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At least 703 records · Page 39Linked to original sources
USGS2019

Screening and biosecurity for White-nose Fungus Pseudogymnoascus destructans (Ascomycota: Pseudeurotiaceae) in Hawai‘i

Introduced pathogens causing emerging infectious diseases (EIDs) are serious contemporary threats to animal, plant, and ecosystem health. The invasive fungus, Pseudogymnoascus destructans , has established populations of European origin in North America, resulting in mass mortality of several hibernating bat species. Extensive monitoring for this pathogen exists in Europe and North America, but limited screening is taking place elsewhere. We report results from cave surveys on Hawai‘i Island. Substrates in 10 lava-tube caves with elevations up to 3,045 m were swabbed providing samples for screening P. destructans . Interior cave air temperatures spanned temperatures suitable for the growth and survival of P. destructans . Using quantitative PCR, all 85 samples tested were negative for the presence of P. destructans . The biology of the Hawaiian hoary bat ( Lasiurus cinereus semotus ) in relation to its unusual use of high elevation caves is discussed because these bats could come into contact with P. destructans should it arrive in Hawai‘i. Large numbers of cave enthusiasts visit Hawaiian caves from across the world after having been inside caves elsewhere including areas with P. destructans . Thus, resource managers in Hawai‘i and other remote areas may want to consider the potential for P. destructans to arrive unintentionally via human activities. Biosecurity measures and periodic screening for P. destructans are especially important in Hawai‘i given the presence of high elevation caves with suitable temperatures for its growth. If P. destructans was introduced to Hawaiian caves, it could affect the local fauna but also act as a source population for colonisations elsewhere.

Hawaii↗
USGS1984

Assessment of ground-water contamination by coal-tar derivatives, St. Louis Park area, Minnesota

Operation of a coal-tar distillation and wood-preserving facility in St. Louis Park, Minnesota, during 1918-72 contaminated ground water with coal-tar derivatives and inorganic chemicals. Coal-tar derivatives entered the groundwater system through three major paths: (1) Spills and drippings that percolated to the water table, (2) surface runoff and plant process water that was discharged to wetlands south of the former plant site, and (3) movement of coal tar directly into bedrock aquifers through a multiaquifer well on the site. In the drift, Platteville, and St. Peter aquifers, ground water flows laterally from west to east and vertically downward. Near the former plant site, creosote-like organic fluids have migrated vertically downward through the drift and are being partially dissolved by ground water. Ground water has preferentially mobilized low-molecular-weight compounds such as phenolic compounds, alkyl-benzenes, and naphthalene, although polynuclear aromatic hydrocarbons as heavy as benzo(a)pyrene have been mobilized at low concentrations. Sorption of high-molecular-weight compounds has retarded their migration down the hydraulic gradient compared to low-molecular-weight compounds in the plume. Some simple phenolic compounds are being degraded to methane and carbon dioxide by bacteria under anaerobic conditions in the drift-PlattevilleSt. Peter aquifer system. Other low-molecular-weight aromatic compounds are apparently being degraded by aerobic bacteria at the periphery of the plume where oxygen is available. Intermediate degradation products such as volatile fatty acids are likely present, but complete conversion of the organic contaminants to innocuous inorganic substances has not been demonstrated. Near and south of 36th and Wooddale Avenues, contaminants enter the St. Peter aquifer where the Glenwood confining unit has been eroded in a buried bedrock valley. Contaminants previously entered the Prairie du Chien-Jordan aquifer through at least one multiaquif er well (W38). Other sources of contaminants and the low concentrations of contaminants hamper delineation of the maximum areal extent of contaminants that are resistant to biologic degradation. These biorefractory compounds will probably continue to migrate down the hydraulic gradients in the drift and Platteville and St. Peter aquifers. Of particular concern with respect to the health risk to humans are the polynuclear aromatic hydrocarbons, which are a major constituent of coal tar and are found in municipal wells near the site that are completed in the Prairie du Chien-Jordan aquifer. The Prairie du Chien-Jordan aquifer lies 250 to 500 feet below land surface and is relatively well protected from nearsurface sources of contamination by overlying rocks. However, the aquifer has been contaminated since at least 1932 because coal-tar derivatives have entered the aquifer through multiaquifer wells. The most significant single source of contamination in the aquifer is a well drilled on the site in 1917 (well W23) that has contained liquid coal-tar since at least 1958. The introduction, dissolution, and movement of this coal-tar in ground water has contaminated nearby municipal wells. The composition of the tar in well W23, and the ratio of concentrations of individual compounds in water from well W23 to those in municipal well SLP15, are consistent with known hydrologic, chemical, and biologic processes, and the conclusion that contaminants in well SLP15 are due primarily to contaminants introduced at well W23. Most of the major polynuclear aromatic hydrocarbons in the tar, although slightly soluble in water and strongly sorbed by aquifer materials, have moved greater distances at higher concentrations than have the lower-molecular-weight, more soluble compounds such as phenolic compounds and naphthalene. The latter are apparently being degraded by bacteria. The direction and rate of contaminant movement within the Prairie du Chien-Jordan aquifer changes with time because the ground-water-flow system continually adjusts to hydraulic stresses caused by ground-water withdrawals and flow through multiaquifer wells. Contaminants can move rapidly through the Prairie du Chien-Jordan because the upper part of the aquifer is a carbonate rock having fracture and solution-channel permeability, low effective porosity, and relatively small surface area for sorption. Consequently, the concentration and composition of contaminants in water pumped from individual industrial and municipal wells completed in the aquifer fluctuate with time. Although contaminants have been in the aquifer for at least 50 years and their spatial distribution is complex, concentrations remain highest near their points of introduction through multiaquifer wells near and on the site of the former plant. Contaminants reached the Ironton-Galesville aquifer through at least two deep multiaquifer wells (W23 and W38), but the extent of contamination in this aquifer, and in the underlying Mount Simon-Hinckley aquifer, is not known.

Minnesota↗
USGS2015

Forecasting the effects of fertility control on overabundant ungulates: White-tailed deer in the National Capital Region

Overabundant populations of ungulates have caused environmental degradation and loss of biological diversity in ecosystems throughout the world. Culling or regulated harvest is often used to control overabundant species. These methods are difficult to implement in national parks, other types of conservation reserves, or in residential areas where public hunting may be forbidden by policy. As a result, fertility control has been recommended as a non-lethal alternative for regulating ungulate populations. We evaluate this alternative using white-tailed deer in national parks in the vicinity of Washington, D.C., USA as a model system. Managers seek to reduce densities of white-tailed deer from the current average (50 deer per km 2 ) to decrease harm to native plant communities caused by deer. We present a Bayesian hierarchical model using 13 years of population estimates from 8 national parks in the National Capital Region Network. We offer a novel way to evaluate management actions relative to goals using short term forecasts. Our approach confirms past analyses that fertility control is incapable of rapidly reducing deer abundance. Fertility control can be combined with culling to maintain a population below carrying capacity with a high probability of success. This gives managers confronted with problematic overabundance a framework for implementing management actions with a realistic assessment of uncertainty.

PLoS ONE↗
USGS2006

Species richness and patterns of invasion in plants, birds, and fishes in the United States

We quantified broad-scale patterns of species richness and species density (mean # species/km 2 ) for native and non-indigenous plants, birds, and fishes in the continental USA and Hawaii. We hypothesized that the species density of native and non-indigenous taxa would generally decrease in northern latitudes and higher elevations following declines in potential evapotranspiration, mean temperature, and precipitation. County data on plants ( n = 3004 counties) and birds ( n =3074 counties), and drainage (6 HUC) data on fishes ( n = 328 drainages) showed that the densities of native and non-indigenous species were strongly positively correlated for plant species ( r = 0.86, P < 0.0001), bird species ( r = 0.93, P <0.0001), and fish species ( r = 0.41, P <0.0001). Multiple regression models showed that the densities of native plant and bird species could be strongly predicted (adj. R 2 = 0.66 in both models) at county levels, but fish species densities were less predictable at drainage levels (adj. R 2 = 0.31, P <0.0001). Similarly, non-indigenous plant and bird species densities were strongly predictable (adj. R 2 = 0.84 and 0.91 respectively), but non-indigenous fish species density was less predictable (adj. R 2 = 0.38). County level hotspots of native and non-indigenous plants, birds, and fishes were located in low elevation areas close to the coast with high precipitation and productivity (vegetation carbon). We show that (1) native species richness can be moderately well predicted with abiotic factors; (2) human populations have tended to settle in areas rich in native species; and (3) the richness and density of non-indigenous plant, bird, and fish species can be accurately predicted from biotic and abiotic factors largely because they are positively correlated to native species densities. We conclude that while humans facilitate the initial establishment, invasions of non-indigenous species, the spread and subsequent distributions of non-indigenous species may be controlled largely by environmental factors.

Biological Invasions↗
USGS2016

Evaluation of the functional roles of fungal endophytes of Phragmites australis from high saline and low saline habitats

Non-native Phragmites australis decreases biodiversity and produces dense stands in North America. We surveyed the endophyte communities in the stems, leaves and roots of collections of P. australis obtained from two sites with a low and high salt concentration to determine differences in endophyte composition and assess differences in functional roles of microbes in plants from both sites. We found differences in the abundance, richness and diversity of endophytes between the low saline collections (18 species distributed in phyla Ascomycota, Basidiomycota and Stramenopiles (Oomycota); from orders Dothideales, Pleosporales, Hypocreales, Eurotiales, Cantharellales and Pythiales; Shannon H = 2.639; Fisher alpha = 7.335) and high saline collections (15 species from phylum Ascomycota; belonging to orders Pleosporales, Hypocreales, Diaporthales, Xylariales and Dothideales; Shannon H = 2.289; Fisher alpha = 4.181). Peyronellaea glomerata , Phoma macrostoma and Alternaria tenuissima were species obtained from both sites. The high salt endophyte community showed higher resistance to zinc, mercury and salt stress compared to fungal species from the low salt site. These endophytes also showed a greater propensity for growth promotion of rice seedlings (a model species) under salt stress. The results of this study are consistent with the ‘habitat-adapted symbiosis hypothesis’ that holds that endophytic microbes may help plants adapt to extreme habitats. The capacity of P. australis to establish symbiotic relationships with diverse endophytic microbes that enhance its tolerance to abiotic stresses could be a factor that contributes to its invasiveness in saline environments. Targeting the symbiotic associates of P. australis could lead to more sustainable control of non-native P. australis .

Biological Invasions↗
USGS2024

Identifying new invasive plants in the face of climate change: A focus on sleeper species

Sleeper populations are established populations of introduced species whose population growth is limited by one or more abiotic or biotic conditions. Sleeper populations pose an invasion risk if a change in those limiting conditions, such as climate change, enables population growth and invasion. With thousands of established introduced species, it is critical that we identify and prioritize potential sleepers. Here, we identified introduced plants established in the northeastern United States with high impacts and the potential to expand with climate change. Of 1795 introduced plants established in one or more northeastern states, we focused on 118 taxa regulated by one or more states outside the Northeast plus 61 taxa recorded as invasive globally and under consideration for regulation in the Northeast. We used the environmental impact classification for alien taxa framework to quantify negative ecological and socioeconomic impacts reported in the scientific literature for these 169 taxa. We compared mean minimum winter temperature and annual precipitation where the species were abundant with current and future climate in the Northeast to evaluate whether climate change could increase risk. We identified 49 plants with ecological impacts linked to loss of native diversity and 94 plants with socioeconomic impacts. 81 species showed an increase in climatic suitability for abundant populations with climate change. Using ecological impact, increased climate suitability, and presence in fewer than 20 Northeastern counties, we highlight 18 species as high priorities for potential management in the Northeast. This approach can inform climate-smart, proactive management of sleeper populations before they become invasive.

Biological Invasions↗
USGS2003

A gentic survey of Salvinia minima in the southern United States

The genetic relationships among 68 samples of Salvinia minima (Salviniaceae) were investigated using RAPD analysis. Neighbor joining, principle components, and AMOVA analyses were used to detect differences among geographically referenced samples within and outside of Florida. Genetic distances (Nei and Li) range up to 0.48, although most are under 0.30, still relatively high levels for an introduced, clonally reproducing plant. Despite the diversity AMOVA analysis yielded no indication that the Florida plants, as a group, were significantly different from the plants sampled elsewhere in its adventive, North American range. A single, genetically dissimilar population probably exists in the recent (1998) horticultural introduction to Mississippi. When the samples were grouped into 10 regional (but artificial) units and analyzed using AMOVA the between region variance was only 7.7%. Genetic similarity among these regions may indicate introduction and dispersal from common sources. The reduced aggressiveness of Florida populations (compared to other states) may be due to herbivory. The weevil Cyrtobagous salviniae , a selective feeder, is found in Florida but not other states. The genetic similarity also suggests that there are no obvious genetic obstacles to the establishment or efficacy of C. salviniae as a biological control agent on S. minima outside of Florida.

Aquatic Botany↗
USGS2016

An international borderland of concern: Conservation of biodiversity in the Lower Rio Grande Valley

The Lower Rio Grande Valley (LRGV) of southern Texas is located on the United States-Mexico borderland and represents a 240-kilometer (150-mile) linear stretch that ends at the Gulf of Mexico. The LRGV represents a unique transition between temperate and tropical conditions and, as such, sustains an exceptionally high diversity of plants and animals—some of them found in few, or no other, places in the United States. Examples include Leopardus pardalis albescens (northern ocelot) and Falco femoralis septentrionalis (northern aplomado falcon)—both endangered in the United States and emblematic of the LRGV. The U.S. Fish and Wildlife Service (USFWS) manages three national wildlife refuges (Santa Ana, Lower Rio Grande Valley, and Laguna Atascosa) that together make up the South Texas Refuge Complex, which actively conserves biodiversity in about 76,006 hectares (187,815.5 acres) of native riparian and upland habitats in the LRGV. These diminished habitats harbor many rare, threatened, and endangered species. This report updates the widely used 1988 USFWS biological report titled “Tamaulipan Brushland of the Lower Rio Grande Valley of South Texas: Description, Human Impacts, and Management Options” by synthesizing nearly 400 peer-reviewed scientific publications that have resulted from biological and sociological research conducted specifically in the four Texas counties of the LRGV in the past nearly 30 years. This report has three goals: (1) synthesize scientific insights gained since 1988 related to the biology and management of the LRGV and its unique biota, focusing on flora and fauna of greatest conservation concern; (2) update ongoing challenges facing Federal and State agencies and organizations that focus on conservation or key natural resources in the LRGV; and (3) redefine conservation opportunities and land-acquisition strategies that are feasible and appropriate today, given the many new and expanding constraints that challenge conservation activities in the LRGV. The LRGV faces every contemporary conservation challenge of the 21st century, but ongoing human population growth and its associated demands, international border issues, and oil, gas, and alternative energy development dominate impacts that affect conservation in the LRGV. Continued careful syntheses of existing and future information collected in the LRGV are needed on many biological and sociological topics to guide conservation activities. Quick response will no doubt be necessary to face contemporary and difficult-to-predict challenges such as climate change, diminished water availability and quality, spread of invasive species, and habitat loss and fragmentation. Complexities of a guarded international borderland add pressure to small patches of native habitat that remain in many places of the LRGV, particularly along the Rio Grande. Large connected corridors of restored native habitat could be the best option to maintain, and even enhance, the exceptional biodiversity of the LRGV in the face of exceptional human demand.

Texas↗
USGS2001

Wetland restoration in the Prairie Pothole Region of North America: A literature review

The landscape of the prairie pothole region (PPR), a grassland biome of the northern U.S. Great Plains and parts of Canada, has been greatly altered by land use since the 1800's. Conversion of grassland to cropland and drainage of wetlands has resulted in wetland losses of up to 90% in some areas. Besides the area providing critical habitat to various wildlife, breeding waterfowl, and migratory birds, its seasonal wetlands support diverse plant and invertebrate communities, play a role in flood attenuation, act as traps for nutrients. store and recharge groundwater. and are valued recreational lands. Most of the restoration of prairie potholes has only occurred since the 1980's, with few follow-up studies performed and little postrestoration monitoring of these restorations. Monitoring and research of wetland restoration in the PPR is less common relative to the number of postrestoration studies done on other wetland types in the United States. This report is a synthesis of current knowledge of restored prairie pothole wetlands and makes suggestions for future wetland restoration-related research. In order to determine the benefits of restored wetlands, it is important to better understand how closely restored wetlands in the PPR resemble their natural analogues in terms of functions and values. The report categorizes PPR literature into five general sections: wildlife, vegetation, invertebrates, fish, and physical and chemical characteristics of restored wetlands. Each of these five sections has a summary of research and is divided into two parts: an overview of research and findings and regional case studies. Most PPR studies have focused on bird and plant communities, whereas research done on the functions of restored wetlands and studies concerning less visible fauna and physical and chemical characteristics are scarce. In addition, there is a scarcity of research in the western and northern portions or the PPR; most studio to date have been conducted in Iowa. Minnesota, or South Dakota. Key Words: wetland restoration, prairie pothole region, PPR, literature review, wetland functions and values. postrestoration studies

Biological Science Report↗
USGS2000

Contaminant Hazard Reviews (compilation)

This compact disc (CD) contains the 35 reports in the Contaminant Hazard Reviews (CHR) that were published originally between 1985 and 1999 in the U.S. Department of the Interior Biological Report series. The CD was produced because printed supplies of these reviews--a total of 105,000--became exhausted and demand remained high. Each review was prepared at the request of environmental specialists of the U.S. Fish and Wildlife Service and each contained specific information on the following: mirex, cadmium, carbofuran, toxaphene, selenium, chromium, polychlorinated biphenyls, dioxins, diazinon, mercury, polycyclic aromatic hydrocarbons, arsenic, chlorpyrifos, lead, tin, index issue, pentachlorophenol, atrazine, molybdenum, boron, chlordane, paraquat, cyanide, fenvalerate, diflubenzuron, zinc, famphur, acrolein, radiation, sodium monofluoroacetate, planar PCBs, silver, copper, nickel, and a cumulative index to chemicals and species. Each report reviewed and synthesized the technical literature on a single contaminant and its effects on terrestrial plants and invertebrates, aquatic plants and animals, avian and mammalian wildlife, and other natural resources. The subtopics include contaminant sources and uses; physical, chemical, and metabolic properties; concentrations in field collections of abiotic materials and living organisms; deficiency effects, where appropriate; lethal and sublethal effects, including effects on survival, growth, reproduction, metabolism, mutagenicity, teratogenicity, and carcinogenicity; proposed criteria for the protection of human health and sensitive natural resources; and recommendations for additional research.

Contaminant Hazard Reviews↗
USGS1984

Reconnaissance of water-quality characteristics of streams in the City of Charlotte and Mecklenburg County, North Carolina

In 1979-81, water samples were collected from 119 sites on streams throughout the City of Charlotte and Mecklenburg County, North Carolina, and were analyzed for specific conductance, dissolved chloride, hardness, pH, total alkalinity, total phosphorus, trace elements, arsenic, cadmium, chromium, copper, iron, lead, manganese, mercury, silver, and zinc and biological measures including dissolved oxygen, biochemical oxygen demand, fecal coliform bacteria, and fecal streptococcus bacteria. Sampling was conducted during both low flow (base flow) and high flow. Several water-quality measures including pH, total arsenic, total cadmium, total chromium, total copper, total iron, total lead, total manganese, total mercury, total silver, total zinc, dissolved oxygen, and fecal coliform bacteria at times exceeded North Carolina water-quality standards in various streams. Runoff from non-point sources appears to contribute more to the deterioration of streams in Charlotte and Mecklenburg County than point-source effluents. Urban and industrial areas contribute various trace elements. Residential and rural areas and municipal waste-water treatment plants contribute high amounts of phosphorus.

North Carolina↗
USGS2001

Food webs including parasites, biomass, body sizes, and life stages for three California/Baja California estuaries

This data set presents food webs for three North American Pacific coast estuaries and a “Metaweb” composed of the species/stages compiled from all three estuaries. The webs have four noteworthy attributes: (1) parasites (infectious agents), (2) body-size information, (3) biomass information, and (4) ontogenetic stages of many animals with complex life cycles. The estuaries are Carpinteria Salt Marsh, California (CSM); Estero de Punta Banda, Baja California (EPB); and Bahía Falsa in Bahía San Quintín, Baja California (BSQ). Most data on species assemblages and parasitism were gathered via consistent sampling that acquired body size and biomass information for plants and animals larger than ∼1 mm, and for many infectious agents (mostly metazoan parasites, but also some microbes). We augmented this with information from additional published sources and by sampling unrepresented groups (e.g., plankton). We estimated free-living consumer–resource links primarily by extending a previously published version of the CSM web (which the current CSM web supplants) and determined most parasite consumer–resource links from direct observation. We recognize 21 possible link types including four general interactions: predators consuming prey, parasites consuming hosts, predators consuming parasites, and parasites consuming parasites. While generally resolved to the species level, we report stage-specific nodes for many animals with complex life cycles. We include additional biological information for each node, such as taxonomy, lifestyle (free-living, infectious, commensal, mutualist), mobility, and residency. The Metaweb includes 500 nodes, 314 species, and 11 270 links projected to be present given appropriate species' co-occurrences. Of these, 9247 links were present in one or more of the estuarine webs. The remaining 2023 links were not present in the estuaries but are included here because they may occur in other places or times. Initial analyses have examined and are examining the interrelationships among consumer strategy, body size, abundance, biomass, trophic level, life stages, and food-web structure and dynamics. Further use of these data may enable a more general exploration how infectious processes and parasites impact communities and ecosystems. Additionally, we present the data and metadata in a standardized format, attempting to provide a system-neutral template for future food-web assembly and publication.

Ecology↗
USGS2016

Autumn olive ( Elaeagnus umbellata ) presence and proliferation on former surface coal mines in Eastern USA

Invasive plants threaten native plant communities. Surface coal mines in the Appalachian Mountains are among the most disturbed landscapes in North America, but information about land cover characteristics of Appalachian mined lands is lacking. The invasive shrub autumn olive ( Elaeagnus umbellata ) occurs on these sites and interferes with ecosystem recovery by outcompeting native trees, thus inhibiting re-establishment of the native woody-plant community. We analyzed Landsat 8 satellite imagery to describe autumn olive’s distribution on post-mined lands in southwestern Virginia within the Appalachian coalfield. Eight images from April 2013 through January 2015 served as input data. Calibration and validation data obtained from high-resolution aerial imagery were used to develop a land cover classification model that identified areas where autumn olive was a primary component of land cover. Results indicate that autumn olive cover was sufficiently dense to enable detection on approximately 12.6 % of post-mined lands within the study area. The classified map had user’s and producer’s accuracies of 85.3 and 78.6 %, respectively, for the autumn olive coverage class. Overall accuracy was assessed in reference to an independent validation dataset at 96.8 %. Autumn olive was detected more frequently on mines disturbed prior to 2003, the last year of known plantings, than on lands disturbed by more recent mining. These results indicate that autumn olive growing on reclaimed coal mines in Virginia and elsewhere in eastern USA can be mapped using Landsat 8 Operational Land Imager imagery; and that autumn olive occurrence is a significant landscape vegetation feature on former surface coal mines in the southwestern Virginia segment of the Appalachian coalfield.

Biological Invasions↗
USGS2014

Non-native fishes in Florida freshwaters: a literature review and synthesis

Non-native fishes have been known from freshwater ecosystems of Florida since the 1950s, and dozens of species have established self-sustaining populations. Nonetheless, no synthesis of data collected on those species in Florida has been published until now. We searched the literature for peer-reviewed publications reporting original data for 42 species of non-native fishes in Florida that are currently established, were established in the past, or are sustained by human intervention. Since the 1950s, the number of non-native fish species increased steadily at a rate of roughly six new species per decade. Studies documented (in decreasing abundance): geographic location/range expansion, life- and natural-history characteristics (e.g., diet, habitat use), ecophysiology, community composition, population structure, behaviour, aquatic-plant management, and fisheries/aquaculture. Although there is a great deal of taxonomic uncertainty and confusion associated with many taxa, very few studies focused on clarifying taxonomic ambiguities of non-native fishes in the State. Most studies were descriptive; only 15 % were manipulative. Risk assessments, population-control studies and evaluations of effects of non-native fishes were rare topics for research, although they are highly valued by natural-resource managers. Though some authors equated lack of data with lack of effects, research is needed to confirm or deny conclusions. Much more is known regarding the effects of lionfish ( Pterois spp.) on native fauna, despite its much shorter establishment time. Natural-resource managers need biological and ecological information to make policy decisions regarding non-native fishes. Given the near-absence of empirical data on effects of Florida non-native fishes, and the lengthy time-frames usually needed to collect such information, we provide suggestions for data collection in a manner that may be useful in the evaluation and prediction of non-native fish effects.

Florida↗
USGS2017

The Bayesian group lasso for confounded spatial data

Generalized linear mixed models for spatial processes are widely used in applied statistics. In many applications of the spatial generalized linear mixed model (SGLMM), the goal is to obtain inference about regression coefficients while achieving optimal predictive ability. When implementing the SGLMM, multicollinearity among covariates and the spatial random effects can make computation challenging and influence inference. We present a Bayesian group lasso prior with a single tuning parameter that can be chosen to optimize predictive ability of the SGLMM and jointly regularize the regression coefficients and spatial random effect. We implement the group lasso SGLMM using efficient Markov chain Monte Carlo (MCMC) algorithms and demonstrate how multicollinearity among covariates and the spatial random effect can be monitored as a derived quantity. To test our method, we compared several parameterizations of the SGLMM using simulated data and two examples from plant ecology and disease ecology. In all examples, problematic levels multicollinearity occurred and influenced sampling efficiency and inference. We found that the group lasso prior resulted in roughly twice the effective sample size for MCMC samples of regression coefficients and can have higher and less variable predictive accuracy based on out-of-sample data when compared to the standard SGLMM.

Journal of Agricultural, Biological, and Environme↗
USGS2026

Estimating submersed aquatic vegetation biomass using a hierarchical Bayesian model of ordinal measurements and structural zeros

This study explores the prediction of a continuous target variable that is primarily measured as an ordinal outcome. Interest in such prediction may occur given data from double- or two-phase sampling designs, where an auxiliary variable is measured at all sampling units and a target and predictor variable, X , at a subset of those units. This study focuses on the case where X is nonnegative, is conditional on a zero process, and is sampled using a cluster sampling design. We model the ordinal outcome using cumulative logistic regression and the conditional regressor X , following log transformation, in a Bayesian setting. Estimation of model parameters and prediction of missing X is generally accurate and precise, particularly with sufficiently large Pr(X > 0) and associated variances. This study is motivated by a need to accurately estimate the biomass of submersed aquatic vegetation on the Upper Mississippi River, where two types of measurements for biomass are available: inexpensive, ordinal biomass scores and expensive, continuous diver-harvested biomass data. Here, X represents plant biomass and Pr(X > 0) is the usual species site occupancy measure. When fit using biomass data from the submerged aquatic vegetation species Vallisneria americana Michx, our model estimates parameters within the parameter space region where the model performed acceptably using synthetic data. We expect this model to appeal to investigators with ordered outcomes, cluster designs, and one or more continuous, positive predictors.

Journal of Agricultural, Biological and Environmen↗
USGS2006

Animal and vegetation patterns in natural and man-made bog pools: implications for restoration

1. Peatlands have suffered great losses following drainage for agriculture, forestry, urbanisation, or peat mining, near inhabited areas. We evaluated the faunal and vegetation patterns after restoration of a peatland formerly mined for peat. We assessed whether bog pools created during restoration are similar to natural bog pools in terms of water chemistry, vegetation structure and composition, as well as amphibian and arthropod occurrence patterns. 2. Both avian species richness and peatland vegetation cover at the site increased following restoration. Within bog pools, however, the vegetation composition differed between natural and man-made pools. The cover of low shrubs, Sphagnum moss, submerged, emergent and floating vegetation in man-made pools was lower than in natural pools, whereas pH was higher than in typical bog pools. Dominant plant species also differed between man-made and natural pools. 3. Amphibian tadpoles, juveniles and adults occurred more often in man-made pools than natural bog pools. Although some arthropods, including Coleoptera bog specialists, readily colonised the pools, their abundance was two to 26 times lower than in natural bog pools. Plant introduction in bog pools, at the stocking densities we applied, had no effect on the occurrence of most groups. 4. We conclude that our restoration efforts were partially successful. Peatland-wide vegetation patterns following restoration mimicked those of natural peatlands, but 4 years were not sufficient for man-made pools to fully emulate the characteristics of natural bog pools.

Freshwater Biology↗
USGS2012

Occurrence of triclosan, triclocarban, and its lesser chlorinated congeners in Minnesota freshwater sediments collected near wastewater treatment plants

The antimicrobial agents triclosan (TCS), triclocarban (TCC) and their associated transformation products are of increasing concern as environmental pollutants due to their potential adverse effects on humans and wildlife, including bioaccumulation and endocrine-disrupting activity. Analysis by tandem mass spectrometry of 24 paired freshwater bed sediment samples (top 10 cm) collected by the U.S. Geological Survey near 12 wastewater treatment plants (WWTPs) in Minnesota revealed TCS and TCC concentrations of up to 85 and 822 ng/g dry weight (dw), respectively. Concentrations of TCS and TCC in bed sediments collected downstream of WWTPs were significantly greater than upstream concentrations in 58% and 42% of the sites, respectively. Dichloro- and non-chlorinated carbanilides (DCC and NCC) were detected in sediments collected at all sites at concentrations of up to 160 and 1.1 ng/g dw, respectively. Overall, antimicrobial concentrations were significantly higher in lakes than in rivers and creeks, with relative abundances decreasing from TCC > TCS > DCC > NCC. This is the first statewide report on the occurrence of TCS, TCC and TCC transformation products in freshwater sediments. Moreover, the results suggest biological or chemical TCC dechlorination products to be ubiquitous in freshwater environments of Minnesota, but whether this transformation occurs in the WWTP or bed sediment remains to be determined.

Minnesota↗