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USGS2012

The U.S. Geological Survey Ecosystem Science Strategy, 2012-2022 - Advancing discovery and application through collaboration

Ecosystem science is critical to making informed decisions about natural resources that can sustain our Nation’s economic and environmental well-being. Resource managers and policy-makers are faced with countless decisions each year at local, state, tribal, territorial, and national levels on issues as diverse as renewable and non-renewable energy development, agriculture, forestry, water supply, and resource allocations at the urban-rural interface. The urgency for sound decision-making is increasing dramatically as the world is being transformed at an unprecedented pace and in uncertain directions. Environmental changes are associated with natural hazards, greenhouse gas emissions, and increasing demands for water, land, food, energy, mineral, and living resources. At risk is the Nation’s environmental capital, the goods and services provided by resilient ecosystems that are vital to the health and well-being of human societies. Ecosystem science—the study of systems of organisms interacting with their environment and the consequences of natural and human-induced change on these systems—is necessary to inform decision-makers as they develop policies to adapt to these changes. This Ecosystems Science Strategy is built on a framework that includes basic and applied science. It highlights the critical roles that USGS scientists and partners can play in building scientific understanding and providing timely information to decision-makers. The strategy underscores the connection between scientific discoveries and the application of new knowledge. The strategy integrates ecosystem science and decision-making, producing new scientific outcomes to assist resource managers and providing public benefits. The USGS is uniquely positioned to play an important role in ecosystem science. With its wide range of expertise, the agency can bring holistic, cross-scale, interdisciplinary capabilities to the design and conduct of monitoring, research, and modeling and to new technologies for data collection, management, and visualization. Collectively, these capabilities can be used to reveal ecological patterns and processes, explain how and why ecosystems change, and forecast change over different spatial and temporal scales. USGS science can provide managers with options and decision-support tools to use resources sustainably. The USGS has long-standing, collaborative relationships with the DOI and other partners in the natural sciences, in both conducting science and its application. The USGS engages these partners in cooperative investigations that otherwise would lack the necessary support or be too expensive for a single bureau to conduct. The heart of this strategy is a framework and vision for USGS ecosystems science that focuses on five long-term goals, which are seen as interconnected and reinforcing components: • Improve understanding of ecosystem structure, function, and processes. The focus for this goal is an understanding of how ecosystems work, including the dynamics of species, their populations, interactions, and genetics, and how they change across spatial and temporal scales. • Advance understanding of how drivers influence ecosystem change. The challenges here are explaining the drivers of ecosystem change, their spatio-temporal patterns, their uncertainties and interactions, and their influence on ecosystem processes and dynamics. • Improve understanding of the services that ecosystems provide to society. Here the emphasis is on the measurement of environmental capital and ecosystem services, and the identification of sources and patterns of change in space and time. • Develop tools, technologies, and capacities to inform decision-making about ecosystems. This includes developing new technologies and approaches for conducting applications-oriented ecosystem science. A principal challenge will be how to quantify uncertainty and incorporate it in decision analysis. • Apply science to enhance strategies for management, conservation, and restoration of ecosystems. These challenges include development of novel approaches to monitoring, assessment, and restoration of ecosystems; new methods to address species of concern and communities at risk; and innovations in decision analysis and support to address imminent ecosystem changes or those that are underway. Closely integrated with the five goals are four strategic approaches that provide the path forward for the USGS Ecosystems Mission Area. These approaches cross-cut all of the goals and are seen as essential to the implementation of this strategy: • Assess information needs for ecosystem science through enhanced partnerships. Work with the DOI and other agencies and institutions to identify, design, and implement priority decision-driven ecological research. • Promote the use of interdisciplinary ecosystem science. Design and conduct interdisciplinary process-oriented research in ecosystem science. • Enhance modeling and forecasting. Build models to forecast ecosystem change, assess future management scenarios, and reduce uncertainties through an adaptive learning process. • Support decision-making. Use quantitative approaches to assess the vulnerabilities of ecosystems, habitats, and species, and evaluate strategies for adaptation, restoration, and sustainable management. Following the strategic approaches are a set of proposed actions that represent a sampling of specific activities that align with this strategy and that address the Nation’s most pressing environmental needs. The strategy emphasizes coordination of activities across the USGS mission areas pursuant to these goals. Ecosystem science is inherently interdisciplinary and requires a broad perspective that incorporates the biological and physical sciences, climate science, information technology, and scientific capacity in mission areas across the Bureau. With its emphasis on coordination, this strategy can provide a critical underpinning for integrated science efforts with scientists from multiple mission areas of the USGS working together. Of course, the USGS will continue to conduct both discipline-specific and interdisciplinary investigations, and both will continue to be vital parts of the ecosystem science portfolio. Finally, the strategy stresses the importance of coordination with other Federal agencies and organizations in the natural resources community. The USGS collaborates with resource agencies in the DOI and other organizations throughout the world to meet societal needs for species and ecosystem management. Working with these agencies and organizations, the USGS will play a key role over the next decade in advancing the scientific foundation for sustaining the natural resources that diverse, productive, resilient ecosystems provide.

Open-File Report↗
USGS2020

Incomplete bioinformatic filtering and inadequate age and growth analysis lead to an incorrect inference of harvested-induced changes

Understanding the evolutionary impacts of harvest on fish populations is important for informing fisheries management and conservation and has become a growing research topic over the last decade. However, the dynamics of fish populations are highly complex, and phenotypes can be influenced by many biotic and abiotic factors. Therefore, it is vital to collect robust data and explore multiple alternative hypotheses before concluding that fish populations are influenced by harvest. In their recently published manuscript, Bowles et al, Evolutionary Applications, 13(6):1128 conducted age/growth and genomic analysis of walleye ( Sander vitreus ) populations sampled 13–15 years (1–2.5 generations) apart and hypothesized that observed phenotypic and genomic changes in this time period were likely due to harvest. Specifically, Bowles et al. (2020) documented differential declines in size-at-age in three exploited walleye populations compared to a separate, but presumably less-exploited, reference population. Additionally, they documented population genetic differentiation in one population pair, homogenization in another, and outlier loci putatively under selection across time points. Based on their phenotypic and genetic results, they hypothesized that selective harvest had led to fisheries-induced evolution (referred to as nascent changes) in the exploited populations in as little as 1–2.5 generations. We re-analyzed their data and found that (a) sizes declined across both exploited and reference populations during the time period studied and (b) observed genomic differentiation in their study was the result of inadequate data filtering, including retaining individuals with high amounts of missing data and retaining potentially undersplit and oversplit loci that created false signals of differentiation between time points. This re-analysis did not provide evidence for phenotypic or genetic changes attributable to harvest in any of the study populations, contrasting the hypotheses presented by Bowles et al. (2020). Our comment highlights the potential pitfalls associated with conducting age/growth analyses with low sample sizes and inadequately filtering genomic datasets.

Quebec↗
USGS2018

The Pleurobemini (Bivalvia: Unionida) revisited: Molecular species delineation using a mitochondrial DNA gene reveals multiple conspecifics and undescribed species

The Pleurobemini (Bivalvia: Unionida) represent approximately one-third of freshwater mussel diversity in North America. Species identification within this group is challenging due to morphological convergence and phenotypic plasticity. Accurate species identification, including characterisation of currently unrecognised taxa, is required to develop effective conservation strategies because many species in the group are imperiled. We examined 575 cox1 sequences from 110 currently recognised species (including 13 Fusconaia and 21 Pleurobema species) to understand phylogenetic relationships among pleurobemine species (mainly Fusconaia and Pleurobema ) and to delineate species boundaries. The results of phylogenetic analyses showed no geographic structure within widespread species and illustrated a close relationship between Elliptio lanceolata and Parvaspina collina . Constraint tests supported monophyly of the genera Fusconaia and Pleurobema , including the subgenus P . ( Sintoxia ). Furthermore, results revealed multiple conspecifics, including P. hanleyianum and P. troschelianum , P. chattanoogaense and P. decisum , P. clava and P. oviforme , P. rubrum and P. sintoxia , F. askewi and F. lananensis , and F. cerina and F. flava . Species delimitation analyses identified three currently unrecognised taxa (two in Fusconaia and one in Pleurobema ). Further investigation using additional genetic markers and other lines of evidence (e.g. morphology, life history, ecology) are necessary before any taxonomic changes are formalised.

Invertebrate Systematics↗
USGS2021

Oases: Finding hidden biodiversity gems in the southern Sonoran Desert

In the arid southern Sonoran Desert, the rugged canyons of the Sierra El Aguaje contain numerous freshwater oases. These habitats are supported by small springs which are usually located along geologic faults in volcanic and granitic bedrock. Genetic evidence from freshwater-obligate species (e.g., fish and frogs) suggests these or similar spring-fed habitats have persisted for thousands to millions of years. Though biologists are just beginning to study these habitats, at least 210 species of aquatic invertebrates have been documented, along with several species of fishes, amphibians, and semi-aquatic reptiles. Additionally, euryhaline fishes occasionally colonize freshwater habitats when hurricane-induced floods connect oases with the sea. At least six new, potentially endemic, species of aquatic invertebrates have been found in recent years, but much work remains to be done to fully document the biota of these oases. Groundwater pumping, introductions of nonnative species, and unmanaged human recreation all threaten the biodiversity of these desert oases. We hope this chapter will draw attention to these beautiful habitats and promote conservation of their unique biota

Sonora↗
USGS2011

Refugial isolation and divergence in the Narrowheaded Gartersnake species complex (Thamnophis rufipunctatus) as revealed by multilocus DNA sequence data

Glacial–interglacial cycles of the Pleistocene are hypothesized as one of the foremost contributors to biological diversification. This is especially true for cold‐adapted montane species, where range shifts have had a pronounced effect on population‐level divergence. Gartersnakes of the Thamnophis rufipunctatus species complex are restricted to cold headwater streams in the highlands of the Sierra Madre Occidental and southwestern USA. We used coalescent and multilocus phylogenetic approaches to test whether genetic diversification of this montane‐restricted species complex is consistent with two prevailing models of range fluctuation for species affected by Pleistocene climate changes. Our concatenated nuDNA and multilocus species analyses recovered evidence for the persistence of multiple lineages that are restricted geographically, despite a mtDNA signature consistent with either more recent connectivity (and introgression) or recent expansion (and incomplete lineage sorting). Divergence times estimated using a relaxed molecular clock and fossil calibrations fall within the Late Pleistocene, and zero gene flow scenarios among current geographically isolated lineages could not be rejected. These results suggest that increased climate shifts in the Late Pleistocene have driven diversification and current range retraction patterns and that the differences between markers reflect the stochasticity of gene lineages (i.e. ancestral polymorphism) rather than gene flow and introgression. These results have important implications for the conservation of T. rufipunctatus (sensu novo), which is restricted to two drainage systems in the southwestern US and has undergone a recent and dramatic decline.

Molecular Ecology↗
USGS2018

Using spatially‐explicit capture–recapture models to explain variation in seasonal density patterns of sympatric ursids

Understanding how environmental factors interact to determine the abundance and distribution of animals is a primary goal of ecology, and fundamental to the conservation of wildlife populations. Studies of these relationships, however, often assume static environmental conditions, and rarely consider effects of competition with ecologically similar species. In many parts of their shared ranges, grizzly bears Ursus arctos and American black bears U. americanus have nearly complete dietary overlap and share similar life history traits. We therefore tested the hypothesis that density patterns of both bear species would reflect seasonal variation in available resources, with areas of higher primary productivity supporting higher densities of both species. We also hypothesized that interspecific competition would influence seasonal density patterns. Specifically, we predicted that grizzly bear density would be locally reduced due to the ability of black bears to more efficiently exploit patchy food resources such as seasonally abundant fruits. To test our hypotheses, we used detections of 309 grizzly and 597 black bears from two independent genetic sampling methods in spatially‐explicit capture–recapture (SECR) models. Our results suggest grizzly bear density was lower in areas of high black bear density during spring and summer, although intraspecific densities were also important, particularly during the breeding season. Black bears had lower densities in areas of high grizzly bear density in spring; however, density of black bears in early and late summer was best explained by primary productivity. Our results are consistent with the hypothesis that smaller‐bodied, more abundant black bears may influence the density patterns of behaviorally‐dominant grizzly bears through exploitative competition. We also suggest that seasonal variation in resource availability be considered in efforts to relate environmental conditions to animal density.

Montana↗
USGS2017

Human interactions with sirenians (manatees and dugongs)

There are three extant sirenian species of the Trichechidae family and one living Dugongidae family member. Given their close ties to coastal and often urbanized habitats, sirenians are exposed to many types of anthropogenic activities that result in challenges to their well-being, poor health, and even death. In the wild, they are exposed to direct and indirect local pressures as well as subject to large-scale stressors such as global climate change acting on regions or entire genetic stocks. In captivity, they are subject to husbandry and management practices based on our collective knowledge, or in some cases lack thereof, of their needs and welfare. It is therefore reasonable to consider that their current imperiled status is very closely linked to our actions. In this chapter, we identify and define human interactions that may impact dugongs and manatees, including hunting, fisheries, boat interactions, negative interactions with man-made structures, disease and contaminants, and global climate change. We examine techniques used to investigate these impacts and the influence of sirenian biology and of changing human behaviors on potential outcomes. We examine how this differs for dugongs and manatees in the wild and for those held in captivity. Finally, we provide possible mitigation strategies and ways to assess the efforts we are making to improve the welfare of individuals and to conserve these species. This chapter identifies how the welfare of these species is intrinsically linked to the human interactions these animals experience, and how the nature of these interactions has changed with societal shifts. We proffer suggested ways to minimize negative impacts. Current knowledge should be used to minimize negative human interactions and impacts, to promote positive impacts, and to protect these animals for the future.

Book chapter↗
USGS2021

Demography and loss of genetic diversity in two insular populations of the bobcat (Lynx rufus)

Among felids worldwide, only 6 of 38 species have stable or increasing populations, and most felid species are threatened by anthropogenic influences, especially habitat loss and fragmentation. We documented changes in genetic diversity in an isolated, reintroduced population of bobcats on Cumberland Island (CUIS), Georgia, USA, compared to another bobcat population on Kiawah Island, South Carolina, USA, that was naturally established and experiences limited immigration from the mainland. The CUIS population declined from 32 reintroduced bobcats in 1989 to 10–24 individuals during 2012–2019, and observed heterozygosity declined from 0.742 to 0.634 (SD = 0.240). Observed heterozygosity of bobcats on Kiawah was 0.699 (SD = 0.153). We estimated that one bobcat immigrated to Kiawah Island every 5.3 years. We compared the predictions of a novel population viability analysis ( PVA ) to empirical estimates of abundance and genetic diversity on CUIS and used our PVA to identify management actions that are likely to support long-term viability. Mean heterozygosity from the PVA (0.588, SD = 0.065) was within 1 standard deviation of the empirical estimate. The PVA estimated the population would decline following population restoration due to loss of genetic diversity and inbreeding depression. Translocations of one female every four years would stabilize allele heterozygosity similar to the Kiawah Island population, but even translocations of two females every two years would not restore heterozygosity to founder levels. The PVA predicted no management action would result in a one in five probability of extinction within 50 years of reintroduction, but all translocation strategies nearly eliminated extinction risk through 100 years.

Georgia, South Carolina↗
USGS2002

On the origin of brucellosis in bison of Yellowstone National Park: a review

Brucellosis caused by Brucella abortus occurs in the free-ranging bison ( Bison bison ) of Yellowstone and Wood Buffalo National Parks and in elk ( Cervus elaphus ) of the Greater Yellowstone Area. As a result of nationwide bovine brucellosis eradication programs, states and provinces proximate to the national parks are considered free of bovine brucellosis. Thus, increased attention has been focused on the wildlife within these areas as potential reservoirs for transmission to cattle. Because the national parks are mandated as natural areas, the question has been raised as to whether Brucella abortus is endogenous or exogenous to bison, particularly for Yellowstone National Park. We synthesized diverse lines of inquiry, including the evolutionary history of both bison and Brucella , wild animals as Brucella hosts, biochemical and genetic information, behavioral characteristics of host and organism, and area history to develop an evaluation of the question for the National Park Service. All lines of inquiry indicated that the organism was introduced to North America with cattle, and that the introduction into the Yellowstone bison probably was directly from cattle shortly before 1917. Fistulous withers of horses was a less likely possibility. Elk on winter feedgrounds south of Yellowstone National Park apparently acquired the disease directly from cattle. Bison presently using Grand Teton National Park probably acquired brucellosis from feedground elk.

Idaho, Montana, Wyoming↗
USGS2016

Golden Eagle fatalities and the continental-scale consequences of local wind-energy generation

Renewable energy production is expanding rapidly despite mostly unknown environmental effects on wildlife and habitats. We used genetic and stable isotope data collected from Golden Eagles (Aquila chrysaetos) killed at the Altamont Pass Wind Resource Area (APWRA) in California in demographic models to test hypotheses about the geographic extent and demographic consequences of fatalities caused by renewable energy facilities. Geospatial analyses of δ 2 H values obtained from feathers showed that ≥25% of these APWRA-killed eagles were recent immigrants to the population, most from long distances away (>100 km). Data from nuclear genes indicated this subset of immigrant eagles was genetically similar to birds identified as locals from the δ 2 H data. Demographic models implied that in the face of this mortality, the apparent stability of the local Golden Eagle population was maintained by continental-scale immigration. These analyses demonstrate that ecosystem management decisions concerning the effects of local-scale renewable energy can have continental-scale consequences.

Conservation Biology↗
USGS2017

Climate change and alpine stream biology: progress, challenges, and opportunities for the future

In alpine regions worldwide, climate change is dramatically altering ecosystems and affecting biodiversity in many ways. For streams, receding alpine glaciers and snowfields, paired with altered precipitation regimes, are driving shifts in hydrology, species distributions, basal resources, and threatening the very existence of some habitats and biota. Alpine streams harbour substantial species and genetic diversity due to significant habitat insularity and environmental heterogeneity. Climate change is expected to affect alpine stream biodiversity across many levels of biological resolution from micro- to macroscopic organisms and genes to communities. Herein, we describe the current state of alpine stream biology from an organism-focused perspective. We begin by reviewing seven standard and emerging approaches that combine to form the current state of the discipline. We follow with a call for increased synthesis across existing approaches to improve understanding of how these imperiled ecosystems are responding to rapid environmental change. We then take a forward-looking viewpoint on how alpine stream biologists can make better use of existing data sets through temporal comparisons, integrate remote sensing and geographic information system (GIS) technologies, and apply genomic tools to refine knowledge of underlying evolutionary processes. We conclude with comments about the future of biodiversity conservation in alpine streams to confront the daunting challenge of mitigating the effects of rapid environmental change in these sentinel ecosystems.

Biological Reviews↗
USGS2018

Rapid discovery of SNPs differentiating hatchery steelhead trout from ESA-listed natural-origin steelhead trout using a 57K SNP array

Natural-origin steelhead trout ( Oncorhynchus mykiss (Walbaum, 1792)) in the Pacific Northwest, USA, are threatened by a number of factors including habitat destruction, disease, decline in marine survival, and a potential erosion of genetic viability due to introgression from hatchery strains. Our major goal was to use a recently developed SNP array containing ∼57 000 SNPs to identify a subset of SNPs that differentiate hatchery and natural-origin populations. We analyzed 35 765 polymorphic SNPs in nine populations of steelhead trout sampled from Puget Sound, Washington, USA. We then conducted two outlier tests and found 360 loci that were candidates for divergent selection between hatchery and natural-origin populations (mean F CT = 0.29, maximum = 0.65) and 595 SNPs that were candidates for selection among natural-origin populations (mean F ST = 0.25, maximum = 0.51). Comparisons with a linkage map revealed that two chromosomes (Omy05 and Omy25) contained significantly more outliers than other chromosomes, suggesting that regions on Omy05 and Omy25 may be of adaptive significance. Our results highlight several advantages of the 57 000 SNP array as a tool for population and conservation genomics studies.

British Columbia, Washington↗
USGS2016

Breeding sites and winter site fidelity of Piping Plovers wintering in The Bahamas, a previously unknown major wintering area

Most of the known wintering areas of Piping Plovers ( Charadrius melodus ) are along the Atlantic and Gulf coasts of the United States and into Mexico, and in the Caribbean. However, 1066 threatened/endangered Piping Plovers were recently found wintering in The Bahamas, an area not previously known to be important for the species. Although representing about 27% of the birds counted during the 2011 International Piping Plover Winter Census, the location of their breeding site(s) was unknown. Thus, our objectives were to determine the location(s) of their breeding site(s) using molecular markers and by tracking banded individuals, identify spring and fall staging sites, and examine site fidelity and survival. We captured and color-banded 57 birds in January and February 2010 in The Bahamas. Blood samples were also collected for genetic evaluation of the likely subspecies wintering in The Bahamas. Band re-sightings and DNA analysis revealed that at least 95% of the Piping Plovers wintering in The Bahamas originated on the Atlantic coast of the United States and Canada. Re-sightings of birds banded in The Bahamas spanned the breeding distribution of the species along the Atlantic coast from Newfoundland to North Carolina. Site fidelity to breeding and wintering sites was high (88–100%). Spring and fall staging sites were located along the Atlantic coast of the United States, with marked birds concentrating in the Carolinas. Our estimate of true survival for the marked birds was 0.71 (95% CI: 0.61–0.80). Our results indicate that more than one third of the Piping Plover population that breeds along the Atlantic coast winters in The Bahamas. By determining the importance of The Bahamas to the Atlantic subspecies of Piping Plovers, future conservation efforts for these populations can be better focused on where they are most needed.

Journal of Field Ornithology↗
USGS2021

Modeling distribution of endemic Bartram’s Bass Micropterus sp. cf. coosae: Disturbance and proximity to invasion source increase hybridization with invasive Alabama Bass

“Bartram’s Bass” Micropterus sp. cf. coosae is endemic to the upper Savannah River basin of the southeastern United States and is threatened by hybridization with invasive Alabama Bass Micropterus henshalli . Bartram’s Bass have been functionally extirpated from reservoirs, and hybrid individuals have been detected in several tributaries. However, the extent of introgression in tributaries is currently unknown. Our objectives were to (1) assess the distribution of Bartram’s Bass, native Largemouth Bass M . salmoides , invasive Alabama Bass, and their hybrids in streams of the upper Savannah River basin and (2) quantify effects of abiotic variables on the distribution of each species. We sampled 154 locations in 2017 and 2018 and assigned genetic identity using hydrolysis probes and microsatellites. We used conditional inference trees to quantify variables affecting the occurrence of each species and hybrids. We observed widespread hybridization across the basin. Pure Bartram’s Bass were collected at 27% (42) of sites, among which only 12 sites contained pure Bartram’s Bass and no other congeners. Thirty sites where pure Bartram’s Bass were collected contained hybrids. In the montane Blue Ridge ecoregion, occurrence of pure Bartram’s Bass was negatively affected by low levels of local-scale developed land cover. In the lower-relief Piedmont ecoregion, pure Bartram’s Bass were positively associated with watershed-scale forest land cover and stream gradient. Distance from a reservoir was positively associated with occurrence of pure Bartram’s Bass in both ecoregions. Pure Bartram’s Bass are likely to occur with high probability in only 16% of nonimpounded stream segments; this represents a conservative estimate, and the true number is likely lower. However, future work accounting for incomplete detection of Bartram’s Bass will help to improve confidence in true extirpations. Conservation efforts may be more successful if implemented on stream segments farther from reservoirs or upstream of dispersal barriers preventing colonization of Alabama Bass.

Georgia, North Carolina, South Carolina↗
USGS2025

How accurately does eDNA reflect the spatial distribution of cold-water fish? Field validation from a temperate lake

Applications of environmental DNA (eDNA) based detection technology to evaluate the distribution of aquatic organisms are increasing; yet field validations of eDNA are important to measure accuracy in study systems. To successfully apply this technology to species conservation, it is critical to understand how both species biology and environmental conditions affect the accuracy of inference from eDNA detection data. We implemented a field assessment of the accuracy and spatial resolution of eDNA-based species distributions for a native cold-water, schooling fish, cisco Coregonus artedi , that has been reintroduced to a deep temperate lake. We leveraged a combination of acoustic telemetry, providing known spatial locations of tagged fish, and lake-wide eDNA sampling to infer their distribution in Keuka Lake, New York, USA. Sub-surface (12 m and 18 m depths) eDNA samples were collected to accommodate the diel vertical migration behaviour of this fish species. The results of this study validated the accuracy of positive eDNA detections with the distribution of tagged fish to coarse spatial scales. Yet, several fine-scale locations revealed a mismatch between eDNA and acoustic telemetry detections; consistent with rapid transport of genetic material via lake currents. Empirical measurements of lake currents using drifters found cisco eDNA detections could deviate from specimens' source locations by as much as 3.3 km at 12 m depth or 1.5 km at 18 m depth over a 24 h transport period. Our study indicates that accurate species distributions estimated from eDNA sampling in lakes may require further understanding of transport mechanisms and persistence of environmental genetic material to relate point detections to source animal locations. Integrating eDNA sampling with additional data collection of species biology and environmental conditions will increase the spatial resolution of fish distribution assessments.

New York↗
USGS2009

Spatial-temporal patterns in Mediterranean carnivore road casualties: Consequences for mitigation

Many carnivores have been seriously impacted by the expansion of transportation systems and networks; however we know little about carnivore response to the extent and magnitude of road mortality, or which age classes may be disproportionately impacted. Recent research has demonstrated that wildlife-vehicle-collisions (WVC) involving carnivores are modulated by temporal and spatial factors. Thus, we investigated road mortality on a guild of small and medium-sized carnivores in southern Portugal using road-kill data obtained from a systematic 36 months monitoring period along highways (260 km) and national roads (314 km) by addressing the following questions: (a) which species and age class are most vulnerable to WVC? (b) are there temporal and/or spatial patterns in road-kill? and (c) which life-history and/or spatial factors influence the likelihood of collisions? We recorded a total of 806 carnivore casualties, which represented an average of 47 ind./100 km/year. Red fox and stone marten had the highest mortality rates. Our findings highlight three key messages: (1) the majority of road-killed individuals were adults of common species; (2) all carnivores, except genets, were more vulnerable during specific life-history phenological periods: higher casualties were observed when red fox and stone marten were provisioning young, Eurasian badger casualties occurred more frequently during dispersal, and higher Egyptian mongoose mortality occurred during the breeding period; and (3) modeling demonstrated that favorable habitat, curves in the road, and low human disturbance were major contributors to the deadliest road segments. Red fox carcasses were more likely to be found on road sections with passages distant from urban areas. Conversely, stone marten mortalities were found more often on national roads with high of cork oak woodland cover; Egyptian mongoose and genet road-kills were found more often on road segments close to curves. Based on our results, two key mitigation measures should help to reduce WVC in Portugal. The first involves the improvement of existing crossings with buried and small mesh size fence to guide the individuals towards to the passages, in road segments with high traffic volume (>1200 vehicles/night) and located in preferred carnivore habitats. The second mitigation involves cutting or removal of dense vegetation in verges of road segments with curves to aid motorists in seeing animals about to cross. ?? 2008 Elsevier Ltd.

Biological Conservation↗
USGS2004

Evaluating mixed samples as a source of error in non-invasive genetic studies using microsatellites

The use of noninvasive genetic sampling (NGS) for surveying wild populations is increasing rapidly. Currently, only a limited number of studies have evaluated potential biases associated with NGS. This paper evaluates the potential errors associated with analysing mixed samples drawn from multiple animals. Most NGS studies assume that mixed samples will be identified and removed during the genotyping process. We evaluated this assumption by creating 128 mixed samples of extracted DNA from brown bear (Ursus arctos) hair samples. These mixed samples were genotyped and screened for errors at six microsatellite loci according to protocols consistent with those used in other NGS studies. Five mixed samples produced acceptable genotypes after the first screening. However, all mixed samples produced multiple alleles at one or more loci, amplified as only one of the source samples, or yielded inconsistent electropherograms by the final stage of the error-checking process. These processes could potentially reduce the number of individuals observed in NGS studies, but errors should be conservative within demographic estimates. Researchers should be aware of the potential for mixed samples and carefully design gel analysis criteria and error checking protocols to detect mixed samples.

Molecular Ecology↗
USGS2017

Gulf Coast vulnerability assessment: Mangrove, tidal emergent marsh, barrier islands and oyster reef

Climate, sea level rise, and urbanization are undergoing unprecedented levels of combined change and are expected to have large effects on natural resources—particularly along the Gulf of Mexico coastline (Gulf Coast). Management decisions to address these effects (i.e., adaptation) require an understanding of the relative vulnerability of various resources to these stressors. To meet this need, the four Landscape Conservation Cooperatives along the Gulf partnered with the Gulf of Mexico Alliance to conduct this Gulf Coast Vulnerability Assessment (GCVA). Vulnerability in this context incorporates exposure and sensitivity to threats (potential impact), coupled with the adaptive capacity to mitigate those threats. Potential impact and adaptive capacity reflect natural history features of target species and ecosystems. The GCVA used an expert opinion approach to qualitatively assess the vulnerability of four ecosystems: mangrove, oyster reef, tidal emergent marsh, and barrier islands, and a suite of wildlife species that depend on them. More than 50 individuals participated in the completion of the GCVA, facilitated via Ecosystem and Species Expert Teams. Of the species assessed, Kemp’s ridley sea turtle was identified as the most vulnerable species across the Gulf Coast. Experts identified the main threats as loss of nesting habitat to sea level rise, erosion, and urbanization. Kemp’s ridley also had an overall low adaptive capacity score due to their low genetic diversity, and higher nest site fidelity as compared to other assessed species. Tidal emergent marsh was the most vulnerable ecosystem, due in part to sea level rise and erosion. In general, avian species were more vulnerable than fish because of nesting habitat loss to sea level rise, erosion, and potential increases in storm surge. Assessors commonly indicated a lack of information regarding impacts due to projected changes in the disturbance regime, biotic interactions, and synergistic effects in both the species and habitat assessments. Many of the assessors who focused on species also identified data gaps regarding genetic information, phenotypic plasticity, life history, and species responses to past climate change and sea level rise. Regardless of information gaps, the results from the GCVA can be used to inform Gulf-wide adaptation plans. Given the scale of climatic impacts, coordinated efforts to address Gulf-wide threats to species and ecosystems will enhance the effectiveness of management actions and also have the potential to maximize the efficacy of limited funding.

Alabama, Florida, Louisiana, Mississippi, Texas↗