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At least 415 records · Page 23Linked to original sources

Resource inventory of marine and estuarine fishes of the West Coast and Alaska: A checklist of North Pacific and Arctic Ocean species from Baja California to the Alaska - Yukon border

This is a comprehensive inventory of the fish species recorded in marine and estuarine waters between the Alaska–Yukon Territory border in the Beaufort Sea and Cabo San Lucas at the southern end of Baja California and out about 300 miles from shore. Our westernmost range includes the eastern Bering Sea and Aleutian Islands. In addition, we have also included our best impressions of the species that might reasonably be expected to be members of the West Coast ichthyofauna but have not yet been captured or reported within our study area. These species are marked with an asterisk (*) and have been reported (1) in the western Bering Sea; (2) off Canada’s Yukon Territory and adjacent portions of the Northwest Territories; (3) along the southern-eastern tip (non-Pacific side) of Baja California; and (4) in waters somewhat beyond 300 miles from shore. Although the term West Coast usually refers to the coast of the continuous western states, our usage herein means the entire study area. The West Coast inventory within this range encompasses fish fauna from 44 orders, 232 families, and a minimum of 1,450 species. Please note that introduced and invasive fish species are marked by double asterisks (**) and that their scientific names are highlighted in gray. We have compiled this document because the most geographically inclusive previous inventories (Jordan and Evermann 1896a, Jordan et al. 1930) are largely of historical interest and are out of date. More recent lists and compilations have either focused on relatively narrow taxonomic groups (e. g., Kramer et al. 1995, Love et al. 2002), are regional in scope (e. g., Hart 1973, Hubbs et al. 1979, Mecklenburg et al. 2002), or focus on commonly observed species (e. g., Miller and Lea 1972, Eschmeyer and Herald 1983). With the explosion of coastal research and environmental assessments, beginning in the 1970s, and more recently, renewed scientific interest in biodiversity (e.g., effects of global climate change), our own studies on related subjects regarding fish populations, assemblages, and biological habitats, suggested this was the appropriate time to update and summarize our knowledge.

Report↗

Recently Active Traces of the Berryessa Fault, California: A Digital Database

The purpose of this map is to show the location of and evidence for recent movement on active fault traces within the Berryessa section and parts of adjacent sections of the Green Valley Fault Zone, California. The location and recency of the mapped traces is primarily based on geomorphic expression of the fault as interpreted from large-scale 2010 aerial photography and from 2007 and 2011 0.5 and 1.0 meter bare-earth LiDAR imagery (that is, high-resolution topographic data). In a few places, evidence of fault creep and offset Holocene strata in trenches and natural exposures have confirmed the activity of some of these traces. This publication is formatted both as a digital database for use within a geographic information system (GIS) and for broader public access as map images that may be browsed on-line or download a summary map . The report text describes the types of scientific observations used to make the map, gives references pertaining to the fault and the evidence of faulting, and provides guidance for use of and limitations of the map.

California↗

Surface Water Records of California, 1961; Volume 1: Colorado River Basin, Southern Great Basin and Pacific Slope Basins excluding Central Valley

The surface-water records for the 1961 water year for gaging stations, partial-record stations, and miscellaneous sites within the State of California are given in this report. For convenience there are also included records for a few pertinent gaging stations in bordering States. The records were collected and computed by the Water Resources Division of the U.S. Geological Survey, under the direction of Walter Hofmann, district engineer, Surface Water Branch. This report marks the beginning of a new method of presenting, annually, basic data on surface-water records by States. Through September 30, 1960, the records of discharge and stage of streams and contents and stage of lakes or reservoirs were published in an annual series of U.S. Geological Survey water-supply papers entitled "Surface Water Supply of the United States." Since 1951 there have been 20 volumes in the series; each volume covered an area whose boundaries coincided with those of certain natural drainage areas. The records in California were contained in Parts 9, 10, and 11 of that series. Beginning with the 1961 water year, streamflow records and related data will be released by the Geological Survey in annual reports on a State-boundary basis. Distribution of these basicdata reports will be limited and primarily for local needs. The records later will be published in Geological Survey water-supply papers at 5-year intervals. These 5-year water-supply papers will show daily discharge and will be compiled on the same geographical areas previously used for the annual series; however, some of the 14 parts of conterminous United States will be further subdivided.

California↗

Surface Water Records of California, 1962; Volume 2: Northern Great Basin and Central Valley

The surface-water records for the 1962 water year for gaging stations, partial-record stations, and miscellaneous sites within the State of California are given in this report. For convenience there are also included records for a few pertinent gaging stations in bordering States. The records were collected and computed by the Water Resources Division of the U.S. Geological Survey, under the direction of Walter Hofmann, district engineer, Surface Water Branch. Through September 30, 1960, the records of discharge and stage of streams,and contents and stage of lakes or reservoirs were published in an annual series of U.S. Geological Survey water-supply papers entitled "Surface Water Supply of the United States." Since 1951 there have been 20 volumes in the series; each volume covered an area whose boundaries coincided with those of certain natural drainage areas. The records in California were contained in parts 9, 10, and 11 of that series. Beginning with the 1961 water year, streamflow records and related data are being released by the Geological Survey in annual reports on a State-boundary basis. Distribution of these basic data reports is limited and primarily for local needs. The records later will be published in Geological Survey water-supply papers at 5-year intervals. These 5-year water-supply papers will show daily discharge and will be compiled on the same geographical areas previously used for the annual series; however, some of the 14 parts of conterminous United States will be further subdivided.

California↗

Surface water records of California, 1963; Volume 2: Northern Great Basin and Central Valley

The surface-water records for the 1963 water year for gaging stations, partial-record stations, and miscellaneous sites within the State of California are given in this report. For convenience there are also included records for a few pertinent gaging stations in bordering States. The records were collected and computed by the Water Resources Division of the U.S. Geological Survey, under the direction of Walter Hofmann, district engineer. Surface Water Branch. Through September 30, 1960, the records of discharge and stage of streams and contents and stage of lakes or reservoirs were published in an annual series of U.S. Geological Survey water-supply papers entitled "Surface Water Supply of the United States." Since 1951 there have been 20 volumes in the series; each volume covered an area whose boundaries coincided with those of certain natural drainage areas. The records in California were contained in parts 9, 10, and 11 of that series. Beginning with the 1961 water year, streamflow records and related data are being released by the Geological Survey in annual reports on a State-boundary basis. Distribution of these basic data reports is limited and primarily for local needs. The records later will be published in Geological Survey water-supply papers at 5-year intervals. These 5-year water-supply papers will show daily discharge and will be compiled on the same geographical areas Previously used for the annual series; however, some of the 14 Parts of conterminous United States will be further subdivided.

California↗

Surface water records of California, 1964; Volume 2: Northern Great Basin and Central Valley

The surface-water records for the 1964 water year for gaging stations, partial-record stations, and miscellaneous sites within the State of California are given in this report. For convenience there are also included records for a few pertinent gaging stations in bordering States. The records were collected and computed by the Water Resources Division of the U.S. Geological Survey, under the direction of Walter Hofmann, district engineer, Surface Water Branch. Through September 30, 1960, the records of discharge and stage of streams and contents and stage of lakes or reservoirs were published in an annual series of U.S. Geological Survey water-supply papers entitled "Surface Water Supply of the United States." Since 1951 there have been 20 volumes in the series; each volume covered an area whose boundaries coincided with those of certain natural drainage areas. The records in California were contained in parts 9, 10, and 11 of that series. Beginning with the 1961 water year, streamflow records and related data are being released by the Geological Survey in annual reports on a State-boundary basis. Distribution of these basic data reports is limited and primarily for local needs. The records later will be published in Geological Survey water-supply papers at 5-year intervals. These 5-year water-supply papers will show daily discharge and will be compiled on the same geographical areas previously used for the annual series; however, some of the 14 parts of conterminous United States will be further subdivided.

California↗

Evaluation of pathogen risks and testing considerations for Chinook salmon egg movements between New Zealand and California

Executive Summary Oncorhynchus tshawytscha (Walbaum in Artedi, 1792; Chinook salmon) were historically abundant in the McCloud River but are now extirpated from this tributary owing to dam construction and lack of passage. Planning efforts to restore populations above Shasta and Keswick Dams are currently underway, including an evaluation of potential source populations. One potential source is New Zealand Chinook salmon, which are believed to have originated from tributaries of the Sacramento River. These fish could be returned to California if reintroduction risks, including risks of pathogen introduction, could be sufficiently mitigated. The U.S. Geological Survey was contracted to provide scientific support for reintroduction efforts, including evaluating the risks of pathogen transmission via the movement of Chinook salmon eggs from New Zealand to the McCloud River. This report estimates pathogen risks associated with egg movement and considers epidemiological and biosecurity measures to minimize these risks. Pathogen risks associated with the movement of Chinook salmon eggs from New Zealand were evaluated based on pathogen virulence, transmission route, and geographic distribution. These criteria identified 14 moderate- and high-risk pathogens out of the 30 pathogens evaluated. Pathogen species and strains were considered high risk if they have the potential for vertical transmission (that is, transmission from parent to offspring), are moderately or highly virulent, and are exotic to the Sacramento River Basin. According to these criteria, we identified the following pathogens as high risk: New Zealand rickettsia-like organisms 1 and 2. —These bacterial pathogens have been associated with mortality events in farmed Chinook salmon from the South Island of New Zealand but have not been detected in other regions. Pilchard orthomyxovirus (POMV). —POMV has been detected in Sardina pilchardus (Walbaum, 1792; pilchards) and Salmo salar (Linnaeus, 1758; Atlantic salmon) from the coasts of southern Australia and Tasmania. POMV can cause relatively high mortality rates and may be indirectly transmitted via contaminated water sources. Infectious pancreatic necrosis virus (IPNV). —IPNV has a wide geographic distribution and is present in the Sacramento River Basin, but the IPNV-like viruses detected in Australia and New Zealand are unique from those found in the United States. Yersinia ruckeri . —This bacterial pathogen is the causative agent of enteric redmouth disease and has a widespread geographic distribution. However, the strains that are present in Australia and New Zealand are unique from those found in North America. Strategic use of testing and biosecurity measures can minimize pathogen risks associated with the movement of eggs. The most effective measures include iodophor treatment of eggs to remove external pathogens, testing of all the adult fish from which gametes are obtained, and a quarantine period after transport to confirm pathogen testing results. Additional measures to enhance biosecurity could include testing the quarantined fish following emergence and (or) developing a fish health history of the source population through pathogen monitoring.

California↗

The Loma Prieta, California, Earthquake of October 17, 1989: Forecasts

The magnitude (Mw) 6.9 Loma Prieta earthquake struck the San Francisco Bay region of central California at 5:04 p.m. P.d.t. on October 17, 1989, killing 62 people and generating billions of dollars in property damage. Scientists were not surprised by the occurrence of a destructive earthquake in this region and had, in fact, been attempting to forecast the location of the next large earthquake in the San Francisco Bay region for decades. This paper summarizes more than 20 scientifically based forecasts made before the 1989 Loma Prieta earthquake for a large earthquake that might occur in the Loma Prieta area. The forecasts geographically closest to the actual earthquake primarily consisted of right-lateral strike-slip motion on the San Andreas Fault northwest of San Juan Bautista. Several of the forecasts did encompass the magnitude of the actual earthquake, and at least one approximately encompassed the along-strike rupture length. The 1989 Loma Prieta earthquake differed from most of the forecasted events in two ways: (1) it occurred with considerable dip-slip in addition to strike-slip motion, and (2) it was much deeper than expected.

California↗

Surface Water Records of California, 1961; Volume 2: Northern Great Basin and Central Valley

The surface-water records for the 1961 water year for gaging stations, partial-record stations, and miscellaneous sites within the State of California are given in this report. For convenience there are also included records for a few pertinent gaging stations in bordering States. The records were collected and computed by the Water Resources Division of the U.S. Geological Survey, under the direction of Walter Hofmann, district engineer, Surface Water Branch. This report marks the beginning of a new method of presenting, annually, basic data on surface-water records by States. Through September 30, 1960, the records of discharge and stage of streams and contents and stage of lakes or reservoirs were published in an annual series of U.S. Geological Survey water-supply papers entitled "Surface Water Supply of the United States." Since 1951 there have been 20 volumes in the series; each volume covered an area whose boundaries coincided with those of certain natural drainage areas. The records in California were contained in Parts 9, 10, and 11 of that series. Beginning with the 1961 water year, streamflow records and related data will be released by the Geological Survey in annual reports on a State-boundary basis. Distribution of these basic data reports will be limited and primarily for local needs. The records later will be published in Geological Survey water-supply papers at 5-year intervals. These 5-year water-supply papers will show daily discharge and will be compiled on the same geographical areas previously used for the annual series; however, some of the 14 parts of conterminous United States will be further subdivided.

California↗

Evaluation of alternative groundwater-management strategies for the Bureau of Reclamation Klamath Project, Oregon and California

The water resources of the upper Klamath Basin, in southern Oregon and northern California, are managed to achieve various complex and interconnected purposes. Since 2001, irrigators in the Bureau of Reclamation Klamath Irrigation Project (Project) have been required to limit surface-water diversions to protect habitat for endangered freshwater and anadromous fishes. The reductions in irrigation diversions have led to an increased demand for groundwater by Project irrigators, particularly in drought years. The potential effects of sustained pumping on groundwater and surface-water resources have caused concern among Federal and state agencies, Indian tribes, wildlife groups, and groundwater users. To aid in the development of a viable groundwater-management strategy for the Project, the U.S. Geological Survey, in collaboration with the Klamath Water and Power Agency and the Oregon Water Resources Department, developed a groundwater-management model that links groundwater simulation with techniques of constrained optimization. The overall goal of the groundwater-management model is to determine the patterns of groundwater pumping that, to the extent possible, meet the supplemental groundwater demands of the Project. To ensure that groundwater development does not adversely affect groundwater and surface-water resources, the groundwater-management model includes constraints to (1) limit the effects of groundwater withdrawal on groundwater discharge to streams and lakes that support critical habitat for fish listed under the Endangered Species Act, (2) ensure that drawdowns do not exceed limits allowed by Oregon water law, and (3) ensure that groundwater withdrawal does not adversely affect agricultural drain flows that supply a substantial portion of water for irrigators and wildlife refuges in downslope areas of the Project. Groundwater-management alternatives were tested and designed within the framework of the Klamath Basin Restoration Agreement (currently [2013] awaiting authorizing Federal legislation), which would establish a permanent limit on the amount of surface water that can be diverted annually to the Project. Groundwater-management scenarios were evaluated for the period 1970•2004; supplemental groundwater demand by the Project was estimated as the part of irrigation demand that would not have been satisfied by the surface-water diversion allowed under the Klamath Basin Restoration Agreement. Over the 35-year management period, 22 years have supplemental groundwater demand, which ranges from a few thousand acre-feet (acre-ft) to about 100,000 acre-ft in the driest years. The results of the groundwater-management model indicate that supplemental groundwater pumping by the Project can be managed to avoid adverse effects to groundwater discharge that supports critical aquatic habitat. The existing configuration of wells in the Project would be able to meet groundwater-pumping goals in 14 of the 22 years with supplemental groundwater demand; however, substantial irrigation shortages can be expected during drought periods when the demand for supplemental groundwater is highest. The maximum irrigation-season withdrawal calculated by the groundwater-management model is about 60,000 acre-ft, the average withdrawal in drought years is about 54,000 acre-ft, and the amount of unmet groundwater demand reaches a maximum of about 45,000 acre-ft. A comparison of optimized groundwater withdrawals by geographic region shows that the highest annual withdrawals are associated with wells in the Tule Lake and Klamath Valley regions of the Project. The patterns of groundwater withdrawal also show that a substantial amount of the available pumping capacity is unused due to the restrictions imposed by drawdown constraints. Subsequent model applications were used to evaluate the sensitivity of optimization results to various factors. A sensitivity analysis quantified the changes in optimized groundwater withdrawals that result from changes in drawdown-constraint limits. The analysis showed the potential for substantial increases in withdrawals of groundwater with less restrictive drawdown limits at drawdown-control sites in the California part of the model. Systematic variation of the drains-constraint limit yielded a trade-off curve between optimized groundwater withdrawals and the allowable reduction in groundwater discharge to the Project drain system. Additional model applications were used to assess the value of increasing the pumping capacity of the network of wells serving the Project, and the relation between reduced off-Project groundwater pumping and increased pumping by Project irrigators.

California;Oregon↗

Geographic Research in the USGS Western Region

The two geography research programs of the U.S. Geological Survey (USGS), Land Remote Sensing and Geographic Analysis and Monitoring, have very strong relevance to the USGS mission and science strategy. In the western United States, the particular niche of these geography programs is in connecting USGS science to people and communities. Reports from the National Academy of Sciences and other organizations invariably encourage the U.S. Geological Survey (USGS) to ensure the quality of its science while finding ways to make it more relevant to important societal issues. Much of the geography research conducted in the USGS Western Region does exactly that. In Menlo Park, California, the geography research team is focused on developing tools and techniques to help people assess risk from natural hazards and environmental impacts. In Flagstaff and Tucson, Arizona, geography scientists explore new ways to use remote sensing to help communities deal with environmental issues.

Fact Sheet↗

Estimating natural recharge in San Gorgonio Pass watersheds, California, 1913–2012

A daily precipitation-runoff model was developed to estimate spatially and temporally distributed recharge for groundwater basins in the San Gorgonio Pass area, southern California. The recharge estimates are needed to define transient boundary conditions for a groundwater-flow model being developed to evaluate the effects of pumping and climate on the long-term availability of groundwater. The area defined for estimating recharge is referred to as the San Gorgonio Pass watershed model (SGPWM) and includes three watersheds: San Timoteo Creek, Potrero Creek, and San Gorgonio River. The SGPWM was developed by using the U.S. Geological Survey INFILtration version 3.0 (INFILv3) model code used in previous studies of recharge in the southern California region, including the San Gorgonio Pass area. The SGPWM uses a 150-meter gridded discretization of the area of interest in order to account for spatial variability in climate and watershed characteristics. The high degree of spatial variability in climate and watershed characteristics in the San Gorgonio Pass area is caused, in part, by the high relief and rugged topography of the area. Daily climate data developed from a network of monitoring sites and published average monthly precipitation maps were used to develop the climate inputs for the SGPWM. Geographic Information System (GIS) data defining land surface altitude, vegetation, soils, surficial geology, and land cover were used to define input parameters representing the physical characteristics of the land surface, root zone, and shallow subsurface underlying the root zone. Model parameterization was based on a previous INFILv3 model developed for an area including the upper parts of the San Timoteo Creek and Potrero Creek drainages and the western part of the San Gorgonio River watershed. The previous INFILv3 model was calibrated by using available streamflow records from the model area. The SGPWM uses an updated INFILv3 version to represent shallow groundwater flow better beneath the root zone that contributes to lateral, downslope seepage rather than deep recharge. The SGPWM calibration was tested by using available streamflow records in the San Gorgonio Pass region. The SGPWM was used to simulate a 100-year water budget, including recharge and runoff, for water years 1913 through 2012. Results indicated that most recharge came from episodic infiltration of surface-water runoff in the larger stream channels. Results also indicated periods of great variability in recharge and runoff in response to variability in precipitation. More recharge was simulated for the area of the groundwater basin underlying the more permeable alluvial fill of the valley floor compared to recharge in the neighboring upland areas of the less permeable mountain blocks. The greater recharge was in response to the episodic streamflow that discharged from the mountain block areas and quickly infiltrated the permeable alluvial fill of the groundwater basin. Although precipitation at the higher altitudes of the mountain block was more than double precipitation at the lower altitudes of the valley floor, recharge for inter-channel areas of the mountain block was limited by the lower permeability bedrock underlying the thin soil cover, and most of the recharge in the mountain block was limited to the main stream channels underlain by alluvial fill.

California↗

Geographic signatures of North American West Coast estuaries

West Coast estuaries are geologically young and composed of a variety of geomorphological types. These estuaries range from large fjords to shallow lagoons; from large to low freshwater flows. Natural hazards include E1 Niños, strong Pacific storms, and active tectonic activity. West Coast estuaries support a wide range of living resources: five salmon species, harvestable shellfish, waterfowl and marine birds, marine mammals, and a variety of algae and plants. Although populations of many of these living resources have declined (salmonids), others have increased (marine mammals). West Coast estuaries are also centers of commerce and increasingly large shipping traffic. The West Coast human population is rising faster than most other areas of the U.S. and Canada, and is distributed heavily in southern California, the San Francisco Bay area, around Puget Sound, and the Fraser River estuary. While water pollution is a problem in many of the urbanized estuaries, most estuaries do not suffer from poor water quality. Primary estuarine problems include habitat alterations, degradation, and loss; diverted freshwater flows; marine sediment contamination; and exotic species introductions. The growing West Coast economy and population are in part related to the quality of life, which is dependent on the use and enjoyment of abundant coastal natural resources.

British Columbia;California;Oregon;Washington↗

Pika ( Ochotona princeps ) losses from two isolated regions reflect temperature and water balance, but reflect habitat area in a mainland region

Although biotic responses to contemporary climate change are spatially pervasive and often reflect synergies between climate and other ecological disturbances, the relative importance of climatic factors versus habitat extent for species persistence remains poorly understood. To address this shortcoming, we performed surveys for American pikas ( Ochotona princeps ) at > 910 locations in 3 geographic regions of western North America during 2014 and 2015, complementing earlier modern (1994–2013) and historical (1898–1990) surveys. We sought to compare extirpation rates and the relative importance of climatic factors versus habitat area for pikas in a mainland-versus-islands framework. In each region, we found widespread evidence of distributional loss—local extirpations, upslope retractions, and encounter of only old sign. Locally comprehensive surveys suggest extirpation of O. princeps from 5 of 9 new sites from the hydrographic Great Basin and from 11 of 29 sites in northeastern California. Although American pikas were recorded as recently as 2011 in Zion National Park and in 2012 from Cedar Breaks National Monument in Utah, O. princeps now appears extirpated from all reported localities in both park units. Multiple logistic regressions for each region suggested that both temperature-related and water-balance-related variables estimated from DAYMET strongly explained pika persistence at sites in the Great Basin and in Utah but not in the Sierra-Cascade “mainland” portion of northeastern California. Conversely, talus-habitat area did not predict American pika persistence in the Great Basin or Utah but strongly predicted persistence in the Sierra-Cascade mainland. These results not only add new areas to our understanding of long-term trend of the American pika’s distribution, but also can inform decisions regarding allocation of conservation effort and management actions. Burgeoning research on species such as O. princeps has collectively demonstrated the heterogeneity and nuance with which climate can act on the distribution of mountain-dwelling mammals.

Journal of Mammalogy↗

Cruise report R/V Surf Surveyor cruise S1-00-CL, mapping the bathymetry of Crater Lake, Oregon

During the Spring of 1999, the US Geological Survey (USGS) Pacific Seafloor Mapping Project (PSMP) was contacted by the US National Park Service Crater Lake National Park (CLNP) to inquire about the plausibility of producing a high-resolution multibeam bathymetric map of Crater Lake. The purpose was to generate a much higher-resolution and more geographically accurate bathymetric map than was produced in 1959, the last time the lake had been surveyed. Scientific interest in various aspects of Crater Lake (aquatic biology, geochemistry, volcanic processes, etc.) has increased during the past decade but the basemap of bathymetry was woefully inadequate. Funds were gathered during the early part of 2000 and the mapping began in late July, 2000. Crater Lake (see fig. 1 in report) is located in south central Oregon (see fig. 2 in report) within the Cascades Range, a chain of volcanoes that stretches from northern California to southern British Columbia. Crater Lake is the collapsed caldera of Mt. Mazama from a climatic eruption about 7700-yr ago (Nelson et al., 1988; Bacon and Lanphere, 1990; Bacon et al., 1997). The floor of Crater Lake has only been mapped three times since the lake was first stumbled upon by gold prospectors in the 1853. The first survey was carried by out by William G. Steel during a joint USGS-US Army expedition under the direction of Maj. Clarence E. Dutton in 1886 (Dutton, 1889). Steel�s mapping survey collected 186 soundings using a Millers lead-line sounding machine (see fig.3 in report). The resulting map (see fig.4 in report) shows only soundings and no attempts were made to generate contours. The second survey, conducted in 1959 by the US Coast and Geodetic Survey, mapped the bathymetry of Crater Lake with an acoustic echo sounder using radar navigation and collected 4000 soundings. The data were contoured by Williams (1961) and Byrne (1962) and the result is a fairly detailed map of the large-scale features of Crater Lake (see fig. 5 in report). The third mapping survey, the one of this report, was a joint USGS-NPS project carried out under a Cooperative Agreement with the Center for Coastal and Ocean Mapping, University of New Hampshire. The 2000 survey used a Kongsberg Simrad EM1002 high-resolution multibeam mapping system owned and operated by C&C Technologies, Inc. of Lafayette, LA.

Oregon↗

Feline immunodeficiency virus cross-species transmission: Implications for emergence of new lentiviral infections

Owing to a complex history of host-parasite coevolution, lentiviruses exhibit a high degree of species specificity. Given the well-documented viral archeology of HIV emergence following human exposures to SIV, understanding processes that promote successful cross-species lentiviral transmissions is highly relevant. We have previously reported natural cross-species transmission of a subtype of feline immunodeficiency virus, puma lentivirus A (PLVA), between bobcats ( Lynx rufus ) and mountain lions ( Puma concolor ) in a small number of animals in California and Florida. In this study we investigate host-specific selection pressures, within-host viral fitness, and inter- vs. intra-species transmission patterns among a larger collection of PLV isolates from free-ranging bobcats and mountain lions. Analysis of proviral and viral RNA levels demonstrates that PLVA fitness is severely restricted in mountain lions compared to bobcats. We document evidence of diversifying selection in three of six PLVA genomes from mountain lions, but did not detect selection among twenty PLVA isolates from bobcats. These findings support that PLVA is a bobcat-adapted virus, which is less fit in mountain lions and under intense selection pressure in the novel host. Ancestral reconstruction of transmission events reveals intraspecific PLVA transmission has occurred among panthers ( Puma concolor coryi ) in Florida following initial cross-species infection from bobcats. In contrast, interspecific transmission from bobcats to mountain lions predominates in California. These findings document outcomes of cross-species lentiviral transmission events among felids that compare to emergence of HIV from nonhuman primates. IMPORTANCE Cross-species transmission episodes can be singular, dead-end events or can result in viral replication and spread in the new species. The factors that determine which outcome will occur are complex, and the risk of new virus emergence is therefore difficult to predict. Here we use molecular techniques to evaluate transmission, fitness, and adaptation of puma lentivirus A (PLVA) between bobcats and mountain lions in two geographic regions. Our findings illustrate that mountain lion exposure to PLVA is relatively common, but does not routinely result in infections communicable in the new host. This is attributed to efficient species barriers that largely prevent lentiviral adaptation. However, the evolutionary capacity for lentiviruses to adapt to novel environments may ultimately overcome host restriction mechanisms over time and under certain ecological circumstances. This phenomenon provides a unique opportunity to examine cross-species transmission events leading to new lentiviral emergence.

California, Florida↗

A report on genetic affinities and relatedness of Agassiz’s desert tortoises (Gopherus agassizii) at opposite ends of the Coachella Valley in California

This report summarizes the results for mtDNA and STR genotyping of 41 desert tortoise (Gopherus agassizii) DNA samples from opposite sides of the Coachella Valley: one sample from the west side at the Mesa wind energy facility in the Whitewater Hills and the other from the mouth of Cottonwood Canyon in Joshua Tree National Park, both within the boundaries of the Coachella Valley Multiple Species Habitat Conservation Plan. Additional samples were collected from tortoises on the northern bajadas of the Orocopia Mountains and from the Santa Rosa Mountains and those results will be presented at a later time in a scientific publication. We tested samples for their mtDNA haplotype and 25 STR loci previously used in other studies. We performed assignment testing to determine the genetic affinity of each individual to the geographic region of collection. Despite apparent isolation, both populations appear to be naturally occurring and do exhibit indications of having experienced increased genetic drift (resulting in increased homozygosity, increased inbreeding or a reduction of genetic diversity). The lack of strong evidence for genetic isolation suggests that long-term maintenance of unfragmented landscapes is an important part of tortoise conservation in the region.

California↗

Atmospheric mercury emissions from substrates and fumaroles associated with three hydrothermal systems in the western United States

This paper quantifies atmospheric mercury (Hg) emissions from substrates and fumaroles associated with three hydrothermal systems: Lassen Volcanic Center, California (LVC); Yellowstone Caldera, Wyoming (YC); and Dixie Valley, Nevada (DV). Substrate Hg fluxes were measured using field chamber methods at thermal and nonthermal sites. The highest Hg fluxes (up to 541 ng m &minus;2 h &minus;1 ) were measured at thermal active areas. Fluxes from altered and unaltered nonthermal sites were <10 ng m &minus;2 h &minus;1 and were comparable to those measured in natural low-Hg background regions for YC and DV, and at LVC they were slightly elevated. Similarly, reactive gaseous mercury concentrations were higher in thermal active areas. Using a Geographic Information System framework for scaling, estimated area-average Hg emissions from substrates were 0.9&ndash;3.8 ng m &minus;2 h &minus;1 at LVC, 0.8&ndash;2.8 ng m &minus;2 h &minus;1 at YC, and 0.4&ndash;0.5 ng m &minus;2 h &minus;1 at DV. At LVC, nonthermal areas were the primary substrate source of atmospheric Hg (>98%). At YC, substrate Hg emissions were dominated (50 to 90%) by acidically altered thermal areas. Substrate emissions at DV were low and primarily from nonthermal areas (66% to 75%). Fumarole emissions at LVC (91&ndash;146 kg yr &minus;1 ) and YC (0.18&ndash;1.6 kg yr &minus;1 for Mud Volcano) were estimated by applying Hg:H 2 O and Hg:CO 2 ratios in hydrothermal gas samples to H 2 O and CO 2 emissions. Applying total area-average emissions from substrates and thermal features at LVC, YC, and DV to similar systems across the conterminous United States, yearly atmospheric Hg emissions from active hydrothermal systems are projected to be 1.3&ndash;2.1 Mg.

Journal of Geophysical Research D: Atmospheres↗