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USGS2019

Relative abundance and molecular evolution of Lake Sinai Virus (Sinaivirus) clades

Lake Sinai Viruses (Sinaivirus) are commonly detected in honey bees ( Apis mellifera ) but no disease phenotypes or fitness consequences have yet been demonstrated. This viral group is genetically diverse, lacks obvious geographic structure, and multiple lineages can co-infect individual bees. While phylogenetic analyses have been performed, the molecular evolution of LSV has not been studied extensively. Here, I use LSV isolates from GenBank as well as contigs assembled from honey bee Sequence Read Archive (SRA) accessions to better understand the evolutionary history of these viruses. For each ORF, substitution rate variation, codon usage, and tests of positive selection were evaluated. Outlier regions of high or low diversity were sought with sliding window analysis and the role of recombination in creating LSV diversity was explored. Phylogenetic analysis consistently identified two large clusters of sequences that correspond to the current LSV1 and LSV2 nomenclature, however lineages sister to LSV1 were the most frequently detected in honey bee SRA accessions. Different expression levels among ORFs suggested the occurrence of subgenomic transcripts. ORF1 and RNA-dependent RNA polymerase had higher evolutionary rates than the capsid and ORF4. A hypervariable region of the ORF1 protein-coding sequence was identified that had reduced selective constraint, but a site-based model of positive selection was not significantly more likely than a neutral model for any ORF. The only significant recombination signals detected between LSV1 and LSV2 initiated within this hypervariable region, but assumptions of the test (single-frame coding and independence of substitution rate by site) were violated. LSV codon usage differed strikingly from that of honey bees and other common honey-bee viruses, suggesting LSV is not strongly co-evolved with that host. LSV codon usage was significantly correlated with that of Varroa destructor , however, despite the relatively weak codon bias exhibited by the latter. While codon usage between the LSV1 and LSV2 clusters was similar for three ORFs, ORF4 codon usage was uncorrelated between these clades, implying rapid divergence of codon use for this ORF only. Phylogenetic placement and relative abundance of LSV isolates reconstructed from SRA accessions suggest that detection biases may be over-representing LSV1 and LSV2 in public databases relative to their sister lineages.

PeerJ↗

USGS2006

Classification tree and minimum-volume ellipsoid analyses of the distribution of ponderosa pine in the western USA

Aim? Ponderosa pine (Pinus ponderosa Douglas ex Lawson & C. Lawson) is an economically and ecologically important conifer that has a wide geographic range in the western USA, but is mostly absent from the geographic centre of its distribution - the Great Basin and adjoining mountain ranges. Much of its modern range was achieved by migration of geographically distinct Sierra Nevada (P. ponderosa var. ponderosa) and Rocky Mountain (P. ponderosa var. scopulorum) varieties in the last 10,000 years. Previous research has confirmed genetic differences between the two varieties, and measurable genetic exchange occurs where their ranges now overlap in western Montana. A variety of approaches in bioclimatic modelling is required to explore the ecological differences between these varieties and their implications for historical biogeography and impending changes in western landscapes. Location? Western USA. Methods? We used a classification tree analysis and a minimum-volume ellipsoid as models to explain the broad patterns of distribution of ponderosa pine in modern environments using climatic and edaphic variables. Most biogeographical modelling assumes that the target group represents a single, ecologically uniform taxonomic population. Classification tree analysis does not require this assumption because it allows the creation of pathways that predict multiple positive and negative outcomes. Thus, classification tree analysis can be used to test the ecological uniformity of the species. In addition, a multidimensional ellipsoid was constructed to describe the niche of each variety of ponderosa pine, and distances from the niche were calculated and mapped on a 4-km grid for each ecological variable. Results? The resulting classification tree identified three dominant pathways predicting ponderosa pine presence. Two of these three pathways correspond roughly to the distribution of var. ponderosa, and the third pathway generally corresponds to the distribution of var. scopulorum. The classification tree and minimum-volume ellipsoid model show that both varieties have very similar temperature limitations, although var. ponderosa is more limited by the temperature extremes of the continental interior. The precipitation limitations of the two varieties are seasonally different, with var. ponderosa requiring significant winter moisture and var. scopulorum requiring significant summer moisture. Great Basin mountain ranges are too cold at higher elevations to support either variety of ponderosa pine, and at lower elevations are too dry in summer for var. scopulorum and too dry in winter for var. ponderosa. Main conclusions? The classification tree analysis indicates that var. ponderosa is ecologically as well as genetically distinct from var. scopulorum. Ecological differences may maintain genetic separation in spite of a limited zone of introgression between the two varieties in western Montana. Two hypotheses about past and future movements of ponderosa pine emerge from our analyses. The first hypothesis is that, during the last glacial period, colder and/or drier summers truncated most of the range of var. scopulorum in the central Rockies, but had less dramatic effects on the more maritime and winter-wet distribution of var. ponderosa. The second hypothesis is that, all other factors held constant, increasing summer temperatures in the future should produce changes in the distribution of var. scopulorum that are likely to involve range expansions in the central Rockies with the warming of mountain ranges currently too cold but sufficiently wet in summer for var. scopulorum. Finally, our results underscore the growing need to focus on genotypes in biogeographical modelling and ecological forecasting.

Journal of Biogeography↗

USGS2005

Environmental exposure modeling and monitoring of human pharmaceutical concentrations in the environment

Human pharmaceuticals are receiving increased attention as environmental contaminants. This is due to their biological activity and the number of monitoring programs focusing on analysis of these compounds in various environmental media and compartments. Risk assessments are needed to understand the implications of reported concentrations; a fundamental part of the risk assessment is an assessment of environmental exposures. The purpose of this chapter is to provide guidance on the use of predictive tools (e.g., models) and monitoring data in exposure assessments for pharmaceuticals in the environment. Methods to predict environmental concentrations from equations based on first principles are presented. These equations form the basis of existing GIS (geographic information systems)-based systems for understanding the spatial distribution of pharmaceuticals in the environment. The pharmaceutical assessment and transport (P h ATE), georeferenced regional exposure assessment tool for European rivers (GREAT-ER), and geographical information system (GIS)-ROUT models are reviewed and recommendations are provided concerning the design and execution of monitoring studies. Model predictions and monitoring data are compared to evaluate the relative utility of each approach in environmental exposure assessments. In summary, both models and monitoring data can be used to define representative exposure concentrations of pharmaceuticals in the environment in support of environmental risk assessments.

Book chapter↗

USGS2017

Geologic sources of energy

This chapter describes the exploration, development, and geologic setting of petroleum resources (including tar sands), coal resources (including coalbed methane), and geothermal energy resources of the Northern Cordillera.For petroleum resources, the chapter describes: (1) the history of petroleum development and production, first for Alaska and then for the Canadian Cordillera; and (2) generalized basin analysis geologic settings for the six major petroleum basins that are illustrated in summary maps and cross sections. Subsequent sections of the chapter describe the nature and geologic setting of tar sand resources, geothermal energy resources, and coal resources. The area distribution of the energy resources of the region are depicted in the Energy Resources Map that has multiple layers that can be displayed in various arrangements. Employing this map in a separate window while reading the text will be greatly beneficial. Many geographic names are employed in the descriptions throughout this chapter. While reading this chapter, viewing the Geographic Regions Layer of the Energy Resources Map, as needed, will be valuable.

Book chapter↗

USGS2023

Trends in tree cover change over three decades related to interannual climate variability and wildfire in California

The U.S. State of California has experienced frequent drought events, hotter temperatures and other disruptions to the climate system whose effects on ecosystems have been widely reported in recent decades. Studies primarily confined to specific vegetation communities or species, individual drought incidents, or analysis over a relatively short intervals, has limited our understanding of the broad-scale effects on tree cover and the spatiotemporal variability of effects across broader regions. We focused analysis on multi-annual land cover and land surface change to assess patterns and trends in tree cover loss in tree-dominated Californian ecoregions from 1986 to 2019. The top three years of total tree cover loss for the state were 2018 (1901 km 2 ), 2015 (1556 km 2 ), and 2008 (1549 km 2 ). Overall, annual tree cover loss had upward trends. Tree cover loss rapidly surged later in the study period and was apparently driven by climate stress and wildfires. Underlying geographic variability was apparent in both non-fire and fire-related tree cover loss that sharply increased during hotter multi-year droughts. The increasingly hotter and drier climate conditions were associated with significant increases in fire-induced mortality. Our findings indicate that a possible effect of future hotter and drier climate would lead to further tree cover loss, thereby endangering California's ecosystem goods and services. Geographic variability in tree cover trends indicates that ecoregion-specific mitigation and adaptation strategies would be useful to conserve the region's forest resources. Such strategies may benefit from consideration of historical disturbances, ecoregion's sensitivity to disturbance types, as well as potential ecoregion-specific climate-vegetation-fire feedbacks.

California↗

USGS2015

Stable isotope values in pup vibrissae reveal geographic variation in diets of gestating Steller sea lions Eumetopias jubatus

Multiple factors, including limitation in food resources, have been proposed as possible causes for the lack of recovery of the endangered western segment of the Steller sea lion population in the United States. Because maternal body condition has important consequences on fetal development and neonatal survival, the diets of pregnant females may be particularly important in regulating population sizes. We used the stable carbon and nitrogen isotope values of vibrissae from Steller sea lion pups as an indirect indicator of maternal diets during gestation. Combining these data with isotope data from potential prey species in a Bayesian mixing model, we generated proportional estimates of dietary consumption for key prey. Our analysis indicated that females in the most westerly metapopulations relied heavily on Atka mackerel and squid, whereas females inhabiting the Gulf of Alaska region had a fairly mixed diet, and the metapopulation of Southeast Alaska showed a strong reliance on forage fish. These results are similar to previous data from scat collections; however, they indicate a possible under-representation of soft-bodied prey (squid) or prey with fragile skeletons (forage fish) from analyses of data from scats. This study supports the utility of stable isotope modeling in predicting diet composition in gestating adult female Steller sea lions during winter, using pup vibrissae.

Alaska↗

USGS2017

Dam removal: Listening in

Dam removal is widely used as an approach for river restoration in the United States. The increase in dam removals—particularly large dams—and associated dam-removal studies over the last few decades motivated a working group at the USGS John Wesley Powell Center for Analysis and Synthesis to review and synthesize available studies of dam removals and their findings. Based on dam removals thus far, some general conclusions have emerged: (1) physical responses are typically fast, with the rate of sediment erosion largely dependent on sediment characteristics and dam-removal strategy; (2) ecological responses to dam removal differ among the affected upstream, downstream, and reservoir reaches; (3) dam removal tends to quickly reestablish connectivity, restoring the movement of material and organisms between upstream and downstream river reaches; (4) geographic context, river history, and land use significantly influence river restoration trajectories and recovery potential because they control broader physical and ecological processes and conditions; and (5) quantitative modeling capability is improving, particularly for physical and broad-scale ecological effects, and gives managers information needed to understand and predict long-term effects of dam removal on riverine ecosystems. Although these studies collectively enhance our understanding of how riverine ecosystems respond to dam removal, knowledge gaps remain because most studies have been short (< 5 years) and do not adequately represent the diversity of dam types, watershed conditions, and dam-removal methods in the U.S.

Water Resources Research↗

USGS2007

Diversity, origins and virulence of Avipoxviruses in Hawaiian Forest Birds

We cultured avian pox (Avipoxvirus spp.) from lesions collected on Hawai'i, Maui, Moloka'i, and 'Oahu in the Hawaiian Islands from 15 native or non-native birds representing three avian orders. Phylogenetic analysis of a 538 bp fragment of the gene encoding the virus 4b core polypeptide revealed two distinct variant clusters, with sequences from chickens (fowlpox) forming a third distinct basal cluster. Pox isolates from one of these two clusters appear closely related to canarypox and other passerine pox viruses, while the second appears more specific to Hawai'i. There was no evidence that birds were infected simultaneously with multiple pox virus variants based on evaluation of multiples clones from four individuals. No obvious temporal or geographic associations were observed and strict host specificity was not apparent among the 4b-defined field isolates. We amplified a 116 bp 4b core protein gene fragment from an 'Elepaio (Chasiempis sandwichensis) collected in 1900 on Hawai'i Island that clustered closely with the second of the two variants, suggesting that this variant has been in Hawai'i for at least 100 years. The high variation detected between the three 4b clusters provides evidence for multiple, likely independent introductions, and does not support the hypothesis of infection of native species through introduction of infected fowl. Preliminary experimental infections in native Hawai'i 'Amakihi (Hemignathus virens) suggest that the 4b-defined variants may be biologically distinct, with one variant appearing more virulent. These pox viruses may interact with avian malaria (Plasmodium relictum), another introduced pathogen in Hawaiian forest bird populations, through modulation of host immune responses. ?? 2007 Springer Science+Business Media B.V.

Conservation Genetics↗

USGS2023

Mismatch between conservation status and climate change sensitivity leaves some anurans in the United States unprotected

Species vulnerable to climate change face increased extinction risk, but many sensitive species may be overlooked due to limited data and exclusion from vulnerability assessments. Intrinsic sensitivity, or the inherent risk of species to environmental change due to biological factors, can be assessed with widely available data and may address gaps in multispecies vulnerability assessments. Species that exist in few places (geographically rare) and in fewer climates (smaller realized climate niche breadth) have high intrinsic sensitivity to environmental change. Using point occurrences, we systematically evaluated intrinsic sensitivity based on geographic rarity and realized climate niche breadth for 90 species of frogs and toads native to the United States using over 140 000 occurrence records. To compare sensitivity to perceived extinction risk, we compared intrinsic sensitivity to conservation status at state, federal, and international levels. We found no relationship between intrinsic sensitivity and federal or state conservation status, with some intrinsically sensitive species (i.e., those with small areas of occurrence and narrow climate specificity) not listed as at-risk at any level. Intrinsic sensitivity analysis can serve as an early warning system for species that may be currently at-risk and overlooked.

Biological Conservation↗

USGS2003

Tidal-bundle sequences in the Jordan Sandstone (Upper Cambrian), southeastern Minnesota, U.S.A.: Evidence for tides along inboard shorelines of the Sauk Epicontinental Sea

This study documents for the first time tidal bundling in a lower Paleozoic sheet sandstone from the cratonic interior of North America, providing insights into the hydrodynamics of ancient epicontinental seas. The Jordan Sandstone (Upper Cambrian) in the Upper Mississippi Valley contains large-scale planar tabular cross-sets with tidal-bundle sequences, which were analyzed in detail at an exceptional exposure. Tidal-bundle sequences (neap-spring-neap cycles) were delineated by foreset thickening-thinning patterns and composite shale drapes, the latter of which represent accumulations of mud during the neap tides of neap-spring-neap tidal cycles. Fourier analysis of the bundle thickness data from the 26 measurable bundle sequences revealed cycles ranging from 15 to 34 bundles per sequence, which suggests a semidiurnal or mixed tidal system along this part of the Late Cambrian shoreline. We extend the tidal interpretation to widespread occurrences of the same facies in outcrops of lesser quality, where the facies is recognizable but too few bundles are exposed for tidal cycles to be measured. By doing so, this study shows that tidally generated deposits have a significant geographic and temporal extent in Upper Cambrian strata of central mid-continent North America. The deposition and preservation of tidal facies was related to the intermittent development of shoreline embayments during transgressions. The tidally dominated deposits filled ravined topographies that were repeatedly developed on the updip parts of the shoreface. Resulting coastal geomorphologies, accompanied perhaps by larger-scale changes in basinal conditions and/or configuration, led to changes in depositional conditions from wave-dominated to tide-dominated. Outcrops of the Jordan Sandstone tidal facies in the Upper Mississippi Valley represent the farthest inboard recorded transmission of ocean-generated tides in the Laurentian epicontinental seas, demonstrating that tidal currents were significant agents in the transport of sand along the far cratonic interior shorelines of Cambrian North America. The results of this study improve the facies-level understanding of the genesis of sheet sandstones. Furthermore, tidalites documented here occur in a specific position within a sequence stratigraphic architecture for the Jordan Sandstone. This provides a framework to compare these ancient deposits and processes to younger (e.g., Carboniferous) epicontinental systems where stratal and sediment dynamics are better documented.

Illinois, Indiana, Iowa, Michigan, Minnesota, Miss↗

USGS2009

Land Cover Change in the Boston Mountains, 1973-2000

The U.S. Geological Survey (USGS) Land Cover Trends project is focused on understanding the rates, trends, causes, and consequences of contemporary U.S. land-cover change. The objectives of the study are to: (1) to develop a comprehensive methodology for using sampling and change analysis techniques and Landsat Multispectral Scanner (MSS), Thematic Mapper (TM), and Enhanced Thematic Mapper Plus (ETM+) data to measure regional land-cover change across the United States; (2) to characterize the types, rates, and temporal variability of change for a 30-year period; (3) to document regional driving forces and consequences of change; and (4) to prepare a national synthesis of land-cover change (Loveland and others, 1999). The 1999 Environmental Protection Agency (EPA) Level III ecoregions derived from Omernik (1987) provide the geographic framework for the geospatial data collected between 1973 and 2000. The 27-year study period was divided into five temporal periods: 1973-1980, 1980-1986, 1986-1992, 1992-2000, and 1973-2000, and the data are evaluated using a modified Anderson Land Use Land Cover Classification System (Anderson and others, 1976) for image interpretation. The rates of land-cover change are estimated using a stratified, random sampling of 10-kilometer (km) by 10-km blocks allocated within each ecoregion. For each sample block, satellite images are used to interpret land-cover change for the five time periods previously mentioned. Additionally, historic aerial photographs from similar time frames and other ancillary data, such as census statistics and published literature, are used. The sample block data are then incorporated into statistical analyses to generate an overall change matrix for the ecoregion. Field data of the sample blocks include direct measurements of land cover, particularly ground-survey data collected for training and validation of image classifications (Loveland and others, 2002). The field experience allows for additional observations of the character and condition of the landscape, assistance in sample block interpretation, ground truthing of Landsat imagery, and determination of the driving forces of change identified in an ecoregion.

Open-File Report↗

USGS2022

Understanding rates of change: A case study using fossil pollen records from California to assess the potential for and challenges to a regional data synthesis

Insights into the rates at which ecosystems and vegetation respond to a changing climate is fundamental to anticipating impacts of projected climate change. Characterization of vegetation change over millennia to centuries has potential to make an important contribution toward this goal, and regional scale syntheses of fossil pollen data can provide the foundation for this understanding. However, challenges of data analysis and integration are nontrivial. Here we present a case study in which publicly available fossil pollen data for California are assessed and analyzed. The data are selected according to a clearly defined selection criteria, and a Rate of Change (RoC) value is calculated to assess rates of vegetation change in California from ~15k BP (before A.D. 1950) to the present. Our results highlight several challenges presented by the extant data sets, including temporal sampling variation within and between records, large age control uncertainties, and sparse, geographically biased coverage. Recommendations for methodological refinements to better characterize ecological rates of change include increasing sampling frequency, maintaining a consistent temporal spacing within records, and applying probabilistic approaches to existing pollen data sets.

California↗

USGS2017

The effect of Holocene temperature fluctuations on the evolution and ecology of Neotoma (woodrats) in Idaho and northwestern Utah

Animals respond to climatic change by adapting or by altering distributional patterns. How an animal responds is influenced by where it is positioned within its geographic range; the probability of extirpation is increased near range boundaries. Here, we examine the impact of Holocene climatic fluctuations on a small mammalian herbivore, the bushy-tailed woodrat (Neotoma cinerea), at five locations within south central Idaho and northwestern Utah. Previous work demonstrated that woodrats adapt to temperature shifts by altering body size. We focus here on the relationship between body mass, temperature, and location within the geographic range. Body mass is estimated by measuring fossil fecal pellets, a technique validated in earlier work. Overall, we find the predicted phenotypic response to climate change: Animals were larger during cold periods, and smaller during warmer episodes. However, we also identify several time periods when changes in environmental temperature exceeded the adaptive flexibility of N. cinerea. A smaller-bodied species, the desert woodrat (N. lepida) apparently invaded lower elevation sites during the mid-Holocene, despite being behaviorally and physically subordinate to N. cinerea. Analysis of contemporary patterns of body size and thermal tolerances for both woodrat species suggests this was because of the greater heat tolerance of N. lepida. The robust spatial relationship between contemporary body size and ambient temperature is used as a proxy to reconstruct local climate during the Holocene. ?? 2003 Elsevier Science (USA). All rights reserved.

Quaternary Research↗

USGS2024

Defining the hafnium isotopic signature of the Appalachian orogen through analysis of detrital zircons from modern fluvial sediments

Fluvial sediments are the product of erosion, weathering, and transport of bedrock within a well-defined catchment area, and their constituent grains may therefore record valuable information about the lithological and geochemical properties of geologic units within the upstream drainage. Analysis of U-Pb ages and Lu/Hf isotopic values in detrital zircon grains from major rivers in the eastern USA characterizes these parameters within broad areas of the Appalachian orogen. In this study, five modern fluvial sediment samples, collected across ~1500 km and representing 216,000 km2 of total catchment area, reveal that the relative proportions of Mesoproterozoic to Paleozoic U-Pb crystallization ages vary widely across the former Laurentian margin. However, εHft values in the same samples are largely consistent regardless of their geographic location. Mesoproterozoic (Grenville orogen) zircons display a more limited range of εHft values (approximately 0 to +10 εHft units) compared to the more negative, more variable values (-15 to +10) found in grains from the Paleozoic orogenies. When compared to other published modern detrital samples from the Gulf Coastal Plain, Appalachian samples show more similarity to each other and to the Pleistocene of Florida than to those from the Mississippi River mouth, likely because the latter also sources sediments from the Cordillera of western North America. More negative εHft values in Paleozoic zircons may be genetically related to older Mesoproterozoic grains, as they are compatible with the continued isotopic evolution of Lu/Hf derived from the mantle between 1.2 and 2.0 Ga. Hafnium geochemistry in detrital grains may therefore have some utility in discerning sediment provenance between the Appalachians and other regions, and may also provide useful information regarding the nature of crustal generation through time.

Journal of Geology↗

USGS2016

Genetic diversity of Wolbachia endosymbionts in Culex quinquefasciatus from Hawai`i, Midway Atoll, and Samoa

Incompatible insect techniques are potential methods for controlling Culex quinquefasciatus and avian disease transmission in Hawai‘i without the use of pesticides or genetically modified organisms. The approach is based on naturally occurring sperm-egg incompatibilities within the Culex pipiens complex that are controlled by different strains of the bacterial endosymbiont Wolbachia pipientis (wPip). Incompatibilities can be unidirectional (crosses between males infected with strain A and females infected with strain B are fertile, while reciprocal crosses are not) or bidirectional (reciprocal crosses between sexes with different wPip strains are infertile). The technique depends on release of sufficient numbers of male mosquitoes infected with an incompatible wPip strain to suppress mosquito populations and reduce transmission of introduced avian malaria ( Plasmodium relictum ) and Avipoxvirus in native forest bird habitats. Both diseases are difficult to manage using more traditional methods based on removal and treatment of larval habitats and coordination of multiple approaches may be needed to control this vector. We characterized the diversity of Wolbachia strains in C. quinquefasciatus from Hawai‘i, Kaua‘i, Midway Atoll, and American Samoa with a variety of genetic markers to identify compatibility groups and their distribution within and between islands. We confirmed the presence of wPip with multilocus sequence typing, tested for local genetic variability using 16 WO prophage genes, and identified similarities to strains from other parts of the world with a transposable element (tr1). We also tested for genetic differences in ankyrin motifs (ank2 and pk1) which have been used to classify wPip strains into five worldwide groups (wPip1–wPip5) that vary in compatibility with each other based on experimental crosses. We found a mixture of both widely distributed and site specific genotypes based on presence or absence of WO prophage and transposable element markers on Hawai‘i Island (Volcano, Pu‘u Wa‘awa‘a, Laupāhoehoe, Kaumana, Kahuku, Nīnole, and Maulua Gulch), Kaua‘i Island (Kawaikōī, Mōhihi, Kalāheo, Lāwa‘i and Hanapepe) and Midway Atoll. Genotypes from American Samoa were unique and formed their own clade. Based on analysis of ankyrin motifs, wPip strains from Hawai‘i, Kaua‘i, and Midway Atoll were most similar to wPip5 strains of Australasian origin. By contrast, Wolbachia strains from Culex quinquefasciatus collected in American Samoa were most similar to wPip3 strains of American origin. We detected a single Culex mosquito from Pu‘u Wa‘awa‘a on Hawai‘i Island that was infected with a unique wPip3 genotype. This discovery, plus a rarefaction analysis of genotypes from Kaua‘i and Hawai‘i Islands suggests that limited sampling may have underestimated diversity of wPip in our study. Mosquitoes infected with wPip5 and wPip3 are bidirectionally compatible with each other based on prior studies, which would support their ability to coexist within the same population on Hawai‘i Island. Available evidence from prior studies suggests that genotype wPip4 from Africa, the Middle East, Europe, and Asia is bidirectionally incompatible with genotype wPip5 and varies in compatibility with genotype wPip3 depending on geographic origin. Since wPip5 appears to be the most common compatibility group in Hawai‘i based on limited sampling, logical next steps are to 1) expand the current survey to include additional islands and localities, 2) infect a laboratory colony of Hawaiian Culex with wPip4 through tetracycline treatment of Hawaiian mosquitoes and backcross with Culex from Europe, North Africa, and the Middle East that are naturally infected with wPip4, 3) conduct cage trials to confirm bidirectional incompatibilities between Hawaiian Culex infected with wPip4 and wPip5, and 4) conduct field trials to evaluate whether release of incompatible males can be applied at small scales to suppress local populations.

American Samoa, Hawaii↗

USGS2023

Latency and geofence testing of wireless emergency alerts intended for the ShakeAlert® earthquake early warning system for the West Coast of the United States of America

ShakeAlert, the earthquake early warning (EEW) system for the West Coast of the United States, attempts to provides crucial warnings before strong shaking occurs. However, because the alerts are triggered only when an earthquake is already in progress, and the alert latencies and delivery times are platform dependent, the time between these warnings and the arrival of shaking is variable. The ShakeAlert system uses, among other public alerting platforms like a mobile phone operating system, smartphone apps, and the Federal Emergency Management Agency Integrated Public Alert & Warning System (IPAWS). IPAWS sends Wireless Emergency Alerts (WEAs) informing people via their smartphones and other mobile devices about various events, such as natural hazards, child abductions, or public health information about COVID-19. However, little is known about the IPAWS delivery latencies. Given that people may have only a few seconds of notice after they receive an alert to take a protective action before they feel earthquake shaking, quantifying latencies is critical to understanding whether the IPAWS system is useful for EEW. In this study, we developed new methods to test the IPAWS distribution system's performance, both with devices in a controlled environment and as well as with a 2019 community-based feedback form, in Oakland and San Diego County, California, respectively. The controlled environment test used mobile phones (including smart and non-smart phones) and associated devices to determine alert receipt times; the community research form had participants self-report their receipt times. By triangulating the data between the controlled test environment and the community research, we determined the latency statistics as well as whether the geofence (the geographic area where the alert was intended to be sent) held broadly. We found that the latencies were similar between the two tests despite the large differences in population sizes. WEA messages were received within a median time frame of 6–12 s, and the geofence held with only a few exceptions. We use this latency to assess how the system would have performed in two large earthquakes, the 1989 M6.9 Loma Prieta and 2019 M7.1 Ridgecrest earthquakes, which both occurred near our WEA test locations. Our analysis revealed that had IPAWS been available during those earthquakes, particularly Loma Prieta, it would have provided crucial seconds of notice that damaging shaking was imminent in some locations relatively far from the epicenter. Further, we find affordable non-smart phones can receive WEAs as fast as smartphones. Finally, our new method can be used for latency and geospatial testing going forward for IPAWS and other similar alerting systems.

California↗

USGS2006

Benthic foraminifera from a relict flood tidal delta along the Virginia/North Carolina Outer Banks

Examination of benthic foraminifera from six vibracores collected from a relict flood tidal delta near the Virginia/North Carolina border documents the assemblages associated with a former inlet and provides geologic evidence of this former inlet that once defined the boundary between Virginia and North Carolina along the Outer Banks. Three distinct foraminiferal assemblages were identified. The oldest assemblage contained abundant and diverse forms, dominated by Elphidium excavatum and several other calcareous species typical of shallow nearshore areas. Sediment immediately below and above this diverse calcareous assemblage was barren or nearly barren of foraminifera. A medium-salinity agglutinated marsh assemblage characterized mainly by Trochammina inflata with fewer Tiphotrocha comprimata overlies the uppermost barren unit. The core top assemblage was dominated by low-salinity marsh species Jadammina macrescens, Miliammina petila and Miliammina fusca. A comparison of these vertically-stacked assemblages with the modern geographic distribution of assemblages in the Outer Banks estuarine system and on the nearby continental shelf reveals a succession of depositional environments proceeding from estuarine and flood tidal delta to medium salinity marsh to lower salinity marsh. These changes in depositional environments reflect a rapid and dramatic increase in salinity caused by the opening of an inlet followed by a gradual decrease in salinity due to inlet shoaling and eventual marsh colonization of the flood tidal delta. These changes cannot be determined through sedimentological studies alone; micropaleontological analysis is required. We conclude this distinctive trend of changing depositional environments constitutes paleontological evidence of the origin and evolution of Old Currituck Inlet that breached the barrier spit prior to 1585AD, actively built a flood tidal delta for more than 145 years, and then closed in 1731AD allowing the flood tidal delta to become colonized by marsh species.

North Carolina, Virginia↗

USGS2015

Long-term effects of wildfire on greater sage-grouse - integrating population and ecosystem concepts for management in the Great Basin

Greater sage-grouse ( Centrocercus urophasianus ; hereinafter, sage-grouse) are a sagebrush obligate species that has declined concomitantly with the loss and fragmentation of sagebrush ecosystems across most of its geographical range. The species currently is listed as a candidate for federal protection under the Endangered Species Act (ESA). Increasing wildfire frequency and changing climate frequently are identified as two environmental drivers that contribute to the decline of sage-grouse populations, yet few studies have rigorously quantified their effects on sage-grouse populations across broad spatial scales and long time periods. To help inform a threat assessment within the Great Basin for listing sage-grouse in 2015 under the ESA, we conducted an extensive analysis of wildfire and climatic effects on sage-grouse population growth derived from 30 years of lek-count data collected across the hydrographic Great Basin of Western North America. Annual (1984–2013) patterns of wildfire were derived from an extensive dataset of remotely sensed 30-meter imagery and precipitation derived from locally downscaled spatially explicit data. In the sagebrush ecosystem, underlying soil conditions also contribute strongly to variation in resilience to disturbance and resistance to plant community changes (R&R). Thus, we developed predictions from models of post-wildfire recovery and chronic effects of wildfire based on three spatially explicit R&R classes derived from soil moisture and temperature regimes. We found evidence of an interaction between the effects of wildfire (chronically affected burned area within 5 kilometers of a lek) and climatic conditions (spring through fall precipitation) after accounting for a consistent density-dependent effect. Specifically, burned areas near leks nullifies population growth that normally follows years with relatively high precipitation. In models, this effect results in long-term population declines for sage-grouse despite cyclic periods of high precipitation. Based on 30-year projections of burn and recovery rates, our population model predicted steady and substantial long-term declines in population size across the Great Basin. Further, example management scenarios that may help offset adverse wildfire effects are provided by models of varying levels of fire suppression and post-wildfire restoration that focus on areas especially important to sage-grouse populations. These models illustrate how sage-grouse population persistence likely will be compromised as sagebrush ecosystems and sage-grouse habitat are degraded by wildfire, especially in a warmer and drier climate, and by invasion of annual grasses that can increase wildfire frequency and size in the Great Basin.

California, Idaho, Nevada, Oregon, Utah↗