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USGS2013

Habitat use of breeding green turtles Chelonia mydas tagged in Dry Tortugas National Park: Making use of local and regional MPAs

Use of existing marine protected areas (MPAs) by far-ranging marine turtles can be determined using satellite telemetry. Because of a lack of information on MPA use by marine turtles in the Gulf of Mexico, we used satellite transmitters in 2010 and 2011 to track movements of 11 adult female breeding green turtles ( Chelonia mydas ) tagged in Dry Tortugas National Park (DRTO), in the Gulf of Mexico, south Florida, USA. Throughout the study period, turtles emerged every 9–18 days to nest. During the intervals between nesting episodes (i.e., inter-nesting periods), the turtles consistently used a common core-area within the DRTO boundary, determined using individual 50% kernel-density estimates (KDEs). We mapped the area in DRTO where individual turtle 50% KDEs overlapped using the USGS Along-Track Reef-Imaging System, and determined the diversity and distribution of various benthic-cover types within the mapped area. We also tracked turtles post-nesting as they transited to foraging sites 5–282 km away from tagging beaches; these sites were located both within DRTO and in the surrounding area of the Florida Keys and Florida Keys National Marine Sanctuary (FKNMS), a regional MPA. Year-round residency of 9 out of 11 individuals (82%) both within DRTO and in the FKNMS represents novel non-migratory behavior, which offers an opportunity for conservation of this imperiled species at both local and regional scales. These data comprise the first satellite-tracking results on adult nesting green turtles at this remote study site. Additional tracking could reveal whether the distinct inter-nesting and foraging sites delineated here will be repeatedly used in the future by these and other breeding green turtles.

Florida↗

USGS2004

Cassini/VIMS observation of an Io post-eclipse brightening event

During the Cassini-Jupiter flyby, VIMS observed Io at different phase angles, both in full sunlight and in eclipse. By using the sunlight measurements, we were able to produce phase curves in the visual through all the near infrared wavelengths covered by the VIMS instrument (0.85-5.1 ??m). The phase angle spanned from ???2?? to ???120??. The measurements, done just after Io emerged from Jupiter's shadow, show an increase of about 15% in Io's reflectance with respect to what would be predicted by the phase curve. This behavior is observed at wavelengths >1.2 ??m. Moreover, just after emergence from eclipse an increase of about 25% is observed in the depth of SO2 frost bands at 4.07 and 4.35 ??m. At 0.879<??<1.04 ??m the brightening is 10-24%. Below ??=0.879 ??m the brightening, if present, should be less than the precision of our measurements (???5%). Apparently, these observations are not explained neither by a diverse spatial distribution of SO2 on the Io' surface nor by atmospheric SO2 condensation on the surface during the eclipse. ?? 2004 Elsevier Inc. All rights reserved.

Icarus↗

USGS2024

New uses for ancient middens: Bridging ecological and evolutionary perspectives

Rodent middens provide a fine-scale spatiotemporal record of plant and animal communities over the late Quaternary. In the Americas, middens have offered insight into biotic responses to past environmental changes and historical factors influencing the distribution and diversity of species. However, few studies have used middens to investigate genetic or ecosystem level responses. Integrating midden studies with neoecology and experimental evolution can help address these gaps and test mechanisms underlying eco-evolutionary patterns across biological and spatiotemporal scales. Fully realizing the potential of middens to answer cross-cutting ecological and evolutionary questions and inform conservation goals in the Anthropocene will require a collaborative research community to exploit existing midden archives and mount new campaigns to leverage midden records globally.

Trends in Ecology and Evolution↗

USGS2024

Integrative phylogenetic, phylogeographic and morphological characterisation of the Unio crassus species complex reveals cryptic diversity with important conservation implications

The global decline of freshwater mussels and their crucial ecological services highlight the need to understand their phylogeny, phylogeography and patterns of genetic diversity to guide conservation efforts. Such knowledge is urgently needed for Unio crassus , a highly imperilled species originally widespread throughout Europe and southwest Asia. Recent studies have resurrected several species from synonymy based on mitochondrial data, revealing U. crassus to be a complex of cryptic species. To address long-standing taxonomic uncertainties hindering effective conservation, we integrate morphometric, phylogenetic, and phylogeographic analyses to examine species diversity within the U. crassus complex across its entire range. Phylogenetic analyses were performed using cytochrome c oxidase subunit I (815 specimens from 182 populations) and, for selected specimens, whole mitogenome sequences and Anchored Hybrid Enrichment (AHE) data on ∼600 nuclear loci. Mito-nuclear discordance was detected, consistent with mitochondrial DNA gene flow between some species during the Pliocene and Pleistocene. Fossil-calibrated phylogenies based on AHE data support a Mediterranean origin for the U. crassus complex in the Early Miocene. The results of our integrative approach support 12 species in the group: the previously recognised Unio bruguierianus , Unio carneus, Unio crassus , Unio damascensis , Unio ionicus , Unio sesirmensis , and Unio tumidiformis , and the reinstatement of five nominal taxa: Unio desectus stat. rev. , Unio gontierii stat. rev. , Unio mardinensis stat. rev. , Unio nanus stat. rev. , and Unio vicarius stat. rev. Morphometric analyses of shell contours reveal important morphospace overlaps among these species, highlighting cryptic, but geographically structured, diversity. The distribution, taxonomy, phylogeography, and conservation of each species are succinctly described.

Molecular Phylogenetics and Evolution↗

USGS2008

Reconstructed historical land cover and biophysical parameters for studies of land-atmosphere interactions within the eastern United States

Over the past 350 years, the eastern half of the United States experienced extensive land cover changes. These began with land clearing in the 1600s, continued with widespread deforestation, wetland drainage, and intensive land use by 1920, and then evolved to the present-day landscape of forest regrowth, intensive agriculture, urban expansion, and landscape fragmentation. Such changes alter biophysical properties that are key determinants of land-atmosphere interactions (water, energy, and carbon exchanges). To understand the potential implications of these land use transformations, we developed and analyzed 20-km land cover and biophysical parameter data sets for the eastern United States at 1650, 1850, 1920, and 1992 time slices. Our approach combined potential vegetation, county-level census data, soils data, resource statistics, a Landsat-derived land cover classification, and published historical information on land cover and land use. We reconstructed land use intensity maps for each time slice and characterized the land cover condition. We combined these land use data with a mutually consistent set of biophysical parameter classes, to characterize the historical diversity and distribution of land surface properties. Time series maps of land surface albedo, leaf area index, a deciduousness index, canopy height, surface roughness, and potential saturated soils in 1650, 1850, 1920, and 1992 illustrate the profound effects of land use change on biophysical properties of the land surface. Although much of the eastern forest has returned, the average biophysical parameters for recent landscapes remain markedly different from those of earlier periods. Understanding the consequences of these historical changes will require land-atmosphere interactions modeling experiments.

Journal of Geophysical Research D: Atmospheres↗

USGS2002

A review of bacterial methyl halide degradation: Biochemistry, genetics and molecular ecology

Methyl halide‐degrading bacteria are a diverse group of organisms that are found in both terrestrial and marine environments. They potentially play an important role in mitigating ozone depletion resulting from methyl chloride and methyl bromide emissions. The first step in the pathway(s) of methyl halide degradation involves a methyltransferase and, recently, the presence of this pathway has been studied in a number of bacteria. This paper reviews the biochemistry and genetics of methyl halide utilization in the aerobic bacteria Methylobacterium chloromethanicum CM4 T , Hyphomicrobium chloromethanicum CM2 T , Aminobacter strain IMB‐1 and Aminobacter strain CC495. These bacteria are able to use methyl halides as a sole source of carbon and energy, are all members of the α ‐Proteobacteria and were isolated from a variety of polluted and pristine terrestrial environments. An understanding of the genetics of these bacteria identified a unique gene ( cmuA ) involved in the degradation of methyl halides, which codes for a protein (CmuA) with unique methyltransferase and corrinoid functions. This unique functional gene, cmuA , is being used to develop molecular ecology techniques to examine the diversity and distribution of methyl halide‐utilizing bacteria in the environment and hopefully to understand their role in methyl halide degradation in different environments. These techniques will also enable the detection of potentially novel methyl halide‐degrading bacteria.

Environmental Microbiology↗

USGS2024

Fine-resolution land cover mapping over large and mountainous areas for Lāna‘i, Hawaii using posterior probabilities, and expert knowledge

The task of accurately mapping species-specific vegetation cover in remote and topographically complex regions like those found in Hawaiʻi presents unique challenges. This study leverages a machine learning approach to accurately classify vegetation into fine species-specific classes across the island of Lāna‘i, Hawaii, offering a novel methodology for tackling such challenges. Utilizing high-resolution WordView-2 satellite imagery, a neural network classifier and a custom lidar-based geometric correction, we introduced two new approaches to refine our high-resolution land cover classifications. This included the implementation of prior-based adjustments to class posterior probabilities to enhance land cover classification accuracy. Moreover, we developed mixed hierarchical classification maps that use class posterior probabilities to identify, at the pixel level, the finest land cover class that meets a user-defined confidence threshold. The resulting high-resolution land cover map for Lāna‘i captures the rich diversity and distribution of native and invasive plant species with high overall accuracy, generally exceeding 95%, based on independent ground control data. The capacity to produce wall-to-wall species-level vegetation maps provides a new window into monitoring vegetation dynamics on Lāna‘i and similarly remote and topographically complex regions, and contributes to our broader understanding of ecosystem responses to invasive species, climatic changes, and land management practices such as erosion and sediment control planning. Our approach offers a blueprint for similar efforts in other complex and remote ecosystems.

Hawaii↗

USGS2016

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

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

Fisheries↗

USGS2011

Sensitivity of leaf size and shape to climate: Global patterns and paleoclimatic applications

Paleobotanists have long used models based on leaf size and shape to reconstruct paleoclimate. However, most models incorporate a single variable or use traits that are not physiologically or functionally linked to climate, limiting their predictive power. Further, they often underestimate paleotemperature relative to other proxies. Here we quantify leaf–climate correlations from 92 globally distributed, climatically diverse sites, and explore potential confounding factors. Multiple linear regression models for mean annual temperature (MAT) and mean annual precipitation (MAP) are developed and applied to nine well‐studied fossil floras. We find that leaves in cold climates typically have larger, more numerous teeth, and are more highly dissected. Leaf habit (deciduous vs evergreen), local water availability, and phylogenetic history all affect these relationships. Leaves in wet climates are larger and have fewer, smaller teeth. Our multivariate MAT and MAP models offer moderate improvements in precision over univariate approaches (± 4.0 vs 4.8°C for MAT) and strong improvements in accuracy. For example, our provisional MAT estimates for most North American fossil floras are considerably warmer and in better agreement with independent paleoclimate evidence. Our study demonstrates that the inclusion of additional leaf traits that are functionally linked to climate improves paleoclimate reconstructions. This work also illustrates the need for better understanding of the impact of phylogeny and leaf habit on leaf–climate relationships.

New Phytologist↗

USGS2017

Biocrust ecology: Unifying micro- and macro-scales to confront global change

Biological soil crusts (biocrusts) are communities of microbes, lichens and bryophytes living at the soil surface in drylands (Fig. 1; Belnap et al ., 2016). Biocrusts occur on all continents and can comprise a majority of cover in some systems (Belnap et al ., 2016). While species diversity and distributions have long been a research focus, interest in controls on community composition and cover has expanded as biocrusts are increasingly recognized for their roles in ecosystem functioning (Deane-Coe and Stanton, 2017). For example, biocrust organisms can stabilize soils (Belnap et al ., 2016; Faist et al ., 2017), fix atmospheric carbon (C) (Sancho et al ., 2016), and serve as the foremost source of ‘new’ soil nitrogen (N) in drylands, via N 2 fixation (Barger et al ., 2016) These contributions to gross primary production and soil fertility could be quite large, as high-end estimates suggest biocrusts and similar communities of bryophytes and lichens might account for 10% of terrestrial C- and 50% of N-fixation globally (Elbert et al ., 2012). Yet verifying these and other biocrust roles in ecosystem functioning is complicated by limited knowledge of biocrust cover and composition across the vast dryland biome (Ferrenberg et al ., 2017). It was against this backdrop that ‘Biocrust3: the 3 rd International workshop on biological soil crusts’ was held in Moab, UT, USA, on 26-30 September 2016. The workshop brought together over 50 scientists from 21 countries and six continents, and included numerous biocrust science pioneers (Fig. 2). The meeting was notable for its cross-scale focus, discussion of novel molecular and imaging techniques, and sessions on mapping and restoring biocrusts in a changing world. Here, we synthesize a central theme that emerged from Biocrust3, namely the potential for combining cutting edge tools with studies focused on organismal traits, ecosystem functions, and global change biology to advance the frontier of biocrust ecology.

New Phytologist↗

USGS2022

The consequences of climate change for dryland biogeochemistry

Drylands, which cover more than 40% of Earth’s terrestrial surface, are dominant drivers of global biogeochemical cycling and home to more than one third of the human population. Climate projections predict warming, drought frequency and severity, and evaporative demand will increase in drylands at faster rates than global means. Due to extreme temperatures and high biological dependency on limited water availability, drylands are predicted to be exceptionally sensitive to climate change and, indeed, significant climate impacts are already being observed. Yet our understanding and ability to forecast climate change effects on dryland biogeochemistry and ecosystem functions lag behind many mesic systems. To improve our capacity to forecast ecosystem change, we propose focusing on the controls and consequences of two key characteristics affecting dryland biogeochemistry: i) high spatial and temporal heterogeneity in environmental conditions and ii) generalized resource scarcity. In addition to climate change, drylands are experiencing accelerating land use change. Building our understanding of dryland biogeochemistry in both intact and disturbed systems will better equip us to address the interacting effects of climate change and landscape degradation. Responding to these challenges will require a diverse, globally distributed, and interdisciplinary community of dryland experts united towards better understanding these vast and important ecosystems.

New Phytologist Foundation↗

USGS2016

Spatial variation in nutrient and water color effects on lake chlorophyll at macroscales

The nutrient-water color paradigm is a framework to characterize lake trophic status by relating lake primary productivity to both nutrients and water color, the colored component of dissolved organic carbon. Total phosphorus (TP), a limiting nutrient, and water color, a strong light attenuator, influence lake chlorophyll a concentrations (CHL). But, these relationships have been shown in previous studies to be highly variable, which may be related to differences in lake and catchment geomorphology, the forms of nutrients and carbon entering the system, and lake community composition. Because many of these factors vary across space it is likely that lake nutrient and water color relationships with CHL exhibit spatial autocorrelation, such that lakes near one another have similar relationships compared to lakes further away. Including this spatial dependency in models may improve CHL predictions and clarify how well the nutrient-water color paradigm applies to lakes distributed across diverse landscape settings. However, few studies have explicitly examined spatial heterogeneity in the effects of TP and water color together on lake CHL. In this study, we examined spatial variation in TP and water color relationships with CHL in over 800 north temperate lakes using spatially-varying coefficient models (SVC), a robust statistical method that applies a Bayesian framework to explore space-varying and scale-dependent relationships. We found that TP and water color relationships were spatially autocorrelated and that allowing for these relationships to vary by individual lakes over space improved the model fit and predictive performance as compared to models that did not vary over space. The magnitudes of TP effects on CHL differed across lakes such that a 1 μg/L increase in TP resulted in increased CHL ranging from 2–24 μg/L across lake locations. Water color was not related to CHL for the majority of lakes, but there were some locations where water color had a positive effect such that a unit increase in water color resulted in a 2 μg/L increase in CHL and other locations where it had a negative effect such that a unit increase in water color resulted in a 2 μg/L decrease in CHL. In addition, the spatial scales that captured variation in TP and water color effects were different for our study lakes. Variation in TP–CHL relationships was observed at intermediate distances (~20 km) compared to variation in water color–CHL relationships that was observed at regional distances (~200 km). These results demonstrate that there are lake-to-lake differences in the effects of TP and water color on lake CHL and that this variation is spatially structured. Quantifying spatial structure in these relationships furthers our understanding of the variability in these relationships at macroscales and would improve model prediction of chlorophyll a to better meet lake management goals.

Maine, Michigan, New York, Wisconsin↗

USGS2014

A new species of small-eared shrew (Mammalia, Eulipotyphla, Cryptotis ) from the Lacandona rain forest, Mexico

The diversity and distribution of mammals in the American tropics remain incompletely known. We describe a new species of small-eared shrew (Soricidae, Cryptotis ) from the Lacandona rain forest, Chiapas, southern Mexico. The new species is distinguished from other species of Cryptotis on the basis of a unique combination of pelage coloration, size, dental, cranial, postcranial, and external characters, and genetic distances. It appears most closely related to species in the Cryptotis nigrescens species group, which occurs from southern Mexico to montane regions of Colombia. This discovery is particularly remarkable because the new species is from a low-elevation habitat (approximately 90 m), whereas most shrews in the region are restricted to higher elevations, typically > 1,000 m. The only known locality for the new shrew is in one of the last areas in southern Mexico where relatively undisturbed tropical vegetation is still found. The type locality is protected by the Mexican government as part of the Yaxchilán Archaeological Site on the border between Mexico and Guatemala.

Chiapas↗

USGS2024

An update of the ichthyofauna of West Virginia with notes on historic sportfish stockings

The management and conservation of faunas at regional scales depend on current data on species diversity and distribution. Relative to the ichthyofauna of West Virginia, few studies have recently documented the richness and distribution of fishes in the state, with even the most comprehensive publications rarely discussing either the conservation status of individual fishes or historical sportfish stockings. In this paper, we review the state's historic sportfish stockings. We also clarify inconsistent published data and present new information for several species, delete 3 species from the West Virginia ichthyofaunal list, and add 35 species representing extant or extirpated populations. Lastly, we provide a checklist of 195 species by major drainage of West Virginia's fishes, including their origin (i.e., native or introduced).

West Virginia↗

USGS2016

Model selection and assessment for multi-species occupancy models

While multi-species occupancy models (MSOMs) are emerging as a popular method for analyzing biodiversity data, formal checking and validation approaches for this class of models have lagged behind. Concurrent with the rise in application of MSOMs among ecologists, a quiet regime shift is occurring in Bayesian statistics where predictive model comparison approaches are experiencing a resurgence. Unlike single-species occupancy models that use integrated likelihoods, MSOMs are usually couched in a Bayesian framework and contain multiple levels. Standard model checking and selection methods are often unreliable in this setting and there is only limited guidance in the ecological literature for this class of models. We examined several different contemporary Bayesian hierarchical approaches for checking and validating MSOMs and applied these methods to a freshwater aquatic study system in Colorado, USA, to better understand the diversity and distributions of plains fishes. Our findings indicated distinct differences among model selection approaches, with cross-validation techniques performing the best in terms of prediction.

Ecology↗

USGS1983

Effects of roads on small mammals

(1) The study was designed to determine the effects of roads on the diversity, spatial distribution, and density of small mammals. (2) Forty species of small mammal (5859 individuals) were snap-trapped in the study. Data resulted from 144 360 trap-nights of effort for an average of 4.06 captures per 100 trap-nights. (3) Small mammal community structure and density were both influenced by roads. Community structure in right-of-way (ROW) habitat was different from that in adjacent habitat. Five species did not prefer ROW habitat: the golden mouse, dusky-footed woodrat, brush mouse, pinon mouse, and California red-backed vole. However, there were more species present in ROW habitat than in adjacent habitat. Grassland species generally preferred ROW habitat and many less habitat-specific species were distributed in ROW and adjacent habitat. (4) Small mammal density (all species combined) was greater in interstate ROW habitat than in adjacent habitat. This was also true individually for the eastern harvest mouse, white-footed mouse, meadow vole, prairie vole, vagrant shrew. Townsend's vole, and California vole. Small mammal density was less in county road ROWs than in adjacent habitat, probably because of the small size of these areas. The data indicate that ROW habitat and its accompanying edge are attractive no: only to grassland species but also to many less habitat-specific species that make use of the ROW-edge-adjacent habitat complex. (5) Mortality on interstate highways was greatest for those species with highest densities in ROW habitat, and did not appear to be detrimental to populations of these species.

Journal of Applied Ecology↗

USGS2024

Realizing the potential of eDNA biodiversity monitoring tools in the marine environment with application to offshore renewable energy

The U.S. Geological Survey (USGS) researches the biological diversity and distribution of species to support management, conservation, and resource use decisions. USGS scientists advance detection and monitoring technologies to assess changes in fish and wildlife populations, biodiversity, and the health of ecosystems. The United States is planning to install 30 gigawatts of offshore marine and wind energy by 2030. However, the effects on fish and wildlife and their habitats are not well understood. The USGS is a leader in the field of eDNA technologies and has helped advance robotic eDNA samplers, has extensive experience working in the offshore environment, and has developed novel and actionable statistical methods and standards for eDNA monitoring applications. This fact sheet presents key eDNA research and development advances needed for realizing the potential of eDNA biodiversity monitoring tools in the marine environment and applying eDNA monitoring to offshore renewable energy development. New and cost-effective tools for measuring changes in biodiversity in response to offshore renewable energy development can help to inform natural resource management and project planning and permitting decisions.

Fact Sheet↗

USGS2010

Inter-nesting habitat-use patterns of loggerhead sea turtles: Enhancing satellite tracking with benthic mapping

The loggerhead sea turtle Caretta caretta faces declining nest numbers and bycatches from commercial longline fishing in the southeastern USA. Understanding spatial and temporal habitat-use patterns of these turtles, especially reproductive females in the neritic zone, is critical for guiding management decisions. To assess marine turtle habitat use within the Dry Tortugas National Park (DRTO), we used satellite telemetry to identify core-use areas for 7 loggerhead females inter-nesting and tracked in 2008 and 2009. This effort represents the first tracking of DRTO loggerheads, a distinct subpopulation that is 1 of 7 recently proposed for upgrading from threatened to endangered under the US Endangered Species Act. We also used a rapid, high-resolution, digital imaging system to map benthic habitats in turtle core-use areas (i.e. 50% kernel density zones). Loggerhead females were seasonal residents of DRTO for 19 to 51 d, and individual inter-nesting habitats were located within 1.9 km (2008) and 2.3 km (2009) of the nesting beach and tagging site. The core area common to all tagged turtles was 4.2 km 2 in size and spanned a depth range of 7.6 to 11.5 m. Mapping results revealed the diversity and distributions of benthic cover available in the core-use area, as well as a heavily used corridor to/from the nesting beach. This combined tagging-mapping approach shows potential for planning and improving the effectiveness of marine protected areas and for developing spatially explicit conservation plans.

Dry Tortugas National Park↗