Search

Objective: Environmental DNA (eDNA) methods are crucial for monitoring populations, particularly rare and cryptic species. For confident eDNA application, rigorous assay validation is required including specificity testing with genomic DNA (gDNA). However, this critical step is often difficult to achieve as obtaining fresh tissue samples from at-risk species can be difficult, highly limited, or impossible. Natural history museum collections could serve as a valuable and ethical voucher specimen resource for eDNA assay validation. The present study demonstrates the effectiveness of whole genome amplification (WGA) in providing enough gDNA to assemble high quality mitogenomes from which robust targeted eDNA assays can be designed. Results: Using fresh and historical museum tissue samples from six species spanning fish, birds, and mammals, we successfully developed a WGA method with an average yield of 380 to 1,268 ng gDNA per 20 µL reaction. This gDNA was used for whole genome shotgun sequencing and subsequent assembly of high quality mitogenomes using mtGrasp. These mitogenomes were then used to develop six new robust, targeted quantitative real time polymerase chain reaction-based eDNA assays and 200 ng WGA-enriched yielded satisfactory Cq values and near 100% detection frequencies for all assays tested. This approach offers a cost-effective and non-invasive alternative, streamlining eDNA research processes and aiding in conservation efforts. [ABSTRACT FROM AUTHOR]

Abstract Objective Environmental DNA (eDNA) methods are crucial for monitoring populations, particularly rare and cryptic species. For confident eDNA application, rigorous assay validation is required including specificity testing with genomic DNA (gDNA). However, this critical step is often difficult to achieve as obtaining fresh tissue samples from at-risk species can be difficult, highly limited, or impossible. Natural history museum collections could serve as a valuable and ethical voucher specimen resource for eDNA assay validation. The present study demonstrates the effectiveness of whole genome amplification (WGA) in providing enough gDNA to assemble high quality mitogenomes from which robust targeted eDNA assays can be designed. Results Using fresh and historical museum tissue samples from six species spanning fish, birds, and mammals, we successfully developed a WGA method with an average yield of 380 to 1,268 ng gDNA per 20 µL reaction. This gDNA was used for whole genome shotgun sequencing and subsequent assembly of high quality mitogenomes using mtGrasp. These mitogenomes were then used to develop six new robust, targeted quantitative real time polymerase chain reaction-based eDNA assays and 200 ng WGA-enriched yielded satisfactory Cq values and near 100% detection frequencies for all assays tested. This approach offers a cost-effective and non-invasive alternative, streamlining eDNA research processes and aiding in conservation efforts.

Climate change effects are contributing to widespread declines of amphibians, and pond-breeding species may be particularly sensitive to future drought conditions that restrict wetland hydroperiods and decrease opportunities for successful breeding and recruitment. Pond-breeding amphibian populations can compensate for periodic droughts via episodic booms in recruitment, but studies predict that increased future drought conditions will negatively impact long-term persistence for several species. The southeastern United States is a global hotspot of amphibian biodiversity where future trends in drought conditions are uncertain. This study applied a population viability analysis (PVA) framework for an at-risk amphibian, the gopher frog (Lithobates [Rana] capito), to (i) explore population sensitivity to the frequency of droughts that restrict reproductive events, relative to changes in other demographic rates, and (ii) forecast future population viability over 30 years, given plausible scenarios varying in the frequency and duration of droughts adapted from recent historical patterns in the southeastern United States. Population persistence was highly sensitive to frequency of reproductive success. Persistence was fairly insensitive to all demographic parameters when reproductive success was ≥ 0.7 (i.e., ≤ 3 drought years per decade, on average), but sensitivity to survival of terrestrial stages (juvenile, adults) and initial abundance increased as reproductive success decreased. Persistence probabilities were relatively high (0.63–0.99) across a range of plausible future drought scenarios, with higher persistence probabilities (> 0.89) for all scenarios where drought years did not increase from recent historical conditions. Our results indicate gopher frog populations are likely resilient to periodic droughts that occur in 4 or fewer years per decade, but extirpation of some populations is possible if recent drought patterns repeat or increase during the next 30 years. Estimates of future risk to gopher frog populations can inform forthcoming status assessments and designation decisions of the U.S. Fish and Wildlife Service. More broadly, PVAs incorporating drought dynamics can identify climate thresholds that at-risk, pond-breeding amphibian populations can tolerate, which can inform management actions (e.g., maintaining a range of hydroperiods across proximate wetlands) that provide sufficient frequent breeding opportunities for long-term persistence even under drought conditions.

Abstract Blue Catfish Ictalurus furcatus are an invasive, yet economically important species in the Chesapeake Bay. However, their impact on the trophic ecology of this system is not well understood. In order to provide in‐depth analysis of predation by Blue Catfish, we identified prey items using high‐throughput DNA sequencing (HTS) of entire gastrointestinal tracts from 134 samples using two genetic markers, mitochondrial cytochrome c oxidase I (COI) and the nuclear 18S ribosomal RNA gene. We compared our HTS results to a more traditional “hybrid” approach that coupled morphological identification with DNA barcoding. The hybrid study was conducted on additional Blue Catfish samples (n = 617 stomachs) collected from the same location and season in the previous year. Taxonomic representation with HTS vastly surpassed that achieved with the hybrid methodology in Blue Catfish. Significantly, our HTS study identified several instances of at‐risk and invasive species consumption not identified using the hybrid method, supporting the hypothesis that previous studies using morphological methods may greatly underestimate consumption of critical species. Finally, we report the novel finding that Blue Catfish diet diversity inversely correlates to daily flow rates, perhaps due to higher mobility and prey‐seeking behaviors exhibited during lower flow.

Targeted, single‐species management and ecosystem‐based management are generally considered disparate conservation approaches. In imperiled ecosystems, these approaches may be complementary, when habitat management for targeted at‐risk species provides broad ecosystem benefits through an umbrella or surrogate species effect. In the northeastern United States, extensive management has been ongoing since 2011 to restore declining habitat for an at‐risk shrubland habitat specialist, the New England cottontail (Sylvilagus transitionalis), with the goal that other shrubland‐obligate wildlife will also benefit; yet, the efficacy of these efforts has not been evaluated. In this study, we assessed whether habitat management targeting New England cottontail provides conservation benefits for shrubland‐obligate birds. Specifically, we (1) identified shrubland‐obligate birds that are indicative of the microhabitat conditions and habitat types suitable for New England cottontails, and (2) determined microhabitat and patch‐level influences on shrubland bird occupancy at sites occupied by or managed for New England cottontail. Through avian point count surveys and indicator species analyses, we identified 12 shrubland‐obligate bird species on patches occupied by New England cottontail and in microhabitat conditions suitable for New England cottontail. Occupancy models for five shrubland bird species further identified species‐specific habitat associations. Generalized linear models showed that shrubland bird species richness was positively associated with herbaceous vegetation and low shrubs, indicating that shrublands managed for the purpose of cottontail colonization can also benefit a suite of shrubland birds before the habitat is dense enough to provide cover for cottontails. Our findings show that managing habitat for New England cottontail on a variety of site types can maintain a range of microhabitat conditions to support a high diversity of shrubland‐obligate birds. These findings provide evidence for broad ecosystem benefits of managing for New England cottontail and exemplify the value of at‐risk habitat specialists as conservation surrogates in imperiled ecosystems. [ABSTRACT FROM AUTHOR]

Abstract Targeted, single‐species management and ecosystem‐based management are generally considered disparate conservation approaches. In imperiled ecosystems, these approaches may be complementary, when habitat management for targeted at‐risk species provides broad ecosystem benefits through an umbrella or surrogate species effect. In the northeastern United States, extensive management has been ongoing since 2011 to restore declining habitat for an at‐risk shrubland habitat specialist, the New England cottontail (Sylvilagus transitionalis), with the goal that other shrubland‐obligate wildlife will also benefit; yet, the efficacy of these efforts has not been evaluated. In this study, we assessed whether habitat management targeting New England cottontail provides conservation benefits for shrubland‐obligate birds. Specifically, we (1) identified shrubland‐obligate birds that are indicative of the microhabitat conditions and habitat types suitable for New England cottontails, and (2) determined microhabitat and patch‐level influences on shrubland bird occupancy at sites occupied by or managed for New England cottontail. Through avian point count surveys and indicator species analyses, we identified 12 shrubland‐obligate bird species on patches occupied by New England cottontail and in microhabitat conditions suitable for New England cottontail. Occupancy models for five shrubland bird species further identified species‐specific habitat associations. Generalized linear models showed that shrubland bird species richness was positively associated with herbaceous vegetation and low shrubs, indicating that shrublands managed for the purpose of cottontail colonization can also benefit a suite of shrubland birds before the habitat is dense enough to provide cover for cottontails. Our findings show that managing habitat for New England cottontail on a variety of site types can maintain a range of microhabitat conditions to support a high diversity of shrubland‐obligate birds. These findings provide evidence for broad ecosystem benefits of managing for New England cottontail and exemplify the value of at‐risk habitat specialists as conservation surrogates in imperiled ecosystems.

Public lands alone are insufficient to address the needs of most at-risk wildlife species in the U.S. As a result, a variety of voluntary incentive programs have emerged to recruit private landowners into conservation efforts that restore and manage the habitats needed by specific species. We review the role of one such effort, Working Lands for Wildlife (WLFW), initiated by the Natural Resources Conservation Service in partnership with the U.S. Fish and Wildlife Service. Using two atrisk species in the eastern U.S. (where private lands dominate), we show the substantial potential that WLFW has for restoring and maintaining needed habitats. Monitoring how effective these efforts are on populations of the target species has been challenging, and both monitoring and implementation are being modified in response to new information. Identifying landowner motivations is essential for developing long-term relationships and conservation success. As WLFW projects develop, they are moving toward a more holistic ecosystem approach, within which the conservation goals of at-risk species are embedded. [ABSTRACT FROM AUTHOR]

Blue Catfish Ictalurus furcatus are an invasive, yet economically important species in the Chesapeake Bay. However, their impact on the trophic ecology of this system is not well understood. In order to provide in‐depth analysis of predation by Blue Catfish, we identified prey items using high‐throughput DNA sequencing (HTS) of entire gastrointestinal tracts from 134 samples using two genetic markers, mitochondrial cytochrome c oxidase I (COI) and the nuclear 18S ribosomal RNA gene. We compared our HTS results to a more traditional "hybrid" approach that coupled morphological identification with DNA barcoding. The hybrid study was conducted on additional Blue Catfish samples (n = 617 stomachs) collected from the same location and season in the previous year. Taxonomic representation with HTS vastly surpassed that achieved with the hybrid methodology in Blue Catfish. Significantly, our HTS study identified several instances of at‐risk and invasive species consumption not identified using the hybrid method, supporting the hypothesis that previous studies using morphological methods may greatly underestimate consumption of critical species. Finally, we report the novel finding that Blue Catfish diet diversity inversely correlates to daily flow rates, perhaps due to higher mobility and prey‐seeking behaviors exhibited during lower flow. [ABSTRACT FROM AUTHOR]

Public lands alone are insufficient to address the needs of most at-risk wildlife species in the U.S. As a result, a variety of voluntary incentive programs have emerged to recruit private landowners into conservation efforts that restore and manage the habitats needed by specific species. We review the role of one such effort, Working Lands for Wildlife (WLFW), initiated by the Natural Resources Conservation Service in partnership with the U.S. Fish and Wildlife Service. Using two at-risk species in the eastern U.S. (where private lands dominate), we show the substantial potential that WLFW has for restoring and maintaining needed habitats. Monitoring how effective these efforts are on populations of the target species has been challenging, and both monitoring and implementation are being modified in response to new information. Identifying landowner motivations is essential for developing long-term relationships and conservation success. As WLFW projects develop, they are moving toward a more holistic ecosystem approach, within which the conservation goals of at-risk species are embedded.

The recent increase in corn ethanol production has drawn attention to the environmental sustainability of biofuel production. Environmental assessments of second-generation biofuel crops ( SGBC) have focused primarily on greenhouse gas emissions and water quality. However, expanding the production of cellulosic biomass resources, especially those that require dedicated agricultural land, is also likely to have impacts on biodiversity. We developed an optimization framework for projecting the spatial pattern of SGBC expansion in the United States and intersected these predictions with occurrence data for at-risk species. In particular, we focused on two candidate perennial grass feedstocks, Panicum virgatum (switchgrass), and Miscanthus × giganteus (Miscanthus). Tradeoffs between biodiversity and economic profitability are assessed using county level data sets of SGBC yield, agricultural land availability, land rents, and at-risk species occurrences. Results show that future SGBC expansion is likely to occur outside of the Corn Belt, where conventional biofuel feedstocks are currently grown. The set of at-risk species that could potentially be impacted is therefore likely to be different from the at-risk species prevalent in the agroecological landscapes of the Upper Midwest that are dominated by corn and soy production. The total number and type of potentially impacted taxa is influenced by several factors, including the total demand for cellulosic biomass, the type of agricultural land used for production, and the method for defining at-risk species. SGBC production is also concentrated in fewer counties when a national species conservation constraint is combined with a biofuel production mandate. This analysis provides a foundation for future research on species conservation in bioenergy production landscapes and highlights the importance of incorporating biodiversity into broader environmental assessments of biofuel sustainability. [ABSTRACT FROM AUTHOR]

Aim Biodiversity and drinking water share a common interest in land conservation. Our objective was to identify where that common interest occurs geographically to inform conservation planning. Location The study focused on 2112 eight-digit hydrologic units (watersheds) occurring in the conterminous United States. Methods Data on aquatic-dependent species occurrence, drinking water intakes, protected land status and land cover change were compiled for each watershed. We compared these four datasets after defining 'hotspots' based on attribute-specific thresholds that included (1) the 90th percentile of at-risk aquatic biodiversity, (2) with and without drinking water intakes, (3) above and below the median percentage of protected land and (4) increase in urban land above and below a 1% threshold between 2001 and 2006. Geographic intersections were used to address a number of questions relevant to conservation planning including the following: What watersheds important to aquatic biodiversity are also important to drinking water? Which watersheds with a shared stake in biodiversity and drinking water protection have inadequate land protection? Which watersheds with potentially inadequate amounts of protected lands are also undergoing relatively rapid urbanization? Results Over 60% of the watersheds that were determined to be aquatic biodiversity hotspots also had drinking water intakes, and approximately 50% of these watersheds had less than the United States median amount of protected land. A total of seven watersheds were found to have shared aquatic biodiversity/drinking water values, relatively low proportions of protected lands and a relatively high rate of urbanization. The majority of these watershed occurred in the south-eastern United States, with secondary occurrences in California. Main conclusions Geographic analysis of multiple ecosystem services can identify areas of shared land conservation interest. Locations where ecosystem commodities and species conservation overlap has the potential to increase stakeholder buy-in and leverage scarce resources to conserve land that, in this case study, protects both biodiversity and drinking water. [ABSTRACT FROM AUTHOR]

Engaging private landowners in conservation activities for imperiled species is critical to maintaining and enhancing biodiversity. Market-based approaches can incentivize conservation behaviors on private lands by shifting the benefit-cost ratio of engaging in activities that result in net conservation benefits for target species. In the United States and elsewhere, voluntary conservation agreements with financial incentives are becoming an increasingly common strategy. While the influence of program design and delivery of voluntary conservation programs is often overlooked, these aspects are critical to achieving the necessary participation to attain landscape-scale outcomes. Using a sample of familyforest landowners in the southeast United States, we show how preferences for participation in a conservation program to protect an at-risk species, the gopher tortoise (Gopherus polyphemus), are related to program structure, delivery, and perceived efficacy. Landowners were most sensitive to programs that are highly controlling, require permanent conservation easements, and put landowners at risk for future regulation. Programs designed with greater levels of compensation and that support landowners' autonomy to make land management decisions can increase participation and increase landowner acceptance of program components that are generally unfavorable, like long-term contracts and permanent easements. There is an inherent trade-off between maximizing participation and maximizing the conservation benefits when designing a conservation incentive program. For conservation programs targeting private lands to achieve landscape-level benefits, they must attract a critical level of participation that creates a connected mosaic of conservation benefits. Yet, programs with attributes that strive to maximize conservation benefits within a single agreement (and reduce risks of failure) are likely to have lower participation, and thus lower landscape benefits. Achieving levels of landowner participation in conservation agreement programs that deliver lasting, landscape-level benefits requires careful attention not only to how the program structure influences potential conservation benefits, but also how it influences landowners and their potential to participate. [ABSTRACT FROM AUTHOR]

In 2012, the United States Forest Service (USFS) promulgated new planning regulations in accordance with the National Forest Management Act (NFMA). These regulations represent the most significant change in federal forest policy in decades and have sweeping implications for wildlife populations. We provide a brief overview of the history of the NFMA planning regulations and their wildlife provisions and review the current science on planning for effective wildlife conservation at the landscape scale. We then discuss the approach to wildlife conservation planning in the 2012 rule and compare it to alternatives that were not selected and previous iterations of the planning rule. The new planning rule is of concern because of its highly discretionary nature and the inconsistency between its intent on the one hand and operational requirements on the other. Therefore, we recommend that the USFS include in the Directives for implementing the rule commitments to directly monitor populations of selected species of conservation concern and focal species and to maintain the viability of both categories of species. Additional guidance must be included to ensure the effective selection of species of conservation concern and focal species, and these categories should overlap when possible. If the USFS determines that the planning unit is not inherently capable of maintaining viable populations of a species, this finding should be made available for scientific review and public comment, and in such cases the USFS should commit to doing nothing that would further impair the viability of such species. In cases where extrinsic factors decrease the viability of species, the USFS has an increased, not lessened, responsibility to protect those species. Monitoring plans must include trigger points that will initiate a review of management actions, and plans must include provisions to ensure monitoring takes place as planned. If wildlife provisions in forest plans are implemented so that they are enforceable and ensure consistency between intent and operational requirements, this will help to prevent the need for additional listings under the Endangered Species Act and facilitate delisting. Although the discretionary nature of the wildlife provisions in the planning rule gives cause for concern, forward-thinking USFS officials have the opportunity under the 2012 rule to create a robust and effective framework for wildlife conservation planning. © 2013 The Wildlife Society. [ABSTRACT FROM AUTHOR]

Bycatch of turtles in passive inland fyke net fisheries has been poorly studied, yet bycatch is an important conservation issue given the decline in many freshwater turtle populations. Delayed maturity and low natural adult mortality make turtles particularly susceptible to population declines when faced with additional anthropogenic adult mortality such as bycatch. When turtles are captured in fyke nets, the prolonged submergence can lead to stress and subsequent drowning. Fish die within infrequently checked passive fishing nets and dead fish are a potential food source for many freshwater turtles. Dead fish could thus act as attractants and increase turtle captures in fishing nets. We investigated the attraction of turtles to decomposing fish within fyke nets in eastern Ontario. We set fyke nets with either 1 kg of one-day or five-day decomposed fish, or no decomposed fish in the cod-end of the net. Decomposing fish did not alter the capture rate of turtles or fish, nor did it alter the species composition of the catch. Thus, reducing fish mortality in nets using shorter soak times is unlikely to alter turtle bycatch rates since turtles were not attracted by the dead fish. Interestingly, turtle bycatch rates increased as water temperatures did. Water temperature also influences turtle mortality by affecting the duration turtles can remain submerged. We thus suggest that submerged nets to either not be set or have reduced soak times in warm water conditions (e.g., >20 °C) as turtles tend to be captured more frequently and cannot withstand prolonged submergence. [ABSTRACT FROM AUTHOR]

Species at risk of extinction are not uniformly distributed in space. Concentrations of threatened species may occur where threatening processes are intense, in refuges from those processes, or in areas of high species diversity. However, there have been few attempts to identify the processes that explain the distribution of at‐risk species. Here, we identified the relative importance of biological traits, environmental factors, and anthropogenic stressors in driving the spatial patterns of both total and at‐risk species richness of North American mammals and birds. Environmental factors are the predominant drivers of both total and at‐risk species richness. Strikingly, the directions of variable relationships differ substantially between models of total and at‐risk species richness. Understanding how environmental gradients differentially drive variation in total and at‐risk species richness can inform conservation action. Moreover, our approach can predict shifts in at‐risk species concentrations in response to projected environmental change and anthropogenic stressors. [ABSTRACT FROM AUTHOR]