Geology topics

John Y. Takekawa

Publications and source records attributed to John Y. Takekawa.

At least 181 records · Page 10Linked to original sources

USGS2009

Avian response to early tidal salt marsh restoration at former commercial salt evaporation ponds in San Francisco Bay, California, USA

Restoration of former commercial salt evaporation ponds in the San Francisco Bay estuary is intended to reverse a severe decline (>79%) in tidal salt marshes. San Francisco Bay is a critical migratory stopover site and wintering area for shorebirds and waterfowl, and salt ponds are important high tide roosting and foraging areas. Conservation of past bird abundance is a stated goal of area restoration projects, and early adaptive management will be critical for achieving this objective. However, initial avian response at sites restored to tidal flow may not be indicative of long-term results. For example, winter shorebirds at a 529 ha pond breached in 2002 showed a marked increase in shorebird abundance following breaching. Shorebirds comprised 1% of area totals during 1999-2002 and increased to 46% during 2003-2008. These changes accompanied increased tidal range and sedimentation, but minimal vegetation establishment. Conversely, a fully vegetated, restored 216 ha pond in the same system consistently supported less than 2% of all waterbirds in the region. Early restoration may temporarily increase habitat, but managed ponds will be needed for long-term waterbird abundance within a restored pond-marsh system.

California↗

USGS2009

Integrating terrestrial LiDAR and stereo photogrammetry to map the Tolay lakebed in northern San Francisco Bay

The Tolay Creek Watershed drains approximately 3,520 ha along the northern edge of San Francisco Bay. Surrounded by a mosaic of open space conservation easements and public wildlife areas, it is one of the only watersheds in this urbanized estuary that is protected from its headwaters to the bay. Tolay Lake is a seasonal, spring-fed lake found in the upper watershed that historically extended over 120 ha. Although the lakebed was farmed since the early 1860s, the majority of the lakebed was recently acquired by the Sonoma County Regional Parks Department to restore its natural habitat values. As part of the restoration planning process, we produced a digital elevation model (DEM) of the historic extent of Tolay Lake by integrating terrestrial LiDAR (light detection and ranging) and stereo photogrammetry datasets, and real-time kinematic (RTK) global positioning system (GPS) surveys. We integrated the data, generated a DEM of the lakebed and upland areas, and analyzed errors. The accuracy of the composite DEM was verified using spot elevations obtained from the RTK GPS. Thus, we found that by combining photogrammetry, terrestrial LiDAR, and RTK GPS, we created an accurate baseline elevation map to use in watershed restoration planning and design.

California↗

USGS2009

Sexing California Clapper Rails using morphological measurements

California Clapper Rails (Rallus longirostris obsoletus) have monomorphic plumage, a trait that makes identification of sex difficult without extensive behavioral observation or genetic testing. Using 31 Clapper Rails (22 females, 9 males), caught in south San Francisco Bay, CA, and using easily measurable morphological characteristics, we developed a discriminant function to distinguish sex. We then validated this function on 33 additional rails. Seven morphological measurements were considered, resulting in three which were selected in the discriminate function: culmen length, tarsometatarsus length, and flat wing length. We had no classification errors for the development or testing datasets either with resubstitution or cross-validation procedures. Male California Clapper Rails were 6-22% larger than females for individual morphological traits, and the largest difference was in body mass. Variables in our discriminant function closely match variables developed for sexing Clapper Rails of Gulf Coast populations. However, a universal discriminant function to sex all Clapper Rail subspecies is not likely because of large and inconsistent differences in morphological traits among subspecies.

North American Bird Bander↗

USGS2008

Low prevalence of avian influenza virus in shorebirds on the Pacific coast of North America

The emergence of highly pathogenic avian influenza (HPAI) H5N1 has elevated concerns about wild birds as virus hosts; however, little is known about the ecological and epidemiological factors of transmission by shorebirds. Here we summarize results for 2,773 shorebirds that were live-trapped on the Pacific coast of the United States during 2006-2007 and tested for avian influenza virus using real-time reverse transcriptase-polymerase chain reaction (RT-PCR) and virus isolation. As was the case throughout North America, HPAI H5N1 was not detected in shorebirds during this interval. Contrary to other wild bird groups, most notably waterfowl, the prevalence of even low pathogenicity virus among shorebirds in our study areas in California, Washington, and Alaska was extremely low (0.5%). Virus was detected by RT-PCR from four different species, including, Dunlin (Calidris alpina; N = 3), Western Sandpiper (C. mauri; N = 8), Long-billed Dowitcher (Limnodromus scolopaceus; N = 1), and American Avocet (Recurvirostra americana; N = 1), with the detections in the latter three constituting the first published records for these birds. Based on studies in the eastern United States, we expected, but did not detect (H 1 = 1.6, P = 0.21) elevated avian influenza prevalence among shorebirds during spring migration. Diagnostic tests, which were designed to evaluate testing and sampling methods, indicated poor functioning of traditional virus isolation methods and no improvement in detection likelihood by collecting oropharyngeal swabs in addition to cloacal swab samples for low pathogenicity viruses (Z 1 = 0.7, P = 0.48).

Waterbirds↗

USGS2008

Mercury correlations among six tissues for four waterbird species breeding in San Francisco Bay, California, USA

Despite a large body of research concerning mercury (Hg) in birds, no single tissue has been used consistently to assess Hg exposure, and this has hampered comparisons across studies. We evaluated the relationships of Hg concentrations among tissues in four species of waterbirds (American avocets [Recurvirostra americana], black-necked stilts [Himantopus mexicanus], Caspian terns [Hydroprogne caspia; formerly Sterna caspia], and Forster's terns [Sterna forsteri]) and across three life stages (prebreeding adults, breeding adults, and chicks) in San Francisco Bay, California, USA. Across species and life stages, Hg concentrations (least square mean ?? standard error) were highest in head feathers (6.45 ?? 0.31 ??g/g dry wt) and breast feathers (5.76 ?? 0.28 ??g/g dry wt), followed by kidney (4.54 ?? 0.22 ??g/g dry wt), liver (4.43 ?? 0.21 ??g/g dry wt), blood (3.10 ?? 0.15 ??g/g dry wt), and muscle (1.67 ?? 0.08 ??g/g dry wt). Relative Hg distribution among tissues, however, differed by species and life stage. Mercury concentrations were highly correlated among internal tissues (r 2 ??? 0.89). Conversely, the relationships between Hg in feathers and internal tissues were substantially weaker (r2 ??? 0.42). Regression slopes sometimes differed among species and life stages, indicating that care must be used when predicting Hg concentrations in one tissue based on those in another. However, we found good agreement between predictions made using a general tissue-prediction equation and more specific equations developed for each species and life stage. Finally, our results suggest that blood is an excellent, nonlethal predictor of Hg concentrations in internal tissues but that feathers are relatively poor indicators of Hg concentrations in internal tissues. ?? 2008 SETAC Printed in the USA.

Environmental Toxicology and Chemistry↗

USGS2008

Evidence of infection by H5N2 highly pathogenic avian influenza viruses in healthy wild waterfowl

The potential existence of a wild bird reservoir for highly pathogenic avian influenza (HPAI) has been recently questioned by the spread and the persisting circulation of H5N1 HPAI viruses, responsible for concurrent outbreaks in migratory and domestic birds over Asia, Europe, and Africa. During a large-scale surveillance programme over Eastern Europe, the Middle East, and Africa, we detected avian influenza viruses of H5N2 subtype with a highly pathogenic (HP) viral genotype in healthy birds of two wild waterfowl species sampled in Nigeria. We monitored the survival and regional movements of one of the infected birds through satellite telemetry, providing a rare evidence of a non-lethal natural infection by an HP viral genotype in wild birds. Phylogenetic analysis of the H5N2 viruses revealed close genetic relationships with H5 viruses of low pathogenicity circulating in Eurasian wild and domestic ducks. In addition, genetic analysis did not reveal known gallinaceous poultry adaptive mutations, suggesting that the emergence of HP strains could have taken place in either wild or domestic ducks or in non-gallinaceous species. The presence of coexisting but genetically distinguishable avian influenza viruses with an HP viral genotype in two cohabiting species of wild waterfowl, with evidence of non-lethal infection at least in one species and without evidence of prior extensive circulation of the virus in domestic poultry, suggest that some strains with a potential high pathogenicity for poultry could be maintained in a community of wild waterfowl.

PLoS Pathogens↗

USGS2008

Potential effects of mercury on threatened California black rails

San Francisco Bay (SFB) estuary sediments contain high levels of mercury (Hg), and tidal marsh resident species may be vulnerable to Hg contamination. We examined Hg concentrations in California black rails, a threatened waterbird species that inhabits SFB tidal salt marshes. We captured 127 black rails during the prebreeding and postbreeding seasons and examined the influence of site, sex, and year on Hg, methylmercury (MeHg), and also selenium (Se) concentrations in feathers and blood. Feather Hg concentrations averaged 6.94 ??g/g dry weight (dw) and MeHg and Se concentrations in blood averaged 0.38 and 0.42 ??g/g wet weight (ww). We used Akaike's information criterion model selection process to evaluate the importance of year, site, sex, and age on patterns of MeHg concentrations; sex and year were the most important of these factors. Feather Hg concentrations (dw) were higher in males (8.22 ??g/g) than females (6.63 ??g/g) and higher in adult birds (7.36 ??g/g) than in hatch-year birds (4.61 ??g/g). A substantial portion of SFB black rail populations may be at risk of reproductive effects due to MeHg contamination, as 32-78% of feathers and <10% of blood samples exceeded no observed adverse effect levels. Sea level rise and other anthropogenic threats to endemic tidal marsh species such as black rails may be exacerbated by the presence of MeHg. Further study of population demographics and toxicological effects would further elucidate the effects of MeHg contamination on black rail populations in SFB. ?? 2008 Springer Science+Business Media, LLC.

Archives of Environmental Contamination and Toxico↗

USGS2008

Wintering site fidelity and movement patterns of Western Sandpipers Calidris mauri in the San Francisco Bay estuary

Western Sandpipers Calidris mauri are the most numerous shorebird species in the San Francisco Bay estuary during winter. A sample of 106 Western Sandpipers was captured in mist nets and radio-marked with 1-g transmitters to examine their wintering site fidelity and movements. Differences in distances moved, home range extent and core area size were examined by age, sex, season, site, time of day and tide. All birds remained in the south San Francisco Bay region during winter and exhibited strong site fidelity, with a mean home range of 22.0 km 2 or only 8% of the study area. First-year birds had larger home ranges (26.6 ± 3.6 km 2 ) than adults (17.2 ± 2.5 km 2 ) in winter, but home range sizes of males and females were not significantly different in any period. Home range sizes were similar between seasons, but core areas were smaller in spring (6.3 ± 1.2 km 2 ) than in early (9.6 ± 4.0 km 2 ) or late (11.6 ± 1.6 km 2 ) winter. Movements and home range size were similar for radio-marked birds located during day and night. The high degree of regional and local site fidelity demonstrated that the mixture of natural mud fiats and artificial salt ponds in southern San Francisco Bay provided sufficient resources for large wintering populations of Western Sandpipers.

Ibis↗

USGS2008

Distribution of Xantus' Murrelet Synthliboramphus hypoleucus at sea in the Southern California Bight, 1995-97

We radiomarked 153 Xantus' Murrelets Synthliboramphus hypoleucus captured at sea near Santa Barbara Island (SBI), the largest murrelet colony in the California Channel Islands, USA. We tracked these radiomarked murrelets in the Southern California Bight (SCB) off coastal southern California during the 1995-97 breeding seasons. In 1995 during mild El Niño conditions, the murrelets were distributed in non-upwelling areas. In 1996-97, they were distributed in dense patches, aggregating in cool upwelled waters near the northern Channel Islands or south of San Nicolas Island. Murrelets flew longer distances from SBI to foraging areas in 1997 (x̄= 111 ± 44 km) than in 1996 (x̄= 62 ± 25 km), but the distances they travelled did not differ between months (Apr and May) within years. Mean foraging distances from SBI were similar for ‘incubating’ murrelets (determined on the basis of repeated visits to SBI) and ‘non-incubating’ murrelets during the colony attendance period. We attributed the low return rate of radiomarked murrelets to SBI to the capture and marking of a large proportion of birds that were not actively incubating rather than to any adverse effects of radio attachment. We believe changes in murrelet foraging patterns between the 1970s and 1990s are associated with changes in prey resources in the SCB. Flexibility in the foraging strategies of these murrelets may be related to the highly variable marine environment at the southern end of the California Current Up welling System.

California↗

USGS2008

Survival of postfledging Forster's terns in relation to mercury exposure in San Francisco Bay

We examined factors influencing mercury concentrations in 90 fledgling Forster's terns (Sterna forsteri) and evaluated whether mercury influenced postfledging survival in San Francisco Bay, California. Mercury concentrations (??SE) in chicks 21-29 days old (just before fledging) were 0.33 ?? 0.01 ??g g-1 ww for blood and 6.44 ?? 0.28 ??g g -1 fw for breast feathers. Colony site had an overriding influence on fledgling contamination, however hatching date and age also affected blood, but not feather, mercury concentrations. Blood mercury concentrations decreased by 28% during the 50-day hatching period and increased with chick age by 30% during the last week prior to fledging. Using radio-telemetry, we calculated that cumulative survival during the 35-day postfledging time period was 0.81 ?? 0.09 (SE). Postfledging survival rates increased with size-adjusted mass, and cumulative survival probability was 61% lower for terns with the lowest, compared to the highest, observed masses. Conversely, survival was not influenced by blood mercury concentration, time since fledging, sex, or hatch date. Mercury concentrations in breast feathers of fledglings found dead at nesting colonies also were no different than those in live chicks. Our results indicate that colony site, hatching date, and age influenced mercury concentrations in fledgling Forster's terns, but that mercury did not influence postfledging survival. ?? 2008 Springer Science+Business Media, LLC.

Ecotoxicology↗

USGS2008

Mercury concentrations in blood and feathers of prebreeding Forster's terns in relation to space use of San Francisco Bay, California, USA, habitats

We examined mercury concentrations and space use of prebreeding Forster's terns (Sterna forsteri) in San Francisco Bay, California, USA, to assess factors influencing mercury levels in piscivorous birds. In 2005 and 2006, we collected blood and feathers from 122 Forster's terns and radio-marked and tracked 72 terns to determine locations of dietary mercury uptake. Capture site and capture date were the most important factors explaining variation in blood mercury concentrations (geometric mean ?? standard error: 1.09 ?? 0.89 ??g/g wet wt), followed by sex and year. Accordingly, radiotelemetry data revealed that Forster's terns generally remained near their site of capture and foraged in nearby salt ponds, managed and tidal marshes, and tidal flats. In contrast, capture site and capture date were not important factors explaining variation in feather mercury concentrations, probably because feathers were grown on their wintering grounds several months prior to our sampling. Instead, sex and year were the most important factors explaining mercury concentrations in breast feathers (9.57 ?? 8.23 ??g/g fresh wt), and sex was the most important factor for head feathers (6.94 ?? 7.04 ??g/g fresh wt). Overall, 13 and 22% of prebreeding Forster's terns were estimated to be at high risk for deleterious effects due to mercury concentrations in blood (>3.0 ??g/g wet wt) and feathers (>20.0 ??g/g fresh wt), respectively. Breeding terns are likely to be even more at risk because blood mercury concentrations more than tripled during the 45-d prebreeding time period. These data illustrate the importance of space use and tissue type in interpreting mercury concentrations in birds. ?? 2008 SETAC.

Environmental Toxicology and Chemistry↗

USGS2008

Fecal indicator bacteria and Salmonella in ponds managed as bird habitat, San Francisco Bay, California, USA

Throughout the world, coastal resource managers are encouraging the restoration of previously modified coastal habitats back into wetlands and managed ponds for their ecosystem value. Because many coastal wetlands are adjacent to urban centers and waters used for human recreation, it is important to understand how wildlife can affect water quality. We measured fecal indicator bacteria (FIB) concentrations, presence/absence of Salmonella, bird abundance, and physico-chemical parameters in two coastal, managed ponds and adjacent sloughs for 4 weeks during the summer and winter in 2006. We characterized the microbial water quality in these waters relative to state water-quality standards and examined the relationship between FIB, bird abundance, and physico-chemical parameters. A box model approach was utilized to determine the net source or sink of FIB in the ponds during the study periods. FIB concentrations often exceeded state standards, particularly in the summer, and microbial water quality in the sloughs was generally lower than in ponds during both seasons. Specifically, the inflow of water from the sloughs to the ponds during the summer, more so than waterfowl use, appeared to increase the FIB concentrations in the ponds. The box model results suggested that the ponds served as net wetland sources and sinks for FIB, and high bird abundances in the winter likely contributed to net winter source terms for two of the three FIB in both ponds. Eight serovars of the human pathogen Salmonella were isolated from slough and pond waters, although the source of the pathogen to these wetlands was not identified. Thus, it appeared that factors other than bird abundance were most important in modulating FIB concentrations in these ponds.

Water Research↗

USGS2008

Space use by Forster's Terns breeding in South San Francisco Bay

Parental care behaviors often differ in dimorphic seabirds, leading to sex-specific differences in foraging behaviors. However, few studies have examined sex-specific foraging behaviors in monomorphic seabirds. Using radio-telemetry, we studied Forster's Terns (Sterna forsteri) - a monomorphic and socially monogamous seabird - breeding in the South San Francisco Bay, California. Space use did not differ between males and females. Instead, space use varied by breeding stage and colony affiliation. Forster's Terns were located farthest from the nest during pre-breeding and post-breeding time periods, and closest to the nest during incubation and chick-rearing. Home-range size and core-use areas decreased as the breeding season progressed and were most concentrated in the post-breeding stage. The results of this and other studies indicate that tems, unlike other monomorphic seabirds studied, do not exhibit sex-specific differences in space use.

Waterbirds↗

USGS2008

Breeding stage influences space use of female American avocets in San Francisco Bay, California

Female American Avocets (Recurvirostra americana) were radio-marked (N=15) and tracked in the South San Francisco Bay, California, to determine if space use varied by breeding stage. Visual observations were used to determine breeding stage (pre-incubation, incubation, brood-rearing, post-breeding) of marked avocets. Space use measurements (linear movements, home ranges, core areas, and average distance from nest) varied significantly among breeding stages. Space use was greatest for the post-breeding stage, followed by pre-incubation, incubation, and brood-rearing. Most avocet nests (93%) were located within their pre-incubation core area boundaries, whereas only 36% of nests were within post-breeding core areas. Distance between daily location and future nest sites decreased significantly as the number of days prior to incubation decreased, suggesting that avocets prospected future nest sites several weeks prior to nesting. These data indicate that breeding stage influences space use of female American Avocets and illustrates the importance of delineating breeding stages to better understand space use of avian species.

Waterbirds↗

USGS2008

Gender identification of Caspian Terns using external morphology and discriminant function analysis

Caspian Tern (Sterna caspia) plumage characteristics are sexually monochromatic and gender cannot easily be distinguished in the field without extensive behavioral observations. We assessed sexual size dimorphism and developed a discriminant function to assign gender in Caspian Terns based on external morphology. We collected and measured Caspian Terns in San Francisco Bay, California, and confirmed their gender based on necropsy and genetic analysis. Of the eight morphological measurements we examined, only bill depth at the gonys and head plus bill length differed between males and females with males being larger than females. A discriminant function using both bill depth at the gonys and head plus bill length accurately assigned gender of 83% of terns for which gender was known. We improved the accuracy of our discriminant function to 90% by excluding individuals that had less than a 75% posterior probability of correctly being assigned to gender. Caspian Terns showed little sexual size dimorphism in many morphometries, but our results indicate they can be reliably assigned to gender in the field using two morphological measurements.

Wilson Journal of Ornithology↗

USGS2008

Relation between species assemblages of fishes and water quality in salt ponds and sloughs in South San Francisco Bay

This study was conducted to characterize fishery resources inhabiting salt-evaporation ponds and sloughs in South San Francisco Bay, and to identify key environmental variables that influence distribution of fishes. The ponds, which were originally constructed and operated for commercial production of salt, have undergone preliminary modifications (installation of culverts, gates, and other water-control structures) in preparation for full restoration to mostly tidal wetlands over the next 2 decades. We sampled fish from two salt-pond complexes (Alviso complex and Eden Landing complex), each consisting of several pond systems and their associated sloughs. Cluster analysis of species of fish indicated that at least two species assemblages were present, one characteristic of ponds and the other characteristic of sloughs and slough-like ponds. The slough-like ponds exhibited water-quality conditions (especially salinity) that resembled conditions found in the sloughs. Pond fishes were represented by 12 species, whereas slough fishes were represented by 22 species. Except for bay pipefish (Syngnathus leptorhynchus), which was unique to ponds, all species present in ponds also were in sloughs and slough-like ponds. These results indicated that species of fish in ponds originated from the sloughs. According to canonical-discriminant analysis, four environmental variables were useful for discriminating between the two species assemblages. Most discriminatory power was contributed by the index of habitat connectivity, a measure of minimum distance that a fish must travel to reach a particular pond from the nearest slough. Apparently, as fish from sloughs enter and move through interconnected salt ponds, environmental stress factors increase in severity until only the more tolerant species remain. The most likely source of stress is salinity, because this variable was second in importance to the index of habitat connectivity in discriminating between the two species assemblages. Water temperature and concentration of dissolved oxygen also seemingly influenced spatial distribution of fishes, although they were less important than salinity.

Southwestern Naturalist↗

USGS2008

Dissolved Oxygen in Guadalupe Slough and Pond A3W, South San Francisco Bay, California, August and September 2007

Initial restoration of former salt evaporation ponds under the South Bay Salt Pond Restoration Project in San Francisco Bay included the changing of water-flow patterns and the monitoring of water quality of discharge waters from the ponds. Low dissolved oxygen (DO) concentrations became evident in discharge waters when the ponds first were opened in 2004. This was a concern, because of the potential for low-DO pond discharge to decrease the DO concentrations in the sloughs that receive water from the ponds. However, as of summer 2007, only limited point-measurements of DO concentrations had been made in the receiving sloughs adjacent to the discharge ponds. In this report, we describe two short studies aimed at understanding the natural variability of slough DO and the effect of pond discharge on the DO concentrations in the sloughs. Pond A3W (a discharge pond) and the adjacent Guadalupe Slough were instrumented in August and September 2007 to measure DO, temperature, conductivity, and pH. In addition, Mowry and Newark Sloughs were instrumented during the August study to document DO variability in nearby sloughs that were unaffected by pond discharge. The results showed that natural tidal variability in the slough appeared to dominate and control the slough DO concentrations. Water-quality parameters between Guadalupe Slough and Mowry and Newark Sloughs could not be directly compared because deployment locations were different distances from the bay. Pond-discharge water was identified in Guadalupe Slough using the deployed instruments, but, counter to the previous assumption, the pond discharge, at times, increased DO concentrations in the slough. The effects of altering the volume of pond discharge were overwhelmed by natural spring-neap tidal variability in the slough. This work represents a preliminary investigation by the U.S. Geological Survey of the effects of pond discharge on adjacent sloughs, and the results will be used in designing a comprehensive DO study to determine normal variability for this region.

Open-File Report↗

USGS2008

Duck migration and past influenza A (H5N1) outbreak areas

In 2005 and 2006, the highly pathogenic avian influenza (HPAI) virus subtype H5N1 rapidly spread from Asia through Europe, the Middle East, and Africa. Waterbirds are considered the natural reservoir of low pathogenic avian influenza viruses (1), but their potential role in the spread of HPAI (H5N1), along with legal and illegal poultry and wildlife trade (2), is yet to be clarified.

Emerging Infectious Diseases↗