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At least 613 records · Page 34Linked to original sources
USGS2021

eDNA metabarcoding outperforms traditional fisheries sampling and reveals fine-scale heterogeneity in a temperate freshwater lake

Understanding biodiversity in aquatic systems is critical to ecological research and conservation efforts, but accurately measuring species richness using traditional methods can be challenging. Environmental DNA (eDNA) metabarcoding, which uses high-throughput sequencing and universal primers to amplify DNA from multiple species present in an environmental sample, has shown great promise for augmenting results from traditional sampling to characterize fish communities in aquatic systems. Few studies, however, have compared exhaustive traditional sampling with eDNA metabarcoding of corresponding water samples at a small spatial scale. We intensively sampled Boardman Lake (1.4 km 2 ) in Michigan, USA, from May to June in 2019 using gill and fyke nets and paired each net set with lake water samples collected in triplicate. We analyzed water samples using eDNA metabarcoding with 12S and 16S fish-specific primers and compared estimates of fish diversity among methods. In total, we set 60 nets and analyzed 180 1 L lake water samples. We captured a total of 12 fish species in our traditional gear and detected 40 taxa in the eDNA water samples, which included all the species observed in nets. The 12S and 16S assays detected a comparable number of taxa, but taxonomic resolution varied between the two genes. In our traditional gear, there was a clear difference in the species selectivity between the two net types, and there were several species commonly detected in the eDNA samples that were not captured in nets. Finally, we detected spatial heterogeneity in fish community composition across relatively small scales in Boardman Lake with eDNA metabarcoding, but not with traditional sampling. Our results demonstrated that eDNA metabarcoding was substantially more efficient than traditional gear for estimating community composition, highlighting the utility of eDNA metabarcoding for assessing species diversity and informing management and conservation.

Michigan↗
USGS2023

Toward a national eDNA strategy for the United States

Environmental DNA (eDNA) data make it possible to measure and monitor biodiversity at unprecedented resolution and scale. As use-cases multiply and scientific consensus grows regarding the value of eDNA analysis, public agencies have an opportunity to decide how and where eDNA data fit into their mandates. Within the United States, many federal and state agencies are individually using eDNA data in various applications and developing relevant scientific expertise. A national strategy for eDNA implementation would capitalize on recent scientific developments, providing a common set of next-generation tools for natural resource management and public health protection. Such a strategy would avoid patchwork and possibly inconsistent guidelines in different agencies, smoothing the way for efficient uptake of eDNA data in management. Because eDNA analysis is already in widespread use in both ocean and freshwater settings, we focus here on applications in these environments. However, we foresee the broad adoption of eDNA analysis to meet many resource management issues across the nation because the same tools have immediate terrestrial and aerial applications.

Environmental DNA↗
USGS2023

The Government eDNA Working Group 6th Annual eDNA Technical Exchange Workshop

The 6th annual Environmental DNA (eDNA) Technical Exchange Workshop was a virtual workshop hosted and coordinated by the Government eDNA Working Group (GEDWG) on January 24–26, 2023. GEDWG is a no-cost consortium that focuses on bringing together stakeholders associated with federal, state, provincial, municipal, and other government and non-government agencies interested in eDNA and related fields, for the purposes of sharing technical expertise and experience during monthly discussion meetings and annual workshops. Over 400 participants registered for the virtual Workshop, which featured four keynote speakers, 23 platform talks, eight short-form poster presentations, and an extended discussion session. Workshop attendees represented a broad cross-section of disciplines and backgrounds, including research scientists, natural resource managers, and conservation policy experts, and many different government agencies, private environmental consulting firms, trade organizations, non-governmental organizations, and others in the environmental management sector. Key takeaways from the workshop included moving the application of eDNA into resource management and discovering ways to improve policy uptake in the development of nationwide biodiversity monitoring, some of which is happening in the development of eDNA networks and national strategies. Future research directions discussed include studies of fate and transport, autonomous sampling/sample processing, and reference library curation. Additionally, co-design of studies and improved engagement and communication among scientists and managers are needed to ensure clear expectations and outcomes.

Environmental DNA↗
USGS2024

How, what, and where you sample environmental DNA affects diversity estimates and species detection

Environmental DNA (eDNA) is a complex mixture of DNA, varying in particle sizes and distributed heterogeneously in aquatic systems. Optimizing eDNA sampling is crucial for maximizing species detection, particularly in high-risk scenarios like invasive species management. In this study, we compare two eDNA sampling methods - namely tow net and grab sample, where the tow nets process large volumes of water (3500–7000 L) through a 64 μm pore size and the grab samples process 1 L sample at a single point through 0.45–1.2 μm pore size membranes. We compared these methods to ascertain what most influences (1) the detection of invasive species ( Dreissena mussels and Burmese pythons) using qPCR or ddPCR and (2) total diversity monitoring of metazoan, protist, and fungi community using a COI marker and plant communities using the ITS marker. Sampling was conducted across a wide geography and diverse aquatic environments in Minnesota and Florida, USA, and Switzerland. The tow net samples had significantly higher eDNA yield compared to grab samples; however, they exhibited equal or lower alpha diversity of OTUs (Operational Taxonomic Units). The two sampling methods measured different beta diversity of communities detected with the COI marker across all three regions, highlighting the impact of the sampling method on the diversity of eDNA captured. In comparison, the beta diversity of plant eDNA was less impacted by the sampling method. We found no clear difference in detection for the invasive species targets based on the eDNA sampling method. These results underscore the need for pilot studies before conducting biodiversity inventory and monitoring, and a need for a greater understanding of not just how much, but also what, eDNA is captured depending on method choice, considering both spatial and particle size heterogeneity.

Florida, Minnesota↗
USGS2017

Impacts of climate change on mangrove ecosystems: A region by region overview

Inter-related and spatially variable climate change factors including sea level rise, increased storminess, altered precipitation regime and increasing temperature are impacting mangroves at regional scales. This review highlights extreme regional variation in climate change threats and impacts, and how these factors impact the structure of mangrove communities, their biodiversity and geomorphological setting. All these factors interplay to determine spatially variable resiliency to climate change impacts, and because mangroves are varied in type and geographical location, these systems are good models for understanding such interactions at different scales. Sea level rise is likely to influence mangroves in all regions although local impacts are likely to be more varied. Changes in the frequency and intensity of storminess are likely to have a greater impact on N and Central America, Asia, Australia, and East Africa than West Africa and S. America. This review also highlights the numerous geographical knowledge gaps of climate change impacts, with some regions particularly understudied (e.g., Africa and the Middle East). While there has been a recent drive to address these knowledge gaps especially in South America and Asia, further research is required to allow researchers to tease apart the processes that influence both vulnerability and resilience to climate change. A more globally representative view of mangroves would allow us to better understand the importance of mangrove type and landscape setting in determining system resiliency to future climate change.

Ecosystem Health and Sustainability↗
USGS2023

Bioaccumulation kinetics of model pharmaceuticals in the freshwater unionid pondmussel, Sagittunio subrostratus

Bioaccumulation of ionizable pharmaceuticals has been increasingly studied, with most reported aquatic tissue concentrations in field or laboratory experiments being from fish. However, higher levels of antidepressants have been observed in bivalves compared with fish from effluent-dominated and dependent surface waters. Such observations may be important for biodiversity because approximately 70% of freshwater bivalves in North America are considered to be vulnerable to extinction. Because experimental bioaccumulation information for freshwater bivalves is lacking, we examined accumulation dynamics in the freshwater pondmussel, Sagittunio subrostratus , following exposure to a model weak acid, acetaminophen (mean (±SD) = 4.9 ± 1 µg L –1 ), and a model weak base, sertraline (mean (±SD) = 1.1 ± 1.1 µg L –1 ) during 14-day uptake and 7-day depuration experiments. Pharmaceutical concentrations were analyzed in water and tissue using isotope dilution liquid chromatography–tandem mass spectrometry. Mussels accumulated two orders of magnitude higher concentrations of sertraline (31.7 ± 9.4 µg g –1 ) compared to acetaminophen (0.3 ± 0.1 µg g –1 ). Ratio and kinetic-based bioaccumulation factors of 28,836.4 (L kg –1 ) and 34.9 (L kg –1 ) were calculated for sertraline and for acetaminophen at 65.3 (L kg –1 ) and 0.13 (L kg –1 ), respectively. However, after 14 days sertraline did not reach steady-state concentrations, although it was readily eliminated by S. subrostratus . Acetaminophen rapidly reached steady-state conditions but was not depurated over a 7-day period. Future bioaccumulation studies of ionizable pharmaceuticals in freshwater bivalves appear warranted. Environ Toxicol Chem 2023;00:1–7. © 2023 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Missouri↗
USGS2020

Disturbance refugia within mosaics of forest fire, drought, and insect outbreaks

Disturbance refugia – locations that experience less severe or frequent disturbances than the surrounding landscape – provide a framework to highlight not only where and why these biological legacies persist as adjacent areas change but also the value of those legacies in sustaining biodiversity. Recent studies of disturbance refugia in forest ecosystems have focused primarily on fire, with a growing recognition of important applications to land management. Given the wide range of disturbance processes in forests, developing a broader understanding of disturbance refugia is important for scientists and land managers, particularly in the context of anthropogenic climate change. We illustrate the framework of disturbance refugia through the individual and interactive effects of three prominent forest disturbance agents: fire, drought, and insect outbreaks. We provide examples of disturbance refugia and related applications to natural resource management in western North America, demonstrate methods for characterizing refugia, identify research priorities, and discuss why a more comprehensive definition of disturbance refugia is relevant to conservation globally.

Frontiers in Ecology and the Environment↗
USGS2020

Validating climate‐change refugia: Empirical bottom‐up approaches to support management actions

Efforts to conserve biodiversity increasingly focus on identifying climate‐change refugia – areas relatively buffered from contemporary climate change over time that enable species persistence. Identification of refugia typically includes modeling the distribution of a species’ current habitat and then extrapolating that distribution given projected changes in temperature and precipitation, or by mapping topographic features that buffer species from regional climate extremes. However, the function of those hypothesized refugia must be validated (or challenged) with independent data not used in the initial identification of the refugia. Although doing so would facilitate the incorporation of climate‐change refugia into conservation and management decision making, a synthesis of validation methods is currently lacking. We reviewed the literature and defined four methods to test refugia predictions. We propose that such bottom‐up approaches can lead to improved protected‐area designations and on‐the‐ground management actions to reduce influences from non‐climate stressors within potential refugia.

Idaho, Montana, Wyoming↗
USGS2022

Trade-offs between utility-scale solar development and ungulates on western rangelands

Utility-scale solar energy (USSE) has become an efficient and cost-effective form of renewable energy, with an expanding footprint into rangelands that provide important habitat for many wild ungulate populations. Using global positioning system data collected before and after construction, we documented the potential impacts of USSE on pronghorn ( Antilocapra americana ), including direct habitat loss, indirect habitat loss, and barrier effects to both resident and migratory population segments. Our case study highlights the challenges that USSE poses to ungulate conservation, including (1) impermeable security fencing that blocks access to and reduces connectivity between formerly available habitats, and (2) the lack of guidelines for minimizing USSE impacts on ungulates. Improved siting and ungulate-specific best management practices would help to minimize habitat loss and retain landscape connectivity. Ungulate biodiversity and ecosystem services (for example, services provided by long-distance migratory species) in arid rangelands are important considerations when balancing the global benefits of renewable energy with local wildlife impacts.

Wyoming↗
USGS2026

Annual grass invasion is transforming the sagebrush biome’s songbird communities

Novel stressors like climate change and biological invasions alter ecological communities, resulting in changes to ecosystem services and biodiversity (that is, ecological transformation). Most ecological transformation research focuses on plants, but animals are likely affected by and plausibly mediate the extent, impact, and pace of transformations. In western North America, where invasive annual grasses are transforming sagebrush-steppe ecosystems, we quantified how transformation in vegetation drives songbird community change. We hypothesized that transformation of vegetation communities via invasion alters wildlife communities by favoring generalists over specialists, albeit with extinction debts that may temporarily obscure transformations’ consequences. Although local-scale songbird diversity increased with grass invasion, we found that this shift was accompanied by ongoing reorganization of songbird communities at larger scales (across the sagebrush biome), driven by heterogeneous impacts of invasion among species and guilds. Through our biome-wide analysis, we were also able to identify high-priority regions for conservation of sensitive songbird species. Our research provides evidence that wildlife communities are transforming alongside vegetation communities and offers insight into the approaches required to quantify nascent community turnover.

western United States↗
USGS2020

Perceived ecological threats and economic benefits of non-native black bass in the United States

Black bass Micropterus spp. are highly sought-after sport fish and, where introduced, are emblematic of the tradeoffs between ensuring productive fisheries and conserving native biodiversity. To disentangle these potentially conflicting interests, we administered a survey of fisheries biologists in the United States to assess perceptions regarding ecological and economic impacts of non-native black bass between anthropogenic and natural habitats. Our results indicate that non-native black bass are generally considered economically beneficial in both habitat types. Contrastingly, these species were perceived to have significantly more negative ecological impacts in natural than anthropogenic habitats. Our findings suggest that habitat may be an important factor to partition the conflicting ecological–economic dynamic of non-native black bass. Implications of this study suggest that challenges remain for managers attempting to balance the paradoxical nature of these species as both desired sport fishes and as potentially harmful invaders when found outside their native range.

Fisheries Magazine↗
USGS2022

Native fish need a natural flow regime

Water development has threatened the ecological integrity of riverine ecosystems. Increasing water demand, persistent drought, and climate change exacerbate the effects of habitat degradation and loss in altered systems such as the Colorado River basin. Today, biologists are challenged to identify management actions that benefit native fishes while not hindering water development or management. Herein, we discuss the importance of the natural flow regime for functioning riverine ecosystems and provide examples from four tributaries to the Green River, a major headwater branch of the Colorado River. These tributaries represent a gradient of impacts ranging from water abstraction to the point of complete seasonal desiccation to a relatively natural flow regime, and consequently have maintained different levels of instream habitat complexity and native fish persistence. Despite decades of management, endangered species lack self-sustaining populations and other native species have been extirpated from over half their ranges, which begs the question: can water development and fish conservation be balanced under current water laws and climate change-driven declines in runoff? Given the continued decline in freshwater biodiversity and abundance occurring across the globe, we contend that immediate designation of rivers with natural flow regimes as freshwater conservation areas will enhance native species recovery.

Arizona, Colorado, Utah, Wyoming↗
USGS2026

Adaptive capacity of freshwater organisms in North America: Current understanding and future applications

Freshwater species are increasingly threatened by climate change, yet our ability to assess their vulnerability remains incomplete. Typically, climate change vulnerability assessments (CCVAs) evaluate three components: exposure, sensitivity, and adaptive capacity. Adaptive capacity, defined as the ability of a species to adjust to changing conditions, provides critical insight into how species may persist under future scenarios and can strengthen conservation planning by highlighting opportunities for resilience and targeted management strategies. Trait-based approaches offer a promising path for managers to operationalize adaptive capacity by identifying measurable biological and ecological traits that influence climate change response strategies. However, these insights are rarely integrated into broader vulnerability frameworks that support conservation decision making. We build on previous research to synthesize current understanding of adaptive capacity for three freshwater taxa in North America: fishes, mussels, and crayfishes. Our objectives were to: (1) assess the relevance of adaptive capacity factors for fishes, mussels, and crayfishes; (2) identify key opportunities and gaps in linking trait-based information into adaptive capacity assessments; and (3) illustrate how incorporating adaptive capacity can enhance management decisions for freshwater species under climate change. We used an expert workshop, literature review, and case studies to identify relevant adaptive capacity factors, assess available information, and evaluate inclusion in management contexts. We found that all three taxa had sufficient information to inform adaptive capacity assessments. In addition to existing adaptive capacity factors, we identified Morphology as an important yet underutilized cross-cutting diagnostic category when information was limited. By explicitly linking trait-based approaches with adaptive capacity frameworks, we offer practical guidance for improving climate adaptation strategies and prioritizing management actions for freshwater biodiversity under accelerating global change.

Global Change Biology Communications↗
USGS2015

Wide-area estimates of evapotranspiration by red gum ( Eucalyptus camaldulensis ) and associated vegetation in the Murray-Darling River Basin, Australia

Floodplain red gum forests ( Eucalyptus camaldulensis plus associated grasses, reeds and sedges) are sites of high biodiversity in otherwise arid regions of southeastern Australia. They depend on periodic floods from rivers, but dams and diversions have reduced flood frequencies and volumes, leading to deterioration of trees and associated biota. There is a need to determine their water requirements so environmental flows can be administered to maintain or restore the forests. Their water requirements include the frequency and extent of overbank flooding, which recharges the floodplain soils with water, as well as the actual amount of water consumed in evapotranspiration (ET). We estimated the flooding requirements and ET for a 38 134 ha area of red gum forest fed by the Murrumbidgee River in Yanga National Park, New South Wales. ET was estimated by three methods: sap flux sensors placed in individual trees; a remote sensing method based on the Enhanced Vegetation Index from MODIS satellite imagery and a water balance method based on differences between river flows into and out of the forest. The methods gave comparable estimates yet covered different spatial and temporal scales. We estimated flood frequency and volume requirements by comparing Normalized Difference Vegetation Index values from Landsat images with flood history from 1995 to 2014, which included both wet periods and dry periods. ET during wet years is about 50% of potential ET but is much less in dry years because of the trees' ability to control stomatal conductance. Based on our analyses plus other studies, red gum trees at this location require environmental flows of 2000 GL yr −1 every other year, with peak flows of 20 000 ML d −1 , to produce flooding sufficient to keep them in good condition. However, only about 120–200 GL yr −1 of river water is consumed in ET, with the remainder flowing out of the forest where it enters the Murray River system.

Murray-Darling River Basin↗
USGS2020

Ecohydrological responses to surface flow across borders: Two decades of changes in vegetation greenness and water use in the riparian corridor of the Colorado River Delta

Hydrological and bioclimatic processes that lead to drought may stress plants and wildlife, restructure plant community type and architecture, increase monotypic stands and bare soils, facilitate the invasion of non‐native plant species and accelerate soil erosion. Our study focuses on the impact of a paucity of Colorado River surface flows from the United States (U.S.) to Mexico. We measured change in riparian plant greenness and water use over the past two decades using remotely sensed measurements of vegetation index (VI), evapotranspiration (ET), and a new annualized Phenology Assessment Metric (PAM) for ET. We measure these long‐term (2000‐2019) metrics and their short‐term (2014‐2019) response to an environmental, pulse flow in 2014, as prescribed under Minute 319 of the 1944 Water Treaty between the two nations. In subsequent years, small directed flows were provided to restoration areas under Minute 323. We use 250 m MODIS and 30 m Landsat imagery to evaluate three vegetation indices (NDVI, EVI, EVI2). We select EVI2 to parameterize an optical‐based ET algorithm and test the relationship between ET from Landsat and MODIS by regression approaches. Our analyses show significant decreases in VIs and ET for both the 20‐year and post‐pulse 5‐year periods. Over the last 20 years, EVI Landsat declined 34% (30% by EVI MODIS ) and ET Landsat‐EVI declined 38% (27% by ET MODIS‐EVI ), overall ca. 1.61 mmd ‐1 or 476 mmyr ‐1 drop in ET. Over the 5 years since the 2014 pulse flow, EVI Landsat declined 20% (13% by EVI MODIS ) and ET Landsat‐EVI declined 23% (4% by ET MODIS‐EVI ) with a 0.77 mmd ‐1 or a 209 mmyr ‐1 5‐year drop in ET. Data and change maps show the pulse flow contributed enough water to slow the rate of loss, but only for the very short‐term (1‐2 years). These findings are critically important as they suggest further deterioration of biodiversity, wildlife habitat and key ecosystem services due to anthropogenic diversions of water in the U.S. and Mexico and from land clearing, fires, and plant‐related drought which affect hydrological processes.

Colorado River delta↗
USGS2024

Using life history traits to assess climate change vulnerability in understudied species

Climate change is a primary threat to biodiversity, but for many species, we still lack information required to assess their relative vulnerability to changes. Climate change vulnerability assessment (CCVA) is a widely used technique to rank relative vulnerability to climate change based on species characteristics, such as their distributions, habitat associations, environmental tolerances, and life-history traits. However, for species that we expect are vulnerable to climate change yet are understudied, like many amphibians, we often lack information required to construct CCVAs using existing methods. We used the CCVA framework to construct trait-based models based on life history theory, using empirical evidence of traits and distributions that reflected sensitivity of amphibians to environmental perturbation. We performed CCVAs for amphibians in 7 states in the north-central USA, focusing on 31 aquatic-breeding species listed as species of greatest conservation need by at least 1 state. Because detailed information on habitat requirements is unavailable for most amphibian species, we used species distributions and information on traits expected to influence vulnerability to a drying climate (e.g., clutch size and habitat breadth). We scored species vulnerability based on changes projected for mid-century (2040−2069) from 2 climate models representing “least-dry” and “most-dry” scenarios for the region. Species characteristics useful for discriminating vulnerability in our models included small range size, small clutch size, inflexible diel activity patterns, and smaller habitat breadth. When projected climate scenarios included a mix of drier and wetter conditions in the future, the exposure of a species to drying conditions was most important to relative rankings. When the scenario was universally drier, species characteristics were more important to relative rankings. Using information typically available even for understudied species and a range of climate projections, our results highlight the potential of using life history traits as indicators of relative climate vulnerability. The commonalities we identified provide a framework that can be used to assess other understudied species threatened by climate change.

Colorado, Kansas, Montana, Nebraska, North Dakota,↗
USGS2016

Application of genetics and genomics to wildlife epidemiology

Wildlife diseases can have significant impacts on wildlife conservation and management. Many of the pathogens that affect wildlife also have important implications for domestic animal and human health. However, management interventions to prevent or control wildlife disease are hampered by uncertainties about the complex interactions between pathogens and free-ranging wildlife. We often lack crucial knowledge about host ecology, pathogen characteristics, and host–pathogen dynamics. The purpose of this review is to familiarize wildlife biologists and managers with the application of genetic and genomic methodologies for investigating pathogen and host biology to better understand and manage wildlife diseases. The genesis of this review was a symposium at the 2013 annual Wildlife Society Conference. We reviewed the scientific literature and used our personal experiences to identify studies that illustrate the application of genetic and genomic methods to advance our understanding of wildlife epidemiology, focusing on recent research, new techniques, and innovative approaches. Using examples from a variety of pathogen types and a broad array of vertebrate taxa, we describe how genetics and genomics can provide tools to detect and characterize pathogens, uncover routes of disease transmission and spread, shed light on the ways that disease susceptibility is influenced by both host and pathogen attributes, and elucidate the impacts of disease on wildlife populations. Genetic and increasingly genomic methodologies will continue to contribute important insights into pathogen and host biology that will aid efforts to assess and mitigate the impacts of wildlife diseases on global health and conservation of biodiversity.

Journal of Wildlife Management↗
USGS2018

Use of created snags by cavity‐nesting birds across 25 years

Snags are important habitat features for many forest‐dwelling species, so reductions in the number of snags can lead to the loss of biodiversity in forest ecosystems. Intentional snag creation is often used in managed forests to mitigate the long‐term declines of naturally created snags, yet information regarding the use of snags by wildlife across long timescales (>20 yr) is lacking and prevents a complete understanding of how the value of created snags change through time. We used a long‐term experiment to assess how harvest treatment (i.e., small‐patch group selection, 2‐story, and clearcut) and snag configuration (i.e., scattered and clustered) influenced nesting in and foraging on 25–27‐year‐old Douglas‐fir ( Pseudotsuga menziesii ) snags by cavity‐nesting birds. In addition, we compared our contemporary measures of bird use to estimates obtained from historical surveys conducted on the same group of snags to quantify how bird use changed over time. Despite observing created snags for >750 hours across 2 consecutive breeding seasons, we found limited evidence of nesting activity. Only 11% of created snags were used for breeding, with nesting attempts by 4 bird species ( n = 36 nests); however, we detected 12 cavity‐nesting species present on our study sites. Furthermore, nearly all nests (94%) belonged to the chestnut‐backed chickadee ( Poecile rufescens ), a weak cavity‐excavating species that requires well‐decayed wood for creating nest cavities. Our surveys also recorded few observations of birds using created snags as foraging substrates, with only 1 foraging event recorded for every 20 hours of observation. We detected 82% fewer nests and recorded 7% fewer foraging observations during contemporary field work despite spending >7.5 times more effort observing created snags relative to historical surveys. We conclude that 25–27‐year‐old created Douglas‐fir snags provided limited opportunities for nesting and foraging by most cavity‐nesting birds, and that the period of greatest use by this group occurred within 5–15 years of creation.

Journal of Wildlife Management↗