Geology topics

John Y. Takekawa

Publications and source records attributed to John Y. Takekawa.

At least 109 records · Page 6Linked to original sources

USGS2014

Mercury in birds of San Francisco Bay-Delta, California: trophic pathways, bioaccumulation, and ecotoxicological risk to avian reproduction

San Francisco Bay Estuary in northern California has a legacy of mercury contamination, which could reduce the health and reproductive success of waterbirds in the estuary. The goal of this study was to use an integrated field and laboratory approach to evaluate the risks of mercury exposure to birds in the estuary. We examined mercury bioaccumulation, and other contaminants of concern, in five waterbird species that depend heavily on San Francisco Bay Estuary for foraging and breeding habitat: American avocets ( Recurvirostra americana ), black-necked stilts ( Himantopus mexicanus ), Forster’s terns ( Sterna forsteri ), Caspian terns ( Hydroprogne caspia ), and surf scoters ( Melanitta perspicillata ). These species have different foraging habitats and diets that represent three distinct foraging guilds within the estuary’s food web. In this report, we provide an integrated synthesis of the primary findings from this study and results are synthesized from 54 peer-reviewed publications generated to date with other unpublished results.

California↗

USGS2014

The critical role of islands for waterbird breeding and foraging habitat in managed ponds of the South Bay Salt Pond Restoration Project, South San Francisco Bay, California

The South Bay Salt Pond Restoration Project aims to restore 50–90 percent of former salt evaporation ponds into tidal marsh in South San Francisco Bay, California. However, large numbers of waterbirds use these ponds annually as nesting and foraging habitat. Islands within ponds are particularly important habitat for nesting, foraging, and roosting waterbirds. To maintain current waterbird populations, the South Bay Salt Pond Restoration Project plans to create new islands within former salt ponds in South San Francisco Bay. In a series of studies, we investigated pond and individual island attributes that are most beneficial to nesting, foraging, and roosting waterbirds.

California↗

USGS2014

Pacific Continental Shelf Environmental Assessment (PaCSEA): aerial seabird and marine mammal surveys off northern California, Oregon, and Washington, 2011-2012

Marine birds and mammals comprise an important community of meso- and upper-trophic-level predators within the northern California Current System (NCCS). The NCCS is located within one of the world’s four major eastern boundary currents and is characterized by an abundant and diverse marine ecosystem fuelled seasonally by wind-driven upwelling which supplies nutrient-rich water to abundant phytoplankton inhabiting the surface euphotic zone. The oceanographic conditions throughout the NCCS fluctuate according to well-described seasonal, inter-annual, and decadal cycles. Such oceanographic variability can influence patterns in the distribution, abundance, and habitat use among marine birds and mammals. Although there are an increasing number of studies documenting distributions and abundances among birds and mammals in various portions of the NCCS, there have been no comprehensive, large-scale, multi-seasonal surveys completed throughout this region since the early 1980s (off northern California; Briggs et al. 1987) and early 1990s (off Oregon and Washington; Bonnell et al. 1992, Briggs et al. 1992, Green et al. 1992). During 2011 and 2012, we completed the Pacific Continental Shelf Environmental Assessment (PaCSEA) which included replicated surveys over the continental shelfslope from shore to the 2000-meter (m) isobath along 32 broad-scale transects from Fort Bragg, California (39° N) through Grays Harbor, Washington (47° N). Additionally, surveys at a finer scale were conducted over the continental shelf within six designated Focal Areas: Fort Bragg, CA; Eureka, CA; Siltcoos Bank, OR; Newport, OR; Nehalem Bank, OR; and Grays Harbor, WA. We completed a total of 26,752 km of standardized, low-elevation aerial survey effort across three bathymetric domains: inner-shelf waters (<100-m depth), outer shelf waters (100 – 200-m depth) and continental slope waters (200 – 2000-m depth). Survey effort was similar among seasons (winter, summer, and fall) and between years and varied according to the three bathymetric domains: 47% (12,646 km) covered the continental slope, 33% (8887 km) covered the inner-shelf (0 – 100-m depth), and 20% (5,219 km) covered the outer-shelf. Overall, we recorded 15,403 sightings of 59,466 individual marine birds (12 families, 54 species). During winter, seven species groupings comprised >90% of the total number of birds counted (19,033) with Common Murres (Uria aalge) representing the majority of individuals counted (70.4% of total). The remaining six most abundant taxa included: Surf/White-winged Scoters (Melanitta perspicillata/M. fusca; 4.8% of total), Herring/Thayer’s Gulls (Larus argentatus/L. thayeri; 3.8% of total), Cassin’s Auklets (Ptychoramphus aleuticus; 3.8% of total), Glaucous-winged Gulls (Larus glaucescens; 3.7% of total), Black-legged Kittiwakes (Rissa tridactyla; 2.0% of total), and Western Gulls (Larus occidentalis; 1.9% of total). During summer, five species comprised >95% of the total number of birds counted (17,063) with the majority comprised of Common Murres (54.1% of total) and Sooty Shearwaters (Puffinus griseus; 34.4% of total). The remaining most abundant three taxa included: Fork-tailed Storm-Petrels (Oceanodroma furcata; 3.3% of total), Western Gulls (2.1% of total), and Leach’s Storm-Petrels (Oceanodroma leucorhoa; 1.1% of total). During fall, nine species comprised >85% of the total number of birds counted (23,376) with the majority comprised of Common Murres (50.0% of total) and Sooty Shearwaters (10.5% of total). The remaining seven taxa included Cassin’s Auklets (5.2% of total), Surf/White-winged Scoters (5.1% of total), Fork-tailed Storm-Petrels (3.8% of total), Red/Red-necked Phalaropes (Phalaropus fulicarius/P. lobatus; 3.2% of total), California Gulls (Larus californicus; 3.1% of total), Northern Fulmars (Fulmarus glacialis; 2.7% of total), and Sabine’s Gulls (Xema sabini; 2.2% of total). Throughout the entire PaCSEA survey area, average densities (± SE) at sea for all marine birds combined were similar between fall (23.7 ± 1.9 birds km -2 ) and winter (24.0 ± 1.9 birds km -2 ) and least during summer (16.3 ± 2.2 birds km -2 ). Marine bird densities at sea varied according to bathymetric domain and season. Throughout the entire PaCSEA study area average densities (± SE) for all marine birds combined were greatest over the inner-shelf domain (<100-m depth) during fall (49.4 ± 5.0 birds km -2 ) and similar during winter (37.4 ± 4.6 birds km -2 ) and summer (37.5 ± 6.4 birds km -2 ). Within the outer-shelf domain (100 – 200-m depth), average densities for all marine birds combined were greatest during winter (34.6 ± 4.2 birds km-2), lesser during fall (16.2 ± 1.7 birds km-2), and least during summer (6.9 ± 1.1 birds km-2). Within the farthest offshore waters over the continental slope domain (200 – 2000-m depth) average densities for all marine birds combined were greatest during fall (10.0 ± 2.2 birds km -2 ) and winter (9.3 ± 1.5 birds km -2 ), and lesser during summer (6.2 ± 1.4 birds km -2 ). We observed 16 cetacean species and five pinniped species. Among the Mysticeti (baleen whales), humpback whales (Megaptera novaeangliae) were most frequently observed (114 sightings of 264 individuals) during summer and fall mostly over the outer-shelf and slope waters, however, individuals were also seen within the Siltcoos, Nehalem, Fort Bragg, and Eureka Focal Areas. We recorded 11 Odontoceti (toothed whale) species. Harbor porpoises (Phocoena phocoena) were the most frequently sighted (164 sightings of 270 individuals). Harbor porpoises were present year-round and most frequently sighted within the inner-shelf domain throughout the entire study area in all seasons. Harbor porpoises occurred in all six Focal Areas, with noteworthy aggregations within the Eureka, Siltcoos, and Grays Harbor Focal Areas. We recorded 246 sightings of 375 individual pinnipeds (5 species). California sea lions (Zalophus californianus) were the most frequently sighted and were present year-round with slightly more sightings recorded during the fall. California sea lions showed a decreasing frequency of sightings and relative abundance with distance from shore across the bathymetric domains surveyed, being most frequently observed over the inner-shelf. Northern elephant seals (Mirounga angustirostris), harbor seals (Phoca vitulina), and northern fur seals (Callorhinus ursinus) were observed occasionally during all seasons with harbor seals occurring nearshore (usually within 10 km of the coast) and northern fur seals almost exclusively beyond the shelf break (> 200-m depth), especially during winter off Oregon and Washington. Northern (Steller’s) sea lions (Eumetopias jubatus) were uncommonly sighted during winter and fall.

California;Oregon;Washington↗

USGS2013

Importance of biogeomorphic and spatial properties in assessing a tidal salt marsh vulnerability to sea-level rise

We evaluated the biogeomorphic processes of a large (309 ha) tidal salt marsh and examined factors that influence its ability to keep pace with relative sea-level rise (SLR). Detailed elevation data from 1995 and 2008 were compared with digital elevation models (DEMs) to assess marsh surface elevation change during this time. Overall, 37 % (113 ha) of the marsh increased in elevation at a rate that exceeded SLR, whereas 63 % (196 ha) of the area did not keep pace with SLR. Of the total area, 55 % (169 ha) subsided during the study period, but subsidence varied spatially across the marsh surface. To determine which biogeomorphic and spatial factors contributed to measured elevation change, we collected soil cores and determined percent and origin of organic matter (OM), particle size, bulk density (BD), and distance to nearest bay edge, levee, and channel. We then used Akaike Information Criterion (AICc) model selection to assess those variables most important to determine measured elevation change. Soil stable isotope compositions were evaluated to assess the source of the OM. The samples had limited percent OM by weight (<5.5 %), with mean bulk densities of 0.58 g cm -3 , indicating that the soils had high mineral content with a relatively low proportion of pore space. The most parsimonious model with the highest AICc weight (0.53) included distance from bay's edge (i.e., lower intertidal) and distance from levee (i.e., upper intertidal). Close proximity to sediment source was the greatest factor in determining whether an area increased in elevation, whereas areas near landward levees experienced subsidence. Our study indicated that the ability of a marsh to keep pace with SLR varied across the surface, and assessing changes in elevation over time provides an alternative method to long-term accretion monitoring. SLR models that do not consider spatial variability of biogeomorphic and accretion processes may not correctly forecast marsh drowning rates, which may be especially true in modified and urbanized estuaries. In light of SLR, improving our understanding of elevation change in these dynamic marsh systems will play a crucial role in forecasting potential impacts to their sustainability and the survival of these ecosystems.

Estuaries and Coasts↗

USGS2013

Relative contribution of lipid sources to eggs of lesser scaup

Studies of how birds mobilize nutrients to eggs have traditionally considered a continuum of possible allocation strategies ranging from income breeding (rely on food sources found on the breeding grounds) to capital breeding (rely on body reserves stored prior to the breeding season). For capital breeding, stored body reserves can be acquired either on or away from the breeding grounds, but it has been difficult to quantify the relative contribution of each, precluding identification of key habitats for acquiring nutrients for clutch formation. During 2006–2009, we explored the importance of spring-staging habitats versus breeding-area habitats for egg-lipid formation in female lesser scaup Aythya affinis using stable carbon (δ 13 C) isotope analyses. Although δ 13 C values for abdominal lipid reserves brought to the breeding grounds overlapped those of local amphipods, we were able to quantify the importance of local plant carbohydrates (seeds of emergent wetland plants) to the production of eggs. We compared the importance of local wetland seeds (overall δ 13 C: −29.1 ± 0.9‰ SD) to combined lipid stores and lipids from local amphipods (overall δ 13 C: −23.8 ± 2.2‰). Local seeds and stored body lipids contributed equally to egg lipid formation across years but we found evidence of annual variation in their relative importance. Wetland seeds contributed 39% (SE = 10%) to egg lipid production, and the importance of this source varied by year (90% CI = 47–75% in 2006, 13–42% in 2007, 29–65% in 2008, and 7–30% in 2009). In contrast to earlier studies that suggest lesser scaup predominantly employ a capital breeding strategy, our results suggest that in some years females may attain half of their energy for clutch formation from foods on the breeding grounds.

Journal of Avian Biology↗

USGS2013

Animal migration and risk of spread of viral infections

The potential contribution of migration towards the spread of disease is as varied as the ecology of the pathogens themselves and their host populations. This chapter outlines multiple examples of viral diseases in animal populations and their mechanisms of viral spread. Many species of insects, mammals, fish, and birds exhibit migratory behavior and have the potential to disperse diseases over long distances. The majority of studies available on viral zoonoses have focused on birds and bats, due to their highly migratory life histories. A number of studies have reported evidence of changes in the timing of animal migrations in response to climate change. The majority indicate an advancement of spring migration, with few or inconclusive results for fall migration. Predicting the combined effects of climate change on migratory patterns of host species and epidemiology of viral pathogens is complex and not fully realistic.

Book chapter↗

USGS2013

Wetland Accretion Rate Model of Ecosystem Resilience (WARMER) and its application to habitat sustainability for endangered species in the San Francisco Estuary

Salt marsh faunas are constrained by specific habitat requirements for marsh elevation relative to sea level and tidal range. As sea level rises, changes in relative elevation of the marsh plain will have differing impacts on the availability of habitat for marsh obligate species. The Wetland Accretion Rate Model for Ecosystem Resilience (WARMER) is a 1-D model of elevation that incorporates both biological and physical processes of vertical marsh accretion. Here, we use WARMER to evaluate changes in marsh surface elevation and the impact of these elevation changes on marsh habitat for specific species of concern. Model results were compared to elevation-based habitat criteria developed for marsh vegetation, the endangered California clapper rail (Rallus longirostris obsoletus), and the endangered salt marsh harvest mouse (Reithrodontomys raviventris) to determine the response of marsh habitat for each species to predicted >1-m sea-level rise by 2100. Feedback between vertical accretion mechanisms and elevation reduced the effect of initial elevation in the modeled scenarios. Elevation decreased nonlinearly with larger changes in elevation during the latter half of the century when the rate of sea-level rise increased. Model scenarios indicated that changes in elevation will degrade habitat quality within salt marshes in the San Francisco Estuary, and degradation will accelerate in the latter half of the century as the rate of sea-level rise accelerates. A sensitivity analysis of the model results showed that inorganic sediment accumulation and the rate of sea-level rise had the greatest influence over salt marsh sustainability.

California↗

USGS2013

Movements of wild ruddy shelducks in the Central Asian Flyway and their spatial relationship to outbreaks of highly pathogenic avian influenza H5N1

Highly pathogenic avian influenza H5N1 remains a serious concern for both poultry and human health. Wild waterfowl are considered to be the reservoir for low pathogenic avian influenza viruses; however, relatively little is known about their movement ecology in regions where HPAI H5N1 outbreaks regularly occur. We studied movements of the ruddy shelduck ( Tadorna ferruginea ), a wild migratory waterfowl species that was infected in the 2005 Qinghai Lake outbreak. We defined their migration with Brownian Bridge utilization distribution models and their breeding and wintering grounds with fixed kernel home ranges. We correlated their movements with HPAI H5N1 outbreaks, poultry density, land cover, and latitude in the Central Asian Flyway. Our Akaike Information Criterion analysis indicated that outbreaks were correlated with land cover, latitude, and poultry density. Although shelduck movements were included in the top two models, they were not a top parameter selected in AICc stepwise regression results. However, timing of outbreaks suggested that outbreaks in the flyway began during the winter in poultry with spillover to wild birds during the spring migration. Thus, studies of the movement ecology of wild birds in areas with persistent HPAI H5N1 outbreaks may contribute to understanding their role in transmission of this disease.

Viruses↗

USGS2013

Flying with the wind: Scale dependency of speed and direction measurements in modelling wind support in avian flight

Background : Understanding how environmental conditions, especially wind, influence birds' flight speeds is a prerequisite for understanding many important aspects of bird flight, including optimal migration strategies, navigation, and compensation for wind drift. Recent developments in tracking technology and the increased availability of data on large-scale weather patterns have made it possible to use path annotation to link the location of animals to environmental conditions such as wind speed and direction. However, there are various measures available for describing not only wind conditions but also the bird's flight direction and ground speed, and it is unclear which is best for determining the amount of wind support (the length of the wind vector in a bird’s flight direction) and the influence of cross-winds (the length of the wind vector perpendicular to a bird’s direction) throughout a bird's journey. Results : We compared relationships between cross-wind, wind support and bird movements, using path annotation derived from two different global weather reanalysis datasets and three different measures of direction and speed calculation for 288 individuals of nine bird species. Wind was a strong predictor of bird ground speed, explaining 10-66% of the variance, depending on species. Models using data from different weather sources gave qualitatively similar results; however, determining flight direction and speed from successive locations, even at short (15 min intervals), was inferior to using instantaneous GPS-based measures of speed and direction. Use of successive location data significantly underestimated the birds' ground and airspeed, and also resulted in mistaken associations between cross-winds, wind support, and their interactive effects, in relation to the birds' onward flight. Conclusions : Wind has strong effects on bird flight, and combining GPS technology with path annotation of weather variables allows us to quantify these effects for understanding flight behaviour. The potentially strong influence of scaling effects must be considered and implemented in developing sampling regimes and data analysis.

Movement Ecology↗

USGS2013

The paradox of extreme high-altitude migration in bar-headed geese Anser indicus

Bar-headed geese are renowned for migratory flights at extremely high altitudes over the world's tallest mountains, the Himalayas, where partial pressure of oxygen is dramatically reduced while flight costs, in terms of rate of oxygen consumption, are greatly increased. Such a mismatch is paradoxical, and it is not clear why geese might fly higher than is absolutely necessary. In addition, direct empirical measurements of high-altitude flight are lacking. We test whether migrating bar-headed geese actually minimize flight altitude and make use of favourable winds to reduce flight costs. By tracking 91 geese, we show that these birds typically travel through the valleys of the Himalayas and not over the summits. We report maximum flight altitudes of 7290 m and 6540 m for southbound and northbound geese, respectively, but with 95 per cent of locations received from less than 5489 m. Geese travelled along a route that was 112 km longer than the great circle (shortest distance) route, with transit ground speeds suggesting that they rarely profited from tailwinds. Bar-headed geese from these eastern populations generally travel only as high as the terrain beneath them dictates and rarely in profitable winds. Nevertheless, their migration represents an enormous challenge in conditions where humans and other mammals are only able to operate at levels well below their sea-level maxima.

Proceedings of the Royal Society B↗

USGS2013

Post-release survival of surf scoters following an oil spill: an experimental approach to evaluating rehabilitation success

Birds are often the most numerous vertebrates damaged and rehabilitated in marine oil spills; however, the efficacy of avian rehabilitation is frequently debated and rarely examined experimentally. We compared survival of three radio-marked treatment groups, oiled, rehabilitated (ORHB), un-oiled, rehabilitated (RHB), and un-oiled, non-rehabilitated (CON), in an experimental approach to examine post-release survival of surf scoters ( Melanitta perspicillata ) following the 2007 M/V Cosco Busan spill in San Francisco Bay. Live encounter-dead recovery modeling indicated that survival differed among treatment groups and over time since release. The survival estimate (±SE) for ORHB was 0.143 ± 0.107 compared to CON (0.498 ± 0.168) and RHB groups (0.772 ± 0.229), suggesting scoters tolerated the rehabilitation process itself well, but oiling resulted in markedly lower survival. Future efforts to understand the physiological effects of oil type and severity on scoters are needed to improve post-release survival of this species.

California↗

USGS2013

American Avocet (Recurvirostra americana)

This large, striking shorebird with long bluish-gray legs, a long recurved bill, and a black-and-white chevron pattern on its back and wings is one of four Avocet species in the world, the only one with distinct breeding and non-breeding plumages -- its grayish-white head and neck feathers become cinnamon in early spring as birds begin to form pairs and migrate to breeding areas.

Book chapter↗

USGS2013

Final report for sea-level rise response modeling for San Francisco Bay estuary tidal marshes

The International Panel on Climate Change has identified coastal ecosystems as areas that will be disproportionally affected by climate change. Current sea-level rise projections range widely with 0.57 to 1.9 meters increase in mea sea level by 2100. The expected accelerated rate of sea-level rise through the 21 st century will put many coastal ecosystems at risk, especially those in topographically low-gradient areas. We assessed marsh accretion and plant community state changes through 2100 at 12 tidal salt marshes around San Francisco Bay estuary with a sea-level rise response model. Detailed ground elevation, vegetation, and water level data were collected at all sites between 2008 and 2011 and used as model inputs. Sediment cores (taken by Callaway and others, 2012) at four sites around San Francisco Bay estuary were used to estimate accretion rates. A modification of the Callaway and others (1996) model, the Wetland Accretion Rate Model for Ecosystem Resilience (WARMER), was utilized to run sea-level rise response models for all sites. With a mean sea level rise of 1.24 m by 2100, WARMER projected that the vast majority, 95.8 percent (1,942 hectares), of marsh area in our study will lose marsh plant communities by 2100 and to transition to a relative elevation range consistent with mudflat habitat. Three marshes were projected to maintain marsh vegetation to 2100, but they only composed 4.2 percent (85 hectares) of the total marsh area surveyed.

California↗

USGS2013

Internal nutrient sources and nutrient distributions in Alviso Pond A3W, California

Within the Alviso Salt Pond complex, California, currently undergoing avian-habitat restoration, pore-water profilers (U.S. Patent 8,051,727 B1) were deployed in triplicate at two contrasting sites in Pond A3W (“Inlet”, near the inflow, and “Deep”, near the middle of the pond; figs. 1 and 2; table 1, note that tables in this report are provided online only as a .xlsx workbook at http://pubs.usgs.gov/of/2013/1128/). Deployments were conducted in 2010 and 2012 during the summer algal-growth season. Specifically, three deployments, each about 7 weeks apart, were undertaken each summer. This study provides the first measurements of the diffusive flux of nutrients across the interface between the pond bed and water column (that is, benthic nutrient flux). These nutrient fluxes are crucial to pond restoration efforts because they typically represent a major (if not the greatest) source of nutrients to the water column in both ponds and other lentic systems. For soluble reactive phosphorus (SRP, the most biologically available form in solution), benthic flux was positive both years (that is, out of the sediment into the water column; table 2), with the exception of the August 2010 deployment, which exhibited nearly negligible but negative flux. Overall, the average SRP flux was significantly greater at Deep (23.9 ± 8.6 micromoles per square meter per hour (µmol-m -2 -h -1 ); all errors shown reflect the 95-percent confidence interval) than Inlet (12.6 ± 4.9 µmol-m -2 -h -1 ). There was much greater temporal variability in SRP flux in the pond than reported for the lower estuary (Topping and others, 2001). For dissolved ammonia, benthic flux was consistently positive on all six sampling trips, and similar to SRP, the fluxes at Deep (258 ± 49 µmol-m -2 -h -1 ) were consistently greater than those at Inlet (28 ± 11 µmol-m -2 -h -1 ). Dissolved ammonia fluxes reported for South San Francisco Bay by Topping and others (2001) fall in between these values. Once again, greater variability for benthic fluxes determined in the pond was observed relative to adjacent South San Francisco Bay. With the near absence of any measurable concentration gradient, dissolved-nitrate fluxes were consistently negligible in the pond. Silica fluxes are often used to represent sediment diagenetic processes that biogeochemically cycle silica (an important algal macronutrient) between biogenic and inorganic phases (Fanning and Pilson, 1974; Emerson and others, 1984). For South San Francisco Bay, those values are consistently positive from core-incubation experiments. In Pond A3W, dissolved-silica fluxes averaged 49 ± 25 µmol-m -2 -h -1 at Inlet and were much higher at Deep (482 ± 370 µmol-m -2 -h -1 ), similar to the spatially variability observed for SRP and dissolved ammonia. An elevated silica flux can stimulate diatom production and subsequent eutrophication effects. Variability in these silica fluxes is consistent with season patterns in pond primary productivity. On the basis of comparisons of dissolved-oxygen flux measurements by profilers and core incubations, it appears that diffusive flux estimates for the sediment in this pond, as one might expected in such benthically productive environments, result in a significant underestimation of true sediment oxygen demand. Therefore, a core incubation experiment was conducted to better quantify the demand. To complement these benthic-flux studies, a diurnal study of nutrient advective flux into and out of the pond was measured during neap and spring tides to provide comparative estimates for allochthonous solute transport (Garret, 2012). Using the two different tides as the probable upper and lower boundaries, we can estimate a range of probable values throughout the year. After converting this advective flux into kg/yr, we can compare it directly to benthic flux estimates for the pond extrapolated over the 2.27 square kilometer (km 2 ) pond surface. Benthic flux of nitrogen species, averaged over all sites and dates, was about 80,000 kilograms per year (kg/yr), well above the adjective flux range of -50 to 1,500 kg/yr. By contrast, the average benthic flux of orthophosphate was about 12,000 kg/yr, well below the advective flux range of 21,500 to 30,000 kg/yr. Initial benthic flux estimates were also made for trace metals, including copper, nickel, iron, and manganese. These analyses indicated that the two sites, Inlet and Deep, have different pore-water profiles, with Inlet exhibiting much higher benthic flux estimates for nickel, iron, and manganese. These initial benthic-flux values reported for macronutrients are particularly impressive in magnitude when one considers that diffusive flux of dissolved solutes based on pore-water profiles provides a conservative determination that may be enhanced by other biogeochemical processes. These enhancement processes (Boudreau and Jorgensen, 2001) include bioturbation, bioirrigation, wind resuspension, and potential groundwater inflows, some of which are captured in core-incubation experiments (Kuwabara and others, 2009). Hence, the values reported herein represent lower bounds to indicate the potential importance of such internal solute sources. The elevated diffusive fluxes for nutrients in the pond relative to the adjacent estuary indicate that vertical nutrient transport between the pond bed and water column is consistently an important (and at times the most important) source of nutrients that stimulate phytoplankton growth in the water column. One might therefore reasonably hypothesize that this benthic transport of biologically reactive solutes (both nutrients and toxicants) represents the most important step at the base of the food web for trophic transfer.

California↗

USGS2013

Niche overlap, threshold food densities, and limits to prey depletion for a diving duck assemblage in an estuarine bay

Planning for marine conservation often requires estimates of the amount of habitat needed to support assemblages of interacting species. During winter in subtidal San Pablo Bay, California, the 3 main diving duck species are lesser scaup Aythya affinis (LESC), greater scaup A. marila (GRSC), and surf scoter Melanitta perspicillata (SUSC), which all feed almost entirely on the bivalve Corbula amurensis . Decreased body mass and fat, increased foraging effort, and major departures of these birds appeared to result from food limitation. Broad overlap in prey size, water depth, and location suggested that the 3 species responded similarly to availability of the same prey. However, an energetics model that accounts for differing body size, locomotor mode, and dive behavior indicated that each species will become limited at different stages of prey depletion in the order SUSC, then GRSC, then LESC. Depending on year, 35 to 66% of the energy in Corbula standing stocks was below estimated threshold densities for profitable foraging. Ectothermic predators, especially flounders and sturgeons, could reduce excess carrying capacity for different duck species by 4 to 10%. A substantial quantity of prey above profitability thresholds was not exploited before most ducks left San Pablo Bay. Such pre-depletion departure has been attributed in other taxa to foraging aggression. However, in these diving ducks that showed no overt aggression, this pattern may result from high costs of locating all adequate prey patches, resulting reliance on existing flocks to find food, and propensity to stay near dense flocks to avoid avian predation. For interacting species assemblages, modeling profitability thresholds can indicate the species most vulnerable to food declines. However, estimates of total habitat needed require better understanding of factors affecting the amount of prey above thresholds that is not depleted before the predators move elsewhere.

Marine Ecology Progress Series↗

USGS2013

Mapping risk of avian influenza transmission at the interface of domestic poultry and wild birds

Emergence of avian influenza viruses with high lethality to humans, such as the currently circulating highly pathogenic A(H5N1) (emerged in 1996) and A(H7N9) cause serious concern for the global economic and public health sectors. Understanding the spatial and temporal interface between wild and domestic populations, from which these viruses emerge, is fundamental to taking action. This information, however, is rarely considered in influenza risk models, partly due to a lack of data. We aim to identify areas of high transmission risk between domestic poultry and wild waterfowl in China, the epicenter of both viruses. Two levels of models were developed: one that predicts hotspots of novel virus emergence between domestic and wild birds, and one that incorporates H5N1 risk factors, for which input data exists. Models were produced at 1 and 30 km spatial resolution, and two temporal seasons. Patterns of risk varied between seasons with higher risk in the northeast, central-east, and western regions of China during spring and summer, and in the central and southeastern regions during winter. Monte-Carlo uncertainty analyses indicated varying levels of model confidence, with lowest errors in the densely populated regions of eastern and southern China. Applications and limitations of the models are discussed within.

Frontiers in Public Health↗

USGS2013

GPS location history data mining and anomalous detection: the scenario of bar-headed geese migration

It is important to discover common movement sequences and uncommon behaviors during the migration of wild birds. In this paper, we propose a new approach to analyze the GPS location history data of migratory birds. The stopover sites are first extracted from the location history data of birds, and their movement sequences are generated automatically. Then, a consistency calculation method is introduced for calculating the movement sequence consistency degrees among the birds. The common movement sequences and uncommon behaviors can be recognized on the basis of consistency. We conducted experiments on the data collected from bar-headed geese captured in the Qinghai Lake region. The experiment results indicate the correctness of our approach.

Book chapter↗

USGS2013

Storm surges and climate change implications for tidal marshes: Insight from the San Francisco Bay Estuary, California, USA

Tidal marshes are dynamic ecosystems, which are influenced by oceanic and freshwater processes and daily changes in sea level. Projected sea-level rise and changes in storm frequency and intensity will affect tidal marshes by altering suspended sediment supply, plant communities, and the inundation duration and depth of the marsh platform. The objective of this research was to evaluate if regional weather conditions resulting in low-pressure storms changed tidal conditions locally within three tidal marshes. We hypothesized that regional storms will increase sea level heights locally, resulting in increased inundation of the tidal marsh platform and plant communities. Using site-level measurements of elevation, plant communities, and water levels, we present results from two storm events in 2010 and 2011 from the San Francisco Bay Estuary (SFBE), California, USA. The January 2010 storm had the lowest recorded sea level pressure in the last 30 years for this region. During the storm episodes, the duration of tidal marsh inundation was 1.8 and 3.1 times greater than average for that time of year, respectively. At peak storm surges, over 65% in 2010 and 93% in 2011 of the plant community was under water. We also discuss the implications of these types of storms and projected sea-level rise on the structure and function of the tidal marshes and how that will impact the hydro-geomorphic processes and marsh biotic communities.

California↗