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At least 1,279 records · Page 71Linked to original sources
USGS2002

Trends in late Maastrichtian calcareous nannofossil distribution patterns, Western North Atlantic margin

First and last occurrences of several Maastrichtian calcareous nannofossil species are shown to be diachronous across paleodepth and paleoenvironment using the graphic correlation method. Calcareous nannofossil assemblages examined from eleven cores from a deep- to shallow-water transect along the eastern United States Atlantic margin document that the first occurrence of Micula murus (Martini 1961) Bukry 1973 is diachronous, appearing 2.0 million years earlier in open ocean sites than in shallow marine sites. The first occurrence (FO) of Lithraphidites kennethii Perch-Nielsen 1984 is also nonsynchronous, appearing in the deep ocean before its FO in neritic waters. The last occurrence (LO) of L. praequadratus Roth 1978 is diachronous across paleodepth, going locally extinct first in deeper water. The LO of Watznaueria bybelliae Self-Trail 1999 is also diachronous, going locally extinct first in shallow-water settings. Ceratolithoides amplector Burnett 1997, C. pricei Burnett 1997, C. self-trailiae Burnett 1997, C. ultimus Burnett 1997, Cribrocorona gallica (Stradner 1963) Perch-Nielsen 1973. Micula praemurus (Bukry 1973) Stradner and Steinmetz 1984, Pseudomicula quadratus Perch-Nielsen et al. 1978, and Semihololithus spp. are present consistently in common to frequent abundances in ODP holes 1050C and 1052E on the Blake Nose, but they are rare or absent from neritic sections in Coastal Plain cores. It is apparent that these species flourished in an open ocean setting, suggesting that differences in assemblage abundance and diversity between deep ocean and nearshore areas were controlled by paleoceanographic factors. These species are not used for biostratigraphy, but may be useful indicators of open ocean conditions. The line of correlation (LOC) for nine Coastal Plain cores clearly defines the Cretaceous-Tertiary (K/T) boundary unconformity at the top of the Maastrichtian section (Peedee Formation) and the Campanian-Maastrichtian (C/M) unconformity at the base of the Maastrichtian section (Peedee/Donoho Creek formational contact). The K/T boundary unconformity is undulatory in nature; updip Maastrichtian sections have been stripped to a greater depth than the downdip sections. The uppermost Campanian, all of the lowermost Maastrichtian, and the basal upper Maastrichtian sediments are missing from the study area.

Micropaleontology↗
USGS2009

Sediment characterization and dynamics in Lake Pontchartrain, Louisiana

Lake Pontchartrain in southeastern Louisiana is the largest of several shallow estuaries that together cover over 15,000 km 2 . Wetlands, forests, and large urban areas surround the lake. Primary transport mechanisms of sediments to Lake Pontchartrain include urban runoff, major diversions of the Mississippi River, discharge from streams along the north and west shores, and tidal circulation. Sediments deposited in Lake Pontchartrain are subjected to resuspension and mixing by natural and human activities. Bioturbation and water turbulence throughout the lake are the major mixing agents, and mechanical shell dredging has reworked much of the lake bottom over the last century. Sediment characterization through direct sampling and geophysical surveys indicates that these processes continually rework the top meter of sediment. The lake receives discharge from roadways and industrial and agricultural sources. Contaminants from these sources accumulate in the lake sediments and are an important contributor to the degradation of the estuary. Decline in populations of various benthic organisms, such as shrimp and clams, has been documented in the lake. To characterize the health of this important estuary, the U.S. Geological Survey (USGS) conducted a comprehensive evaluation of the geology, geomorphology, coastal processes, and environmental condition of the Pontchartrain Basin from 1994 to 1997. This report presents an assessment of sediment distribution and quality using a multidisciplinary approach to characterize the influence of various physical and chemical parameters: nearsurface stratigraphy, major trace metal concentrations (Cu, Pb, Zn, and Ni), and short-lived radionuclides ( 210 Pb, 7 Be, and 137 Cs). The results are compared with water-circulation patterns to determine high-resolution sedimentation patterns in the lake. The data show a significant increase in trace metals in the top 1 m of lake sediments. Above this horizon, pollen analysis indicates a correlation with land clearing in the area, a proxy for increasing human development of the surrounding landscape and an increase in surface run-off. The data also show that the top meter of sediment undergoes frequent resuspension during high-energy circulation events and via circulation gyres in the lake. This regular turnover does not allow stratification of recently deposited sediments, restricting the sequestration of contaminated material that enters the lake.

Louisiana↗
USGS1997

Imperiled mammalian fauna of aquatic ecosystems in the Southeast: A historical perspective

About 100 species of mammals are endemic to the southeastern United States, an area of diverse habitat types and high biodiversity. Many of these species are either formally considered aquatic or semi-aquatic, or they are otherwise closely associated with aquatic ecosystems. In the southeastern United States, greater than 80 percent of mammalian species are listed in some category of concern throughout all or at least a portion of their ranges (i.e., endangered, threatened, under review for possible listing as endangered or threatened, species of special concern, species deemed in need of management, etc.). Almost all of these species are imperiled because their populations have declined to dangerously low levels due to habitat loss, habitat degradation, or other human-related factors. Most imperiled mammal taxa can be categorized as belonging to one of two general groups: habitat generalists or habitat specialists. Typically, habitat generalists have become imperiled mainly due to human exploitation, while habitat specialists have suffered primarily from habitat loss or habitat degradation. The passage of the U.S. Endangered Species Act of 1973 resulted in an increased need for information concerning distribution and status of all native species. However, relatively little is known concerning the historical distribution and current status of many mammalian taxa, and this is particularly so for small non-game species. In this chapter we provide species accounts of mammals commonly associated with aquatic ecosystems that we consider to be imperiled in the southeastern United States. In these accounts we have included information which we feel is valuable toward best understanding the threats that challenge each considered taxon.

Book chapter↗
USGS2022

Engaging stakeholders to develop a decision support model of conservation risk and management capacity to prioritize investments in Bull Trout recovery

Rarely are sufficient resources available to support the full suite of management actions to promote recovery of a species across their entire distribution. Decision support models are a tool that can inform natural resource management decisions with consideration of the perspectives from a variety of stakeholders who work across large geographic and jurisdictional extents. We offer an example of a decision support model that was developed by several Federal and State natural resource agencies to rank Bull Trout Salvelinus confluentus core areas for prioritizing conservation investment within Oregon, USA. We engaged State level decision makers to identify parameters believed to be influential in determining funding allocations for Bull Trout core areas. Parameters were linked in a model framework that was further refined with input from local Bull Trout experts with knowledge specific to the various core areas. The model produces a relative priority value that is a combination of the conservation risk to the species and the management capacity to address threats. A series of sensitivity analyses suggests that Bull Trout persistence and threat score are most influential in determining the relative priority of a core area, and life-history and genetic diversity are least influential. One of the more powerful products from this work is an interactive web-based application ( https://das.ecosphere.fws.gov/public/obts/ ) that anyone can use to explore how their beliefs in parameter values will affect the relative priority of Bull Trout core areas across Oregon. Our modeling effort is an example of engaging stakeholders with different roles in species recovery and across a large geographic area to create a clearer path forward in allocating limited resources for species recovery. This approach can be employed to address a number of natural resource management situations across species and habitats.

Oregon↗
USGS2022

Acetylenotrophic and diazotrophic Bradyrhizobium sp. strain I71 from TCE-contaminated soils

Abstract Acetylene (C 2 H 2 ) is a molecule rarely found in nature, with very few known natural sources, but acetylenotrophic microorganisms can use acetylene as their primary carbon and energy source. As of 2018 there were 15 known strains of aerobic and anaerobic acetylenotrophs; however, we hypothesize there may yet be unrecognized diversity of acetylenotrophs in nature. This study expands the known diversity of acetylenotrophs by isolating the aerobic acetylenotroph, Bradyrhizobium sp. strain I71, from trichloroethylene (TCE)-contaminated soils. Strain I71 is a member of the class Alphaproteobacteria and exhibits acetylenotrophic and diazotrophic activities, the only two enzymatic reactions known to transform acetylene. This unique capability in the isolated strain may increase the genus’ economic impact beyond agriculture as acetylenotrophy is closely linked to bioremediation of chlorinated contaminants. Computational analyses indicate that the Bradyrhizobium sp. strain I71 genome contains 522 unique genes compared to close relatives. Moreover, applying a novel hidden Markov model of known acetylene hydratase (AH) enzymes identified a putative AH enzyme. Protein annotation with I-TASSER software predicted the AH from the microbe Syntrophotalea acetylenica as the closest structural and functional analog. Furthermore, the putative AH was flanked by horizontal gene transfer (HGT) elements, like that of AH in anaerobic acetylenotrophs, suggesting an unknown source of acetylene or acetylenic substrate in the environment that is selecting for the presence of AH. Importance The isolation of Bradyrhizobium strain I71 expands the distribution of acetylene-consuming microbes to include a group of economically important microorganisms. Members of Bradyrhizobium are well studied for their abilities to improve plant health and increase crop yields by providing bioavailable nitrogen. Additionally, acetylene-consuming microbes have been shown to work in tandem with other microbes to degrade soil contaminants. Based on genome, cultivation, and protein prediction analysis, the ability to consume acetylene is likely not widespread within the genus Bradyrhizobium . These findings suggest that the suite of phenotypic capabilities of strain I71 may be unique and make it a good candidate for further study in several research avenues.

California↗
USGS2024

2023-2024 Coastal sage scrub and chaparral community monitoring for western San Diego County

Western San Diego County is dominated by shrublands supporting biologically diverse native plant and animal communities. Widespread urbanization has led to regional habitat loss and fragmentation, and many species in these shrubland communities are rare, threatened, or endangered. Large-scale, multiple-species conservation planning has resulted in a regional preserve system that focuses on these shrubland communities. Several large-scale threats are leading to type conversion from shrub-dominated to non-native invasive annual grass-dominated vegetation. To understand the changes that are occurring to native shrublands, we have developed a vegetation monitoring program with several components at multiple spatial scales, focused on quantifying coastal sage scrub (CSS) and chaparral vegetation community characteristics. Several drivers of change associated with type conversion of native shrubland to non-native annual grassland have been identified by previous research including increasing fire frequency, nitrogen deposition from air pollution, and prolonged and intense drought associated with changing climate. Loss of ecological integrity indices have been proposed as useful measures of the threat of degradation and type conversion of shrublands in San Diego County. For this study, ecological integrity is defined as a system’s ability to maintain species’ relationships and functions comparable to natural habitat in the region. Previous studies have identified the percent cover of invasive non-native annual grasses as a proxy for overall ecological degradation (loss of integrity) that is consistent across native taxonomic groups. Increased cover of non-native grass is associated with lower integrity of the shrubland vegetation community as shrub-associated plant and animal species are replaced by species preferring grassy and disturbed habitats. The objectives of this CSS and chaparral vegetation community monitoring plan are to: 1) Determine the distribution, composition, structure, and integrity of CSS and chaparral vegetation communities on conserved lands in western San Diego County, 2) Identify whether these attributes of the vegetation communities are changing over time, and 3) Evaluate relationships of known drivers of change (threats) and environmental factors in association with changes in vegetation community attributes. The CSS and chaparral vegetation community monitoring program is divided into four components: 1) vegetation mapping, 2) GIS/remote sensing office analysis of landscape-scale data, 3) permanent field plots using Unmanned Aerial Systems (UAS) and field data collections, and 4) animal and target species surveys and rapid assessment protocols. The first component, which is not detailed in this vegetation monitoring plan, aims to map vegetation communities every 10-15 years based on a classification developed for western San Diego County. High resolution aerial imagery will be used to update the 2012 vegetation map and expand it across the entire study area. The second component uses remote sensing models to annually track ecological integrity of shrublands across the study area and will include a map of areas of change and areas of stability over several decades. These landscape-scale integrity classifications will be used to analyze ecological processes, threats, and abiotic factors relative to changes to shrubland ecological integrity over time and space. The third component includes field surveys of 100 permanent plots across areas historically mapped as shrublands. Surveys in the 1930s mapped vegetation types using plot data. By using this historical classification map, we included areas that have already type-converted from shrubland to non-native annual grassland. The plots were split between CSS (55 plots) and chaparral (45 plots) and stratified into four geographical eco-subregions to guarantee coverage over small patches of habitat along the heavily developed coast. Surveys will include the collection of UAS imagery at a very high resolution. Species-level identifications will be made from the imagery based on a plant list compiled of all species detected in the plot during a thorough field survey by botanists, combined with geo-referenced samples of plant species locations. In addition, herbaceous cover will be estimated in the field using nine 1-m diameter circles (one per subplot) to obtain ocular estimates of cover for each plant species within the circle frame. Soil samples will be collected and analyzed for important element compositions. These data will be analyzed to evaluate plot-level ecological integrity based on species composition and cover. Repeated monitoring will allow evaluation of changes in vegetation attributes over time with known drivers or threats and other environmental factors. In addition, analyses will focus on indicator species and various measures of biological diversity for the vegetation communities. Finally, animal species and rare plants will be assessed using either taxa-based rapid assessment protocols or specialized species-specific protocols for rarer species. The purpose of these assessments is to document the status, habitat, and threat covariates of specific species and confirm the species composition and diversity of animal taxonomic groups (e.g., pollinators). Diversity and abundance of animal species at vegetation plots will be used to refine measures and thresholds of ecological integrity. Rapid assessment protocols for animal taxonomic groups can include multiple detection methods such as, camera traps, cover boards, and bird point counts. Pollinators will be monitored at plots using a protocol currently being developed in conjunction with but separately from this plan. Target rare plant species will be monitored using the regional Inspect and Manage (IMG) protocol that measures the status of rare plant occurrences and habitat and threat covariates over time. Species-specific animal survey methods will be refined as these species are prioritized for future monitoring. The goal of this monitoring program is to classify CSS and chaparral vegetation community integrity, identify areas of degradation across western San Diego County, and characterize drivers, and environmental factors associated with loss of ecological integrity. A combination of vegetation mapping, landscape-scale remote sensing, and field plots will be used to address all the aspects of our research questions. Data compiled and collected will be available to conservation partners to help inform future management decisions.

California↗
USGS2014

Ephemeral stream reaches preserve the evolutionary and distributional history of threespine stickleback in the Santa Clara and Ventura River watersheds of southern California

Much remains to be understood about the evolutionary history and contemporary landscape genetics of unarmored threespine stickleback in southern California, where populations collectively referred to as Gasterosteus aculeatus williamsoni have severely declined over the past 70+ years and are now endangered. We used mitochondrial sequence and microsatellite data to assess the population genetics and phylogeography of unarmored populations sampled immediately downstream from the type locality of G. a. williamsoni in the upper Santa Clara River, and assessed their distinctiveness with respect to low-armor populations in the downstream sections of the river and the adjacent Ventura River. We also characterized the geographic limits of different plate morphs and evaluated the congruence of those boundaries with barriers to dispersal in both river systems and to neutral genetic variation. We show substantial population structuring within the upper reach of the Santa Clara River, but little partitioning between the lower Santa Clara and Ventura Rivers—we attribute these patterns to different ancestry between spatially subdivided populations within the same drainage, a predominance of downstream gene flow, and ability for coastal dispersal between the Santa Clara and Ventura Rivers. We also show that alleles from introduced low-plate stock have infiltrated a native population in at least one upper Santa Clara River tributary, causing this formerly unarmored population to become gradually low-plated over a 30 + year time period. Measures of genetic diversity, census surveys, and severe habitat disturbance all indicate that unarmored stickleback near the type locality are currently at high risk of extinction.

California↗
USGS2013

Effects of climate change and urban development on the distribution and conservation of vegetation in a Mediterranean type ecosystem

Climate and land-use changes are projected to threaten biodiversity over this century. However, few studies have considered the spatial and temporal overlap of these threats to evaluate how ongoing land-use change could affect species ranges projected to shift outside conservation areas. We evaluated climate change and urban development effects on vegetation distribution in the Southwest ecoregion, California Floristic Province, USA. We also evaluated how well a conservation network protects suitable habitat for rare plant species under these change projections and identified primary sources of uncertainty. We used consensus-based maps from three species distribution models (SDMs) to project current and future suitable habitat for 19 species representing different functional types (defined by fire-response – obligate seeders, resprouting shrubs – and life forms – herbs, subshrubs), and range sizes (large/common, small/rare). We used one spatially explicit urban growth projection; two climate models, emission scenarios, and probability thresholds applied to SDMs; and high-resolution (90 m) environmental data. We projected that suitable habitat could disappear for 4 species and decrease for 15 by 2080. Averaged centroids of suitable habitat (all species) were projected to shift tens (up to hundreds) of kilometers. Herbs showed a small-projected response to climate change, while obligate seeders could suffer the greatest losses. Several rare species could lose suitable habitat inside conservation areas while increasing area outside. We concluded that (i) climate change is more important than urban development for vegetation habitat loss in this ecoregion through 2080 due to diminishing amounts of undeveloped private land in this region; (ii) the existing conservation plan, while extensive, may be inadequate to protect plant diversity under projected patterns of climate change and urban development, (iii) regional assessments of the dynamics of the drivers of biodiversity change based on high-resolution environmental data and consensus predictive mapping, such as this study, are necessary to identify the species expected to be the most vulnerable and to meaningfully inform regional-scale conservation.

California↗
USGS2005

A 40,000-year woodrat-midden record of vegetational and biogeographical dynamics in north-eastern Utah

Aim A conspicuous climatic and biogeographical transition occurs at 40-45° N in western North America. This pivot point marks a north–south opposition of wet and dry conditions at interannual and decadal time-scales, as well as the northern and southern limits of many dominant western plant species. Palaeoecologists have yet to focus on past climatic and biotic shifts along this transition, in part because it requires comparisons across dissimilar records [i.e. pollen from lacustrine sediments to the north and plant macrofossils from woodrat ( Neotoma ) middens to the south]. To overcome these limitations, we are extending the woodrat-midden record northward into the lowlands of the central Rocky Mountains. Location Woodrat middens were collected from crevices and rock shelters on south-facing slopes of Dutch John Mountain (2000-2200 m, 40°57′ N, 109°25′ W), situated on the eastern flanks of the Uinta Mountains in north-eastern Utah. The site is near the regional limits for Pinus ponderosa, P. edulis, P. contorta, Cercocarpus ledifolius var. intricatus, Abies concolor, Ephedra viridis and other important western species. Methods We analysed pollen and plant macrofossils from the 40,000-year midden sequence. The middens represent brief, depositional episodes (mostly years to decades). Four middens represent the early to full-glacial period (40,000–18,000 cal-yr bp), eight middens are from the late-glacial/early Holocene transition (13,500–9000 cal yr bp), and 33 middens span the mid-to-late Holocene (last 7500 years). Temporal density of our Holocene middens (one every c. 210 years) is comparable with typical Holocene pollen sequences from lake sediments. Results Early to full-glacial assemblages are characterized by low diversity and occurrence of montane conifers ( Picea pungens, Pseudotsuga menziesii, P. flexilis, Juniperus communis ) absent from the site today. Diversity increases in the late-glacial samples with the addition of J. scopulorum, J. horizontalis, C. montanus, C. ledifolius var. intricatus and mesic understory species. The coniferous trees and J. communis declined and J. osteosperma appeared during the late-glacial/Holocene transition. Juniperus osteosperma populations have occupied the site throughout the Holocene. Pinus ponderosa was established by 7500 cal-yr bp, and has occurred at least locally ever since. Montane conifers and J. horizontalis persisted until c. 5500 cal-yr bp. The signature events of the late Holocene were the invasions of P. edulis and Ephedra viridis and establishment of pinyon–juniper woodland in the last 800 years. Main conclusions The Dutch John Mountain midden record adds to an emerging picture in which mid-elevation conifers ( P. flexilis, Pseudotsuga menziesii, Picea pungens, J. scopulorum, J. communis ) dominated vegetation over a wide area of the Colorado Plateau and adjacent Rocky Mountains. Rather than being fragmented, as often assumed in phylogeographical studies, these species had broader and more-connected distributions than they do in the region today. Paradoxically, subalpine conifers ( Picea engelmannii, A. lasiocarpa ) occurred at higher elevations to the south, possibly representing declining precipitation from south to north owing to southward displacement of the polar jet stream. The Dutch John Mountain record displays a series of extinction and invasion events. Most of the extinctions were local in scale; nearly all constituents of fossil midden assemblages occur within a few kilometres of Dutch John Mountain, and some occur at least locally on its slopes. The sole exception is J. horizontalis , which is regionally extinct. In contrast to extinctions, Holocene invasions were regional in scale; J. osteosperma, P. ponderosa, P. edulis and Ephedra viridis immigrated from glacial-age source populations far to the south.

Utah↗
USGS2021

Current distribution and abundance of Kohala forest birds in Hawai‘i

The Kohala volcano is home to the most spatially isolated population of Hawaiian forest birds on Hawai‘i Island and contains one of the few native bird populations in the state that has not been monitored since the original Hawai‘i Forest Bird Survey (HFBS) in 1979. We surveyed 143 stations across 13 transects in Pu‘u ‘O ‘Umi Natural Area Reserve on Kohala from February through April 2017 and compared our results to data from the 1979 HFBS conducted at 80 stations across three transects in the same location as our study site. We detected 2806 individuals of 15 species and measured relative abundance, relative occurrence, and density for seven species. We observed changes in species densities ranging from −8.4% (Hawai‘i ‘Elepaio, Chasiempis sandwichensis ) to +714% (‘I‘iwi, Drepanis coccinea ). Equivalence testing showed meaningful increases in population densities for all but one species, the Hawai‘i ‘Elepaio. The increases in population densities on Kohala are in stark contrast to the widespread declines in population densities of native species elsewhere in Hawai‘i. Relative occurrence was greater in 2017 than in 1979 for all species except Hawai‘i ‘Elepaios and House Finches ( Haemorhous mexicanus ), and relative abundance increased for all species except Hawai‘i ‘Elepaios, House Finches, and Melodious Laughing Thrushes ( Garrulax canorus ). We also documented the range expansion of Japanese Bush Warblers ( Cettia diphone ) in Kohala. Our results indicate that this spatially isolated avian community remains biologically diverse, and most population densities are increasing in the study area. Our results provide a framework for future surveys and a baseline for understanding possible changes in population and community dynamics as birds respond to climate change and avian disease on Kohala volcano.

Hawai'i↗
USGS2019

Wetland drying linked to variations in snowmelt runoff across Grand Teton and Yellowstone national parks

In Grand Teton and Yellowstone national parks wetlands offer critical habitat and play a key role in supporting biological diversity. The shallow depths and small size of many wetlands make them vulnerable to changes in climate compared with larger and deeper aquatic habitats. Here, we use a simple water balance model to generate estimates of biophysical drivers of wetland change. We then examine the relationship between wetland inundation status and four principal drivers (i.e., temperature, precipitation, evapotranspiration, and runoff) spanning varying meteorological conditions over an 8-year time series from Grand Teton and Yellowstone national parks. We found that a higher percentage of surveyed wetlands were dry in years characterized by lower snowmelt runoff. While runoff-based models were most supported, wetland drying was also related to variations in April to June precipitation and temperatures. Our work shows that wetland drying was widespread across both parks, but sub-regional variations were best described at the hydrologic subbasin-level. Documenting the varying responses of wetlands to meteorological drivers is a necessary first step to identifying which subbasins are most sensitive to recent change and contemplating how future change may alter the distribution of wetlands and their dependent taxa.

Idaho, Montana, Wyoming↗
USGS2020

Occurrence of a suite of stream-obligate amphibians in timberlands of Mendocino County, California, examined using environmental DNA

Stream-obligate amphibians are important indicators of ecosystem health in the Pacific Northwest, but distributional information to improve forest management is lacking in many regions. We analyzed archived DNA extracted from water samples in 60 pools in streams on private timberlands in Mendocino County, California, for 3 California Species of Special Concern—Coastal Tailed Frogs ( Ascaphus truei ), Foothill Yellow-legged Frogs ( Rana boylii ), and Southern Torrent Salamanders ( Rhyacotriton variegatus )—to better understand their distributions in the region. Detection probabilities for eDNA of Foothill Yellow-legged Frogs and Coastal Tailed Frogs were positively influenced by water temperature. eDNA occurrence for both frogs was affected by whether silt or organic matter was a dominant substrate in the sampled pool, and Foothill Yellow-legged Frog eDNA occurrence was also affected by water temperature. Foothill Yellow-legged Frog eDNA occurrence had a strong, positive association with water temperature, with occurrence unlikely below 14°C and very likely above 16°C, and a positive association with silt or organic substrates in pools, which was likely an indicator of higher-order stream reaches. In contrast, Coastal Tailed Frogs had a negative association with silt or organic substrates. Historical visual detections were generally congruent with findings using eDNA, but differences highlight important areas for further study. We did not detect Southern Torrent Salamanders using eDNA at any sites. Our study reinforces that ecological relationships of these species are varied, and shows the importance of maintaining the integrity of streams with diverse characteristics for conserving stream amphibians.

California↗
USGS2019

Integrating fish assemblage data, modeled stream temperatures, and thermal tolerance metrics to develop thermal guilds for water temperature regulation: Wyoming case study

Many streams are experiencing increased average temperatures due to anthropogenic activity and climate change. As a result, surface water temperature regulation is critical for preserving a diverse stream fish species assemblage. The development of temperature regulations has generally been based on laboratory measurements of individual species' thermal tolerances rather than community response to temperature in the field, despite multiple limitations of using laboratory data for this purpose. Using field data to develop temperature regulations may avoid some of the limitations of laboratory data, but the use of field data comes with additional challenges that prevent its widespread adoption. We used Wyoming stream fish assemblages as a case study to examine the feasibility of addressing the limitations of field and laboratory data through a hybrid approach that integrates both types of data to classify species into thermal guilds that can potentially inform regulatory standards. We identified coldwater, coolwater, and warmwater classes of sites with modeled mean August temperatures of <15.5, 15.5–19.9, and >19.9°C, respectively. We used species' associations with these temperature classes to place species into site‐groups. Finally, we used standardized laboratory measures of species' upper acute and chronic thermal tolerances to identify and reclassify species with unusual thermal distributions. Through this process we classified species into five thermal guilds that may be useful for surface water temperature regulation in Wyoming. Our approach addresses the limitations identified for field and laboratory data and demonstrates a framework that could be used for incorporating multiple types of data to develop temperature standards.

Wyoming↗
USGS2022

Reference genome of the California glossy snake, Arizona elegans occidentalis: A declining California Species of Special Concern

The glossy snake ( Arizona elegans ) is a polytypic species broadly distributed across southwestern North America. The species occupies habitats ranging from California’s coastal chaparral to the shortgrass prairies of Texas and southeastern Nebraska, to the extensive arid scrublands of central México. Three subspecies are currently recognized in California, one of which is afforded state-level protection based on the extensive loss and modification of its preferred alluvial coastal scrub and inland desert habitat. We report the first genome assembly of A. elegans occidentalis as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technologies to produce a de novo assembled genome. The assembly comprises a total of 140 scaffolds spanning 1,842,602,218 base pairs, has a contig NG50 of 61 Mb, a scaffold NG50 of 136 Mb, and a BUSCO complete score of 95.9%, and is one of the most complete snake genome assemblies. The A. e. occidentalis genome will be a key tool for understanding the genomic diversity and the basis of adaptations within this species and close relatives within the hyperdiverse snake family Colubridae.

California↗
USGS2023

Revealing the extent of sea otter impacts on bivalve prey through multi-trophic monitoring and mechanistic models

Sea otters are apex predators that can exert considerable influence over the nearshore communities they occupy. Since facing near extinction in the early 1900s, sea otters are making a remarkable recovery in Southeast Alaska, particularly in Glacier Bay, the largest protected tidewater glacier fjord in the world. The expansion of sea otters across Glacier Bay offers both a challenge to monitoring and stewardship and an unprecedented opportunity to study the top-down effect of a novel apex predator across a diverse and productive ecosystem. Our goal was to integrate monitoring data across trophic levels, space, and time to quantify and map the predator–prey interaction between sea otters and butter clams Saxidomus gigantea , one of the dominant large bivalves in Glacier Bay and a favoured prey of sea otters. We developed a spatially-referenced mechanistic differential equation model of butter clam dynamics that combined both environmental drivers of local population growth and estimates of otter abundance from aerial survey data. We embedded this model in a Bayesian statistical framework and fit it to clam survey data from 43 intertidal and subtidal sites across Glacier Bay. Prior to substantial sea otter expansion, we found that butter clam density was structured by an environmental gradient driven by distance from glacier (represented by latitude) and a quadratic effect of current speed. Estimates of sea otter attack rate revealed spatial heterogeneity in sea otter impacts and a negative relationship with local shoreline complexity. Sea otter exploitation of productive butter clam habitat substantially reduced the abundance and altered the distribution of butter clams across Glacier Bay, with potential cascading consequences for nearshore community structure and function. Spatial variation in estimated sea otter predation processes further suggests that community context and local environmental conditions mediate the top-down influence of sea otters on a given prey. Overall, our framework provides high-resolution insights about the interaction among components of this food web and could be applied to a variety of other systems involving invasive species, epidemiology or migration.

Journal of Animal Ecology↗
USGS2017

A comprehensive survey of faults, breccias, and fractures in and flanking the eastern Española Basin, Rio Grande rift, New Mexico

A comprehensive survey of geologic structures formed in the Earth’s brittle regime in the eastern Española Basin and flank of the Rio Grande rift, New Mexico, reveals a complex and protracted record of multiple tectonic events. Data and analyses from this representative rift flank-basin pair include measurements from 53 individual fault zones and 22 other brittle structures, such as breccia zones, joints, and veins, investigated at a total of just over 100 sites. Structures were examined and compared in poorly lithified Tertiary sediments, as well as in Paleozoic sedimentary and Proterozoic crystalline rocks. Data and analyses include geologic maps; field observations and measurements; orientation, kinematic, and paleostress analyses; statistical examination of fault trace lengths derived from aeromagnetic data; mineralogy and chemistry of host and fault rocks; and investigation of fault versus bolide-impact hypotheses for the origin of enigmatic breccias found in the Proterozoic basement rocks. Fault kinematic and paleostress analyses suggest a record of transitional, and perhaps partitioned, strains from the Laramide orogeny through Rio Grande rifting. Normal faults within Tertiary basin-fill sediments are consistent with more typical WNW-ESE Rio Grande rift extension, perhaps decoupled from bedrock structures due to strength contrasts favoring the formation of new faults in the relatively weak sediments. Analyses of the fault-length data indicate power-law length distributions similar to those reported from many geologic settings globally. Mineralogy and chemistry in Proterozoic fault-related rocks reveal geochemical changes tied to hydrothermal alteration and nearly isochemical transformation of feldspars to clay minerals. In sediments, faulted minerals are characterized by mechanical entrainment with minor secondary chemical changes. Enigmatic breccias in rift-flanking Proterozoic rocks are autoclastic and isochemical with respect to their protoliths and exist near shatter cones believed to be related to a previously reported pre-Pennsylvanian impact event. A weak iridium anomaly is associated with the breccias as well as adjacent protoliths, thus an impact shock wave cannot be ruled out for their origin. Major fault zones along the eastern rift-flank mountain front are discontinuous and unlikely to impede regional groundwater flow into Española Basin aquifers. The breccia bodies are not large enough to constitute aquifers, and no fault- or breccia-related geochemical anomalies were identified as potential contamination sources for ground or surface waters. The results of this work provide a broad picture of structural diversity and tectonic evolution along the eastern flank of the central Rio Grande rift and the adjacent Española Basin representative of the rift as a whole and many rifts worldwide.

New Mexico↗
USGS2018

Continuous water-quality and suspended-sediment transport monitoring in the San Francisco Bay, California, water years 2014–15

The U.S. Geological Survey (USGS) monitors water quality and suspended-sediment transport in the San Francisco Bay (bay) as part of a multi-agency effort to address management, water supply, and ecological concerns. The San Francisco Bay area is home to millions of people, and the bay teems both with resident and with migratory wildlife, plants, and fish. Freshwater mixes with salt water in the bay, which is subject both to riverine influences (floods, droughts, managed reservoir releases and freshwater diversions) and to marine influences (tides, waves, effects of salt water). To understand this environment, the USGS, along with its partners (see “Acknowledgements”), has been monitoring the bay’s waters continuously since 1988. Several water-quality variables are of particular importance to State and Federal resource managers and are monitored at key locations throughout the bay (fig. 1). Salinity, which indicates the relative mixing of fresh and ocean waters in the bay, is derived from specific conductance measurements. Water temperature, along with salinity, affects the density of water, which controls gravity-driven circulation patterns and stratification in the water column. Turbidity, a measure of light scattered from suspended particles in the water, is used to estimate suspended-sediment concentration (SSC). Suspended sediment affects the bay in multiple ways: attenuation of sunlight in the water column, affecting phytoplankton growth; deposition on tidal marsh and intertidal mudflats, which can help sustain these habitats as sea level rises; deposition in ports and shipping channels, which can necessitate dredging; and often, adsorption of contaminants, affecting their distribution and concentrations in the environment. Dissolved oxygen concentration, essential to a healthy ecosystem and a fundamental indicator of water quality, is affected by water temperature, salinity, ecosystem metabolism, tidal currents, and wind. Tidal currents in the bay reverse four times a day, and wind direction and intensity typically vary on a daily cycle. Consequently, salinity, water temperature, SSC, and dissolved-oxygen concentration vary spatially and temporally throughout the bay. Therefore, continuous measurements are needed to observe these changes. The purpose of this fact sheet is to provide information about these variables, as well as internet links to access these continuous water-quality data collected by the USGS.

California↗
USGS2021

Impacts of climate changes and amplified natural disturbance on global ecosystems

Natural disturbances maintain biological diversity and landscape heterogeneity and initiate ecosystem renewal and reorganization. However, the severity, frequency, and extent of many disturbances have increased substantially in recent decades as the result of anthropogenic climate change. Disturbances can be discrete, short-duration events, such as wildfires or hurricanes, or can exert persistent, cumulative stresses on an ecosystem (for example, ongoing warming of ocean or land surface temperatures). Landscape and ecosystem impacts can occur from a single disturbance, from several disturbances acting independently, or from the interactions of multiple, linked disturbances. Key, climate-related disturbances affecting global biomes and ecosystems include shifting temperature and hydrologic regimes (for example, warming surface temperatures and increasing aridity), increased frequency and magnitude of extreme events such as heatwaves, severe droughts, storms, and hurricanes, warming-induced permafrost thaw, and heightened wildfire activity and insect-caused tree mortality. For ecosystems and landscapes, the consequences of climate-amplified disturbance include forced poleward and upward movement of plant and animal species, widespread tree mortality and reduced forest productivity, changes in plant community structure and species distributions, reduced biodiversity, increased erosion, debris flows, wetland dynamism, declining sea ice extent, more frequent storm-driven tides and saltwater intrusion, and increased landscape flammability.

Book chapter↗