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USGS2021

Intended consequences statement

As the biodiversity crisis accelerates, the stakes are higher for threatened plants and animals. Rebuilding the health of our planet will require addressing underlying threats at many scales, including habitat loss and climate change. Conservation interventions such as habitat protection, management, restoration, predator control, translocation, genetic rescue, and biological control have the potential to help threatened or endangered species avert extinction. These existing, well-tested methods can be complemented and augmented by more frequent and faster adoption of new technologies, such as powerful new genetic tools. In addition, synthetic biology might offer solutions to currently intractable conservation problems. We believe that conservation needs to be bold and clear-eyed in this moment of great urgency.

Conservation Science and Practice↗

USGS2016

Applications of genetic data to improve management and conservation of river fishes and their habitats

Environmental variation and landscape features affect ecological processes in fluvial systems; however, assessing effects at management-relevant temporal and spatial scales is challenging. Genetic data can be used with landscape models and traditional ecological assessment data to identify biodiversity hotspots, predict ecosystem responses to anthropogenic effects, and detect impairments to underlying processes. We show that by combining taxonomic, demographic, and genetic data of species in complex riverscapes, managers can better understand the spatial and temporal scales over which environmental processes and disturbance influence biodiversity. We describe how population genetic models using empirical or simulated genetic data quantify effects of environmental processes affecting species diversity and distribution. Our summary shows that aquatic assessment initiatives that use standardized data sets to direct management actions can benefit from integration of genetic data to improve the predictability of disturbance–response relationships of river fishes and their habitats over a broad range of spatial and temporal scales.

Fisheries↗

USGS2021

An inventory and typology of permanent floodplain lakes in the Mississippi alluvial valley: A first step to conservation planning

The alluvial valley of the Mississippi River is an extensive area harboring hundreds of lakes created by fluvial dynamics. These floodplain lakes are scattered throughout the valley and carved over thousands of years by shifting river courses and other hydro-fluvial processes associated with contemporary and prehistoric rivers. These lakes have significant ecological importance as they support a large component of North American biodiversity. We used remote sensing to catalog lakes, to characterize morphology, and to construct a typology via cluster analysis. We identified over 1,300 permanent lakes totaling over 100,000 ha. The lakes were classified into 12 types according to lake size, shape, depth, connectivity, inundation frequency, and surrounding landcover. We anticipate that biotic characteristics differ among the 12 types, but large-scale systematic analyses of biotic assemblages of floodplain lakes in the region are mostly absent. Our typology can provide the framework essential for organizing research to define water dynamics, water quality, and ecological conditions such as forests, mussel, fish, and avian communities to construct conservation plans. The typology encourages a large-scale view of the properties of floodplain lakes in the alluvial valley. It is a functional tool that can be used to begin identifying conservation and research needs, adapt monitoring and management programs, customize environmental programs, and use conservation resources more effectively to achieve large-scale management objectives.

Mississippi River↗

USGS2022

Mangroves provide blue carbon ecological value at a low freshwater cost

“Blue carbon” wetland vegetation has a limited freshwater requirement. One type, mangroves, utilizes less freshwater during transpiration than adjacent terrestrial ecoregions, equating to only 43% (average) to 57% (potential) of evapotranspiration ( E T "> E T ). Here, we demonstrate that comparative consumptive water use by mangrove vegetation is as much as 2905 kL H 2 O ha −1 year −1 less than adjacent ecoregions with E c "> E c -to- E T "> E T ratios of 47–70%. Lower porewater salinity would, however, increase mangrove E c "> E c -to- E T "> E T ratios by affecting leaf-, tree-, and stand-level eco-physiological controls on transpiration. Restricted water use is also additive to other ecosystem services provided by mangroves, such as high carbon sequestration, coastal protection and support of biodiversity within estuarine and marine environments. Low freshwater demand enables mangroves to sustain ecological values of connected estuarine ecosystems with future reductions in freshwater while not competing with the freshwater needs of humans. Conservative water use may also be a characteristic of other emergent blue carbon wetlands.

Scientific Reports↗

USGS2023

Towards a better future for biodiversity and people: Modelling Nature Futures

The Nature Futures Framework (NFF) is a heuristic tool for co-creating positive futures for nature and people. It seeks to open up a diversity of futures through mainly three value perspectives on nature – Nature for Nature, Nature for Society, and Nature as Culture. This paper describes how the NFF can be applied in modelling to support decision-making. First, we describe key considerations for the NFF in developing qualitative and quantitative scenarios: i) multiple value perspectives on nature as a state space where pathways improving nature toward a frontier can be represented, ii) mutually reinforcing key feedbacks of social-ecological systems that are important for nature conservation and human wellbeing, iii) indicators of multiple knowledge systems describing the evolution of complex social-ecological dynamics. We then present three approaches to modelling Nature Futures scenarios in the review, screening, and design phases of policy processes. This paper seeks to facilitate the integration of relational values of nature in models and strengthen modelled linkages across biodiversity, nature’s contributions to people, and quality of life.

Global Environmental Change↗

USGS2007

New ecological knowledge and practices for society and sustainability

As attributes of the Earth's ecosystems shift in the face of human impact and sustainability of ecosystem services becomes less certain, one important tool at the disposal of the scientific community and other groups is a blueprint for understanding, evaluating, and communicating the value of ecological services. The blueprint presented here is based on (1) an examination of the ecological and societal trade-offs accompanying any given action, (2) revised methods of communication, and (3) coordination of actions at many different scales. The Mexican National Commission for the Knowledge and Use of Biodiversity (CONABIO) is a good example of a demand-driven “bridging institution” between academia, government, and civil society, and it works to collect and convert scientific information into information for policy, management, and conservation. Intergovernmental organizations like the United Nations Educational, Scientific and Cultural Organization (UNESCO) are well placed to facilitate such coordination at the international level, through their work with member states. Through collaboration with the constituencies of such organizations as the Ecological Society of America, the blueprint described below has the potential to become an important tool for assessing and managing threats to ecosystem services that are essential to life.

Frontiers in Ecology and the Environment↗

USGS2020

Avian community responses to management of vegetation and water levels in restored wetlands at the Humacao Nature Reserve, Puerto Rico

Coastal wetlands of the Caribbean have been greatly reduced in area and quality, and information on wildlife responses to management is lacking. We applied wetland management practices (disking, control of water levels) in a site historically disturbed by Saccharum spp. (sugarcane) cultivation at the Humacao Nature Reserve, southeastern Puerto Rico, and evaluated avian community response. We conducted weekly bird surveys and nest searches on disked and non-disked plots within recently constructed impoundments. The avian community shifted from 16 upland dominated species pre-restoration, to 67 wetland-dependent species at the end of our study (2001–2002). Ordination analysis indicated avian guild use of plots varied with environmental variables. Bird species diversity was not influenced by treatment, month, or salinity levels but was influenced by water depth and vegetation cover. Bird abundance was influenced by water depth, but not by treatment, month, salinity or vegetation cover. Furthermore, water depths of 0.10–0.20 m and salinity of ≤15 ppt promoted habitat conditions suitable for a diverse wetland avian community. We located 268 nests of 8 wetland bird species and observed adults with young of various other waterbirds, including species of conservation concern such as Dendrocygna arborea (West Indian Whistling Duck) and Porzana flaviventer (Yellow-breasted Crake). Bird community responses suggest that management practices (i.e., soil disturbance and control of water levels) can improve wetland biodiversity in abandoned sugarcane fields of Puerto Rico. Moreover, these practices may benefit wetland biodiversity in other Caribbean islands with a similar history of land use and habitat degradation.

Humacao Nature Reserve↗

USGS2012

Wetland hydrodynamics and long-term use of spring migration areas by lesser scaup in eastern South Dakota

Lesser scaup ( Aythya affinis [Eyton]) populations remain below their long-term average despite improved habitat conditions along spring migration routes and at breeding grounds. Scaup are typically associated with large, semipermanent wetlands and exhibit regional preferences along migration routes. Identifying consistently used habitats for conservation and restoration is complicated by irregular wetland availability due to the dynamic climate. We modeled long-term wetland use by lesser scaup in eastern South Dakota based on surveys conducted during below-average (1987-1989) and above-average (1993-2002) water condition years. Wetland permanence, longitude, and physiographic region were all significant determinants of use (P<0.01). Long-term use was best described by a quadratic equation including wetland surface area variability, an index of wetland hydrodynamics that is linked to productivity, biodiversity, and value to waterfowl. Contrary to previous findings, our study shows that over the long term, lesser scaup are more than twice as likely to use permanent wetlands as they are semipermanent wetlands. The northern region of South Dakota's Prairie Coteau, which holds the highest density of hydrologically dynamic permanent wetlands, should be considered an area of conservation concern for lesser scaup. The criteria we identified may be used to identify important lesser scaup habitats in other regions of the Prairie Pothole Region.

South Dakota↗

USGS2021

Widespread Ranavirus and Perkinsea infections in Cuban treefrogs (Osteopilus septentrionalis) invading New Orleans, USA

Invasive species can negatively impact ecosystems in numerous ways, including vectoring pathogenic organisms. In amphibians, a lineage globally threatened by multiple pathogens, this spread of disease via invasive species could contribute to declines in native populations. The Cuban Treefrog (Osteopilus septentrionalis) is invasive in the southeastern USA. To assess whether O. septentrionalis is a potential reservoir host for the pathogens Batrachochytrium dendrobatidis (Bd; Amphibian Chytrid Fungus), Ranavirus (Rv), and Perkinsea (Pr), we sampled 82 individuals from a recently invaded site in New Orleans, Louisiana, USA. We used quantitative PCR to assess prevalence and intensity of Bd, Rv, and Pr in mouthparts and tail clips from 22 larvae and in toe clips from 60 metamorphosed frogs. We compared infection prevalence and intensity across host characteristics, including Fulton’s Body Condition, sex, and life stage. None of the individuals were infected with Bd, 72% were infected with Rv, and 44% were infected with Pr. Twenty-three individuals (28%) were co-infected with Rv and Pr, but co-infection did not significantly predict the prevalence or intensity of either Rv or Pr. Although we did not observe any disease signs, Pr infections were significantly associated with lower body condition, suggesting sub-lethal fitness costs. Our study establishes that invasive O. septentrionalis in New Orleans are infected with two pathogens of global concern for amphibians. Understanding host-pathogen dynamics in O. septentrionalis in Louisiana is a critical step towards understanding how this invasive species could threaten amphibian biodiversity in the region by transmitting infectious pathogens.

Louisiana↗

USGS2020

A call for global action to conserve native trout in the 21st century and beyond

Trout and char (hereafter, trout ) represent some of the more culturally, economically and ecologically important taxa of freshwater fishes worldwide (Kershner, Williams, Gresswell, & Lobón‐Cerviá, 2019a ). Native to all continents in the Northern Hemisphere (as well as western Mediterranean Africa), trout belong to seven genera ( Oncorhynchus , Salvelinus, Salmo , Hucho, Parahucho, Brachymystax and Salvethymus ), which are distributed across more than 60 countries (Muhlfeld et al., 2019 ). Despite their broad importance as indicators of biodiversity in cold‐water ecosystems (Haak & Williams, 2013 ), as well as cultural icons for food and recreation, nearly half of the world's recognised trout species (IUCN, 2018 ) are imperilled or at risk of global extinction (Muhlfeld et al., 2018 , 2019 ). The root causes of their vulnerability include broad‐scale alteration of landscapes and watersheds, dams, overharvest, pollution, interactions with hatchery‐bred conspecifics and non‐native species. However, emerging threats such as climate change and related problems such as the spread of diseases and parasites pose significant challenges and uncertainties to native trout and their habitats (Kovach et al., 2016 ; Muhlfeld et al., 2018 ). Ultimately, conservation of native trout depends on understanding their diversity, a willingness to address threats at their root causes and implementing progressive conservation solutions that promote persistence of these iconic species in the face of growing human pressures.

Ecology of Freshwater Fish↗

USGS2019

Spatial sampling bias and model complexity in stream-based species distribution models: A case study of Paddlefish (Polyodon spathula) in the Arkansas River basin, USA

Leveraging existing presence records and geospatial datasets, species distribution modeling has been widely applied to informing species conservation and restoration efforts. Maxent is one of the most popular modeling algorithms, yet recent research has demonstrated Maxent models are vulnerable to prediction errors related to spatial sampling bias and model complexity. Despite elevated rates of biodiversity imperilment in stream ecosystems, the application of Maxent models to stream networks has lagged, as has the availability of tools to address potential sources of error and calculate model evaluation metrics when modeling in nonraster environments (such as stream networks). Herein, we use Maxent and customized R code to estimate the potential distribution of paddlefish ( Polyodon spathula ) at a stream-segment level within the Arkansas River basin, USA, while accounting for potential spatial sampling bias and model complexity. Filtering the presence data appeared to adequately remove an eastward, large-river sampling bias that was evident within the unfiltered presence dataset. In particular, our novel riverscape filter provided a repeatable means of obtaining a relatively even coverage of presence data among watersheds and streams of varying sizes. The greatest differences in estimated distributions were observed among models constructed with default versus AIC C -selected parameterization. Although all models had similarly high performance and evaluation metrics, the AIC C -selected models were more inclusive of westward-situated and smaller, headwater streams. Overall, our results solidified the importance of accounting for model complexity and spatial sampling bias in SDMs constructed within stream networks and provided a roadmap for future paddlefish restoration efforts in the study area.

Arkansas, Colorado, Kansas, Missouri, Nebraska, Ne↗

USGS2020

Calibrating environmental DNA metabarcoding to conventional surveys for measuring fish species richness

The ability to properly identify species present in a landscape is foundational to ecology and essential for natural resource management and conservation. However, many species are often unaccounted for due to ineffective direct capture and visual surveys, especially in aquatic environments. Environmental DNA metabarcoding is an approach that overcomes low detection probabilities and should consequently enhance estimates of biodiversity and its proxy, species richness. Here, we synthesize 37 studies in natural aquatic systems to compare species richness estimates for bony fish between eDNA metabarcoding and conventional methods, such as nets, visual census, and electrofishing. In freshwater systems with fewer than 100 species, we found eDNA metabarcoding detected more species than conventional methods. Using multiple genetic markers further increased species richness estimates with eDNA metabarcoding. For more diverse freshwater systems and across marine systems, eDNA metabarcoding reported similar values of species richness to conventional methods; however, more studies are needed in these environments to better evaluate relative performance. In systems with greater biodiversity, eDNA metabarcoding will require more populated reference databases, increased sampling effort, and multi-marker assays to ensure robust species richness estimates to further validate the approach. eDNA metabarcoding is reliable and provides a path for broader biodiversity assessments that can outperform conventional methods for estimating species richness.

Frontiers in Ecology and Evolution↗

USGS2021

Soil reservoir dynamics of ophidiomyces ophidiicola, the causative agent of snake fungal disease

Wildlife diseases pose an ever-growing threat to global biodiversity. Understanding how wildlife pathogens are distributed in the environment and the ability of pathogens to form environmental reservoirs is critical to understanding and predicting disease dynamics within host populations. Snake fungal disease (SFD) is an emerging conservation threat to North American snake populations. The causative agent, Ophidiomyces ophidiicola (Oo), is detectable in environmentally derived soils. However, little is known about the distribution of Oo in the environment and the persistence and growth of Oo in soils. Here, we use quantitative PCR to detect Oo in soil samples collected from five snake dens. We compare the detection rates between soils collected from within underground snake hibernacula and associated, adjacent topsoil samples. Additionally, we used microcosm growth assays to assess the growth of Oo in soils and investigate whether the detection and growth of Oo are related to abiotic parameters and microbial communities of soil samples. We found that Oo is significantly more likely to be detected in hibernaculum soils compared to topsoils. We also found that Oo was capable of growth in sterile soil, but no growth occurred in soils with an active microbial community. A number of fungal genera were more abundant in soils that did not permit growth of Oo, versus those that did. Our results suggest that soils may display a high degree of both general and specific suppression of Oo in the environment. Harnessing environmental suppression presents opportunities to mitigate the impacts of SFD in wild snake populations.

Journal of Fungi↗

USGS2026

Tropical and subtropical coral reefs

Global declines in coral cover persist, owing to increasing ocean temperatures associated with climate change, continued coastal development, pollution, sedimentation, diseases and the destruction and overextraction of marine resources (through fishing and coral harvesting). These stressors have an impact on coral biodiversity, reef-associated fauna and the architectural complexity of reef frameworks, compromising the food security and livelihoods of the millions of people who depend on these ecosystems (virtually certain, well established). The frequency and severity of disturbances caused by heatwaves, disease outbreaks and tropical storms have increased (virtually certain, established but incomplete), curtailing the recovery time between such disturbances. This pattern is projected to continue on its current trajectory (at best) or accelerate (very likely). The ecosystem services provided by coral reefs are substantial, not only in terms of biodiversity, but also in terms of direct economic benefits (including coastal protection, livelihoods for millions and nurseries for commercial species), as well as less tangible benefits, such as cultural and aesthetic (intrinsic) value (virtually certain, well established). Conservation, restoration and regeneration efforts are under way on a global scale, but few initiatives are implemented on a long-term, sustainable basis, with socioeconomic considerations, such as livelihoods, taken into account (virtually certain, well established). A wide range of approaches and tools is being developed, many of which are designed to mitigate or halt reef declines. These are often restricted to local reef-wide projects, however, and the potential for upscaling is sometimes criticized (unresolved). Documented results are also almost always undermined by a clear disconnect between these and other policy decisions, such as the extraction and burning of fossil fuels and coastal development (likely). Regardless of scalability concerns, all programmes need to be embedded within a broader evidence-based conservation framework. Global efforts are required to facilitate reef ecosystem survival and continued function by reducing emissions and ongoing climate change (virtually certain, established but incomplete). The reefs of today will not be the reefs of tomorrow (virtually certain) and shifting baselines need to be considered when setting objectives with respect to conservation, restoration and regeneration (virtually certain, established but incomplete).

Report↗

USGS2025

The scientific benefits of a statewide, standardized, coastal wetland monitoring program in Hawaiʻi

In this viewpoint, we provide a scientific justification for a statewide, standardized, coastal wetland monitoring program for Hawaiʻi, USA. Hawaiian coastal wetlands provide important habitat for endangered waterbirds, invertebrates, plants, and the Hawaiian hoary bat (ʻōpeʻapeʻa; Lasiurus semotus ) as well as support Indigenous food systems. Currently, numerous agencies and groups in Hawaiʻi collect data on coastal wetlands, but information is not typically shared and methods are not standardized. A statewide, standardized, coastal wetland monitoring program with a centralized database would allow managers to keep better track of progress toward restoration goals, population changes of conservation-reliant species, outbreaks and impacts of avian botulism, rates of coastal salinization, and many other critical issues across space and time. Monitoring combined with targeted research could fill critical knowledge gaps about the types, functions, values, and biodiversity of Hawaiian coastal wetlands. Ultimately, the improved knowledge gained from long-term coastal wetland monitoring could inform landscape-scale restoration actions and adaptive management of coastal wetlands under sea-level rise and climate change.

Hawaii↗

USGS2024

From eDNA to decisions using a multi-method approach to restoration planning in streams

Reintroduction efforts are increasingly used to mitigate biodiversity losses, but are frequently challenged by inadequate planning and uncertainty. High quality information about population status and threats can be used to prioritize reintroduction and restoration efforts and can transform ad hoc approaches into opportunities for improving conservation outcomes at a landscape scale. We conducted comprehensive environmental DNA (eDNA) and visual encounter surveys to determine the distribution of native and non-native aquatic species in two high-priority watersheds to address key uncertainties—such as the distribution of threats and the status of existing populations—inherent in restoration planning. We then used these occurrence data to develop a menu of potential conservation actions and a decision framework to benefit an endangered vertebrate (foothill yellow-legged frog, Rana boylii ) in dynamic stream systems. Our framework combines the strengths of multiple methods, allowing managers and conservation scientists to incorporate conservation science and site-specific knowledge into the planning process to increase the likelihood of achieving conservation goals.

Scientific Reports↗

USGS2021

Quantifying the representation of plant communities in the protected areas of the U.S.: An analysis based on the U.S. National Vegetation Classification Groups

Plant communities represent the integration of ecological and biological processes and they serve as an important component for the protection of biological diversity. To measure progress towards protection of ecosystems in the United States for various stated conservation targets we need datasets at the appropriate thematic, spatial, and temporal resolution. The recent release of the LANDFIRE Existing Vegetation Data Products (2016 Remap) with a legend based on U.S. National Vegetation Classification allowed us to assess the conservation status of plant communities of the U.S. The map legend is based on the Group level of the USNVC, which characterizes the regional differences in plant communities based on dominant and diagnostic plant species. By combining the Group level map with the Protected Areas Database of the United States (PAD-US Ver 2.1), we quantified the representation of each Group. If the mapped vegetation is assumed to be 100% accurate, using the Aichi Biodiversity target (17% land in protection by 2020) we found that 159 of the 265 natural Groups have less than 17% in GAP Status 1 & 2 lands and 216 of the 265 Groups fail to meet a 30% representation target. Only four of the twenty ecoregions have >17% of their extent in Status 1 & 2 lands. Sixteen ecoregions are dominated by Groups that are under-represented. Most ecoregions have many hectares of natural or ruderal vegetation that could contribute to future conservation efforts and this analysis helps identify specific targets and opportunities for conservation across the U.S.

Forests↗

USGS2026

Influence of new residential construction varying in housing density on bird species, human tolerance guilds, and communities

Human population growth and changing settlement patterns fuel the development of urban fringe lands worldwide, with implications for biodiversity. We conducted a 12-year study of birds in the fast-developing urban fringe lands of the central Puget Sound region, Washington, USA, to examine the effect of development configuration on birds. We hypothesized that lower-intensity conservation developments, compared to higher-intensity planned community developments, would benefit the overall bird community, as well as native forest birds (avoiders of human development) and avian generalist species (adapters to human development), but that higher-intensity planned community developments would benefit synanthropic species (exploiters of human development). We fit single-species and multi-species occupancy models to test these hypotheses. Consistent with our hypotheses, we found that a greater proportion of the overall community, avoiders, and adapters occupied lower-intensity conservation developments compared to higher-intensity planned community developments. However, we did not detect an effect of development type on the exploiter guild, and we found that species in the exploiter guild are variable in their response to the configuration of suburban developments. We also hypothesized that human tolerance guilds would be a useful predictor of individual species responses to development type. This hypothesis was somewhat supported: we found that, for avoiders, 87% of species in the guild had the same response to development type as the overall guild; for adapters, 63% had the same response as the overall guild, and for exploiters, only 44% had the same response as the overall guild. Our results indicate that the configuration of suburban developments can have a meaningful impact on bird communities, particularly on those species that are most sensitive to any level of development.

Washington↗