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The use of coverboards in estimating patterns of reptile and amphibian biodiversity
No abstract available at this time
Biodiversity and zoogeography of non-marine turtles in Southeast Asia
No abstract available at this time
Biodiversity and ecosystem function in mediterranean-climate California,
No abstract available at this time
Influence of eastern hemlock on aquatic biodiversity in Delaware Water Gap National Recreation Area
No abstract available at this time
Defining conservation priorities for freshwater fishes according to taxonomic, functional, and phylogenetic diversity
To date, the predominant use of systematic conservation planning has been to evaluate and conserve areas of high terrestrial biodiversity. Although studies in freshwater ecosystems have received recent attention, research has rarely considered the potential trade-offs between protecting different dimensions of biodiversity and the ecological processes that maintain diversity. We provide the first systematic prioritization for freshwaters (focusing on the highly threatened and globally distinct fish fauna of the Lower Colorado River Basin, USA) simultaneously considering scenarios of: taxonomic, functional, and phylogenetic diversity; contemporary threats to biodiversity (including interactions with nonnative species); and future climate change and human population growth. There was 75% congruence between areas of highest conservation priority for different aspects of biodiversity, suggesting that conservation efforts can concurrently achieve strong complementarity among all types of diversity. However, sizable fractions of the landscape were incongruent across conservation priorities for different diversity scenarios, underscoring the importance of considering multiple dimensions of biodiversity and highlighting catchments that contribute disproportionately to taxonomic, functional, and phylogenetic diversity in the region. Regions of projected human population growth were not concordant with conservation priorities; however, higher human population abundance will likely have indirect effects on native biodiversity by increasing demand for water. This will come in direct conflict with projected reductions in precipitation and warmer temperatures, which have substantial overlap with regions of high contemporary diversity. Native and endemic fishes in arid ecosystems are critically endangered by both current and future threats, but our results highlight the use of systematic conservation planning for the optimal allocation of limited resources that incorporates multiple and complementary conservation values describing taxonomic, functional, and phylogenetic diversity.
Using structural equation modeling to investigate relationships among ecological variables
Structural equation modeling is an advanced multivariate statistical process with which a researcher can construct theoretical concepts, test their measurement reliability, hypothesize and test a theory about their relationships, take into account measurement errors, and consider both direct and indirect effects of variables on one another. Latent variables are theoretical concepts that unite phenomena under a single term, e.g., ecosystem health, environmental condition, and pollution (Bollen, 1989). Latent variables are not measured directly but can be expressed in terms of one or more directly measurable variables called indicators. For some researchers, defining, constructing, and examining the validity of latent variables may be the end task of itself. For others, testing hypothesized relationships of latent variables may be of interest. We analyzed the correlation matrix of eleven environmental variables from the U.S. Environmental Protection Agency's (USEPA) Environmental Monitoring and Assessment Program for Estuaries (EMAP-E) using methods of structural equation modeling. We hypothesized and tested a conceptual model to characterize the interdependencies between four latent variables-sediment contamination, natural variability, biodiversity, and growth potential. In particular, we were interested in measuring the direct, indirect, and total effects of sediment contamination and natural variability on biodiversity and growth potential. The model fit the data well and accounted for 81% of the variability in biodiversity and 69% of the variability in growth potential. It revealed a positive total effect of natural variability on growth potential that otherwise would have been judged negative had we not considered indirect effects. That is, natural variability had a negative direct effect on growth potential of magnitude -0.3251 and a positive indirect effect mediated through biodiversity of magnitude 0.4509, yielding a net positive total effect of 0.1258. Natural variability had a positive direct effect on biodiversity of magnitude 0.5347 and a negative indirect effect mediated through growth potential of magnitude -0.1105 yielding a positive total effects of magnitude 0.4242. Sediment contamination had a negative direct effect on biodiversity of magnitude -0.1956 and a negative indirect effect on growth potential via biodiversity of magnitude -0.067. Biodiversity had a positive effect on growth potential of magnitude 0.8432, and growth potential had a positive effect on biodiversity of magnitude 0.3398. The correlation between biodiversity and growth potential was estimated at 0.7658 and that between sediment contamination and natural variability at -0.3769.
Saproxylic beetles' morphological traits and higher trophic guilds indicate boreal forest naturalness
Forests contribute to numerous ecosystem functions and services and contain a large proportion of terrestrial biodiversity, but they are being negatively impaced by anthropogenic activities. Forests that have never been clear-cut and have old growth characteristics, termed “near-natural,” often harbor different and richer species assemblages than managed forests. Alternative management strategies may be able to balance the needs of biodiversity with the demands of forestry, but evaluation efforts are limited by the challenges of measuring biodiversity. Species richness is frequently used as a simple measure of biodiversity, but research indicates that it may not adequately capture community-level changes. Alternatively, trait-based measures of biodiversity may prove to be useful, but research is lacking. In this paper, we use a large dataset that includes 339 obligate saproxylic beetle species collected over a decade in the boreal region throughout southern Norway to: (1) establish if there is a difference in beetle community composition between near-natural and managed forests; and (2) determine which measures of beetle biodiversity best indicate forest naturalness. We arranged the sites in an ordination space and tested for differences in community composition between these forest types. We also tested different measures of biodiversity to determine which were the most predictive of forest naturalness. We found a clear difference in community composition between near-natural and managed forests. Additionally, three measures of biodiversity were most predictive of forest naturalness: proportional abundance of predators, community weighted mean (CWM) of wing length, and CWM of body roundness. The probability that a forest was near-natural increased with the proportional abundance of predators but decreased with CWM wing length and body roundness. Although species richness was higher in near-natural forests, the effect was not significant. Overall, our findings underscore the conservation value of near-natural forests and highlight the potential of several measures of biodiversity for determining forest quality.
Towards a global terrestrial species monitoring program
Introduction: The Convention for Biological Diversity’s (CBD) Strategic Plan for Biodiversity 2011-2020 envisions that “By 2050, biodiversity is valued, conserved, restored and wisely used, maintaining ecosystem services, sustaining a healthy planet and delivering benefits essential for all people.” Although 193 parties have adopted these goals, there is little infrastructure in place to monitor global biodiversity trends. Recent international conservation policy requires such data to be up-to-date, reliable, comparable among sites, relevant, and understandable; as is becoming obvious from the work plan adopted by the Intergovernmental Panel for Biodiversity and Ecosystem Services (IPBES: www.ipbes.net/; http://tinyurl.com/ohdnknq). In order to meet the five strategic goals of the Strategic Plan for Biodiversity 2011-2020 and its 20 accompanying Aichi Targets for 2020 (www.cbd.int/sp/targets/), advances need to be made in coordinating large-scale biodiversity monitoring and linking these with environmental data to develop a comprehensive Global Observation Network, as is the main idea behind GEOSS the Global Earth Observation System of Systems (Christian 2005)...Here we identify ten requirements important for the successful implementation of a global biodiversity monitoring network under the flag of GEO BON and especially a global terrestrial species monitoring program.
Using the value of information to improve conservation decision making
Conservation decisions are challenging, not only because they often involve difficult conflicts among outcomes that people value, but because our understanding of the natural world and our effects on it is fraught with uncertainty. Value of Information (VoI) methods provide an approach for understanding and managing uncertainty from the standpoint of the decision maker. These methods are commonly used in other fields (e.g., economics, public health) and are increasingly used in biodiversity conservation. This decision analytical approach can identify the best management alternative to select where the effectiveness of interventions is uncertain, and can help to decide when to act and when to delay action until after further research. We review the use of VoI in the environmental domain, reflect on the need for greater uptake of VoI, particularly for strategic conservation planning, and suggest promising areas for new research. We also suggest common reporting standards as a means of increasing the leverage of this powerful tool. The environmental science, ecology and biodiversity categories of the Web of Knowledge were searched using the terms ‘Value of Information,’ ‘Expected Value of Perfect Information,’ and the abbreviation ‘EVPI.’ Google Scholar was searched with the same terms, and additionally the terms decision and biology, biodiversity conservation, fish, or ecology. We identified 1225 papers from these searches. Included studies were limited to those that show an application of VoI in biodiversity conservation rather than simply describing the method. All examples of use of VOI were summarised regarding the application of VoI, the management objectives, the uncertainties, models used, how the objectives were measured, and the type of VoI. While the use of VoI appears to be on the increase in biodiversity conservation, the reporting of results is highly variable, which can make it difficult to understand the decision context and which uncertainties were considered. Moreover, it was unclear if, and how, the papers informed management and policy interventions, which is why we suggest a range of reporting standards that would aid the use of VoI. The use of VoI in conservation settings is at an early stage. There are opportunities for broader applications, not only for species-focussed management problems, but also for setting local or global research priorities for biodiversity conservation, making funding decisions, or designing or improving protected area networks and management. The long-term benefits of applying VoI methods to biodiversity conservation include a more structured and decision-focused allocation of resources to research.
A gap analysis and comprehensive conservation strategy for riverine ecosystems of Missouri
North America harbors an astounding proportion of the world's freshwater species, but it is facing a freshwater biodiversity crisis. A first step to slowing the loss of biodiversity involves identifying gaps in existing efforts to conserve biodiversity and prioritizing opportunities to fill these gaps. In this monograph we detail two separate, but complementary, conservation planning efforts - a Gap Analysis (GAP) and a State Wildlife Action Plan (WAP) - for Missouri that address this first step. The goal of the Missouri Aquatic GAP Project was to identify riverine ecosystems, habitats, and species not adequately represented (i.e., gaps) within existing conservation lands. The goal of the freshwater component of the Missouri Wildlife Action Plan was to identify and map a set of conservation-opportunity areas (COAs) that holistically represent all riverine ecosystems, habitats, and species in Missouri. Since conservation planning is a geographical exercise, both efforts utilized geographic information systems (GIS). Four principal GIS data sets were used in each planning effort: (1) a hierarchical riverine ecosystem classification, (2) predicted species distributions, (3) public ownership/stewardship, and (4) a human-threat index. Results of the gap analyses are not encouraging. Forty five, mostly rare, threatened, or endangered, species are not represented in lands set aside for conserving biodiversity. Results also illustrate the fragmented nature of conservation lands, which are mainly situated in the uplands and fail to provide connectivity among riverine habitats. Furthermore, many conservation lands are severely threatened by an array of human disturbances. In contrast, results of the WAP provide hope that relatively intact riverine ecosystems still exist. A total of 158 COAs, representing ∼6% of the total kilometers of stream in Missouri, were selected for the WAP. This illustrates that a wide spectrum of biodiversity can be represented within a small portion of the total resource base, but the area of conservation concern is often much larger. Identifying priority riverscapes for conservation is an important first step toward effective biodiversity conservation. Yet, achieving the ultimate goal of conserving biodiversity will require vigilance on the part of all responsible parties, with particular attention to addressing and coordinating the many remaining logistical tasks.
Comparison of two benthic assemblage sampling gears for use on intertidal oyster reefs in Louisiana
Background Estuarine biodiversity plays a vital role in supporting ecosystem functions yet remains threatened by climate change and anthropogenic activity. Tracking and identifying estuarine biodiversity trends helps management ensure long-term provisions of human and environmental benefits by contributing to the estimation of habitat loss and the monitoring of restoration and conservation progress. However, the sampling gear and biodiversity metric used may indicate different conclusions, which can lead to uncertainty in the actual state of the ecosystem-level biodiversity. Sampling benthic biodiversity in complex estuarine habitats, such as oyster reefs, is particularly challenging because no one gear type captures entire target assemblages, and differences in gear efficiency on these complex habitats make comparisons across gear types challenging. Methods We investigated how estimates of oyster reef-associated benthic taxa abundance, richness, Pielou’s evenness, and Shannon-Wiener diversity differed across three Crassostrea virginica reefs in Louisiana between suction sampler and substrate tray sampling gears ( n = 6), and how gear influenced comparisons across reefs (3 reefs × 6 replicates × 2 gears). Results Abundance and richness were higher, and Pielou’s evenness was lower, in trays compared to suction samples at all reefs. Shannon-Wiener diversity was similar in suction samples and trays at two out of three reefs. Amphipod taxa were numerically dominant in trays, skewing the distribution of abundances and driving the reef assemblage differences between gears. Abundance and Shannon-Wiener diversity were similar across reefs within each gear. However, there were significant differences in richness across reefs in tray samples only, while evenness differed across reefs only in suction samples. Our results highlight that gear choices, along with biodiversity metrics tracked, can result in different conclusions in biodiversity trends, ultimately affecting conservation decisions and management.
A metadata checklist and data formatting guidelines to make eDNA FAIR (Findable, Accessible, Interoperable and Reusable)
The success of environmental DNA (eDNA) approaches for species detection has revolutionized biodiversity monitoring and distribution mapping. Targeted eDNA amplification approaches, such as quantitative PCR, have improved our understanding of species distribution, and metabarcoding-based approaches have enabled biodiversity assessment at unprecedented scales and taxonomic resolution. eDNA datasets, however, are often scattered across repositories with inconsistent formats, varying access restrictions, and inadequate metadata; this limits their interoperation, reuse, and overall impact. Adopting FAIR (Findable, Accessible, Interoperable, and Reusable) data practices with eDNA data can transform the monitoring of biodiversity and individual species and support data-driven biodiversity management across broad scales. FAIR practices remain underdeveloped in the eDNA community, partly due to gaps in adapting existing vocabularies, such as Darwin Core (DwC) and Minimum Information about any (x) Sequence (MIxS), to eDNA-specific needs and workflows. To address these challenges, we propose a comprehensive FAIR eDNA (FAIRe) Metadata Checklist, which integrates existing data standards and introduces new terms tailored to eDNA workflows. Metadata are systematically linked to both raw data (e.g., metabarcoding sequences, Ct/Cq values of targeted qPCR assays) and derived biological observations (e.g., Amplicon Sequence Variant (ASV)/Operational Taxonomic Unit (OTU) tables, species presence/absence). Along with formatting guidelines, tools, templates, and example datasets, we introduce a standardized, ready-to-use approach for FAIR eDNA practices. Through broad collaboration, we seek to integrate these guidelines into established biodiversity and molecular data standards, promote journal data policies, and foster user-driven improvements and uptake of FAIR practices among eDNA data producers. In proposing this standardized approach and developing a long-term plan with key databases and data standard organizations, the goal is to enhance accessibility, maximize reuse, and elevate the scientific impact of these valuable biodiversity data resources.
A census of marine life: Unknowable or just unknown?
As an introduction to the entire volume, this article outlines the relationships among the five elements of the Census of Marine Life (CoML) that create new knowledge: (1) The Ocean Biogeographic Information System (OBIS), a marine component of the Global Biodiversity Information Facility, links marine databases around the world to provide an Internet accessible, dynamic interface for comparing species-level, geo-referenced biodiversity data in relation to ocean habitats. The entire CoML field project data will be managed in and accessible through OBIS. (2) The History of Marine Animal Populations (HMAP) is a unique new synthesis of historical and biological research that will document marine biodiversity, globally, up to 500 years ago, before significant human impact, and store it in formats compatible with modern data in OBIS. (3) The Scientific Committee on Oceanic Research Working Group 118 monitors and recommends advanced marine technologies, ready to be routinely used in CoML field projects. (4) CoML Initial Field Projects develop and calibrate these technologies in selected regions to facilitate and accelerate global biodiversity research. As calibrated technologies and protocols are adopted in many regions, qualitative and quantitative biodiversity discoveries accumulate. (5) The Future of Marine Animal Populations (FMAP) program will insure that the data in OBIS are suitable for modeling and predicting changes in global biodiversity in response to fishing, pollution, and climate change challenges. It will make datasets available for hindcasting and forecasting analyses linked to physical ocean observations and assist in documenting the impacts of conservation efforts on sustainability.
Fishing for conservation of freshwater tropical fish in the Anthropocene
1. Biodiversity and fisheries are two important assets of freshwater ecosystems that are currently at risk from external threats. Establishing an equitable resolution to these threats is a major challenge of the Anthropocene. 2. This is particularly pertinent in developing nations where hotspots for biodiversity converge with rapid, and often environmentally degrading, economic development, and high dependency on aquatic biota and fisheries by local communities. 3. Here, we present global case studies that demonstrate how building upon a shared need for healthy environments and ecological integrity can meet both biodiversity conservation and fishery objectives. 4. These case studies provide evidence that addressing biodiversity conservation needs is possible through partnerships (especially with fishers), shared knowledge, and innovation in fisheries management. 5. In the pursuit of sustainable use of fresh water in development, both conservation and fisheries agendas are better served if efforts focused on synergising fishing activities with local ecosystem functioning and yield long-term livelihood and food security perspectives. 6. A partnership between conservationists (e.g., practitioners, environmental NGOs) and fisheries communities provides a unified voice advocating for biodiversity and social interests in freshwater governance decisions, which has more socio-economic and political capital than when voices are independent or in competition.
Seasonal impoundment alters patterns of tidal wetland plant diversity across spatial scales
Understanding patterns of biodiversity is a key goal of ecology and is especially pressing in the current human‐caused biodiversity crisis. In wetland ecosystems, human impacts are centered around hydrologic manipulation including the common practice of wetland diking and impoundment. Constraining how wetland management influences plant biodiversity patterns across spatial scales will provide information on how best to modify actions to preserve biodiversity and ecosystem function in managed wetlands. Here, we compare patterns of plant diversity and species presence, abundance, and community composition at several spatial scales among tidal wetlands along an estuarine salinity gradient and managed wetlands that were formerly tidal. Managed impounded wetlands had decreased alpha and gamma diversity of rare species, with less than 60% of the species richness found in tidal brackish wetlands at several spatial scales. There was little change in the overall pattern of alpha, beta, and gamma diversity for common species in impounded wetlands; however, dominant tidal brackish species, primarily perennial rhizomatous graminoids, were replaced with management target plants and non‐native annual grasses in impounded wetlands. This species replacement led to over 60% of impounded sites being classified as containing novel plant assemblages. An additional 25% of impounded sites were classified as containing tidal saline plant assemblages, suggesting potential soil salinization. Along the estuarine gradient, patchiness and codominance of common plant species drove high diversity and turnover in tidal brackish wetlands, while it remains unclear whether tidal fresh or brackish wetlands maximize rare plant diversity. With reduced species richness, altered functional dominants, and novel or saline assemblages, impounded brackish wetlands may require careful water management to balance native plant biodiversity, associated ecosystem processes, and waterfowl requirements.
Predicting intensity of white-tailed deer herbivory in the Central Appalachian Mountains
In eastern North America, white-tailed deer ( Odocoileus virginianus ) can have profound influences on forest biodiversity and forest successional processes. Moderate to high deer populations in the central Appalachians have resulted in lower forest biodiversity. Legacy effects in some areas persist even following deer population reductions or declines. This has prompted managers to consider deer population management goals in light of policies designed to support conservation of biodiversity and forest regeneration while continuing to support ample recreational hunting opportunities. However, despite known relationships between herbivory intensity and biodiversity impact, little information exists on the predictability of herbivory intensity across the varied and spatially diverse habitat conditions of the central Appalachians. We examined the predictability of browsing rates across central Appalachian landscapes at four environmental scales: vegetative community characteristics, physical environment, habitat configuration, and local human and deer population demographics. In an information - theoretic approach, we found that a model fitting the number of stems browsed relative to local vegetation characteristics received most (62%) of the overall support of all tested models assessing herbivory impact. Our data suggest that deer herbivory responded most predictably to differences in vegetation quantity and type. No other spatial factors or demographic factors consistently affected browsing intensity. Because herbivory, vegetation communities, and productivity vary spatially, we suggest that effective broad-scale herbivory impact assessment should include spatially-balanced vegetation monitoring that accounts for regional differences in deer forage preference. Effective monitoring is necessary to avoid biodiversity impacts and deleterious changes in vegetation community composition that are difficult to reverse and/or may not be detected using traditional deer-density based management goals.
Shotgun sequencing of airborne eDNA achieves rapid assessment of whole biomes, population genetics and genomic variation
Biodiversity and its associated genetic diversity are being lost at an unprecedented rate. Simultaneously, the distributions of flora, fauna, fungi, microbes and pathogens are rapidly changing. Novel technology can help to capture and record genetic diversity before it is lost and to measure population shifts and pathogen distributions. Here we report the rapid application of shotgun long-read environmental DNA (eDNA) analysis for non-invasive biodiversity, genetic diversity and pathogen assessments from air. We also compared air eDNA with water and soil eDNA. Coupling long-read sequencing with established cloud-based biodiversity pipelines enabled a 2-day turnaround from airborne sample collection to completed analysis by a single investigator. To determine the full utility of airborne eDNA, we also conducted a local bioinformatic analysis and deep short-read shotgun sequencing. From outdoor air eDNA alone, comprehensive genetic analysis was performed, including population genetics (phylogenetic placement) of a charismatic mammal (bobcat, Lynx rufus ) and a venomous spider (golden silk orb weaver, Trichonephila clavipes ), and haplotyping humans ( Homo sapiens ) from natural complex community settings, such as subtropical forests and temperate locations. The rich datasets also enabled deeper analysis of specific species and genomic regions of interest, including viral variant calling, human variant analysis and antimicrobial resistance gene surveillance from airborne DNA. Our results highlight the speed, versatility and specificity of pan-biodiversity monitoring via non-invasive eDNA sampling using current benchtop/portable and cloud-based approaches. Furthermore, they reveal the future feasibility of scaling down (equipment and temporally) these approaches for near real-time analysis. Together these approaches can enable rapid simultaneous detection of all life and its genetic diversity from air, water and sediment samples for unbiased non-targeted information-rich genomics-empowered (1) biodiversity monitoring, (2) population genetics, (3) pathogen and disease-vector genomic surveillance, (4) allergen and narcotic surveillance, (5) antimicrobial resistance surveillance and (6) bioprospecting.