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At least 739 records · Page 41Linked to original sources
USGS2020

A round-robin evaluation of the repeatability and reproducibility of environmental DNA assays for dreissenid mussels

Resource managers may be hesitant to make decisions based on environmental (e)DNA results alone since eDNA is an indirect method of species detection. One way to reduce the uncertainty of eDNA is to identify laboratory‐based protocols that ensure repeatable and reproducible results. We conducted a double‐blind round‐robin analysis of probe‐based assays for DNA of dreissenid ( Dreissena spp.) mussels, which are prolific aquatic invaders that can cause significant economic and ecological impacts. DNA extract from water samples spiked with known amounts of dreissenid DNA and from water samples collected from waters with and without dreissenids were analyzed by four independent research laboratories. We used results to calculate detection repeatability within laboratories and assays, detection reproducibility among laboratories and assays, and estimated dreissenid DNA copy number precision and accuracy. Laboratory and assay repeatability and reproducibility of detection results were high, 91% and 92%, respectively. The estimated copy numbers were neither precise nor accurate for samples spiked with <773 gene copies. These results suggest that eDNA surveillance of dreissenid mussels, using the protocols evaluated herein, can generate reliable detection data for decision‐making. However, managers should be cautious about using the quantitative information often associated with eDNA detections, especially when DNA is at lower abundance. Our results provide strong support that eDNA has the potential to provide repeatable and reproducible evidence under varying laboratory conditions and for different sample water chemistries. This is reassuring since the demand for eDNA surveillance is widespread and number of laboratories that process eDNA samples is growing steadily.

California, Montana, Nevada, New York, Oregon, Was↗
USGS2022

Risk-based prioritization of organic chemicals and locations of ecological concern in sediment from Great Lakes tributaries

With improved analytical techniques, environmental monitoring studies are increasingly able to report the occurrence of tens or hundreds of chemicals per site, making it difficult to identify the most relevant chemicals from a biological standpoint. For this study, organic chemical occurrence was examined, individually and as mixtures, in the context of potential biological effects. Sediment was collected at 71 Great Lakes tributary sites and analyzed for 87 chemicals. Multiple risk-based lines of evidence were used to prioritize chemicals and locations, including comparing sediment concentrations and estimated porewater concentrations to established whole-organism benchmarks (i.e., sediment and water quality criteria and screening values) and to high-throughput toxicity screening data from the U.S. Environmental Protection Agency's ToxCast database, estimating additive effects of chemical mixtures on common ToxCast endpoints, and estimating toxic equivalencies for mixtures of alkylphenols and polycyclic aromatic hydrocarbons (PAHs). This multiple-lines-of-evidence approach enabled the screening of more chemicals, mitigated the uncertainties of individual approaches, and strengthened common conclusions. Collectively, at least one benchmark/screening value was exceeded for 54 of the 87 chemicals, with exceedances observed at all 71 of the monitoring sites. Chemicals with the greatest potential for biological effects, both individually and as mixture components, were bisphenol A, 4-nonylphenol, indole, carbazole, and several polycyclic aromatic hydrocarbons (PAHs). Potential adverse outcomes based on ToxCast gene targets and putative adverse outcome pathways relevant to individual chemicals and chemical mixtures included tumors, skewed sex ratios, reproductive dysfunction, hepatic steatosis, and early mortality, among others. Results provide a screening level prioritization of chemicals with the greatest potential for adverse biological effects and an indication of sites where they are most likely to occur.

Illinois, Indiana, Michigan, Minnesota, New York, ↗
USGS2019

An old tree and its many‐shaped leaves

Plant leaf shape is highly variable. The beauty of leaves can be purely aesthetic, but also derives from the mystery of adaptive significance. This mystery is especially compelling for species with strongly varying leaf shape on a single tree. The desert poplar (Populus euphratica Oliv.) is an ancient and protected species, and forms riparian forests in deserts of mid and west Asia, north Africa and southern Europe. More than half of all desert poplar forest is found along the Tarim River within the Taklamakan, a desert in northwest China. The Taklamakan is in the rain shadow of the Himalayas and the world’s second largest shifting sand desert. There, forest extent has been greatly reduced, mostly due to flow diversion for agriculture, but many old trees persist. The tree in the picture is the oldest recorded living desert poplar. The innermost ring in a core dates back to 1709 or earlier. The leaves on this tree vary widely in shape, from smooth to dentate, from narrow to broad, and from linear to lanceolate to ovate. Drought is a dominant stressor in this hyperarid environment with highly variable temperature and soil salinity. Leaf shape may relate to tradeoffs among water conservation, thermoregulation and growth rate. Is this extremely wide variation in leaf shape on a single tree an adaptation to the large temporal fluctuations in the environment? Alternatively, could leaf polymorphism be a neutral and thus non-adaptive consequence of variable gene expressions related to developmental stages. Answers to these questions can enrich the ecological and evolutionary understanding of trees and ecological drought.

Frontiers in Ecology and the Environment↗
USGS2023

Climate change risks to freshwater subsistence fisheries in Arctic Alaska: Insights and uncertainty from broad whitefish Coregonus nasus

Arctic freshwater ecosystems and fish populations are largely shaped by seasonal and long-term watershed hydrology. In this paper, we hypothesize how changing air temperature and precipitation will alter freeze and thaw processes, hydrology, and instream habitat to assess potential indirect effects, such as the change to the foraging and behavioral ecology, on Arctic fishes, using Broad Whitefish Coregonus nasus as an indicator species. Climate change is expected to continue to alter hydrologic pathways, flow regimes, and, therefore, habitat suitability, connectivity, and availability for fishes. Warming and lengthening of the growing season will likely increase fish growth rates; however, the exceedance of threshold stream temperatures will likely increase physiological stress and alter life histories. We expect these changes to have mixed effects on Arctic subsistence fishes and fisheries. Management and conservation approaches focused on preserving the processes that create heterogeneity in aquatic habitats, genes, and communities will help maintain the resilience of Broad Whitefish and other important subsistence fisheries. Long-term effects are uncertain, so filling scientific knowledge gaps, such as identifying important habitats or increasing knowledge of abiotic variables in priority watersheds, is key to understanding and potentially mitigating likely impacts to Arctic fishes in a rapidly changing landscape.

Alaska↗
USGS2015

Density, distribution, and genetic structure of grizzly bears in the Cabinet-Yaak Ecosystem

The conservation status of the 2 threatened grizzly bear ( Ursus arctos ) populations in the Cabinet-Yaak Ecosystem (CYE) of northern Montana and Idaho had remained unchanged since designation in 1975; however, the current demographic status of these populations was uncertain. No rigorous data on population density and distribution or analysis of recent population genetic structure were available to measure the effectiveness of conservation efforts. We used genetic detection data from hair corral, bear rub, and opportunistic sampling in traditional and spatial capture–recapture models to generate estimates of abundance and density of grizzly bears in the CYE. We calculated mean bear residency on our sampling grid from telemetry data using Huggins and Pledger models to estimate the average number of bears present and to correct our superpopulation estimates for lack of geographic closure. Estimated grizzly bear abundance (all sex and age classes) in the CYE in 2012 was 48–50 bears, approximately half the population recovery goal. Grizzly bear density in the CYE (4.3–4.5 grizzly bears/1,000 km 2 ) was among the lowest of interior North American populations. The sizes of the Cabinet ( n = 22–24) and Yaak ( n = 18–22) populations were similar. Spatial models produced similar estimates of abundance and density with comparable precision without requiring radio-telemetry data to address assumptions of geographic closure. The 2 populations in the CYE were demographically and reproductively isolated from each other and the Cabinet population was highly inbred. With parentage analysis, we documented natural migrants to the Cabinet and Yaak populations by bears born to parents in the Selkirk and Northern Continental Divide populations. These events supported data from other sources suggesting that the expansion of neighboring populations may eventually help sustain the CYE populations. However, the small size, isolation, and inbreeding documented by this study demonstrate the need for comprehensive management designed to support CYE population growth and increased connectivity and gene flow with other populations.

Idaho, Montana↗
USGS2016

Proximate influences on female dispersal in white-tailed deer

Ultimate causes of animal dispersal have been hypothesized to benefit the dispersing individual because dispersal reduces competition for local resources, potential for inbreeding, and competition for breeding partners. However, proximate cues influence important features of dispersal behavior, including when dispersal occurs, how long it lasts, and direction, straightness, and distance of the dispersal path. Therefore, proximate cues that affect dispersal influence ecological processes (e.g., population dynamics, disease transmission, gene flow). We captured and radio-marked 277 juvenile female white-tailed deer ( Odocoileus virginianus ), of which 27 dispersed, to evaluate dispersal behavior and to determine proximate cues that may influence dispersal behavior. Female dispersal largely occurred at 1 year of age and coincided with the fawning season. Dispersal paths varied but generally were non-linear and prolonged. Physical landscape features (i.e., roadways, rivers, residential areas) influenced dispersal path direction and where dispersal terminated. Additionally, forays outside of the natal range that did not result in dispersal occurred among 52% of global positioning system (GPS)-collared deer ( n = 25) during the dispersal period. Our results suggest intra-specific social interactions and physical landscape features influence dispersal behavior in female deer. Female dispersal behavior, particularly the lack of directionality, the semi-permeable nature of physical barriers, and the frequency of forays outside of the natal range, should be considered in regard to population management and controlling the spread of disease.

Pennsylvania↗
USGS2021

Evaluation of connectivity among black bear populations in Georgia

Habitat fragmentation and loss contribute to isolation of wildlife populations and increased extinction risks for various species, including many large carnivores. We studied a small and isolated population of American black bears ( Ursus americanus ) that is of conservation concern in central Georgia, USA (i.e., central Georgia bear population [CGBP]). Our goal was to evaluate the potential for demographic and genetic interchange from neighboring bear populations to the CGBP. To evaluate resource selection and movement potential, we used 35,487 global positioning system locations collected every 20 minutes from 2012 to 2014 from 33 male bears in the CGBP. We then developed a step selection function model based on conditional logistic regression. Male bears chose steps that avoided crops, roads, and human developments and were closer to forests and woody wetlands than expected based on availability. We used a geographic information system to simulate 300 bear movement paths from nearby bear populations in northern Florida, northern Georgia, and southern Georgia to estimate the potential for immigration to the CGBP. Only 4 simulated movement paths from the nearby populations intersected the CGBP. The creation of a hypothetical 1-km-wide corridor between the southern Georgia population and the CGBP produced only minor improvements in interchange. Our findings suggest that demographic connectivity between the CGBP and surrounding bear populations may be limited, and coupled with previous works showing genetic isolation in the CGBP, that creation of corridors may have only marginal effects on restoring gene flow, at least in the near term. Management actions such as translocation and the establishment of stepping stone populations may be needed to increase the genetic diversity and demographic stability of bears in the CGBP. © 2021 The Wildlife Society.

Florida Georgia, North Carolina, South Carolina↗
USGS2022

Density, harvest rates, and growth of a reintroduced American black bear population

Less than 30% of all species reintroductions have been successful and it is important that factors associated with success or failure be identified. Officials experimentally translocated 14 adult female American black bears ( Ursus americanus ) from Great Smoky Mountains National Park, North Carolina and Tennessee, USA, to Big South Fork National River and Recreation Area in the Cumberland Plateau of Kentucky and Tennessee, USA, in 1996–1997. Since that time, the reintroduced bear population has continued to expand in size and range so our study objective was to use spatially explicit capture-recapture methods across a wide spatial extent to estimate bear population abundance and growth. We constructed 440 (223 in KY, 217 in TN) hair traps in our primary sampling area in 2019 arranged in clusters of 4–9 traps/cluster, which we augmented with data from 138 hair traps in a secondary sampling area in Tennessee collected in 2018. We extracted and genotyped DNA from hair samples to construct spatially explicit capture histories, using spatial covariates to model inhomogeneous densities. Population abundance estimates across our 36,035-km 2 study area were 411 males and 406 females excluding cubs. Based on an initial standing population of 18 adult and subadult bears, the mean annual growth rate ( λ ) from 1998 to 2019 was 1.199. The mean annual harvest rate in Kentucky from 2013 to 2019 was 5.1% and in Tennessee from 2014 to 2019 was 13.2%. Based on simulations, the hunting seasons reduced mean λ from 1.217 to 1.199, but growth was rapid despite harvest. Genetic diversity was retained, with similar expected heterozygosity as in the source population. The lack of conspecifics, highly productive habitat, and an initial age and sex distribution that was skewed toward the most fecund members of the population likely contributed to the rapid growth and high levels of gene retention in this bear population.

Kentucky, Tennessee↗
USGS2025

Bait trapping of waterfowl increases the environmental contamination of avian influenza virus (AIV)

Highly pathogenic avian influenza virus (HPAIV) H5Nx clade 2.3.4.4b has circulated in North America since late 2021, resulting in higher rates of morbidity and mortality in wild birds than observed in this region before. The objective of this study was to determine whether baiting, which is widely conducted in Canada and the United States as part of waterfowl management practices (e.g., duck banding), influences the occurrence of avian influenza virus (AIV) in wetlands. We used a quasi-experimental design, collecting superficial sediment samples ( n = 336) and fecal samples ( n = 242) from paired baited (treatment) and non-baited (control) sites at 2 wetlands in Saskatchewan, Canada, between August and September 2022. We visited sampling sites 3 times during the sampling period: prior to the commencement of baiting activities ( t0 ), approximately 14 days after t0 ( t1 ), and 24 days after t0 ( t2 ). We screened samples for AIV using real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) targeting the matrix gene and subjected the PCR-positive samples to next-generation sequencing. We used a mixed-effects logistic regression model to estimate the effect of baiting on the odds of AIV positivity in sediment samples, while controlling for clustering by wetland. At control sites, we did not detect evidence for a difference in the odds of AIV detection in sediment at t1 or t2 versus t0 ; however, at baited sites, the odds of AIV detection at t1 were 5.43 (95% CI = 1.99, 14.79) times the odds at t0 and at t2 the odds of AIV detection were 8.73 (95% CI = 3.29, 23.18) times the odds at t0 . We detected HPAIV clade 2.3.4.4b H5N1 in sediment at 1 treatment site following baiting. There was also a trend towards increased fecal AIV positivity and increased fecal and sediment AIV diversity in baited versus non-baited sites; however, there was insufficient power to determine if these findings were statistically significant. Overall, our results indicate that baiting is associated with localized increases in AIV environmental contamination, with baiting potentially creating concentrated areas of AIV accumulation. As such, wetland baiting activities may pose a risk to wildlife population health through the propagation of AIV in wetlands and the waterfowl using those environments and efforts to replace, refine, or reduce this activity may be warranted depending on local ecosystem contexts and cost-benefit analyses.

Saskatchewan↗
USGS2023

Genetic structure of the Silver Chub indicates distinctiveness of Lake Erie population

Objective Silver Chub Macrhybopsis storeriana is a small riverine minnow endemic to North American fresh waters. Its range extends from the southern USA to southcentral Canada; the latter includes a rare lacustrine population in Lake Erie. Anthropogenic activities pose an immediate threat to several Silver Chub populations, currently categorized from special concern to threatened at the state level in the USA and federally and provincially not-at-risk to endangered in Canada. Several studies have examined the anthropogenic causes for the decline of Silver Chub populations, but conservation efforts have been hindered by the lack of knowledge of the population genetics of this species. Methods Here, we provide an assessment of the genetic diversity of Silver Chub populations across the USA and Canada using a fast-evolving mitochondrial gene, with particular focus on the Lake Erie population. Result We found the Lake Erie population to be divergent from all other populations, with nearly all the haplotypes sampled there being private. Conclusion Our study provides genetic evidence that the Silver Chub population in Lake Erie could be considered a separate conservation unit.

Lake Erie↗
USGS2023

Spatial and temporal overlap between hatchery- and natural-origin steelhead and Chinook salmon during spawning in the Klickitat River, Washington, USA

A goal of many segregated salmonid hatchery programs is to minimize potential interbreeding between hatchery- and natural-origin fish. To assess this on the Klickitat River, Washington, USA, we used radiotelemetry during 2009–2014 to evaluate spatiotemporal spawning overlap between hatchery-origin and natural-origin steelhead Oncorhynchus mykiss and spring Chinook Salmon O. tshawytscha. We estimated percentages of tagged fish that spawned naturally in the Klickitat River subbasin, emigrated from the Klickitat River, or died before spawning. For steelhead, 12% of hatchery-origin and 50% of natural-origin fish spawned naturally. For spring Chinook Salmon, 18% of hatchery-origin and 44% of natural-origin fish spawned naturally. Tag loss may result in underestimates in these percentages. Most hatchery-origin steelhead (90%) spawned downstream of rkm 32 and 75% spawned from November to mid-March, while the majority of natural-origin steelhead (64%) spawned upstream of rkm 32 and 75% spawned from mid-March to late May. Spawn timing of hatchery-origin Chinook Salmon (early August to mid-September) overlapped with that of natural-origin Chinook Salmon (late July to late September), and fish of both origins spawned in the same 30-km reach of the river. We estimated the percent of hatchery-origin spawners on the natural spawning grounds (pHOS) to be 12% for steelhead and 40% for spring Chinook Salmon across all study years. A kernel density analysis was used to estimate probability of spatiotemporal overlap between hatchery- and natural-origin spawners. For steelhead, we estimated this overlap to be 25% (95% CI 22.5–28%). For spring Chinook Salmon, tight spatial clustering of hatchery-origin fish resulted in a lower overlap estimate of 21% (13%-31%). We suggest adjusting pHOS estimates using these overlap estimates or similar spatiotemporal data on actual spawner proximity and possible interactions, and that these types of analyses be used in conjunction with gene flow analysis to accurately evaluate effects of individual hatchery programs.

Washington↗
USGS2010

Agronomic and environmental implications of enhanced s-triazine degradation

Novel catabolic pathways enabling rapid detoxification of s -triazine herbicides have been elucidated and detected at a growing number of locations. The genes responsible for s -triazine mineralization, i.e. atzABCDEF and trzNDF , occur in at least four bacterial phyla and are implicated in the development of enhanced degradation in agricultural soils from all continents except Antarctica. Enhanced degradation occurs in at least nine crops and six crop rotation systems that rely on s -triazine herbicides for weed control, and, with the exception of acidic soil conditions and s -triazine application frequency, adaptation of the microbial population is independent of soil physiochemical properties and cultural management practices. From an agronomic perspective, residual weed control could be reduced tenfold in s -triazine-adapted relative to non-adapted soils. From an environmental standpoint, the off-site loss of total s -triazine residues could be overestimated 13-fold in adapted soils if altered persistence estimates and metabolic pathways are not reflected in fate and transport models. Empirical models requiring soil pH and s -triazine use history as input parameters predict atrazine persistence more accurately than historical estimates, thereby allowing practitioners to adjust weed control strategies and model input values when warranted.

Pest Management Science↗
USGS2023

High-resolution thermal imagery reveals how interactions between crown structure and genetics shape plant temperature

Understanding interactions between environmental stress and genetic variation is crucial to predict the adaptive capacity of species to climate change. Leaf temperature is both a driver and a responsive indicator of plant physiological response to thermal stress, and methods to monitor it are needed. Foliar temperatures vary across leaf to canopy scales and are influenced by genetic factors, challenging efforts to map and model this critical variable. Thermal imagery collected using unoccupied aerial systems (UAS) offers an innovative way to measure thermal variation in plants across landscapes at leaf-level resolutions. We used a UAS equipped with a thermal camera to assess temperature variation among genetically distinct populations of big sagebrush ( Artemisia tridentata ), a keystone plant species that is the focus of intensive restoration efforts throughout much of western North America. We completed flights across a growing season in a sagebrush common garden to map leaf temperature relative to subspecies and cytotype, physiological phenotypes of plants, and summer heat stress. Our objectives were to (1) determine whether leaf-level stomatal conductance corresponds with changes in crown temperature; (2) quantify genetic (i.e., subspecies and cytotype) contributions to variation in leaf and crown temperatures; and (3) identify how crown structure, solar radiation, and subspecies-cytotype relate to leaf-level temperature. When considered across the whole season, stomatal conductance was negatively, non-linearly correlated with crown-level temperature derived from UAS. Subspecies identity best explained crown-level temperature with no difference observed between cytotypes. However, structural phenotypes and microclimate best explained leaf-level temperature. These results show how fine-scale thermal mapping can decouple the contribution of genetic, phenotypic, and microclimate factors on leaf temperature dynamics. As climate-change-induced heat stress becomes prevalent, thermal UAS represents a promising way to track plant phenotypes that emerge from gene-by-environment interactions.

Idaho↗
USGS2018

Neutral genetic and phenotypic variation within and among isolated headwater Brook Trout populations

Isolated populations are challenging to manage and conserve as they are particularly vulnerable to genetic drift, allelic fixation, inbreeding, and may express markedly reduced phenotypic variability. We sought to improve our understanding of how spatial isolation, occupancy range, and restricted gene flow influence contemporary phenotypic variation within and among native populations of Brook Trout Salvelinus fontinalis by examining the neutral genetic and phenotypic characteristics of 35 isolated headwater populations from Great Smoky Mountains National Park. Across a suite of 13 neutral microsatellite loci, we observed high levels of allelic fixation and considerable genetic differentiation among populations, subwatersheds, and watersheds that were consistent with patterns of isolation. We observed significant, positive correlations between allelic diversity and estimates of effective population sizes. In contrast, we observed considerably less phenotypic structure among streams, subwatersheds, and watersheds. Much of the phenotypic variation observed occurred among individuals within populations. Pairwise Mann‐Whitney tests revealed no significant phenotypic differences among the populations of Brook Trout we examined. Similarly, we observed no significant relationship between the amount of phenotypic variation within populations and any of the examined measures of genetic diversity or the amount of occupied habitat sampled, which suggests that unmeasured variables may be influencing morphometric and meristic variation within isolated populations. The observed patterns of isolation, genetic drift, and allelic fixation highlight the importance of enhancing population connectivity, but also suggest considerable phenotypic variability may persist within small, fragmented populations. Our results elucidate some challenges associated with managing and conserving isolated populations of Brook Trout, and reinforce the importance of conducting genetic studies on fragmented populations to inform management decisions.

Transactions of the American Fisheries Society↗
USGS2019

Nonlethal detection of Asian fish tapeworm in the federally-endangered Humpback Chub using a molecular screening tool

Optimal spawning habitat of federally endangered Humpback Chub Gila cypha exists within the Little Colorado River; however, temperatures in the Little Colorado River are also ideal for proliferation of the invasive pathogenic Asian fish tapeworm Schyzocotyle acheilognathi . The current standard for positive identification of the parasite is necropsy and visual examination of the gut via microscopy, a methodology undesirable for assessing infection in endangered fishes. A swab taken at the rectum of the fish and analyzed using a novel DNA primer targeting the cestode cytochrome oxidase I subunit mtDNA gene region offers a convenient nonlethal sampling tool. To validate the nonlethal methodology, primer sensitivity (51.9%) and specificity (79.5%) were calculated by exposing captive fish to the parasite and comparing results using the lethal standard method (i.e., visual examination). Subsequently, we utilized this nonlethal methodology to address prevalence of infection and infection frequency across a range of size-classes in a wild population of Humpback Chub and addressed possible patterns and mechanisms of infection in the Little Colorado River. When wild Humpback Chub were screened for infection prevalence in spring 2015 (21.4%, n = 140) and fall 2015 (6.6%, n = 258), the relative frequency of infection was highest in juveniles and subadult fish (200–300 mm). Elevated levels of infection near the major spawning grounds of Humpback Chub in the Little Colorado River promote parasitic infection, which may continue to persist without treatment or actions to control infections. We demonstrated that rectal swabs, in conjunction with PCR and primer-specific identification, offer a time-efficient nonlethal method to detect infection of Asian fish tapeworm in an endangered fish.

Transactions of the American Fisheries Society↗
USGS2020

Genetic structure of Smallmouth Bass in the Lake Michigan and Upper Mississippi River drainages relates to habitat, distance, and drainage boundaries: Smallmouth bass population genetic structure

Analysis of genetic connectivity helps to define stock boundaries and provides information on interpopulation dynamics, such as migration and spawning site fidelity. We used 16 microsatellite loci to describe the genetic population structure of 1,215 Smallmouth Bass Micropterus dolomieu from 32 sites throughout the upper Mississippi River and Lake Michigan watersheds. We found that Smallmouth Bass populations formed two genetically distinct units separated by the Mississippi River–Lake Michigan drainage boundary. Smallmouth Bass from the Lake Michigan drainage could be parsimoniously grouped into two or six genetically distinct units that largely corresponded with either river or lake habitats, while fish from the Mississippi River drainage grouped into two, six, or nine genetic units that were mostly associated with watershed boundaries. In the Lake Michigan and Mississippi River drainages, relative migration was limited between lake and river sites, suggesting that gene flow between neighboring sites with different habitat attributes can be low. Our research provides a higher‐resolution assessment of Smallmouth Bass genetic structure in a core portion of the species’ range and provides strong evidence that Smallmouth Bass populations are structured at small spatial scales that are potentially associated with habitat type. These results demonstrate the importance of evaluating genetic structure at small spatial scales and adopting management strategies that preserve genetic diversity of black bass populations at both the watershed level and the habitat level.

Michigan, Wisconsin↗
USGS2026

Cotton farming pesticides affect ileal microbiota activity expressions of virulome but not resistome or metabolic pathways in a sedentary wild passerine

The increased use of agrochemicals to enhance crop production has had detrimental environmental effects including implication in the sharp decline of North American farmland-breeding birds. Here, using a combination of deep shotgun metatranscriptomics and pesticide exposure data, we sought to assess whether exposure to cotton ( Gossypium spp.) production had a differential effect on ileum multi-kingdom microbial activity, metabolism, anti-microbial resistance, and virulence factors of sedentary northern mockingbirds ( Mimus polyglottos ) sampled from two cotton-producing areas (16 birds in total) and one uncultivated area (7 birds) in Texas, USA. Both Shannon Index values (Adj. r 2 = 0.174, F (1,21) = 5.633, p = 0.027) and a Mantel test (Spearman ρ = 0.184, p = 0.013) supported a relationship between metabolically active microbiota Bray–Curtis dissimilarities and differences in pesticide mixtures among study areas. Virulence factor richness (Adj. r 2 = 0.182, F (1,21) = 5.890, p = 0.024), Shannon Index (Adj. r 2 = 0.231, F (1,21) = 7.612, p = 0.012), and load (sum of virulence factor abundances; Adj. r 2 = 0.160, F (1,21) = 5.194, p = 0.033) were related to total pesticide load (total quantity of pesticides). We found no pesticide effects on expression of either antimicrobial resistance genes or metabolic pathways.

Texas↗
USGS2016

Concordance in diagnostic testing for respiratory pathogens of bighorn sheep

Reliable diagnostic tests are essential for disease investigation and management. This is particularly true for diseases of free-ranging wildlife where sampling is logistically difficult precluding retesting. Clinical assays for wildlife diseases frequently vary among laboratories because of lack of appropriate standardized commercial kits. Results of diagnostic testing may also be called into question when investigators report different etiologies for disease outbreaks, despite similar clinical and pathologic findings. To evaluate reliability of diagnostic testing for respiratory pathogens of bighorn sheep ( Ovis canadensis ), we conducted a series of ring tests across 6 laboratories routinely involved in detection of Mycoplasma ovipneumoniae , Pasteurellaceae, lktA (the Pasteurellaceae gene encoding leukotoxin), and 3 reference laboratories. Consistency of results for replicate samples within laboratories was high (median agreement = 1.0). Agreement between laboratories was high for polymerase chain reaction (PCR) detection of M. ovipneumoniae and culture isolation of Mannheimia spp. and Bibersteinia trehalosi (median agreement = 0.89–0.95, Kappa = 0.65–0.74), and lower for PCR detection of Mannheimia spp. lktA (median agreement = 0.58, Kappa = 0.12). Most errors on defined status samples were false negatives, suggesting test sensitivity was a greater problem than specificity. However, tests for M. haemolytica and lktA yielded some false positive results. Despite differences in testing protocols, median agreement among laboratories and correct classification of controls for most agents was ≥0.80, meeting or exceeding the standard required by federal proficiency testing programs. This information is valuable for interpreting test results, laboratory quality assessments, and advancing diagnosis of respiratory disease in wild sheep. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

Wildlife Society Bulletin↗