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At least 433 records · Page 24Linked to original sources
USGS2024

Using models of local environmental conditions for biological assessment

A common approach for biological assessment is to compare current observations of biota at a site to predictions of the biota that would occur if the site were in reference condition. To estimate these reference expectations, predictive bioassessment models use only data collected at reference sites and estimate relationships between biota and environmental variables that are unaffected by human activities (i.e., immutable variables). However, in some areas where human activities are pervasive, few reference sites are available. Here, we introduce a new approach for bioassessment, in which we first estimate relationships between widely available measurements of both immutable and human-influenced landscape variables and local environmental conditions (conductivity, dissolved total P, total suspended solids, percentage of sand and fines in the substrate, and dissolved organic C), and then we estimate the relationship between these local environmental variables and total macroinvertebrate richness. We then calculate the values of the local environmental variables under reference conditions by adjusting predictors that are strongly influenced by human activities to levels that are consistent with those observed at reference sites. Reference values of local environmental variables are then combined with the model for taxon richness to calculate taxon richness expected under reference conditions. Predictions of total taxon richness in validation data using the new approach are similar in accuracy and precision as predictions calculated using a traditional approach that focuses only on reference site data. The new approach complements existing bioassessment methods by highlighting types of sites in which estimates of reference expectations are uncertain and by improving our understanding of how instream stressors affect expected total taxon richness.

conterminous United States↗
USGS2003

Supraglacial sulfur springs and associated biological activity in the Canadian high arctic - signs of life beneath the ice

Unique springs, discharging from the surface of an arctic glacier, release H2S and deposit native sulfur, gypsum, and calcite. The presence of sulfur in three oxidation states indicates a complex series of redox reactions. Physical and chemical conditions of the spring water and surrounding environment, as well as mineralogical and isotopic signatures, suggest biologically mediated reactions. Cell counts and DNA analyses confirm bacteria are present in the spring system, and a limited number of sequenced isolates suggests that complex communities of bacteria live within the glacial system.

Astrobiology↗
USGS2020

An overview of agent-based models in plant biology and ecology

Agent-based modeling (ABM) has become an established methodology in many areas of biology, ranging from the cellular to the ecological population and community levels. In plant science, two different scales have predominated in their use of ABM. One is the scale of populations and communities, through the modeling of collections of agents representing individual plants, interacting with each other and with the environment. The other is the scale of the individual plant, through the modeling, by functional-structural plant models (FSPMs), of agents representing plant building blocks, or metamers, to describe the development of plant architecture and functions within individual plants. The purpose of this review is to show key results and parallels in ABM for growth, mortality, carbon allocation, competition, and reproduction across the scales from the plant organ to populations and communities on a range of spatial scale to the whole landscape. Several areas of application of ABMs are reviewed, showing that some issues are addressed by both population-level ABMs and FSPMs. Continued increase in the relevance of ABM to environmental science and management will be helped by greater integration of ABMs across these two scales.

Annals of Botany↗
USGS2000

The AOU Conservation Committee Review of the biology, status, and management of Cape Sable Seaside Sparrows: Final report

The Cape Sable Seaside Sparrow ( Ammodramus maritimus mirabilis ) was listed as an original member of the federal list of endangered species in 1968. It is restricted to seasonally flooded prairies of extreme southern Florida and is disjunct from all other conspecific breeding populations (Kushlan et al 1982, McDonald 1988). Since the subspecies was described in 1919, its populations have been discovered and rediscovered, often only to disappear or decline to a handful of individuals (Werner and Woolfenden 1983, Kushlan and Bass 1983). Although the sparrow historically is known from six distinct areas, at present only two of these areas support populations numbering in the hundreds or low thousands of individuals. Debates swirl around the status of these remnant populations. The main controversy encompasses whether the sparrow, now largely restricted to Everglades National Park, is in jeopardy of global extinction and if so, what actions must be taken to prevent this from happening. In November 1998, a panel of scientists was assembled under the auspices of the Conservation Committee of the American Ornithologists' Union (AOU) to evaluate the scientific evidence relevant to this controversy. The Panel was charged with scrutinizing the evidence for the existence and probable causes of global population decline in this subspecies, evaluating proposed management actions, and suggesting further research necessary to manage the remaining populations to maximize their chances of long-term persistence. This document presents the conclusions of the Panel, which are based on our reading of the peer-reviewed and “gray” literature, interactions during a workshop held 9 to 11 February 1999 at Florida International University in Miami with researchers investigating the sparrow's biology, and site visits associated with the workshop. In addition, researchers provided the Panel with position papers summarizing their findings and conclusions prior to the workshop and provided information in response to specific questions following the workshop. Further information was obtained through public comment on an initial draft of this report.

The Auk↗
USGS2025

Prioritizing chemicals of emerging concern in the Great Lakes Basin using covariance of chemical concentrations and diverse biological responses from a variety of species

The Great Lakes Restoration Initiative aims to protect and restore the nation’s largest freshwater resource, in part, by furthering our understanding of the effects of contaminants of emerging concern (CECs) and chemical mixtures on aquatic and terrestrial organisms. To address this goal, an interagency team conducted field studies at sites along the Maumee River in Ohio, USA, in 2016–2017, monitoring CEC levels along with diverse in vitro and in vivo biological effects in ecologically relevant species (fathead minnows, tree swallows, and golden clams). The objective of the present work was to prioritize the CECs in these studies for further monitoring and assessment by determining if there are patterns in chemical–bioeffect relations across data sets, species, and response types that indicate relatively high or low hazard to aquatic life from CEC exposure. Of the 748 monitored chemicals, 425 were detected and were analyzed for covariance with bioeffects. All 748 chemicals were placed into 10 bins based on their frequencies of monitoring, detection, and covariance with bioeffects across studies and species. We describe how chemicals can be prioritized across bins to aid monitoring and assessment efforts. Our approach using effects-based monitoring data is especially useful for prioritizing chemicals with little or no traditional toxicity testing data. Similar evidence-based prioritizations will allow agencies to more efficiently allocate limited resources to improve the ability to protect aquatic and terrestrial organisms from adverse impacts due to contaminant exposure.

Ohio↗
USGS2025

Biological implications for contaminants of emerging concern in the Great Lakes–Upper St Lawrence River drainage: An effect-based ecological hazard assessment in fish

Contaminants of emerging concern (CECs) are released widely and continuously into the Great Lakes Basin–Upper St Lawrence River study area, with many detected in surface water at concentrations known to adversely affect fish. We applied a recent ecological hazard assessment methodology to identify the biological significance of a database of 21,441 surface water CEC concentrations compiled from 7,162 surface water samples collected at 1,021 sampling sites in 387 individual waterbodies throughout the Great Lakes Basin. We assessed hazard to fish in 12 effect categories (e.g., mortality, developmental, reproductive) from aqueous exposure to 16 emerging contaminants. Our hazard assessment used pairs of screening values to generate contaminant- and effect-specific ordinal hazard scores. Using this novel methodology, we generated a database of 93,864 hazard scores. We found the highest level of hazard to fish, indicating probable adverse impacts, was broadly distributed and often associated with municipalities. Mortality, reproductive, and developmental effect categories combined accounted for 17.5% of high hazard observations. Low hazard, indicating possible adverse effects, was prevalent for numerous effect categories and occurred throughout the period 1991–2021. For mortality, reproductive, and developmental effect categories, the incidence of elevated hazard (low or high hazard) among assessed water samples was 20.4%, 39.5%, and 20.3%, respectively. On a local scale, effect-based assessment is an efficient and conceptually simple tool for natural resource managers to obtain effect- and site-specific hazard information concerning CEC effects in fish that can be used in project planning and results interpretation for natural resource monitoring, restoration, and protection.

Great Lakes–Upper St Lawrence River study area↗
USGS1996

Comparative biology of zebra mussels in Europe and North America: an overview

SYNOPSIS. Since the discovery of the zebra mussel, Dreissena polymorpha , in the Great Lakes in 1988 comparisons have been made with mussel populations in Europe and the former Soviet Union. These comparisons include: Population dynamics, growth and mortality rates, ecological tolerances and requirements, dispersal rates and patterns, and ecological impacts. North American studies, mostly on the zebra mussel and a few on a second introduced species, the quagga mussel, Dreissena bugensis , have revealed some similarities and some differences. To date it appears that North American populations of zebra mussels are similar to European populations in their basic biological characteristics, population growth and mortality rates, and dispersal mechanisms and rates. Relative to European populations differences have been demonstrated for: (1) individual growth rates; (2) life spans; (3) calcium and pH tolerances and requirements; (4) potential distribution limits; and (5) population densities of veligers and adults. In addition, studies on the occurrence of the two dreissenid species in the Great Lakes are showing differences in their modes of life, depth distributions, and growth rates. As both species spread throughout North America, comparisons between species and waterbodies will enhance our ability to more effectively control these troublesome species.

American Zoologist↗
USGS2012

Dryland biological soil crust cyanobacteria show unexpected decreases in abundance under long-term elevated CO 2

Biological soil crusts (biocrusts) cover soil surfaces in many drylands globally. The impacts of 10 years of elevated atmospheric CO 2 on the cyanobacteria in biocrusts of an arid shrubland were examined at a large manipulated experiment in Nevada, USA. Cyanobacteria-specific quantitative PCR surveys of cyanobacteria small-subunit (SSU) rRNA genes suggested a reduction in biocrust cyanobacterial biomass in the elevated CO 2 treatment relative to the ambient controls. Additionally, SSU rRNA gene libraries and shotgun metagenomes showed reduced representation of cyanobacteria in the total microbial community. Taxonomic composition of the cyanobacteria was similar under ambient and elevated CO 2 conditions, indicating the decline was manifest across multiple cyanobacterial lineages. Recruitment of cyanobacteria sequences from replicate shotgun metagenomes to cyanobacterial genomes representing major biocrust orders also suggested decreased abundance of cyanobacteria sequences across the majority of genomes tested. Functional assignment of cyanobacteria-related shotgun metagenome sequences indicated that four subsystem categories, three related to oxidative stress, were differentially abundant in relation to the elevated CO 2 treatment. Taken together, these results suggest that elevated CO 2 affected a generalized decrease in cyanobacteria in the biocrusts and may have favoured cyanobacteria with altered gene inventories for coping with oxidative stress.

Nevada↗
USGS2016

Uncertainty in biological monitoring: a framework for data collection and analysis to account for multiple sources of sampling bias

Biological monitoring programmes are increasingly relying upon large volumes of citizen-science data to improve the scope and spatial coverage of information, challenging the scientific community to develop design and model-based approaches to improve inference. Recent statistical models in ecology have been developed to accommodate false-negative errors, although current work points to false-positive errors as equally important sources of bias. This is of particular concern for the success of any monitoring programme given that rates as small as 3% could lead to the overestimation of the occurrence of rare events by as much as 50%, and even small false-positive rates can severely bias estimates of occurrence dynamics. We present an integrated, computationally efficient Bayesian hierarchical model to correct for false-positive and false-negative errors in detection/non-detection data. Our model combines independent, auxiliary data sources with field observations to improve the estimation of false-positive rates, when a subset of field observations cannot be validated a posteriori or assumed as perfect. We evaluated the performance of the model across a range of occurrence rates, false-positive and false-negative errors, and quantity of auxiliary data. The model performed well under all simulated scenarios, and we were able to identify critical auxiliary data characteristics which resulted in improved inference. We applied our false-positive model to a large-scale, citizen-science monitoring programme for anurans in the north-eastern United States, using auxiliary data from an experiment designed to estimate false-positive error rates. Not correcting for false-positive rates resulted in biased estimates of occupancy in 4 of the 10 anuran species we analysed, leading to an overestimation of the average number of occupied survey routes by as much as 70%. The framework we present for data collection and analysis is able to efficiently provide reliable inference for occurrence patterns using data from a citizen-science monitoring programme. However, our approach is applicable to data generated by any type of research and monitoring programme, independent of skill level or scale, when effort is placed on obtaining auxiliary information on false-positive rates.

Methods in Ecology and Evolution↗
USGS2021

A roadmap for sampling and scaling biological nitrogen fixation in terrestrial ecosystems

Accurately quantifying rates and patterns of biological nitrogen fixation (BNF) in terrestrial ecosystems is essential to characterize ecological and biogeochemical interactions, identify mechanistic controls, improve BNF representation in conceptual and numerical modelling, and forecast nitrogen limitation constraints on future carbon (C) cycling. While many resources address the technical advantages and limitations of different methods for measuring BNF, less systematic consideration has been given to the broader decisions involved in planning studies, interpreting data, and extrapolating results. Here, we present a conceptual and practical road map to study design, study execution, data analysis and scaling, outlining key considerations at each step. We address issues including defining N‐fixing niches of interest, identifying important sources of temporal and spatial heterogeneity, designing a sampling scheme (including method selection, measurement conditions, replication, and consideration of hotspots and hot moments), and approaches to analysing, scaling and reporting BNF. We also review the comparability of estimates derived using different approaches in the literature, and provide sample R code for simulating symbiotic BNF data frames and upscaling. Improving and standardizing study design at each of these stages will improve the accuracy and interpretability of data, define limits of extrapolation, and facilitate broader use of BNF data for downstream applications. We highlight aspects—such as quantifying scales of heterogeneity, statistical approaches for dealing with non‐normality, and consideration of rates versus ecological significance—that are ripe for further development.

Methods in Ecology and Evolution↗
USGS2024

Thinking beyond the closure assumption: Designing surveys for estimating biological truth with occupancy models

Occupancy models estimate distributions of imperfectly detected species, but violations of the closure assumption can bias results. However, researchers working with mobile animals may find it impossible to eliminate such violations. Here, we tested the hypothesis that occupancy models fit to realistic sampling data can generate unbiased occupancy estimates for an itinerant Wood Thrush ( Hylocichla mustelina ) population. In 2013 and 2014, we tracked movements of 41 breeding Wood Thrush males. We modelled territory shift probabilities using logistic exposure models and within-territory movements using continuous-time stochastic process models. We then constructed an individual-based model, simulated (1000 iterations) spatiotemporal locations for individuals and simulated sampling these populations using 162 different point count protocols with variable spatial (sampling radius and point placement method), and temporal (survey length, between-survey intervals and number of surveys) characteristics. We compared occupancy estimates with true values of instantaneous, daily and seasonal occupancy from the simulations. We parameterized continuous time stochastic process models based on movements within 34 unique territories and estimated a daily territory shift probability of 0.0099 (95% CI: 0.0060, 0.0152). Simulated data indicated that estimates of occupancy ranged from 0.18 (0.06, 1.00) to 0.80 (0.71, 0.89) depending on protocol characteristics. Occupancy estimates increased with increasing survey radius, survey length and between-survey interval. Protocols using shorter surveys and between-survey intervals were good estimators for instantaneous occupancy (low bias and mean-squared error) but poor estimators for daily and seasonal occupancy; longer surveys and intervals generated unbiased estimators of daily occupancy but underestimated seasonal occupancy. Logistic regression models that ignored imperfect detection outperformed occupancy models for estimating instantaneous occupancy but not daily or seasonal occupancy. For mobile animals, occupancy of sampling sites changes in space and time. Consequently, the spatial and temporal aspects of a sampling protocol have strong, but predictable, effects on occupancy model parameter estimates. Our results demonstrate that how these factors interact is critical for designing surveys that produce occupancy estimates representative of the biological process of interest to a researcher.

Methods in Ecology and Evolution↗
USGS2023

Monitoring status and trends in genetic diversity for the Convention on Biological Diversity: An ongoing assessment of genetic indicators in nine countries

Recent scientific evidence shows that genetic diversity must be maintained, managed, and monitored to protect biodiversity and nature's contributions to people. Three genetic diversity indicators, two of which do not require DNA-based assessment, have been proposed for reporting to the Convention on Biological Diversity and other conservation and policy initiatives. These indicators allow an approximation of the status and trends of genetic diversity to inform policy, using existing demographic and geographic information. Application of these indicators has been initiated and here we describe ongoing efforts in calculating these indicators with examples. We specifically describe a project underway to apply these indicators in nine countries, provide example calculations, address concerns of policy makers and implementation challenges, and describe a roadmap for further development and deployment, incorporating feedback from the broader community. We also present guidance documents and data collection tools for calculating indicators. We demonstrate that Parties can successfully and cost-effectively report these genetic diversity indicators with existing biodiversity observation data, and, in doing so, better conserve the Earth's biodiversity.

Conservation Letters↗
USGS2006

Correlates of biological soil crust abundance across a continuum of spatial scales: Support for a hierarchical conceptual model

1. Desertification negatively impacts a large proportion of the global human population and > 30% of the terrestrial land surface. Better methods are needed to detect areas that are at risk of desertification and to ameliorate desertified areas. Biological soil crusts are an important soil lichen-moss-microbial community that can be used toward these goals, as (i) bioindicators of desertification damage and (ii) promoters of soil stability and fertility. 2. We identified environmental factors that correlate with soil crust occurrence on the landscape and might be manipulated to assist recovery of soil crusts in degraded areas. We conducted three studies on the Colorado Plateau, USA, to investigate the hypotheses that soil fertility [particularly phosphorus (P), manganese (Mn) and zinc (Zn)] and/or moisture limit soil crust lichens and mosses at four spatial scales. 3. In support of the soil fertility hypothesis, we found that lichen-moss crusts were positively correlated with several nutrients [Mn, Zn, potassium (K) and magnesium (Mg) were most consistent] at three of four spatial scales ranging from 3.5 cm2 in area to c. 800 km2. In contrast, P was negatively correlated with lichen-moss crusts at three scales. 4. Community composition varied with micro-aspect on ridges in the soil crust. Three micro-aspects [north-north-west (NNW), east-north-east (ENE) and TOP] supported greater lichen and moss cover than the warmer, windward and more xeric micro-aspects [west-south-west (WSW) and south-south-east (SSE)]. This pattern was poorly related to soil fertility; rather, it was consistent with the moisture limitation hypothesis. 5. Synthesis and application. Use of crusts as desertification bioindicators requires knowledge of a site's potential for crust cover in the absence of desertification. We present a multi-scale model of crust potential as a function of site properties. Future quantitative studies can use this model to guide sampling efforts. Also, our results suggest new directions in restoration research: enhancement of moisture residence time and fertilization with key nutrients (Mn, Zn, K and Mg). Re-establishment of soil crusts in desertified lands will help regain lost soil stability and fertility, and facilitate plant re-establishment. ?? 2006 British Ecological Society.

Journal of Applied Ecology↗
USGS2007

Three distinct clades of cultured heterocystous cyanobacteria constitute the dominant N2-fixing members of biological soil crusts of the Colorado Plateau, USA

The identity of the numerically dominant N2-fixing bacteria in biological soil crusts of the Colorado Plateau region and two outlying areas was determined using multiple approaches, to link the environmental diversity of nifH gene sequences to cultured bacterial isolates from the regions. Of the nifH sequence-types detected in soil crusts of the Colorado Plateau, 89% (421/473) were most closely related to nifH signature sequences from cyanobacteria of the order Nostocales. N2-fixing cyanobacterial strains were cultured from crusts and their morphotypes, 16S rRNA gene and nifH gene sequences were characterized. The numerically dominant diazotrophs in the Colorado Plateau crusts fell within three clades of heterocystous cyanobacteria. Two clades are well-represented by phylogenetically and morphologically coherent strains, corresponding to the descriptions of Nostoc commune and Scytonema hyalinum, which are widely recognized as important N2-fixing components of soil crusts. A third, previously-overlooked clade was represented by a phylogenetically coherent but morphologically diverse group of strains that encompass the morphogenera Tolypothrix and Spirirestis. Many of the strains in each of these groups contained at least two nifH copies that represent different clusters in the nifH environmental survey. ?? 2007 Federation of European Microbiological Societies.

FEMS Microbiology Ecology↗
USGS2012

Nutrient enrichment and fish nutrient tolerance: Assessing biologically relevant nutrient criteria

Relationships between nutrient concentrations and fish nutrient tolerance were assessed relative to established nutrient criteria. Fish community, nitrate plus nitrite (nitrate), and total phosphorus (TP) data were collected during summer low-flow periods in 2003 and 2004 at stream sites along a nutrient-enrichment gradient in an agricultural basin in Indiana and Ohio and an urban basin in the Atlanta, Georgia, area. Tolerance indicator values for nitrate and TP were assigned for each species and averaged separately for fish communities at each site (TIV o ). Models were used to predict fish species expected to occur at a site under minimally disturbed conditions and average tolerance indicator values were determined for nitrate and TP separately for expected communities (TIV e ). In both areas, tolerance scores (TIV o /TIV e ) for nitrate increased significantly with increased nitrate concentrations whereas no significant relationships were detected between TP tolerance scores and TP concentrations. A 0% increase in the tolerance score (TIV o /TIV e = 1) for nitrate corresponded to a nitrate concentration of 0.19 mg/l (compared with a USEPA summer nitrate criterion of 0.17 mg/l) in the urban area and 0.31 mg/l (compared with a USEPA summer nitrate criterion of 0.86 mg/l) in the agricultural area. Fish nutrient tolerance values offer the ability to evaluate nutrient enrichment based on a quantitative approach that can provide insights into biologically relevant nutrient criteria.

Georgia, Indiana, Ohio↗
USGS2015

Genetic signatures of historical dispersal of fish threatened by biological invasions: the case of galaxiids in South America

Aim The ecological effects of biological invasions are well documented, but little is known about the effects of invaders on the genetic structure of native species. We examined the phylogeography, genetic variation and population structuring of two galaxiid fishes, Aplochiton zebra and A. taeniatus , threatened by non-native salmonids, and whose conservation is complicated by misidentification and limited knowledge of their genetic diversity. Location Chile and the Falkland Islands. Methods We combined microsatellite and mitochondrial DNA (16S rDNA and COI) markers to compare genetic diversity, effective population size and gene flow of Aplochiton spp. populations differentially affected by salmonid presence. Results We identified two 16S rDNA haplotypes among A. zebra – one dominant in coastal populations and another dominant in inland populations. Populations living on the island of Chiloé displayed a mixture of coastal and inland haplotypes, as well as high microsatellite diversity, as one would expect if the island had been a refugium during the Last Glacial Maximum, or a contact zone among populations. Microsatellite data revealed strong population structuring, indicative of current isolation patterns, and a negative correlation between the genetic diversity of A. zebra and the relative abundance of invasive salmonids. Main conclusions Our study indicates that population structuring of A. zebra reflects the influence of historical patterns of migration, but also the current levels of reduced gene flow among watersheds. Invasive salmonids, known to compete with and prey on native galaxiids, may have had negative impacts on the genetic diversity of Aplochiton spp. The low genetic variation found in some populations, coupled with potential biases in abundance estimates due to species misidentification, highlight the urgent need for more research into the conservation status of the two species of Aplochiton .

Journal of Biogeography↗