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USGS2012

Temporal analysis of mtDNA variation reveals decreased genetic diversity in least terns

The Least Tern (Sternula antillarum) has undergone large population declines over the last century as a result of direct and indirect anthropogenic factors. The genetic implications of these declines are unknown. We used historical museum specimens (pre-1960) and contemporary (2001–2005) samples to examine range-wide phylogeographic patterns and investigate potential loss in the species' genetic variation. We obtained sequences (522 bp) of the mitochondrial gene for NADH dehydrogenase subunit 6 (ND6) from 268 individuals from across the species' range. Phylogeographic analysis revealed no association with geography or traditional subspecies designations. However, we detected potential reductions in genetic diversity in contemporary samples from California and the Atlantic coast Least Tern from that in historical samples, suggesting that current genetic diversity in Least Tern populations is lower than in their pre-1960 counterparts. Our results offer unique insights into changes in the Least Tern's genetic diversity over the past century and highlight the importance and utility of museum specimens in studies of conservation genetics.

The Condor↗

USGS2007

Effects of flow diversions on water and habitat quality: Examples from California's highly manipulated Sacramento–San Joaquin Delta

We use selected monitoring data to illustrate how localized water diversions from seasonal barriers, gate operations, and export pumps alter water quality across the Sacramento-San Joaquin Delta (California). Dynamics of water-quality variability are complex because the Delta is a mixing zone of water from the Sacramento and San Joaquin Rivers, agricultural return water, and the San Francisco Estuary. Each source has distinct water-quality characteristics, and the contribution of each source varies in response to natural hydrologic variability and water diversions. We use simulations with a tidal hydrodynamic model to reveal how three diversion events, as case studies, influence water quality through their alteration of Delta-wide water circulation patterns and flushing time. Reduction of export pumping decreases the proportion of Sacramento- to San Joaquin-derived fresh water in the central Delta, leading to rapid increases in salinity. Delta Cross Channel gate operations control salinity in the western Delta and alter the freshwater source distribution in the central Delta. Removal of the head of Old River barrier, in autumn, increases the flushing time of the Stockton Ship Channel from days to weeks, contributing to a depletion of dissolved oxygen. Each shift in water quality has implications either for habitat quality or municipal drinking water, illustrating the importance of a systems view to anticipate the suite of changes induced by flow manipulations, and to minimize the conflicts inherent in allocations of scarce resources to meet multiple objectives.

California↗

USGS1997

Multiscale sampling of plant diversity: Effects of minimum mapping unit size

Only a small portion of any landscape can be sampled for vascular plant diversity because of constraints of cost (salaries, travel time between sites, etc.). Often, the investigator decides to reduce the cost of creating a vegetation map by increasing the minimum mapping unit (MMU), and/or by reducing the number of vegetation classes to be considered. Questions arise about what information is sacrificed when map resolution is decreased. We compared plant diversity patterns from vegetation maps made with 100-ha, 50-ha, 2-ha, and 0.02-ha MMUs in a 754-ha study area in Rocky Mountain National Park, Colorado, United States, using four 0.025-ha and 21 0.1-ha multiscale vegetation plots. We developed and tested species–log(area) curves, correcting the curves for within-vegetation type heterogeneity with Jaccard’s coefficients. Total species richness in the study area was estimated from vegetation maps at each resolution (MMU), based on the corrected species–area curves, total area of the vegetation type, and species overlap among vegetation types. With the 0.02-ha MMU, six vegetation types were recovered, resulting in an estimated 552 species (95% ci = 520–583 species) in the 754-ha study area (330 plant species were observed in the 25 plots). With the 2-ha MMU, five vegetation types were recognized, resulting in an estimated 473 species for the study area. With the 50-ha MMU, 439 plant species were estimated for the four vegetation types recognized in the study area. With the 100-ha MMU, only three vegetation types were recognized, resulting in an estimated 341 plant species for the study area. Locally rare species and keystone ecosystems (areas of high or unique plant diversity) were missed at the 2-ha, 50-ha, and 100-ha scales. To evaluate the effects of minimum mapping unit size requires: (1) an initial stratification of homogeneous, heterogeneous, and rare habitat types; and (2) an evaluation of within-type and between-type heterogeneity generated by environmental gradients and other factors. We suggest that at least some portions of vegetation maps created at a coarser level of resolution be validated at a higher level of resolution.

Ecological Applications↗

USGS1999

Characterizing fish community diversity across Virginia landscapes: Prerequisite for conservation

The number of community types occurring within landscapes is an important, but often unprotected, component of biological diversity. Generally applicable protocols for characterizing community diversity need to be developed to facilitate conservation. We used several multivariate techniques to analyze geographic variation in the composition of fish communities in Virginia streams. We examined relationships between community composition and six landscape variables: drainage basin, physiography, stream order, elevation, channel slope, and map coordinates. We compared patterns at two scales (statewide and subdrainage-specific) to assess sensitivity of community classification to spatial scale. We also compared patterns based on characterizing communities by species composition vs. ecological composition. All landscape variables explained significant proportions of the variance in community composition. Statewide, they explained 32% of the variance in species composition and 48% of the variance in ecological composition. Typical communities in each drainage or physiography were statistically distinctive. Communities in different combinations of drainage, physiography, and stream size were even more distinctive, but composition was strongly spatially autocorrelated. Ecological similarity and species similarity of community pairs were strongly related, but replacement by ecologically similar species was common among drainage–physiography combinations. Landscape variables explained significant proportions of variance in community composition within selected subdrainages, but proportions were less than at the statewide scale, and the explanatory power of individual variables varied considerably among subdrainages. Community variation within subdrainages appeared to be much more closely related to environmental variation than to replacement among ecologically similar species. Our results suggest that taxonomic and ecological characterizations of community composition are complementary; both are useful in a conservation context. Landscape features such as drainage, physiography, and water body size generally may provide a basis for assessing aquatic community diversity, especially in regions where the biota is poorly known. Systematic conservation of community types would be a major advance relative to most current conservation programs, which typically focus narrowly on populations of imperiled species. More effective conservation of aquatic biodiversity will require new approaches that recognize the value of both species and assemblages, and that emphasize protection of key landscape-scale processes.

Ecological Applications↗

USGS2016

Resource waves: phenological diversity enhances foraging opportunities for mobile consumers

Time can be a limiting constraint for consumers, particularly when resource phenology mediates foraging opportunity. Though a large body of research has explored how resource phenology influences trophic interactions, this work has focused on the topics of trophic mismatch or predator swamping, which typically occur over short periods, at small spatial extents or coarse resolutions. In contrast many consumers integrate across landscape heterogeneity in resource phenology, moving to track ephemeral food sources that propagate across space as resource waves. Here we provide a conceptual framework to advance the study of phenological diversity and resource waves. We define resource waves, review evidence of their importance in recent case studies, and demonstrate their broader ecological significance with a simulation model. We found that consumers ranging from fig wasps ( Chalcidoidea) to grizzly bears ( Ursus arctos ) exploit resource waves, integrating across phenological diversity to make resource aggregates available for much longer than their component parts. In model simulations, phenological diversity was often more important to consumer energy gain than resource abundance per se. Current ecosystem-based management assumes that species abundance mediates the strength of trophic interactions. Our results challenge this assumption and highlight new opportunities for conservation and management. Resource waves are an emergent property of consumer–resource interactions and are broadly significant in ecology and conservation.

Ecology↗

USGS2021

Habitat diversity influences puma (Puma concolor) diet in the Chihuahuan Desert

Habitat heterogeneity and corresponding diversity in potential prey species should increase the diet breadth of generalist predators. Many previous studies describing puma Puma concolor diets in the arid regions of the southwestern United States were focused within largely xeric locations, overlooking the influence of heterogeneity created by riparian forests. Such habitat heterogeneity and corresponding prey diversity could influence prey availability and puma diet composition. We examined seasonal prey composition of pumas occupying areas with different habitat conditions representing riparian areas adjacent to the Rio Grande and xeric Chihuahuan Desert uplands in southern New Mexico. We collected prey composition data from 686 kill sites made by 17 (9 males and 8 females) GPS-collared pumas from 2014 to 2018. Diet composition included 32 different avian, aquatic, small mammal, and ungulate prey species. Prey composition varied, with more ungulate prey consumed by pumas inhabiting the upland desert areas and more aquatic prey consumed in the riparian bosque. Prey composition differed between seasons, with ungulate prey decreasing and aquatic prey increasing during the hot–dry season. Prey composition also varied between puma sex and habitat with females in the desert uplands consuming more small mammals than either males or females in riparian areas. The diverse diets of the pumas inhabiting the heterogeneous landscapes in southern New Mexico provide additional evidence that pumas have broad diets that are strongly influenced by the habitat and prey community that their home range encompasses.

New Mexico↗

USGS2011

A survey of alterations in microbial community diversity in marine sediments in response to oil from the Deepwater Horizon spill: Northern Gulf of Mexico shoreline, Texas to Florida

Microbial community genomic DNA was extracted from sediment samples collected from the northern Gulf of Mexico (NGOM) coast. These samples had a high probability of being impacted by Macondo-1 (M-1) well oil from the Deepwater Horizon (DWH) drilling site. The hypothesis for this project was that presence of M-1 oil in coastal sediments would significantly alter the diversity within the microbial communities associated with the impacted sediments. To determine if community-level changes did or did not occur following exposure to M-1 oil, microbial community-diversity fingerprints were generated and compared. Specific sequences within the community's genomic DNA were first amplified using the polymerase chain reaction (PCR) using a primer set that provides possible resolution to the species level. A second nested PCR that was performed on the primary PCR products using a primer set on which a GC-clamp was attached to one of the primers. These nested PCR products were separated using denaturing-gradient gel electrophoresis (DGGE) that resolves the nested PCR products based on sequence dissimilarities (or similarities), forming a genomic fingerprint of the microbial diversity within the respective samples. Sediment samples with similar fingerprints were grouped and compared to oil-fingerprint data from Rosenbauer and others (2010). The microbial community fingerprints grouped closely when identifying those sites that had been impacted by M-1 oil (N=12) and/or some mixture of M-1 and other oil (N=4), based upon the oil fingerprints. This report represents some of the first information on naturally occurring microbial communities in sediment from shorelines along the NGOM coast. These communities contain microbes capable of degrading oil and related hydrocarbons, making this information relevant to response and recovery of the NGOM from the DWH incident.

Gulf Of Mexico↗

USGS2015

Lake Michigan Diversion Accounting land cover change estimation by use of the National Land Cover Dataset and raingage network partitioning analysis

The U.S. Army Corps of Engineers (USACE), Chicago District, is responsible for monitoring and computation of the quantity of Lake Michigan water diverted by the State of Illinois. As part of this effort, the USACE uses the Hydrological Simulation Program–FORTRAN (HSPF) with measured meteorological data inputs to estimate runoff from the Lake Michigan diversion special contributing areas (SCAs), the North Branch Chicago River above Niles and the Little Calumet River above South Holland gaged basins, and the Lower Des Plaines and the Calumet ungaged that historically drained to Lake Michigan. These simulated runoffs are used for estimating the total runoff component from the diverted Lake Michigan watershed, which is accountable to the total diversion by the State of Illinois. The runoff is simulated from three interpreted land cover types in the HSPF models: impervious, grass, and forest. The three land cover data types currently in use were derived from aerial photographs acquired in the early 1990s. This study used the National Land Cover Dataset (NLCD) and developed an automated process for determining the area of the three land cover types, thereby allowing faster updating of future models, and for evaluating land cover changes by use of historical NLCD datasets. The study also carried out a raingage partitioning analysis so that the segmentation of land cover and rainfall in each modeled unit is directly applicable to the HSPF modeling. Historical and existing impervious, grass, and forest land acreages partitioned by percentages covered by two sets of raingages for the Lake Michigan diversion SCAs, gaged basins, and ungaged basins are presented.

Illinois↗

USGS2004

Evaluation of Streamflow Losses Along the Gunnison River from Whitewater Downstream to the Redlands Canal Diversion Dam, near Grand Junction, Colorado, Water Years 1995-2003

In 2003, the U.S. Geological Survey, in cooperation with the Colorado Water Conservation Board, Upper Colorado River Endangered Fish Recovery Program, Colorado River Water Conservation District, Colorado Division of Water Resources, and Bureau of Reclamation, initiated a study to characterize streamflow losses along a reach of the Gunnison River from the town of Whitewater downstream to the Redlands Canal diversion dam. This describes the methods and results of the study that include: (1) a detailed mass-balance analysis of historical discharge records that were available for the three streamflow-gaging stations along the study reach; and (2) two sets of discharge measurements that were made at the three stations and at four additional locations. Data for these existing streamflow-gaging stations were compiled and analyzed: (1) Gunnison River near Grand Junction (Whitewater station); (2) Gunnison River below Redlands Canal diversion dam (below-Redlands-dam station); and (3) Redlands Canal near Grand Junction (Redlands-Canal station). Data for water years 1995-2003 were used for the mass-balance analysis. Four intermediate sites (M1, M2, M3, and M4) were selected for discharge measurements in addition to the existing stations. The study reach is the approximate 12-mile reach of the Gunnison River from the Whitewater station downstream to the Redlands Canal diversion dam, which is about 3 miles upstream from the confluence with the Colorado River. For the mass-balance analysis, differences between the sum of the annual cumulative daily mean discharge at the two downstream stations and the annual cumulative daily mean discharges at the upstream station ranged from about -8,700 to -69,800 acre-feet (about -.8 to -1.1 percent), indicating that the downstream discharges generally were less than the upstream discharges. Moving 3-day daily mean discharge averages also were computed for each of the three stations to smooth out some of the abrupt differences between the downstream and upstream daily mean discharges. During water years 1995-2002, differences between the downstream and upstream moving 3-day daily mean discharges ranged from about -200 to +100 cubic feet per second (ft3/s) during one-half of each year, but the differences had absolute values as large as about 500 to 1,000 ft3/s during the other one-half of the year. The differences as a percentage of the upstream discharge ranged from 0 to -10 percent within the interquartile range and were as small or large as about -60 to +50. Two sets of discharge measurements were obtained during water year 2003. For measurement set 1 (February 5-6), discharge was measured 5-8 times over a 24-hour period at sites M1-M4, where measured discharges ranged from 527 to 608 ft3/s. Discharge was measured once each day at the Whitewater and below-Redlands-dam stations to verify discharge rating shifts; the Redlands Canal was not in operation at this time, so measurements were not needed at the Redlands-Canal station. Recorded 15-minute (unit) discharges ranged from about 575 to 615 ft3/s at the Whitewater station and from about 560 to 600 ft3/s at the below-Redlands-dam station during the February 5-6 period. Because of the inherent error in discharge measurements (5 percent for measurements rated good), and because the mean discharge at the below-Redlands-dam station, about 580 ft3/s, was only about 2.5 percent smaller than the mean discharge at the Whitewater station, about 595 ft3/s, it is concluded that there was no measurable streamflow loss along the study reach during measurement set 1. For measurement set 2 (May 14-15), discharge in the Gunnison River was about 2,000 ft3/s and increasing because of high-elevation snowmelt. Five discharge measurements were made at site M2 and discharge ranged from 1,668 to 2,117 ft3/s. Measured discharges at the gaging stations were 2,730 ft3/s at the Whitewater station, 1,268 ft3/s at the below-Redlands-dam station, and 819 ft3/s at the

Scientific Investigations Report↗

USGS2005

Effects of Surface-Water Diversions on Habitat Availability for Native Macrofauna, Northeast Maui, Hawaii

Effects of surface-water diversions on habitat availability for native stream fauna (fish, shrimp, and snails) are described for 21 streams in northeast Maui, Hawaii. Five streams (Waikamoi, Honomanu, Wailuanui, Kopiliula, and Hanawi Streams) were chosen as representative streams for intensive study. On each of the five streams, three representative reaches were selected: (1) immediately upstream of major surface-water diversions, (2) midway to the coast, and (3) near the coast. This study focused on five amphidromous native aquatic species (alamoo, nopili, nakea, opae, and hihiwai) that are abundant in the study area. The Physical Habitat Simulation (PHABSIM) System, which incorporates hydrology, stream morphology and microhabitat preferences to explore relations between streamflow and habitat availability, was used to simulate habitat/discharge relations for various species and life stages, and to provide quantitative habitat comparisons at different streamflows of interest. Hydrologic data, collected over a range of low-flow discharges, were used to calibrate hydraulic models of selected transects across the streams. The models were then used to predict water depth and velocity (expressed as a Froude number) over a range of discharges up to estimates of natural median streamflow. The biological importance of the stream hydraulic attributes was then assessed with the statistically derived suitability criteria for each native species and life stage that were developed as part of this study to produce a relation between discharge and habitat availability. The final output was expressed as a weighted habitat area of streambed for a representative stream reach. PHABSIM model results are presented to show the area of estimated usable bed habitat over a range of streamflows relative to natural conditions. In general, the models show a continuous decrease in habitat for all modeled species as streamflow is decreased from natural conditions. The PHABSIM modeling results from the intensively studied streams were normalized to develop relations between the relative amount of diversion from a stream and the resulting relative change in habitat in the stream. These relations can be used to estimate changes in habitat for diverted streams in the study area that were not intensively studied. The relations indicate that the addition of even a small amount of water to a dry stream has a significant effect on the amount of habitat available. Equations relating stream base-flow changes to habitat changes can be used to provide an estimate of the relative habitat change in the study area streams for which estimates of diverted and natural median base flow have been determined but for which detailed habitat models were not developed. Stream water temperatures, which could have an effect on stream ecology and taro cultivation, were measured in five streams in the study area. In general, the stream temperatures measured at any of the monitoring sites were not elevated enough, based on currently available information, to adversely effect the growth or mortality of native aquatic macrofauna or to cause wetland taro to be susceptible to fungi and associated rotting diseases.

Scientific Investigations Report↗

USGS2017

Field-trip guide to Columbia River flood basalts, associated rhyolites, and diverse post-plume volcanism in eastern Oregon

The Miocene Columbia River Basalt Group (CRBG) is the youngest and best preserved continental flood basalt province on Earth, linked in space and time with a compositionally diverse succession of volcanic rocks that partially record the apparent emergence and passage of the Yellowstone plume head through eastern Oregon during the late Cenozoic. This compositionally diverse suite of volcanic rocks are considered part of the La Grande - Owyhee eruptive axis (LOEA), an approximately 300-kilometer-long (185 mile), north - northwest - trending, middle Miocene to Pliocene volcanic belt located along the eastern margin of the Columbia River flood basalt province. Volcanic rocks erupted from and preserved within the LOEA form an important regional stratigraphic link between the (1) flood basalt - dominated Columbia Plateau on the north, (2) bimodal basalt - rhyolite vent complexes of the Owyhee Plateau on the south, (3) bimodal basalt-rhyolite and time-transgressive rhyolitic volcanic fields of the Snake River Plain - Yellowstone Plateau, and (4) the High Lava Plains of central Oregon. This field-trip guide describes a 4 - day geologic excursion that will explore the stratigraphic and geochemical relationships among mafic rocks of the Columbia River Basalt Group and coeval and compositionally diverse volcanic rocks associated with the early “Yellowstone track” and High Lava Plains in eastern Oregon. Beginning in Portland, the Day 1 log traverses the Columbia River gorge eastward to Baker City, focusing on prominent outcrops that reveal a distal succession of laterally extensive, large-volume tholeiitic flood lavas of the Grande Ronde, Wanapum, and Saddle Mountains Basalt formations of the CRBG. These “great flows” are typical of the well-studied flood basalt-dominated Columbia Plateau, where interbedded silicic and calc-alkaline lavas are conspicuously absent. The latter part of Day 1 will highlight exposures of middle to late Miocene silicic ash-flow tuffs, rhyolite domes, and calc-alkaline lava flows overlying the CRBG across the northern and central parts of the LOEA. The Day 2 field route migrates to southern parts of the LOEA, where rocks of the CRBG are associated in space and time with lesser known and more complex silicic volcanic stratigraphy associated with middle Miocene, large-volume, bimodal basalt-rhyolite vent complexes. Key stops will provide a broad overview of the structure and stratigraphy of the middle Miocene Mahogany Mountain caldera and middle to late Miocene calc-alkaline lavas of the Owyhee basalt. Stops on Day 3 will progress westward from the eastern margin of the LOEA, examining a transition linking the Columbia River Basalt-Yellowstone province with a northwestward-younging magmatic trend of silicic volcanism that underlies the High Lava Plains of eastern Oregon. Initial field stops on Day 3 will examine key outcrops demonstrating the intercalated nature of middle Miocene tholeiitic CRBG flood basalts, prominent ash-flow tuffs, and “Snake River-type” large-volume rhyolite lava flows exposed along the Malheur River. Subsequent stops on Day 3 will focus upon the volcanic stratigraphy northeast of the town of Burns, which includes regional middle to late Miocene ash-flow tuffs, and lava flows assigned to the Strawberry Volcanics. The return route to Portland on Day 4 traverses across the western axis of the Blue Mountains, highlighting exposures of the widespread, middle Miocene Dinner Creek Tuff and aspects of Picture Gorge Basalt flows and northwest-trending feeder dikes situated in the central part of the CRBG province.

Oregon↗

USGS1990

Trends and comparison of water quality and bottom material of northeastern Arkansas streams, 1974-85, and effects of planned diversions

Water quality of several rivers in Arkansas was compared using median values at individual water quality stations. Differences were detected in several properties, including common dissolved constituents, alkalinity, nutrients, fecal coliform bacteria, trace metals, pesticides, and sediment. In bottom material, organochlorine pesticides were detected much more frequently than organophosphorus pesticides and were higher in rivers with beds of fine-gradient particles. Time trends were examined using the Seasonal Kendall test. Trends in conductance, sodium adsorption ratio, chloride, phosphorus, and ammonia were usually not detectable. Sulfate concentrations were increasing at approximately one-half of the stations studied while fecal-coliform bacteria concentrations decreased at approximately one-half of the stations. The most potentially detrimental effects upon water quality resulting from surface water diversions were related to increases of common dissolved constituents. From available data, the largest of these increases would be caused by diversion from the Arkansas River. Potential effects not specifically examined include resuspension of bottom materials resulting from construction and operation of the diversion system. Use of some surface waters for artificial recharge of the alluvial aquifer may adversely affect the recharge systems or the aquifer. Possible effects include plugging of the injection well and the aquifer. (USGS)

Water-Resources Investigations Report↗

USGS2011

Emergence of viral hemorrhagic septicemia virus in the North American Great Lakes region is associated with low viral genetic diversity

Viral hemorrhagic septicemia virus (VHSV) is a fish rhabdovirus that causes disease in a broad range of marine and freshwater hosts. The known geographic range includes the Northern Atlantic and Pacific Oceans, and recently it has invaded the Great Lakes region of North America. The goal of this work was to characterize genetic diversity of Great Lakes VHSV isolates at the early stage of this viral emergence by comparing a partial glycoprotein (G) gene sequence (669 nt) of 108 isolates collected from 2003 to 2009 from 31 species and at 37 sites. Phylogenetic analysis showed that all isolates fell into sub-lineage IVb within the major VHSV genetic group IV. Among these 108 isolates, genetic diversity was low, with a maximum of 1.05% within the 669 nt region. There were 11 unique sequences, designated vcG001 to vcG011. Two dominant sequence types, vcG001 and vcG002, accounted for 90% (97 of 108) of the isolates. The vcG001 isolates were most widespread. We saw no apparent association of sequence type with host or year of isolation, but we did note a spatial pattern, in which vcG002 isolates were more prevalent in the easternmost sub-regions, including inland New York state and the St. Lawrence Seaway. Different sequence types were found among isolates from single disease outbreaks, and mixtures of types were evident within 2 isolates from individual fish. Overall, the genetic diversity of VHSV in the Great Lakes region was found to be extremely low, consistent with an introduction of a new virus into a geographic region with previously naïve host populations.

Diseases of Aquatic Organisms↗

USGS2023

Stress gradients structure spatial variability in coastal tidal marsh plant composition and diversity in a major Pacific coast estuary

Understanding the drivers of variability in plant diversity from local to landscape spatial scales is a challenge in ecological systems. Environmental gradients exist at several spatial scales and can be nested hierarchically, influencing patterns of plant diversity in complex ways. As plant community dynamics influence ecosystem function, understanding the drivers of plant community variability across space is paramount for predicting potential shifts in ecosystem function from global change. Determining the scales at which stress gradients influence vegetation composition is crucial to inform management and restoration of tidal marshes for specific functions. Here, we analyzed vegetation community composition in 51 tidal marshes from the San Francisco Bay Estuary, California, USA. We used model-based compositional analysis and rank abundance curves to quantify environmental (elevation/tidal frame position, distance to channel, and channel salinity) and species trait (species form, wetland indicator status, and native status) influences on plant community variability at the marsh site and estuary scales. While environmental impacts on plant diversity varied by species and their relationships to each other, overall impacts increased in strength from marsh to estuary scales. Relative species abundance was important in structuring these tidal marsh communities even with the limited species pools dominated by a few species. Rank abundance curves revealed different community structures by region with higher species evenness at plots higher in the tidal frame and adjacent to freshwater channels. By identifying interactions (species–species, species–environment, and environment–trait) at multiple scales (local, landscape), we begin to understand how variability measurements could be interpreted for conservation and land management decisions.

California↗

USGS2021

Phylogeographic genetic diversity in the white sucker hepatitis B Virus across the Great Lakes Region and Alberta, Canada

Hepatitis B viruses belong to a family of circular, double-stranded DNA viruses that infect a range of organisms, with host responses that vary from mild infection to chronic infection and cancer. The white sucker hepatitis B virus (WSHBV) was first described in the white sucker (Catostomus commersonii), a freshwater teleost, and belongs to the genus Parahepadnavirus. At present, the host range of WSHBV and its impact on fish health are unknown, and neither genetic diversity nor association with fish health have been studied in any parahepadnavirus. Given the relevance of genomic diversity to disease outcome for the orthohepadnaviruses, we sought to characterize genomic variation in WSHBV and determine how it is structured among watersheds. We identified WSHBV-positive white sucker inhabiting tributaries of Lake Michigan, Lake Superior, Lake Erie (USA), and Lake Athabasca (Canada). Copy number in plasma and in liver tissue was estimated via qPCR. Templates from 27 virus-positive fish were amplified and sequenced using a primer-specific, circular long-range amplification method coupled with amplicon sequencing on the Illumina MiSeq. Phylogenetic analysis of the WSHBV genome identified phylogeographical clustering reminiscent of that observed with human hepatitis B virus genotypes. Notably, most non-synonymous substitutions were found to cluster in the pre-S/spacer overlap region, which is relevant for both viral entry and replication. The observed predominance of p1/s3 mutations in this region is indicative of adaptive change in the polymerase open reading frame (ORF), while, at the same time, the surface ORF is under purifying selection. Although the levels of variation we observed do not meet the criteria used to define sub/genotypes of human and avian hepadnaviruses, we identified geographically associated genome variation in the pre-S and spacer domain sufficient to define five WSHBV haplotypes. This study of WSHBV genetic diversity should facilitate the development of molecular markers for future identification of genotypes and provide evidence in future investigations of possible differential disease outcomes.

Alberta, Michigan, Minnesota, Ohio, Wisconsin↗

USGS2024

Rapid simulation of wave runup on morphologically diverse, reef-lined coasts with the BEWARE-2 (Broad-range Estimator of Wave Attack in Reef Environments) meta-process model

Low-lying, tropical, coral-reef-lined coastlines are becoming increasingly vulnerable to wave-driven flooding due to population growth, coral reef degradation, and sea-level rise. Early-warning systems (EWSs) are needed to enable coastal authorities to issue timely alerts and coordinate preparedness and evacuation measures for their coastal communities. At longer timescales, risk management and adaptation planning require robust assessments of future flooding hazard considering uncertainties. However, due to diversity in reef morphologies and complex reef hydrodynamics compared to sandy shorelines, there have been no robust analytical solutions for wave runup to allow for the development of large-scale coastal wave-driven flooding EWSs and risk assessment frameworks for reef-lined coasts. To address the need for fast, robust predictions of runup that account for the natural variability in coral reef morphologies, we constructed the BEWARE-2 (Broad-range Estimator of Wave Attack in Reef Environments) meta-process modeling system. We developed this meta-process model using a training dataset of hydrodynamics and wave runup computed by the XBeach Non-Hydrostatic process-based hydrodynamic model for 440 combinations of water level, wave height, and wave period with 195 representative reef profiles that encompass the natural diversity in real-world fringing coral reef systems. Through this innovation, BEWARE-2 can be applied in a larger range of coastal settings than meta-models that rely on a parametric description of the coral reef geometry. In the validation stage, the BEWARE-2 modeling system produced runup results that had a relative root mean square error of 13% and relative bias of 5% relative to runup simulated by XBeach Non-Hydrostatic for a large range of oceanographic forcing conditions and for diverse reef morphologies (root mean square error and bias 0.63 and 0.26 m, respectively, relative to mean simulated wave runup of 4.85 m). Incorporating parametric modifications in the modeling system to account for variations in reef roughness and beach slope allows for systematic errors (relative bias) in BEWARE-2 predictions to be reduced by a factor of 1.5–6.5 for relatively coarse or smooth reefs and mild or steep beach slopes. This prediction provided by the BEWARE-2 modeling system is faster by 4–5 orders of magnitude than the full, process-based hydrodynamic model and could therefore be integrated into large-scale EWSs for tropical, reef-lined coasts and used for large-scale flood risk assessments.

Natural Hazards and Earth System Sciences↗

USGS2023

Genetic diversity, structure, and effective population size of an endangered, endemic hoary bat, ʻōpeʻapeʻa, across the Hawaiian Islands

Island bat species are disproportionately at risk of extinction, and Hawaiʻi’s only native terrestrial land mammal, the Hawaiian hoary bat ( Lasiurus semotus) locally known as ʻōpeʻapeʻa, is no exception. To effectively manage this bat species with an archipelago-wide distribution, it is important to determine the population size on each island and connectivity between islands. We used 18 nuclear microsatellite loci and one mitochondrial gene from 339 individuals collected from 1988–2020 to evaluate genetic diversity, population structure and estimate effective population size on the Islands of Hawaiʻi, Maui, Oʻahu, and Kauaʻi. Genetic differentiation occurred between Hawaiʻi and Maui, both of which were differentiated from Oʻahu and Kauaʻi. The population on Maui presents the greatest per-island genetic diversity, consistent with their hypothesized status as the original founding population. A signature of isolation by distance was detected between islands, with contemporary migration analyses indicating limited gene flow in recent generations, and male-biased sex dispersal within Maui. Historical and long-term estimates of genetic effective population sizes were generally larger than contemporary estimates, although estimates of contemporary genetic effective population size lacked upper bounds in confidence intervals for Hawaiʻi and Kauaʻi. Contemporary genetic effective population sizes were smaller on Oʻahu and Maui. We also detected evidence of past bottlenecks on all islands with the exception of Hawaiʻi. Our study provides population-level estimates for the genetic diversity and geographic structure of ‘ōpeʻapeʻa, that could be used by agencies tasked with wildlife conservation in Hawaiʻi.

Hawaii↗

USGS2002

Wetland macroinvertebrates of Prentiss Bay, Lake Huron, Michigan: diversity and functional group composition

The Great Lakes support many fish and waterbirds that depend directly or indirectly on coastal wetlands during some portion of their life cycle. It is known that macroinvertebrates make up an important part of wetland food webs and ecosystem function; however, our understanding of species distribution within and among wetlands has only recently received attention. We investigated the macroinvertebrates of a freshwater marsh (Prentiss Bay) in the Les Chenaux Island Area of Northern Lake Huron, Michigan. Macroinvertebrate taxa diversity and functional feeding group composition were compared between two habitats. A shallow depositional habitat with higher vegetation diversity and little wave action was compared to a deeper erosional habitat with fewer plant species and more wave action. A total of 83 taxa were collected over the summer of 1996, representing two phyla (Arthropoda and Mollusca) and five classes (Arachnida, Bivalvia, Malacostraca, Gastropoda and Insecta). A total of 79 genera were identified, with 92% being insects (39 families composed of at least 73 genera). Of the total, 42 insect genera were common to both habitats,while relatively fewer were collected exclusively from the erosional compared the depositional habitat. When habitats were pooled, predators comprised about 50% of the functional group taxa, while gathering collectors and shredders each were about 20%. Filtering collectors and scrapers each represented < 10%. When comparing habitats, there was a relatively higher percentage of predators and shredders in the depositional habitat, while all other functional groups were lower. These data suggest that vegetation diversity, depth and wave action affect taxa composition and functional group organization of the Prentiss Bay marsh.

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