaging practices affect avian communities in conifer-dominated forests of the western United States. Specifically, we contrast avian communities in (1) burned vs. unburned forest, and (2) unsalvaged vs. salvage-logged burns. We also examine how variation in burn characteristics (e.g., severity, age, size) and salvage logging can alter avian communities in burns. Of the 41 avian species observed in three or more studies comparing early postfire and adjacent unburned forests, 22% are consistently more abundant in burned forests, 34% are usually more abundant in unburned forests, and 44% are equally abundant in burned and unburned forests or have varied responses. In general, woodpeckers and aerial foragers are more abundant in burned forest, whereas most foliage-gleaning species are more abundant in unburned forests. Bird species that are frequently observed in stand-replacement burns are less common in understory burns; similarly, species commonly observed in unburned forests often decrease in abundance with increasing burn severity. Granivores and species common in open-canopy forests exhibit less consistency among studies. For all species, responses to tire may be influenced by a number of factors including burn severity, fire size and shape, proximity to unburned forests, pre-and post-fire cover types, and time since fire. In addition, postfire management can alter species’ responses to burns. Most cavity-nesting species do not use severely salvaged burns, whereas some cavity-nesters persist in partially salvaged burns. Early post fire specialists, in particular, appear to prefer unsalvaged burns. We discuss several alternatives to severe salvage-logging that will help provide habitat for cavity nesters. We provide an overview of critical research questions and design considerations crucial for evaluating the effects of prescribed fire and other anthropogenic disturbances, such as forest fragmentation. Management of native avifaunas may be most successful if natural disturbance regimes, including fire, are permitted to occur when possible. Natural fires could be augmented with practices, such as prescribed fire (including high-severity fire), that mimic inherent disturbance regimes.

Studies in Avian Biology↗

USGS2020

Diversity of diatoms, benthic macroinvertebrates, and fish varies in response to different environmental correlates in Arctic rivers across North America

Climate change poses a significant threat to Arctic freshwater biodiversity, but impacts depend upon the strength of organism response to climate‐related drivers. Currently, there is insufficient knowledge about Arctic freshwater biodiversity patterns to guide assessment, prediction, and management of biodiversity change. As part of the Circumpolar Biodiversity Monitoring Program's first freshwater assessment, we evaluated diversity of diatoms, benthic macroinvertebrates, and fish in North American Arctic rivers. Alpha diversity was assessed in relation to temperature, water chemistry, bedrock geology, and glaciation history to identify important environmental correlates. Biotic composition was compared among groups to evaluate response to environmental gradients. Macroinvertebrate α‐diversity declined strongly with increasing latitude from 48°N to 82°N, whereas diatom and fish diversity peaked around 70°N without a clear latitudinal decline. Macroinvertebrate diversity was significantly positively related to air temperature. Diatom diversity was related to bedrock geology and temperature, whereas fish diversity was related to glaciation history. Fish and macroinvertebrate assemblages differed between sites in western Canada, where invertebrate composition was more variable, and Alaska, where fish composition was more variable. In sites with both diatom and macroinvertebrate data, diatom composition was distinct in Alaska, where richness was highest in former glacial refugia. Macroinvertebrate composition was distinct in lowest‐latitude eastern and high‐latitude western Canadian sites where temperature was highest. Temperature, precipitation, geology, calcium, and substrate size were important environmental correlates for diatoms and macroinvertebrates, although the relative importance of each correlate differed. Diatom taxa were most strongly associated with water chemistry, whereas benthic invertebrate composition related most strongly to precipitation and temperature. This large‐scale study provides the most substantial integration and analysis of river diatom, macroinvertebrate, and fish data from the North American Arctic to date. Findings suggest that macroinvertebrates will show the strongest response to climate‐related shifts in temperature, whereas diatoms and fish are more likely to respond to climate‐induced shifts in nutrients and hydraulic connectivity. However, significant gaps in data coverage limited our ability to reliably evaluate spatial patterns and detect change. These gaps could be reduced by improving collaborative efforts between the U.S.A. and Canada to harmonise future monitoring.

Arctic↗

USGS2010

Southeast Regional Assessment Project for the National Climate Change and Wildlife Science Center, U.S. Geological Survey

The Southeastern United States spans a broad range of physiographic settings and maintains exceptionally high levels of faunal diversity. Unfortunately, many of these ecosystems are increasingly under threat due to rapid human development, and management agencies are increasingly aware of the potential effects that climate change will have on these ecosystems. Natural resource managers and conservation planners can be effective at preserving ecosystems in the face of these stressors only if they can adapt current conservation efforts to increase the overall resilience of the system. Climate change, in particular, challenges many of the basic assumptions used by conservation planners and managers. Previous conservation planning efforts identified and prioritized areas for conservation based on the current environmental conditions, such as habitat quality, and assumed that conditions in conservation lands would be largely controlled by management actions (including no action). Climate change, however, will likely alter important system drivers (temperature, precipitation, and sea-level rise) and make it difficult, if not impossible, to maintain recent historic conditions in conservation lands into the future. Climate change will also influence the future conservation potential of non-conservation lands, further complicating conservation planning. Therefore, there is a need to develop and adapt effective conservation strategies to cope with the effects of climate and landscape change on future environmental conditions. Congress recognized this important issue and authorized the U.S. Geological Survey (USGS) National Climate Change and Wildlife Science Center (NCCWSC; http://nccw.usgs.gov/) in the Fiscal Year 2008. The NCCWSC will produce science that will help resource management agencies anticipate and adapt to climate change impacts to fish, wildlife, and their habitats. With the release of Secretarial Order 3289 on September 14, 2009, the mandate of the NCCWSC was expanded to address climate change-related impacts on all Department of the Interior (DOI) resources. The NCCWSC will establish a network of eight DOI Regional Climate Science Centers (RCSCs) that will work with a variety of partners to provide natural resource managers with tools and information that will help them anticipate and adapt conservation planning and design for projected climate change. The forecasting products produced by the RCSCs will aid fish, wildlife, and land managers in designing suitable adaptive management approaches for their programs. The DOI also is developing Landscape Conservation Cooperatives (LCCs) as science and conservation action partnerships at subregional scales. The USGS is working with the Southeast Region of the U.S. Fish and Wildlife Service (FWS) to develop science collaboration between the future Southeast RCSC and future LCCs. The NCCWSC Southeast Regional Assessment Project (SERAP) will begin to develop regional downscaled climate models, land cover change models, regional ecological models, regional watershed models, and other science tools. Models and data produced by SERAP will be used in a collaborative process between the USGS, the FWS (LCCs), State and federal partners, nongovernmental organizations, and academia to produce science at appropriate scales to answer resource management questions. The SERAP will produce an assessment of climate change, and impacts on land cover, ecosystems, and priority species in the region. The predictive tools developed by the SERAP project team will allow end users to better understand potential impacts of climate change and sea level rise on terrestrial and aquatic populations in the Southeastern United States. The SERAP capitalizes on the integration of five existing projects: (1) the Multi-State Conservation Grants Program project "Designing Sustainable Landscapes," (2) the USGS multidisciplinary Science Thrust project "Water Availability for Ecological Needs," (3) the USGS Southeast Pilot Project "Climate Change in the Southeastern U.S. and its Impacts on Bird Distributions and Habitats," (4) a sea-level rise impacts study envisioned jointly with the National Oceanic and Atmospheric Administration (NOAA), and (5) two USGS sea-level rise impact assessment projects that address inundation hazards and provide probabilistic forecasts of coastal geomorphic change. The SERAP will expand on these existing projects and include the following tasks, which were initiated in summer 2009: * Regionally downscaled probabilistic climate-change projections * Integrated coastal assessment * Integrated terrestrial assessment * Multi-resolution assessment of potential climate change effects on biological resources: aquatic and hydrologic dynamics * Optimal conservation strategies to cope with climate change The SERAP seeks to formally integrate these tasks to aid conservation planning and design so that ecosystem management decisions can be optimized for providing desirable outcomes across a range of species and environments. The following chapters detail SERAP's efforts in providing a suite of regional climate, watershed, and landscape-change analyses and develop the interdisciplinary framework required for the biological planning phases of adaptive management and strategic conservation. The planning phase will include the identification of conservation alternatives, development of predictive models and decision support tools, and development of a template to address similar challenges and goals in other regions. The project teams will explore and develop ways to link the various ecological models arising from each component. The SERAP project team also will work closely with members of the LCCs and other partnerships throughout the life of the project to ensure that the objectives of the project meet resources mangers needs in the Southeast.

Open-File Report↗

USGS2012

Habitat persistence for sedentary organisms in managed rivers: the case for the federally endangered dwarf wedgemussel (Alasmidonta heterodon) in the Delaware River

1. To manage the environmental flow requirements of sedentary taxa, such as mussels and aquatic insects with fixed retreats, we need a measure of habitat availability over a variety of flows (i.e. a measure of persistent habitat). Habitat suitability measures in current environmental flow assessments are measured on a ‘flow by flow’ basis and thus are not appropriate for these taxa. Here, we present a novel measure of persistent habitat suitability for the dwarf wedgemussel (Alasmidonta heterodon), listed as federally endangered in the U.S.A., in three reaches of the Delaware River. 2. We used a two-dimensional hydrodynamic model to quantify suitable habitat over a range of flows based on modelled depth, velocity, Froude number, shear velocity and shear stress at three scales (individual mussel, mussel bed and reach). Baseline potentially persistent habitat was quantified as the sum of pixels that met all thresholds identified for these variables for flows ≥40 m3 s−1, and we calculated the loss of persistently suitable habitat by sequentially summing suitable habitat estimates at lower flows. We estimated the proportion of mussel beds exposed at each flow and the amount of change in the size of the mussel bed for one reach. 3. For two reaches, mussel beds occupied areas with lower velocity, shear velocity, shear stress and Froude number than the reach average at all flows. In the third reach, this was true only at higher flows. Together, these results indicate that beds were possible refuge areas from the effects of these hydrological parameters. Two reaches showed an increase in the amount of exposed mussel beds with decreasing flow. 4. Baseline potentially persistent habitat was less than half the areal extent of potentially suitable habitat, and it decreased with decreasing flow. Actually identified beds and modelled persistent habitat showed good spatial overlap, but identified beds occupied only a portion of the total modelled persistent habitat, indicating either that additional suitable habitat is available or the need to improve habitat criteria. At one site, persistent beds (beds where mussels were routinely collected) were located at sites with stable substratum, whereas marginal beds (beds where mussels were infrequently collected or that were lost following a large flood event) were located in scoured areas. 5. Taken together, these model results support a multifaceted approach, which incorporates the effects of low and high flow stressors, to quantify habitat suitability for mussels and other sedentary taxa. Models of persistent habitat can provide a more holistic environmental flow assessment of rivers.

Freshwater Biology↗

USGS2017

Contaminants of emerging concern in the Great Lakes Basin: A report on sediment, water, and fish tissue chemistry collected in 2010-2012

Despite being detected at low levels in surface waters and sediments across the United States, contaminants of emerging concern (CECs) in the Great Lakes Basin are not well characterized in terms of spatial and temporal occurrence. Additionally, although the detrimental effects of exposure to CECs on fish and wildlife have been documented for many CECs in laboratory studies, we do not adequately understand the implications of the presence of CECs in the environment. Based on limited studies using current environmentally relevant concentrations of chemicals, however, risks to fish and wildlife are evident. As a result, there is an increasing urgency to address data gaps that are vital to resource management decisions. The U.S. Fish and Wildlife Service, in collaboration with the U.S. Geological Survey, is leading a Great Lakes Basin-wide evaluation of CECs (CEC Project) with the objectives to (a) characterize the spatial and temporal distribution of CECs; (b) evaluate risks to fish and wildlife resources; and (c) develop tools to aid resource managers in detecting, averting, or minimizing the ecological consequences to fish and wildlife that are exposed to CECs. This report addresses objective (a) of the CEC Project, summarizing sediment and water chemistry data collected from 2010 to 2012 and fish liver tissue chemistry data collected in 2012; characterizes the sampling locations with respect to potential sources of CECs in the landscape; and provides an initial interpretation of the variation in CEC concentrations relative to the identified sources. Data collected during the first three years of our study, which included 12 sampling locations and analysis of 134 chemicals, indicate that contaminants were more frequently detected in sediment compared to water. Chemicals classified as alkyphenols, flavors/ fragrances, hormones, PAHs, and sterols had higher average detection frequencies in sediment compared to water, while the opposite was observed for pesticides, pharmaceuticals, and plasticizers/flame retardants. The St. Louis River and Maumee River sampling locations had the most CEC detections in water and sediment, relative to other sites, as well as the largest number of maximum detected concentrations across all sites in the Basin. No consistent temporal CEC occurrence patterns were observed at locations sampled multiple times each day. Most appearances and increases in chemical concentrations in sediments occurred at sites immediately downstream from wastewater treatment plants and at sites with predominantly developed land use. The location with the most observed appearances and increases was the St. Louis River. Perfluorinated compounds were commonly detected in fish liver tissues with detections in 100% of both benthic and pelagic species. The occurrence of these chemicals in liver tissue of benthic and pelagic species was generally similar. Abstract

Great Lakes Basin↗

USGS2022

Influence of offshore oil and gas structures on seascape ecological connectivity

Offshore platforms, subsea pipelines, wells and related fixed structures supporting the oil and gas (O&G) industry are prevalent in oceans across the globe, with many approaching the end of their operational life and requiring decommissioning. Although structures can possess high ecological diversity and productivity, information on how they interact with broader ecological processes remains unclear. Here, we review the current state of knowledge on the role of O&G infrastructure in maintaining, altering or enhancing ecological connectivity with natural marine habitats. There is a paucity of studies on the subject with only 33 papers specifically targeting connectivity and O&G structures, although other studies provide important related information. Evidence for O&G structures facilitating vertical and horizontal seascape connectivity exists for larvae and mobile adult invertebrates, fish and megafauna; including threatened and commercially important species. The degree to which these structures represent a beneficial or detrimental net impact remains unclear, is complex and ultimately needs more research to determine the extent to which natural connectivity networks are conserved, enhanced or disrupted. We discuss the potential impacts of different decommissioning approaches on seascape connectivity and identify, through expert elicitation, critical knowledge gaps that, if addressed, may further inform decision making for the life cycle of O&G infrastructure, with relevance for other industries (e.g. renewables). The most highly ranked critical knowledge gap was a need to understand how O&G structures modify and influence the movement patterns of mobile species and dispersal stages of sessile marine species. Understanding how different decommissioning options affect species survival and movement was also highly ranked, as was understanding the extent to which O&G structures contribute to extending species distributions by providing rest stops, foraging habitat, and stepping stones. These questions could be addressed with further dedicated studies of animal movement in relation to structures using telemetry, molecular techniques and movement models. Our review and these priority questions provide a roadmap for advancing research needed to support evidence-based decision making for decommissioning O&G infrastructure.

Global Change Biology↗

USGS2017

Patterns and magnitude of flow alteration in California, USA

Quantifying the natural flow regime is essential for management of water resources and conservation of aquatic ecosystems. Understanding the degree to which anthropogenic activities have altered flows is critical for developing effective conservation strategies. Assessing flow alteration requires estimates of flows expected in the absence of human influence and under current land use and water management. There are several techniques to predict flows in streams and rivers; however, none have been applied to make predictions of natural flow conditions over large regions and time periods. We utilised machine learning statistical models to predict natural monthly flows (natural streamflows without the influence of water management or anthropogenic land use) in California from 1950 to 2015, using time-dependent and fixed watershed variables from reference stream gages. These models were then used to make estimates of mean, maximum and minimum monthly flows in all streams in the state. We compared observed flows measured at 540 stream gages across the state with expected natural flows at the same locations, to quantify the type, frequency and magnitude of flow alteration over the past 20 years (1996–2015). A gage was considered altered if an observed flow metric (monthly mean, annual maximum, annual minimum) fell outside the 80% prediction interval of the modelled flow estimate. We found that 95% of the 540 stream gages in California had at least 1 month of altered flows over the past 20 years, and 11% of gages were frequently altered (over two-thirds of the months recorded had evidence of altered flows). The type of alteration varied across the state with flows being either depleted, inflated or a mix of both at different times of the year. Most altered gages (68%) exhibited both depletion and inflation in monthly flows over the time period. Inflation of monthly mean flows was most prevalent during the summer months, while depletion of monthly flows was evident throughout the year. Type, frequency and magnitude of flow alteration varied by region. Flow depletion was present at >80% of gages in the North Coast and Central Coast, flow inflation was measured at >80% of gages in the South Coast and San Francisco Bay and both depletion and inflation were evident at >80% of gages in the Sacramento River and San Joaquin and Tulare regions. Annual maximum flows were consistently depleted and annual minimum flows were commonly inflated in the Sierra Nevada and Central Valley (Sacramento River and San Joaquin and Tulare regions). This is the first study to comprehensively assess flow alteration at stream gages across California. Understanding the patterns and degree of alteration can aid in prioritising streams for environmental flow assessment and developing conservation strategies for native freshwater biota.

California↗

USGS2000

Cassin's Sparrow (Aimophila cassinii) status assessment and conservation plan

Executive Summary Cassin’s Sparrow ( Aimophila cassinii ) is a grassland species endemic to the southwestern U.S. and northern Mexico. Its behavior and ecology have been shaped by these arid ecosystems and the health of its populations is dependent on the availability of grasslands that contain a shrub component. Populations of many grassland birds have experienced dramatic declines due to the loss and deterioration of grassland habitats, and there has been concern about the trends in Cassin’s Sparrow populations. Without better information about population trends, ecology, and effects of management activities, and without a stronger emphasis on grassland management, Cassin’s Sparrows and other grassland species may continue to experience declines. Little information exists about historic Cassin’s Sparrow population levels, and current population estimates for states in the breeding range are unknown. Significant survey-wide declines are documented by the Breeding Bird Survey (BBS) between 1966 and 1996. However, closer examination of these data suggest that the survey-wide trends are driven by population declines in the Edwards Plateau and South Texas Brushlands in Texas. No other areas within the core of its range or on the periphery show consistent, significant trends. In fact, there is consensus that in the core of its range in New Mexico Cassin’s Sparrow remains the most abundant breeding bird in grasslands with a shrub component. Understanding of population patterns in this species is complicated by large yearly fluctuations in distribution and numbers at any particular location, apparently in response to precipitation. This is particularly obvious in the periphery of its range. These dramatic fluctuations have hampered a clear assessment of population status, and our understanding has been confounded by the fact that the timing of BBS data collection does not always coincide with the peak breeding season of this species. The lack of information about the Cassin’s Sparrow’s status, ecology, and response to management activities, and the apparent declines indicated by BBS data, have been cause for concern. Habitat disturbance and degradation, mainly due to grazing and rangeland management practices such as shrub control, fire management, and planting of exotics, pose threats to Cassin’s Sparrow populations, as does habitat conversion through suburban development and agriculture. There is evidence that heavy grazing negatively affects populations, but the information is primarily available from the southwestern portion of its range (Arizona) and may not be applicable throughout the Cassin’s Sparrow’s entire range. Any management practice that results in complete removal of the shrub component, or loss of grass cover and an increase in shrub density beyond a threshold preferred by the species, also poses a threat. Lack of standardized or coordinated studies of Cassin’s Sparrow ecology and response to management practices in different geographic portions of its range has made it difficult to assess its status and make specific management recommendations. Limited data are available from the wintering grounds, and from its range (both breeding and wintering) in Mexico. The greatest needs are for determining of the causes of significant declines where they occur, determining of the effects of various management activities on Cassin’s Sparrow throughout its range, improved assessments of population and trends, and a better understanding of the annual population and distribution dynamics of this species, which shows such dramatic annual distributional fluctuations.

Wyoming, Nebraska, Kansas, Oklahoma,Texas, New Mex↗

USGS2013

Native Prairie Adaptive Management: a multi region adaptive approach to invasive plant management on Fish and Wildlife Service owned native prairies

Much of the native prairie managed by the U.S. Fish and Wildlife Service (FWS) in the Prairie Pothole Region (PPR) of the northern Great Plains is extensively invaded by the introduced cool-season grasses, smooth brome ( Bromus inermis ) and Kentucky bluegrass ( Poa pratensis ). Management to suppress these invasive plants has had poor to inconsistent success. The central challenge to managers is selecting appropriate management actions in the face of biological and environmental uncertainties. In partnership with the FWS, the U.S. Geological Survey (USGS) developed an adaptive decision support framework to assist managers in selecting management actions under uncertainty and maximizing learning from management outcomes. This joint partnership is known as the Native Prairie Adaptive Management (NPAM) initiative. The NPAM decision framework is built around practical constraints faced by FWS refuge managers and includes identification of the management objective and strategies, analysis of uncertainty and construction of competing decision models, monitoring, and mechanisms for model feedback and decision selection. Nineteen FWS field stations, spanning four states of the PPR, have participated in the initiative. These FWS cooperators share a common management objective, available management strategies, and biological uncertainties. Though the scope is broad, the initiative interfaces with individual land managers who provide site-specific information and receive updated decision guidance that incorporates understanding gained from the collective experience of all cooperators. We describe the technical components of this approach, how the components integrate and inform each other, how data feedback from individual cooperators serves to reduce uncertainty across the whole region, and how a successful adaptive management project is coordinated and maintained on a large scale. During an initial scoping workshop, FWS cooperators developed a consensus management objective: increase the composition of native grasses and forbs on native sod while minimizing cost. Cooperators agreed that decision guidance should be provided annually and should account for local, real-time vegetation conditions observed on the ground. Over the course of development, two prototypes of the decision framework were considered. The final framework recognized four alternative actions that managers could take in any given year: (1) Graze—targeted use of grazing ungulates to achieve defoliation, (2) Burn—application of prescribed fire as the single form of defoliation, (3) Burn/Graze—a combination treatment, and (4) Rest—no action. The study area included northern mixed-grass and tallgrass prairie. Native vegetation in mixed–grass prairie has a strong cool-season component and thus the dominant native species have a phenology similar to that of smooth brome and Kentucky bluegrass, making management of those species challenging. In contrast, tallgrass prairie has a strong warm-season native component, leading to an existence of cool-season windows, periods of time in the fall and spring when cool‐season invasive grass species are actively growing and vulnerable to damage via select management actions, but warm‐season grass species are not active and are thus less susceptible to damage via the same actions. This dichotomy between prairie types necessitated the development of separate but parallel decision support systems for mixed-grass and tallgrass biomes. Management units are parcels of native prairie that receive a single management treatment at any one time over their entire extent. At any particular time, the vegetation state of each management unit is characterized by the amount of cover of native grasses and forbs and the type of invasive grass that is dominant. In addition, each unit has a defoliation state which reflects the number of years since the last defoliation event and an index to how intensively the unit was managed during the previous 7 years. State-transition models are used to predict the state of a management unit in year t+1 from its state in year t and a prescribed management action that was applied between the two monitoring events. Alternative models are built around key uncertainties that make choice of a management action difficult. Three uncertainties revolve around whether the effect of management actions depends on (1) type of dominant invader, (2) past defoliation history, and (3) level of invasion. Two additional uncertainties are considered when choosing a management action for tallgrass units: (4) the effectiveness of grazing within the cool-season window as a surrogate for burning when smooth brome is the dominant invader, and (5) the differential effect of active management outside the window as compared to rest. Because data on the probability of transitioning from one state to another under the various models were lacking, expert opinion and elicitation were used to parameterize the models. In addition, cooperators participated in elicitation exercises to extract their beliefs regarding the value of having native prairie compared to the cost of achieving it. Quantifying the subjective expression of utility in this way allowed for mathematical representation of the management objective into an objective function. By maximizing the objective function, cumulative utility is maximized, leading to the identification of a sequence of decisions that will achieve the management objective. The NPAM system adopted a vegetation monitoring protocol that was rapid, inexpensive, and familiar to many of the cooperators. The monitoring protocol served three purposes: (1) determining current vegetation and defoliation states of each unit, (2) evaluating progress toward the management objective, and (3) assessing predictive performance of the alternative models. The management year runs from September 1 to August 31. Management can be applied anytime during that period and monitoring takes places from late June to mid-August. Cooperators enter vegetation data and management information into a centralized database by August 25 of each year. Given the current state of the system (vegetation and defoliation states) and the current understanding of the system (or the belief state), identifying the current best management decision is a matter of looking up the combination (that is, system state and belief state) in the appropriate (mixed-grass or tallgrass) optimal decision table. Given complete uncertainty at the outset of decision-making, initial assignment of equal belief weights to each model was believed reasonable. The decisions in the optimal decision table that correspond to the current belief state constitute the current optimal decision policy. By August 31 of each year, individual cooperators are provided with a recommended management action for each of their management units for the upcoming management year. Upon receiving the management recommendations for their units, managers consider the recommendation, along with other relevant information, and at some point during the year one of the management alternatives is carried out. This iterative cycle of making and implementing a management decision, predicting the response, monitoring the outcome, comparing predicted and observed outcomes, updating model weights, and recommending a management action for the next cycle is expected to result in an accumulation of weight on a representative model of system dynamics, thereby increasing understanding needed to effectively manage native prairies. The NPAM system is now entering its second full year of complete operation, and represents one of only a few fully implemented applications of adaptive management within the U.S. Fish and Wildlife Service. NPAM is truly unique in that it originated from the ground up as a result of the leadership and steadfastness of several refuge biologists and managers confronted with a common problem. These biologists recognized that working together across a large landscape presented perhaps the best opportunity for halting and reversing the invasion of native grasslands by non-native cool-season grasses. Importantly, the NPAM system encapsulates the collective thinking and experience of tens if not hundreds of individuals who have battled this vexing problem for much of their careers. The NPAM initiative is rooted in principles of adaptive management, thereby affording the opportunity for grassland managers to pursue management objectives while acquiring information to reduce uncertainty and improve future management. The project introduced a number of technical innovations that will serve as templates for conservation efforts throughout and beyond the U.S. Fish and Wildlife Service. First, NPAM is an on-the-ground implementation of active adaptive management—possibly the first of its kind in conservation management—in which recommended management actions result from a prospective analysis of future learning (Williams, 1996). Second, by the use of dynamic optimization, NPAM demonstrates how decisions can be made that take into account possible future transitions of the system. Third, NPAM demonstrates how models of partial controllability are an effective means of accommodating unpredictable circumstances that cause a manager to follow a different course than was intended. Finally, the database developed for NPAM is an unparalleled system that enables the rapid integration of data from the field for the generation of ‘just-in-time’ management recommendations. In all, NPAM provides an example of how a science-management partnership can be forged to achieve large-scale conservation objectives.

Minnesota;Montana;North Dakota;South Dakota↗

USGS2024

U.S. Geological Survey Karst Interest Group proceedings, Nashville, Tennessee, October 22-24, 2024

Karst hydrogeologic systems represent challenging and unique conditions to scientists studying groundwater flow and contaminant transport. Karst terrains are characterized by distinct and beautiful landscapes, caverns, and springs, and many of the exceptional karst areas are designated as national or state parks. The range and complexity of landforms and groundwater flow systems associated with karst terrains are enormous, perhaps more than any other aquifer type. The U.S. Geological Survey (USGS) Karst Interest Group (KIG), formed in 2000, is a loosely knit, grassroots organization of USGS and non-USGS scientists and researchers devoted to fostering better communication among scientists working on, or interested in, karst aquifers. The primary mission of the KIG is to encourage and support interdisciplinary collaboration and technology transfer among scientists working in karst areas. To accomplish its mission, the KIG has organized a series of workshops. To date (2024), nine KIG workshops, including the workshop documented in this report, have been held. The abstracts and extended abstracts provide a snapshot in time of past and current karst related studies. The USGS Water Availability and Use Science Program funded the workshop and proceedings. The planning committee for the ninth workshop includes Thomas D. Byl (USGS and Tennessee State University), Allan K. Clark (USGS), Laura M. DeMott (USGS), Eve L. Kuniansky (USGS, Emeritus), Benjamin V. Miller (USGS), and Lawrence E. Spangler (USGS, Emeritus). The workshop proceedings are edited by Eve L. Kuniansky and Lawrence E. Spangler. The field trip guide was produced by Benjamin V. Miller and Brian Ham (Tennessee Department of Environment and Conservation) and included in the proceedings from the KIG’s 2021 virtual workshop to be used on the optional field trip held on Thursday, October 24, 2024.

Open-File Report↗

USGS1984

Proceedings of a workshop on fish habitat suitability index models

One of the habitat-based methodologies for impact assessment currently in use by the U.S. Fish and Wildlife Service is the Habitat Evaluation Procedures (HEP) (U.S. Fish and Wildlife Service 1980). HEP is based on the assumption that the quality of an area as wildlife habitat at a specified target year can be described by a single number, called a Habitat Suitability Index (HSI). An HSI of 1.0 represents optimum habitat: an HSI of 0.0 represents unsuitable habitat. The verbal or mathematical rules by which an HSI is assigned to an area are called an HSI model. A series of Habitat Suitability Index (HSI) models, described by Schamberger et al. (1982), have been published to assist users in applying HEP. HSI model building approaches are described in U.S. Fish and Wildlife Service (1981). One type of HSI model described in detail requires the development of Suitability Index (SI) graphs for habitat variables believed to be important for the growth, survival, standing crop, or other measure of well-being for a species. Suitability indices range from 0 to 1.0, with 1.0 representing optimum conditions for the variable. When HSI models based on suitability indices are used, habitat variable values are measured, or estimated, and converted to SI's through the use of a Suitability Index graph for each variable. Individual SI's are aggregated into an HSI. Standard methods for testing this type of HSI model did not exist at the time the studies reported in this document were performed. A workshop was held in Fort Collins, Colorado, February 14-15, 1983, that brought together biologists experienced in the use, development, and testing of aquatic HSI models, in an effort to address the following objectives: (1) review the needs of HSI model users; (2) discuss and document the results of aquatic HSI model tests; and (3) provide recommendations for the future development, testing, modification, and use of HSI models. Individual presentations, group discussions, and group decision techniques were used to develop and present information at the meeting. A synthesis of the resulting concepts, results, and recommendations follows this preface. Subsequent papers describe individual tests of selected HSI models. Most of the tests involved comparison of values from HSI models or Suitability index (SI) curves with standing crop, as required contractually. Time and budget constraints generally limited tests to the use of data previously collected for other purposes. These proceedings are intended to help persons responsible for the development, testing, or use of HSI models by increasing their understanding of potential uses and limitations of testing procedures and models based on aggregated Suitability Indices. Problems encountered when testing HSI models are described, model performance during tests is documents, and recommendations for future model development and testing presented by the participants are listed and interpreted.

Biological Report↗

USGS2018

Global conservation status of turtles and tortoises (order Testudines)

We present a review and analysis of the conservation status and International Union for Conservation of Nature (IUCN) threat categories of all 360 currently recognized species of extant and recently extinct turtles and tortoises (Order Testudines). Our analysis is based on the 2018 IUCN Red List status of 251 listed species, augmented by provisional Red List assessments by the IUCN Tortoise and Freshwater Turtle Specialist Group (TFTSG) of 109 currently unlisted species of tortoises and freshwater turtles, as well as re-assessments of several outdated IUCN Red List assessments. Of all recognized species of turtles and tortoises, this combined analysis indicates that 20.0% are Critically Endangered (CR), 35.3% are Critically Endangered or Endangered (CR+EN), and 51.9% are Threatened (CR+EN+Vulnerable). Adjusting for the potential threat levels of Data Deficient (DD) species indicates that 56.3% of all data-sufficient species are Threatened. We calculated percentages of imperiled species and modified Average Threat Levels (ATL; ranging from Least Concern = 1 to Extinct = 8) for various taxonomic and geographic groupings. Proportionally more species in the subfamily Geoemydinae (Asian members of the family Geoemydidae) are imperiled (74.2% CR+EN, 79.0% Threatened, 3.89 ATL) compared to other taxonomic groupings, but the families Podocnemididae, Testudinidae, and Trionychidae and the superfamily Chelonioidea (marine turtles of the families Cheloniidae and Dermochelyidae) also have high percentages of imperiled species and ATLs (42.9–50.0% CR+EN, 73.8–100.0% Threatened, 3.44–4.06 ATL). The subfamily Rhinoclemmydinae (Neotropical turtles of the family Geoemydidae) and the families Kinosternidae and Pelomedusidae have the lowest percentages of imperiled species and ATLs (0%–7.4% CR+EN, 7.4%–13.3% Threatened, 1.65–1.87 ATL). Turtles from Asia have the highest percentages of imperiled species (75.0% CR+EN, 83.0% Threatened, 3.98 ATL), significantly higher than predicted based on the regional species richness, due to much higher levels of exploitation in that geographic region. The family Testudinidae has the highest ATL (4.06) of all Testudines due to the extinction of several species of giant tortoises from Indian and Pacific Ocean islands since 1500 CE. The family Testudinidae also has an ATL higher than all other larger polytypic families (≥ 5 species) of Reptilia or Amphibia. The order Testudines is, on average, more imperiled than all other larger orders (≥ 20 species) of Reptilia, Amphibia, Mammalia, or Aves, but has percentages of CR+EN and Threatened species and an ATL (2.96) similar to those of Primates and Caudata (salamanders).

Chelonian Conservation and Biology↗

USGS2009

Fire rehabilitation effectiveness: a chronosequence approach for the Great Basin

Federal land management agencies have invested heavily in seeding vegetation for emergency stabilization and rehabilitation (ES&R) of non-forested lands. ES&R projects are implemented to reduce post-fire dominance of non-native annual grasses, minimize probability of recurrent fire, quickly recover lost habitat for sensitive species, and ultimately result in plant communities with desirable characteristics including resistance to invasive species and resilience or ability to recover following disturbance. Land managers lack scientific evidence to verify whether seeding non-forested lands achieves their desired long-term ES&R objectives. The overall objective of our investigation is to determine if ES&R projects increase perennial plant cover, improve community composition, decrease invasive annual plant cover and result in a more desirable fuel structure relative to no treatment following fires while potentially providing habitat for Greater Sage-Grouse, a species of management concern. In addition, we provide the locations and baseline vegetation data for further studies relating to ES&R project impacts. We examined effects of seeding treatments (drill and broadcast) vs. no seeding on biotic and abiotic (bare ground and litter) variables for the dominant climate regimes and ecological types within the Great Basin. We attempted to determine seeding effectiveness to provide desired plant species cover while restricting non-native annual grass cover relative to post-treatment precipitation, post-treatment grazing level and time-since-seeding. Seedings were randomly sampled from all known post-fire seedings that occurred in the four-state area of Idaho, Nevada, Oregon and Utah. Sampling locations were stratified by major land resource area, precipitation, and loam-dominated soils to ensure an adequate spread of locations to provide inference of our findings to similar lands throughout the Great Basin. Nearly 100 sites were located that contained an ES&R project. Of these sites, 61 were seeded by using a drill, 27 were broadcast aerially, and 12 had a combination of both. We randomly sampled three burned and seeded, burned and unseeded, and unburned and unseeded locations in the vicinity of the fire, each within the same ecological site. We measured foliar cover of all plant functional groups (perennial or annual, shrub, grass, forb, native or introduced), biological soil crusts, and abiotic (bare soil and litter) variables using the line-point intercept protocol. Fuel loads and horizontal fuel continuity were measured. We applied linear mixed models to response variables (cover and density of plant groups) relative to the dependent variables (seeding treatments and precipitation/temperature relationships. Post-fire strengths with native perennial grasses or shrubs in mixes did not increase density or cover of these groups significantly relative to unseeded, burned areas. Seeded non-native perennial grasses and the shrub Bassia prostrata were effective in providing more cover in aerial and drill seedings. Seeded non-native perennial grass cover increased with increased annual precipitation regardless of seeding type. Seeding native shrubs, particularly Artemisia tridentata, did not significantly increase shrub cover in burned areas. Cover of undesirable non-native annual grasses was lower in drill seedings relative to unseeded areas but only at higher elevations. Seeding effectiveness after wildfire is unpredictable in drier, low elevation environments, and our findings indicate management objectives are more likely met when focusing efforts on higher elevation or higher precipitation locations where establishment of perennial grasses is more likely. On sites where potential for invasion and dominance of non-native annuals is high, such as lower and drier sites, intensive methods of restoration that include invasive plant control before seeding may be required. Where establishment of native perennial plants is the goal, managers might consider using native-only seed mixtures, because we found that the non-native perennials typically used in Great Basin restoration efforts are selected for their competitive nature and may reduce establishment of less competitive native species. Although we attempted to include information on livestock grazing history after seedings, we were unable to extract sufficient data from files to address this topic that may play an additional role in understanding native plant abundance post-fire seeding. Evaluation of drill and aerial seeding effects on fuel characteristics focused on two metrics that are standard inputs for fire behavior models, fuel load and fuel continuity. Fuel loads were evaluated separately for total fuel load biomass, and the individual components that sum to total biomass, namely herbaceous, shrub, shrub:herbaceous ratio, litter, 10-hour, and 100-hour fuel biomasses. Fuel continuity was evaluated using the following cover categories, total, annual grass, annual forb, perennial forb perennial grass, shrub, litter, vegetative interspace, and perennial interspace. Drill seeding did not affect fuel loads, except to reduce 10-hour fuels, probably due to mechanical destruction of dead and down fuels by the drill seeding equipment. Drill seeding did affect fuel continuity, specifically decreasing total plant cover by increasing perennial grass cover which suppressed annual grass and litter production resulting in a net decrease in continuity, but only at the elevations above approximately 1500m. Aerial seeding had no effect on any fuel load or fuel continuity category. For the Greater Sage-Grouse habitat study, we developed multi-scale empirical models of sage-grouse occupancy in 211 randomly located plots within a 40 million ha portion of the species’ range. We then used these models to predict sage-grouse habitat quality at 101 ES&R seeding projects. We compared conditions at restoration sites to published habitat guidelines. Sage-grouse occupancy was positively related to plot- and landscape-level dwarf sagebrush (Artemisia arbuscula, A. nova, A. tripartita) and big sagebrush steppe, and negatively associated with non-native grass and human development. The predicted probability of sage-grouse occupancy at treated plots was low on average (0.07–0.09) and was not significantly different from burned areas that had not been treated. Restoration was more often successful at higher elevation sites with low annual temperatures, high spring precipitation, and high plant diversity. No plots seeded after fire (n=313) met all overstory guidelines for breeding habitats, but approximately 50% met understory guidelines, particularly for perennial grasses. This trend was similar for summer habitat. Ninety-eight percent of treated plots did not meet winter habitat guidelines. Restoration actions in burned areas did not increase the probability of meeting most guideline criteria. The probability of meeting guidelines was influenced by a latitudinal gradient, local climate, and topography. Post-fire seeding treatments in Great Basin sagebrush shrublands generally have not created high quality habitat for sage-grouse. Understory conditions are more likely to be adequate than those of overstory, but in unfavorable climates, establishing forbs and reducing cheatgrass dominance is unlikely. Reestablishing sagebrush cover will require more than 20 years using the restoration methods of the past two decades. Given current fire frequencies and restoration capabilities, protection of landscapes containing a mix of dwarf sagebrush and big sagebrush steppe, minimal human development, and low non-native plant cover may provide the best opportunity for conservation of sage-grouse habitats. Our database of ES&R locations has used the Land Treatment Digital Library to archive data and location information regarding our study (see Pilliod and Welty 2013). This has contributed to two additional studies. One examined the potential spread of Bassia prostrata (aka Kochia prostrata; forage kochia) from ES&R project locations (Gray and Muir 2013). The second used remote sensing to determine the phenology of vegetation green-up on post-fire seeded sites (Sankey et al. 2013).

California;Idaho;Oregon;Utah↗