SEARCH · Search USGS

Results for “Pacific Studies”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 685 records · Page 38Linked to original sources

USGS2014

Structure and vulnerability of Pacific Northwest tidal wetlands – A summary of wetland climate change research by the Western Ecology Division, U.S. EPA

Climate change poses a serious threat to the tidal wetlands of the Pacific Northwest (PNW) region of the U.S. In response to this threat, scientists at the Western Ecology Division of the U.S. EPA at and the Western Fisheries Research Center of the U.S. Geological Survey, along with other partners, initiated a series of studies on the structure and vulnerability of tidal wetlands to climate change. One research thrust was to evaluate community structure of PNW marshes, experimentally assess the vulnerability of marsh plants to inundation and salinity stress (as would happen with sea level rise), and evaluate the utility of the National Wetland Inventory (NWI) classification system. Another research thrust was to develop tools that provide insights into possible impacts of climate change. This effort included enhancing the Sea Level Affecting Marshes Model (SLAMM) to predict the effects of sea level rise on submerged aquatic vegetation (Zostera marina) distributions, evaluating changes in river flow into coastal estuaries in response to precipitation changes, and synthesizing Pacific Coast estuary, watershed, and climate data in a downloadable tool. Because the research resulting from these efforts was published in multiple venues, we summarized them in this document. We anticipate that future research efforts by the U.S. EPA will continue with a focus on climate change impacts on a regional scale.

California, Oregon, Washington↗

USGS2004

El Nino influence on Holocene reef accretion in Hawai'i

New observations of reef accretion from several locations show that in Hawai'i accretion during early to middle Holocene time occurred in areas where today it is precluded by the wave regime, suggesting an increase in wave energy. Accretion of coral and coralline algae reefs in the Hawaiian Islands today is largely controlled by wave energy. Many coastal areas in the main Hawaiian Islands are periodically exposed to large waves, in particular from North Pacific swell and hurricanes. These are of sufficient intensity to prevent modern net accretion as evidenced by the antecedent nature of the seafloor. Only in areas sheltered from intense wave energy is active accretion observed. Analysis of reef cores reveals patterns of rapid early Holocene accretion in several locations that terminated by middle Holocene time, ca. 5000 yr ago. Previous analyses have suggested that changes in Holocene accretion were a result of reef growth "catching up" to sea level. New data and interpretations indicate that the end of reef accretion in the middle Holocene may be influenced by factors in addition to sea level. Reef accretion histories from the islands of Kaua'i, O'ahu, and Moloka'i may be interpreted to suggest that a change in wave energy contributed to the reduction or termination of Holocene accretion by 5000 yr ago in some areas. In these cases, the decrease in reef accretion occurred before the best estimates of the decrease in relative sea-level rise during the mid-Holocene high stand of sea level in the main Hawaiian Islands. However, reef accretion should decrease following the termination of relative sea-level rise (ca. 3000 yr ago) if reef growth were "catching up" to sea level. Evidence indicates that rapid accretion occurred at these sites in early Holocene time and that no permanent accretion is occurring at these sites today. This pattern persists despite the availability of hard substrate suitable for colonization at a wide range of depths between -30 m and the intertidal zone. We infer that forcing other than relative sea-level rise has altered the natural ability to support reef accretion on Hawaiian insular shelves. The limiting factor in these areas today is wave energy. Numbers of both large North Pacific swell events and hurricanes in Hawai'i are greater during El Nino years. We infer that if these major reef-limiting forces were suppressed, net accretion would occur in some areas in Hawai'i that are now wave-limited. Studies have shown that El Nino/Southern Oscillation (ENSO) was significantly weakened during early-mid Holocene time, only attaining an intensity similar to the current one ca. 5000 yr ago. We speculate that this shift in ENSO may assist in explaining patterns of Holocene Hawaiian reef accretion that are different from those of the present and apparently not related to relative sen-level rise.

Hawaii↗

USGS2009

Composition and variation of noise recorded at the Yellowknife Seismic Array, 1991-2007

We analyze seismic noise recorded on the 18 short-period, vertical component seismometers of the Yellowknife Seismic Array (YKA). YKA has an aperture of 23 km and is sited on cratonic lithosphere in an area with low cultural noise. These properties make it ideal for studying natural seismic noise at periods of 1-3 s. We calculated frequency-wave number spectra in this band for over 6,000 time windows that were extracted once per day for 17 years (1991-2007). Slowness analysis reveals a rich variety of seismic phases originating from distinct source regions: R g waves from the Great Slave Lake; L g waves from the Atlantic, Pacific, and Arctic Oceans; and teleseismic P waves from the north Pacific and equatorial mid-Atlantic regions. The surface wave energy is generated along coastlines, while the body wave energy is generated at least in part in deep-water, pelagic regions. Surface waves tend to dominate at the longer periods and, just as in earthquake seismograms, L g is the most prominent arrival. Although the periods we study are slightly shorter than the classic double-frequency microseismic band of 4-10 s, the noise at YKA has clear seasonal behavior that is consistent with the ocean wave climate in the Northern Hemisphere. The temporal variation of most of the noise sources can be well fit using just two Fourier components: yearly and biyearly terms that combine to give a fast rise in microseismic power from mid-June through mid-October, followed by a gradual decline. The exception is the R g energy from the Great Slave Lake, which shows a sharp drop in noise power over a 2-week period in November as the lake freezes. The L g noise from the east has a small but statistically significant positive slope, perhaps implying increased ocean wave activity in the North Atlantic over the last 17 years. Copyright 2009 by the American Geophysical Union.

Journal of Geophysical Research B: Solid Earth↗

USGS2023

Microfaunal recording of recent environmental changes in the Herschel Basin, western Arctic Ocean

Microfaunal assemblages of benthic foraminifera, ostracods, and tintinnids from two marine sediment cores retrieved from the Herschel Basin of the Canadian Beaufort Sea shelf document relationships with environmental parameters such as salinity, sea-ice cover, and turbulence. Cores YC18-HB-GC01 and PG2303-1 were collected at 18 and 32 m water depth, respectively. At these sites, sediment accumulation rates range between 0.6 and 1.7 cm yr –1 allowing a near-annual temporal resolution over the last 50 years. Multivariate analyses indicate that benthic foraminiferal assemblages respond primarily to food supply. Dissimilarities between the microfaunal assemblages of the two cores are mainly the result of bottom water salinity levels linked to water depth. High abundance of the benthic foraminiferal species Elphidium clavatum and occurrences of Elphidium bartletti point to varying, but relatively low, salinities at the shallow core site YC18-HB-GC01, which may be affected by variations in the summer halocline depth. Higher species diversity and more abundant Cassidulina reniforme and Stainforthia feylingi characterize the deeper core PG2303-1, which might reflect more stable conditions and higher bottom-water salinities throughout the studied time interval. The most important microfaunal shift of the last 50 years, observed in the shallower longer core YC18-HB-GC01, occurred at the turn of the 21 st century. Prior to ∼2000 CE, the presence of Islandiella norcrossi indicates more stable and saline conditions. Since ∼2000 CE, increased abundances of Haynesina nivea and of the ciliate Tintinnopsis fimbriata suggest decreased salinity and increased turbidity. An increased abundance of Eoeponidella pulchella after ∼2000 CE suggests a concurrent increase in productivity in the last two decades. This shift is nearly synchronous with a decrease in mean summer sea-ice concentration, which can play an important role in bottom water stability on the shelf. Easterly winds can induce a reduction in the sea-ice cover, but also foster a westward spreading of the Mackenzie River plume and the upwelling of nutrient-rich Pacific waters onto the shelf. Both factors would explain the increased freshening and productivity of the Herschel Basin. The last two decades were also marked by a decrease in ostracod abundance that may relate to higher water turbidity. This study shows that combining information from benthic foraminifera, ostracods, and tintinnids provides a comprehensive insight into recent hydrographic/climatic changes in nearshore Arctic habitats, where productivity is critical for the food security of local communities.

Herschel Basin↗

USGS2006

The impact of invasive plants on tidal-marsh vertebrate species: common reed (Phragmites australis) and smooth cordgrass (Spartina alterniflora) as case studies

Large areas of tidal marsh in the contiguous US and the Maritime Provinces of Canada are threatened by invasive plant species. Our understanding of the impact these invasions have on tidal-marsh vertebrates is sparse. In this paper, we focus on two successful invasive plant taxa that have spread outside their native range --common reed (Phragmites australis) and smooth cordgrass (Spartina a/terniflora). A cryptic haplotype of common reed has expanded its range in Atlantic Coast tidal marshes and smooth cordgrass, a native dominant plant of Atlantic Coast low-marsh habitat, has expanded its range and invaded intertidal-marsh habitats of the Pacific Coast. The invasions of common reed in Atlantic Coast tidal marshes and smooth cordgrass in Pacific Coast tidal marshes appear to have similar impacts. The structure and composition of these habitats has been altered and invasion and dominance by these two taxa can lead to profound changes in geomorphological processes, altering the vertical relief and potentially affecting invertebrate communities and the entire trophic structure of these systems. Few studies have documented impacts of invasive plant taxa on tidal-marsh vertebrate species in North America. However, habitat specialists that are already considered threatened or endangered are most likely to be affected. Extensive experimental studies are needed to examine the direct impact of invasive plant species on native vertebrate species. Careful monitoring of sites during the initial stages of plant invasion and tracking ecosystem changes through time are essential. Since tidal marshes are the foci for invasion by numerous species, we also need to understand the indirect impacts of invasion of these habitats on the vertebrate community. We also suggest the initiation of studies to determine if vertebrate species can compensate behaviorally for alterations in their habitat caused by invasive plant species, as well as the potential for adaptation via rapid evolution. Finally, we urge natural-resource managers to consider the impact various invasive plant control strategies will have on native vertebrate communities.

Book chapter↗

USGS2013

Observed changes in phenology across the USA: A regional review for the 2013 National Climate Assessment, Pacific Northwest Regional Information Sheet

This is one in a series of eight, geographic region-focused information sheets that summarizes documented changes in plant and animal phenology over the past century across the United States. This summary is based on long-term studies (10 years or more) published in the primary scientific literature since 2001. A forthcoming manuscript synthesizes the findings of the eight regional information sheets. This information was developed in support of the U.S. Global Change Research Program’s National Climate Assessment and can be used to facilitate preparation for the cascading effects of ongoing climate change.

Idaho, Oregon, Washington↗

USGS2013

Observed changes in phenology across the USA: A regional review for the 2013 National Climate Assessment, Hawaii and Pacific Islands Regional Information Sheet

Hawai‘i↗

USGS2016

Seasonal variation exceeds effects of salmon carcass additions on benthic food webs in the Elwha River

Dam removal and other fish barrier removal projects in western North America are assumed to boost freshwater productivity via the transport of marine-derived nutrients from recolonizing Pacific salmon ( Oncorhynchus spp.). In anticipation of the removal of two hydroelectric dams on the Elwha River in Washington State, we tested this hypothesis with a salmon carcass addition experiment. Our study was designed to examine how background nutrient dynamics and benthic food webs vary seasonally, and how these features respond to salmon subsidies. We conducted our experiment in six side channels of the Elwha River, each with a spatially paired reference and treatment reach. Each reach was sampled on multiple occasions from October 2007 to August 2008, before and after carcass placement. We evaluated nutrient limitation status; measured water chemistry, periphyton, benthic invertebrates, and juvenile rainbow trout ( O. mykiss ) response; and traced salmon-derived nutrient uptake using stable isotopes. Outside of winter, algal accrual was limited by both nitrogen and phosphorous and remained so even in the presence of salmon carcasses. One month after salmon addition, dissolved inorganic nitrogen levels doubled in treatment reaches. Two months after addition, benthic algal accrual was significantly elevated. We detected no changes in invertebrate or fish metrics, with the exception of 15 N enrichment. Natural seasonal variability was greater than salmon effects for the majority of our response metrics. Yet seasonality and synchronicity of nutrient supply and demand are often overlooked in nutrient enhancement studies. Timing and magnitude of salmon-derived nitrogen utilization suggest that uptake of dissolved nutrients was favored over direct consumption of carcasses. The highest proportion of salmon-derived nitrogen was incorporated by herbivores (18–30%) and peaked 1–2 months after carcass addition. Peak nitrogen enrichment in predators (11–16%) occurred 2–3 months after addition. All taxa returned to background δ 15 N levels by 7 months. Since this study was conducted, both dams on the Elwha River were removed over 2011–2014 to open over 90% of the basin to anadromous fishes. We anticipate that as the full portfolio of salmon species expands through the basin, nutrient supply and demand will come into better balance.

Ecosphere↗

USGS2014

El Niño–Southern Oscillation diversity and Southern Africa teleconnections during Austral Summer

A wide range of sea surface temperature (SST) expressions have been observed during the El Niño–Southern Oscillation events of 1950–2010, which have occurred simultaneously with different global atmospheric circulations. This study examines the atmospheric circulation and precipitation during December–March 1950–2010 over the African Continent south of 15° ∘ "> S, a region hereafter known as Southern Africa, associated with eight tropical Pacific SST expressions characteristic of El Niño and La Niña events. The self-organizing map method along with a statistical distinguishability test was used to isolate the SST expressions of El Niño and La Niña. The seasonal precipitation forcing over Southern Africa associated with the eight SST expressions was investigated in terms of the horizontal winds, moisture budget and vertical motion. El Niño events, with warm SST across the east and central Pacific Ocean and warmer than average SST over the Indian Ocean, are associated with precipitation reductions over Southern Africa. The regional precipitation reductions are forced primarily by large-scale mid-tropospheric subsidence associated with anticyclonic circulation in the upper troposphere. El Niño events with cooler than average SST over the Indian Ocean are associated with precipitation increases over Southern Africa associated with lower tropospheric cyclonic circulation and mid-tropospheric ascent. La Niña events, with cool SST anomalies over the central Pacific and warm SST over the west Pacific and Indian Ocean, are associated with precipitation increases over Southern Africa. The regional precipitation increases are forced primarily by lower tropospheric cyclonic circulation, resulting in mid-tropospheric ascent and an increased flux of moisture into the region.

Climate Dynamics↗

USGS2009

Endogenic carbonate sedimentation in Bear Lake, Utah and Idaho, over the last two glacial-interglacial cycles

Sediments deposited over the past 220,000 years in Bear Lake, Utah and Idaho, are predominantly calcareous silty clay, with calcite as the dominant carbonate mineral. The abundance of siliciclastic sediment indicates that the Bear River usually was connected to Bear Lake. However, three marl intervals containing more than 50% CaCO 3 were deposited during the Holocene and the last two interglacial intervals, equivalent to marine oxygen isotope stages (MIS) 5 and 7, indicating times when the Bear River was not connected to the lake. Aragonite is the dominant mineral in two of these three high-carbonate intervals. The high-carbonate, aragonitic intervals coincide with warm interglacial continental climates and warm Pacific sea-surface temperatures. Aragonite also is the dominant mineral in a carbonate-cemented microbialite mound that formed in the southwestern part of the lake over the last several thousand years. The history of carbonate sedimentation in Bear Lake is documented through the study of isotopic ratios of oxygen, carbon, and strontium, organic carbon content, CaCO 3 content, X-ray diffraction mineralogy, and HCl-leach chemistry on samples from sediment traps, gravity cores, piston cores, drill cores, and microbialites. Sediment-trap studies show that the carbonate mineral that precipitates in the surface waters of the lake today is high-Mg calcite. The lake began to precipitate high-Mg calcite sometime in the mid-twentieth century after the artificial diversion of Bear River into Bear Lake that began in 1911. This diversion drastically reduced the salinity and Mg 2+ :Ca 2+ of the lake water and changed the primary carbonate precipitate from aragonite to high-Mg calcite. However, sediment-trap and core studies show that aragonite is the dominant mineral accumulating on the lake floor today, even though it is not precipitating in surface waters. The isotopic studies show that this aragonite is derived from reworking and redistribution of shallow-water sediment that is at least 50 yr old, and probably older. Apparently, the microbialite mound also stopped forming aragonite cement sometime after Bear River diversion. Because of reworking of old aragonite, the bulk mineralogy of carbonate in bottom sediments has not changed very much since the diversion. However, the diversion is marked by very distinct changes in the chemical and isotopic composition of the bulk carbonate. After the last glacial interval (LGI), a large amount of endogenic carbonate began to precipitate in Bear Lake when the Pacific moisture that filled the large pluvial lakes of the Great Basin during the LGI diminished, and Bear River apparently abandoned Bear Lake. At first, the carbonate that formed was low-Mg calcite, but ???11,000 years ago, salinity and Mg 2+ :Ca 2+ thresholds must have been crossed because the amount of aragonite gradually increased. Aragonite is the dominant carbonate mineral that has accumulated in the lake for the past 7000 years, with the addition of high-Mg calcite after the diversion of Bear River into the lake at the beginning of the twentieth century. Copyright ?? 2009 The Geological Society of America.

Special Paper of the Geological Society of America↗

USGS2010

Ferromanganese crusts as archives of deep water Cd isotope compositions

The geochemistry of Cd in seawater has attracted significant attention owing to the nutrient-like properties of this element. Recent culturing studies have demonstrated that Cd is a biologically important trace metal that plays a role in the sequestration of inorganic carbon. This conclusion is supported by recent isotope data for Cd dissolved in seawater and incorporated in cultured phytoplankton. These results show that plankton features isotopically light Cd while Cd-depleted surface waters typically exhibit complimentary heavy Cd isotope compositions. Seawater samples from below 900 m depth display a uniform and intermediate isotope composition of ε 114/110 Cd = +3.3 ± 0.5. This study investigates whether ferromanganese (Fe-Mn) crusts are robust archives of deep water Cd isotope compositions. To this end, Cd isotope data were obtained for the recent growth surfaces of 15 Fe-Mn crusts from the Atlantic, Pacific, Indian, and Southern oceans and two USGS Fe-Mn reference nodules using double spike multiple collector inductively coupled plasma mass spectrometry. The Fe-Mn crusts yield a mean ε 114/110 Cd of +3.2 ± 0.4 (2 SE, n = 14). Data for all but one of the samples are identical, within the analytical uncertainty of ±1.1ε 114/110 Cd (2 SD), to the mean deep water Cd isotope value. This indicates that Fe-Mn crusts record seawater Cd isotope compositions without significant isotope fractionation. A single sample from the Southern Ocean exhibits a light Cd isotope composition of ε 114/110 Cd = 0.2 ± 1.1. The origin of this signature is unclear, but it may reflect variations in deep water Cd isotope compositions related to differences in surface water Cd utilization or long-term changes in seawater ε 114/110 Cd. The results suggest that time series analyses of Fe-Mn crusts may be utilized to study changes in marine Cd utilization.

Geochemistry, Geophysics, Geosystems↗

USGS2021

Integrating seabird dietary and groundfish stock assessment data: Can puffins predict pollock spawning stock biomass in the North Pacific?

Information on the annual variability in abundance and growth of juvenile groundfish can be useful for predicting fisheries stocks, but is often poorly known owing to difficulties in sampling fish in their first year of life. In the Western Gulf of Alaska (WGoA) and Eastern Bering Sea (EBS) ecosystems, three species of puffin (tufted and horned puffin, Fratercula cirrhata, Fratercula corniculata, and rhinoceros auklet , Cerorhinca monocerata , Alcidae), regularly prey upon (i.e., “sample”) age-0 groundfish, including walleye pollock ( Gadus chalcogramma , Gadidae) and Pacific cod ( Gadus microcephalus , Gadidae). Here, we test the hypothesis that integrating puffin dietary data with walleye pollock stock assessment data provides information useful for fisheries management, including indices of interannual variation in age-0 abundance and growth. To test this hypothesis, we conducted cross-correlation and regression analyses of puffin-based indices and spawning stock biomass (SSB) for the WGoA and EBS walleye pollock stocks. For the WGoA, SSB leads the abundance of age-0 fish in the puffin diet, indicating that puffins sample the downstream production of the WGoA spawning stock. By contrast, the abundance and growth of age-0 fish sampled by puffins lead SSB for the EBS stock by 1–3 years, indicating that the puffin diet proxies incoming year class strength for this stock. Our study indicates connectivity between the WGoA and EBS walleye pollock stocks. Integration of non-traditional data sources, such as seabird diet data, with stock assessment data appears useful to inform information gaps important for managing US fisheries in the North Pacific.

Alaska↗

USGS2011

Plant invasions in mountains: Global lessons for better management

Mountains are one of few ecosystems little affected by plant invasions. However, the threat of invasion is likely to increase because of climate change, greater anthropogenic land use, and continuing novel introductions. Preventive management, therefore, will be crucial but can be difficult to promote when more pressing problems are unresolved and predictions are uncertain. In this essay, we use management case studies from 7 mountain regions to identify common lessons for effective preventive action. The degree of plant invasion in mountains was variable in the 7 regions as was the response to invasion, which ranged from lack of awareness by land managers of the potential impact in Chile and Kashmir to well-organized programs of prevention and containment in the United States (Hawaii and the Pacific Northwest), including prevention at low altitude. In Australia, awareness of the threat grew only after disruptive invasions. In South Africa, the economic benefits of removing alien plants are well recognized and funded in the form of employment programs. In the European Alps, there is little need for active management because no invasive species pose an immediate threat. From these case studies, we identify lessons for management of plant invasions in mountain ecosystems: (i) prevention is especially important in mountains because of their rugged terrain, where invasions can quickly become unmanageable; (ii) networks at local to global levels can assist with awareness raising and better prioritization of management actions; (iii) the economic importance of management should be identified and articulated; (iv) public acceptance of management programs will make them more effective; and (v) climate change needs to be considered. We suggest that comparisons of local case studies, such as those we have presented, have a pivotal place in the proactive solution of global change issues.

Mountain Research and Development↗

USGS2014

Gross and microscopic pathology of lesions in Pocillopora spp. from the subtropical eastern Pacific

Coral reefs are threatened by a variety of factors including diseases that have caused significant damage in some regions such as in the Caribbean. At present, no data are available on coral diseases in the Mexican Pacific where Pocillopora spp. is a dominant component of coral communities. Here, we describe gross and microscopic morphology of lesions found in pocilloporids at four sites in the Mexican Pacific. Corals were identified and their lesions photographed and quantified in the field. Tissue samples were collected from healthy and affected colonies for histopathology. We recorded seven species of pocilloporids at the study sites with Isla Isabel being the location with the highest coral diversity ( H ′ = 1.27). Lesions were present in 42% of the colonies and included discoloration (32%), predation-induced tissue loss (30%), unexplained tissue loss (3%) and overgrowth by sponges or algae (35%). The most affected species, P . damicornis (50%), was also one of the most common in the region. No species was more prone to a particular lesion, but there was a significant association between location and the presence of lesions. Northern Islas Marietas (61%) and Isla Isabel (41%) had the highest prevalence of lesions, followed by Manzanillo (37%) and Bahías de Huatulco (23%). Histological changes included atrophy of the surface body wall with depletion of zooxanthellae (91%) in corals with discoloration (bleaching). Ablation of tissue from mesoglea (18%) was also observed. Colonies with unexplained tissue loss showed atrophy and thinning of the epidermis (89%), characterized by cuboidal instead of pseudocolumnar cells normally found in healthy pseudocolumnar ciliated epithelium. Bacterial aggregates between the mesoglea and gastrodermis (11%) were very conspicuous in healthy and diseased corals. Lesions produced by fish bites and gastropods were associated with tissue atrophy (40%) and, in some cases, algal overgrowth near the lesion (20%). No infectious agents associated with cell pathology were detected microscopically. Bleaching and overgrowth by algae and sponges, as well as unexplained tissue loss, are common in Pocillopora . These lesions and anatomical changes warrant further study since their incidence is potentially indicative of reef degradation.

Mexican Pacific↗

USGS2002

Changes to Monterey Bay beaches from the end of the 1982-83 El Niño through the 1997-98 El Niño

The shoreline of Monterey Bay, CA, USA demarcates the landward extent of the Monterey Bay National Marine Sanctuary. Along the length of that shoreline, nine beaches were profiled 34 times between 1983 and 1998. The resulting data set provides an understanding of processes that affect beach volume, width, and shape. Monterey Bay, which is open to high-energy waves generated in the Pacific Ocean, comprises a range of beach environments that respond in a dramatic way to major storms such as the anomalously large El Nin??os in 1982-83 and 1997-98. This study relates the profile characteristics of the beaches to storminess, shoreline location, and geomorphic setting. Because the large El Nin??os occurred at the start and end of the study, the surveys cover both periods of nearly constant beach size and periods of extreme erosion, and the data show both the extent of erosion and accretion and the nature of the transition between the two periods.

Marine Geology↗

USGS2011

Comparative evaluation of molecular diagnostic tests for Nucleospora salmonis and prevalence in migrating juvenile salmonids from the Snake River, USA

Nucleospora salmonis is an intranuclear microsporidian that primarily infects lymphoblast cells and contributes to chronic lymphoblastosis and a leukemia-like condition in a range of salmonid species. The primary goal of this study was to evaluate the prevalence of N. salmonis in out-migrating juvenile hatchery and wild Chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss from the Snake River in the U.S. Pacific Northwest. To achieve this goal, we first addressed the following concerns about current molecular diagnostic tests for N. salmonis : (1) nonspecific amplification patterns by the published nested polymerase chain reaction (nPCR) test, (2) incomplete validation of the published quantitative PCR (qPCR) test, and (3) whether N. salmonis can be detected reliably from nonlethal samples. Here, we present an optimized nPCR protocol that eliminates nonspecific amplification. During validation of the published qPCR test, our laboratory developed a second qPCR test that targeted a different gene sequence and used different probe chemistry for comparison purposes. We simultaneously evaluated the two different qPCR tests for N. salmonis and found that both assays were highly specific, sensitive, and repeatable. The nPCR and qPCR tests had good overall concordance when DNA samples derived from both apparently healthy and clinically diseased hatchery rainbow trout were tested. Finally, we demonstrated that gill snips were a suitable tissue for nonlethal detection of N. salmonis DNA in juvenile salmonids. Monitoring of juvenile salmonid fish in the Snake River over a 3-year period revealed low prevalence of N. salmonis in hatchery and wild Chinook salmon and wild steelhead but significantly higher prevalence in hatchery-derived steelhead. Routine monitoring of N. salmonis is not performed for all hatchery steelhead populations. At present, the possible contribution of this pathogen to delayed mortality of steelhead has not been determined.

Journal of Aquatic Animal Health↗

USGS2002

The last interglacial period on the Pacific Coast of North America: Timing and paleoclimate

New, high-precision U-series ages of solitary corals ( Balanophyllia elegans ) coupled with molluscan faunal data from marine terraces on the Pacific Coast of North America yield information about the timing and warmth of the last interglacial sea-level highstand. Balanophyllia elegans takes up U in isotopic equilibrium with seawater during growth and shortly after death. Corals from the second terrace on San Clemente Island (offshore southern California), the third terrace on Punta Banda (on the Pacific Coast of northern Baja California), and the Discovery Point Formation on Isla de Guadalupe (in the Pacific Ocean offshore Baja California) date to the peak of the last interglacial period and have U-series ages ranging from ca. 123 to 114 ka. The first terrace on Punta Banda has corals with ages ranging from ca. 83 to 80 ka, which corresponds to a sea-level highstand formed in the late last interglacial period. U-series analyses of corals from the Cayucos terrace (central California) and the Nestor terrace at Point Loma (southern California) show that these fossils have evidence of open-system history, similar to what has been reported by other workers for the same localities. Nevertheless, a model of continuous, secondary U and Th uptake shows that two ages of corals are likely present at these localities, representing the ca. 105 and ca. 120 ka sea-level highstands reported elsewhere. U-series ages of last interglacial corals from the Pacific Coast overlap with, but are on average younger than the ages of corals from Barbados, the Bahamas, and Hawaii. This age difference is explained by the nature of the geomorphic response to sea-level change: fringing or barrier reefs on low-latitude coastlines have an accretionary growth style that keeps pace with rising sea level, whether on a tectonically rising or stable coastline. In contrast, midlatitude, high-energy coastlines are sites of platform cutting during the early part of a sea-level high stand and terrace scouring and concomitant sediment and fossil deposition as sea level starts to recede. The youngest ages of corals from the Pacific Coast suggest that sea level was still relatively high at ca. 116 ka, which is not in agreement with other estimates of relatively large global ice volume at that time. Reliably dated, ca. 120 ka marine-terrace deposits on the Pacific Coast have fossil mollusks that indicate water temperatures as warm or warmer than at present. In contrast, ca. 80 ka marine deposits reported here and elsewhere have fossil mollusks indicating cooler-than-modern water temperatures. The presence of both ca. 105 ka and ca. 120 ka corals on the Nestor and Cayucos terraces explains a previously enigmatic mixture of warm-water and cool-water mollusks. At ca. 105 ka, a relatively high sea level with cool waters may have "captured" the terrace formed during the 120 ka sea-level highstand, in areas of low uplift rate. The inference of cooler-than-modern waters off the Pacific Coast of North America at ca. 80 ka and ca. 105 ka, based on marine-terrace faunas, does not agree with estimates of sea-surface temperatures derived from alkenone studies in the Santa Barbara Basin. However, cooler water temperatures at these times are in agreement with paleo-temperature estimates from planktonic foraminiferal data for the Santa Barbara Basin. All records, from central California to Baja California, whether from marine terraces or offshore cores, indicate at least seasonably warmer-than-modern waters during the peak of the last interglacial period at ca. 120 ka.

Pacific Coast↗

USGS2016

Exploring climate niches of ponderosa pine (Pinus ponderosa Douglas ex Lawson) haplotypes in the western United States: Implications for evolutionary history and conservation

Ponderosa pine ( Pinus ponderosa Douglas ex Lawson) occupies montane environments throughout western North America, where it is both an ecologically and economically important tree species. A recent study using mitochondrial DNA analysis demonstrated substantial genetic variation among ponderosa pine populations in the western U.S., identifying 10 haplotypes with unique evolutionary lineages that generally correspond spatially with distributions of the Pacific ( P . p . var. ponderosa ) and Rocky Mountain ( P . p . var. scopulorum ) varieties. To elucidate the role of climate in shaping the phylogeographic history of ponderosa pine, we used nonparametric multiplicative regression to develop predictive climate niche models for two varieties and 10 haplotypes and to hindcast potential distribution of the varieties during the last glacial maximum (LGM), ~22,000 yr BP. Our climate niche models performed well for the varieties, but haplotype models were constrained in some cases by small datasets and unmeasured microclimate influences. The models suggest strong relationships between genetic lineages and climate. Particularly evident was the role of seasonal precipitation balance in most models, with winter- and summer-dominated precipitation regimes strongly associated with P . p . vars. ponderosa and scopulorum , respectively. Indeed, where present-day climate niches overlap between the varieties, introgression of two haplotypes also occurs along a steep clinal divide in western Montana. Reconstructed climate niches for the LGM suggest potentially suitable climate existed for the Pacific variety in the California Floristic province, the Great Basin, and Arizona highlands, while suitable climate for the Rocky Mountain variety may have existed across the southwestern interior highlands. These findings underscore potentially unique phylogeographic origins of modern ponderosa pine evolutionary lineages, including potential adaptations to Pleistocene climates associated with discrete temporary glacial refugia. Our predictive climate niche models may inform strategies for further genetic research (e.g., sampling design) and conservation that promotes haplotype compatibility with projected changes in future climate.

PLoS ONE↗