Geology topics

John Y. Takekawa

Publications and source records attributed to John Y. Takekawa.

At least 145 records · Page 8Linked to original sources

USGS2010

Uncloaking a cryptic, threatened rail with molecular markers: origins, connectivity and demography of a recently-discovered population

The threatened California Black Rail lives under dense marsh vegetation, is rarely observed, flies weakly and has a highly disjunct distribution. The largest population of rails is found in 8–10 large wetlands in San Francisco Bay (SF Bay), but a population was recently discovered in the foothills of the Sierra Nevada Mountains (Foothills), within a wetland network comprised of over 200 small marshes. Using microsatellite and mitochondrial analyses, our objectives were to determine the origins, connectivity and demography of this recently-discovered population. Analyses of individuals from the Foothills ( n = 31), SF Bay ( n = 31), the Imperial Valley ( n = 6) and the East Coast ( n = 3), combined with rigorous power evaluations, provided valuable insights into past history and current dynamics of the species in Northern California that challenge conventional wisdom about the species. The Foothills and SF Bay populations have diverged strongly from the Imperial Valley population, even more strongly than from individuals of the East Coast subspecies. The data also suggest a historical presence of the species in the Foothills. The SF Bay and Foothills populations had similar estimated effective population size over the areas sampled and appeared linked by a strongly asymmetrical migration pattern, with a greater probability of movement from the Foothills to SF Bay than vice versa. Random mating was inferred in the Foothills, but local substructure among marshes and inbreeding were detected in SF Bay, suggesting different dispersal patterns within each location. The unexpected dimensions of Black Rail demography and population structure suggested by these analyses and their potential importance for management are discussed.

California↗

USGS2010

Movement patterns of Bar-headed Geese Anser indicus during breeding and post-breeding periods at Qinghai Lake, China

The highly pathogenic avian influenza (HPAI) H5N1 outbreak at Qinghai Lake, China, in 2005 caused the death of over 6,000 migratory birds, half of which were Bar-headed Geese Anser indicus . Understanding the movements of this species may inform monitoring of outbreak risks for HPAI viruses; thus, we investigated the movement patterns of 29 Bar-headed Geese at Qinghai Lake, China during 2007 and 2008 by using high resolution GPS satellite telemetry. We described the movements and distribution of marked Bar-headed Geese during the pre-nesting, nesting, and moulting periods. Of 21 Bar-headed Geese with complete transmission records, 3 moved to other areas during the nesting period: 2 to Jianghe wetland (50 km northwest of Qinghai Lake) and 1 to Cuolongka Lake (220 km northwest of Qinghai Lake) during the nesting period. We identified nesting attempts of 7 of the marked geese at Qinghai Lake. Four completed successful nesting attempts according to our rules of judgment for the breeding status, and 2 geese lost broods soon after hatching (hereafter referred to as unsuccessful breeders). Of 18 geese present at Qinghai Lake during the nesting period, 9 (6 non-breeders, 2 successful breeders and 1 unsuccessful breeder) remained at Qinghai Lake during the moulting period; and 9 (5 non-breeders, 4 unsuccessful breeders) left Qinghai Lake for moulting. Kuhai Lake, Donggeicuona Lake, Alake Lake, Zhaling-Eling Lake area and Huangheyuan wetland area were used as moulting sites. Geese that moulted at Qinghai Lake, Cuolongka Lake, Kuhai Lake, Donggeicuona Lake and Alake Lake also moved to Zhaling-Eling Lake area or Huangheyuan wetland area and stayed there for several days prior to autumn migration. Mean home range and core area estimates did not differ significantly by sex, year and between breeders and non-breeders.

Qinghai Lake↗

USGS2010

Victims and vectors: highly pathogenic avian influenza H5N1 and the ecology of wild birds

The emergence of highly pathogenic avian influenza (HPAI) viruses has raised concerns about the role of wild birds in the spread and persistence of the disease. In 2005, an outbreak of the highly pathogenic subtype H5N1 killed more than 6,000 wild waterbirds at Qinghai Lake, China. Outbreaks have continued to periodically occur in wild birds at Qinghai Lake and elsewhere in Central China and Mongolia. This region has few poultry but is a major migration and breeding area for waterbirds in the Central Asian Flyway, although relatively little is known about migratory movements of different species and connectivity of their wetland habitats. The scientific debate has focused on the role of waterbirds in the epidemiology, maintenance and spread of HPAI H5N1: to what extent are they victims affected by the disease, or vectors that have a role in disease transmission? In this review, we summarise the current knowledge of wild bird involvement in the ecology of HPAI H5N1. Specifically, we present details on: (1) origin of HPAI H5N1; (2) waterbirds as LPAI reservoirs and evolution into HPAI; (3) the role of waterbirds in virus spread and persistence; (4) key biogeographic regions of outbreak; and (5) applying an ecological research perspective to studying AIVs in wild waterbirds and their ecosystems.

Avian Biology Research↗

USGS2010

Circumpolar variation in morphological characteristics of Greater White-fronted Geese Anser albifrons

Capsule: Greater White-fronted Geese show significant variation in body size from sampling locations throughout their circumpolar breeding range. Aims: To determine the degree of geographical variation in body size of Greater White-fronted Geese and identify factors contributing to any apparent patterns in variation. Methods: Structural measures of >3000 geese from 16 breeding areas throughout the Holarctic breeding range of the species were compared statistically. Results: Palearctic forms varied clinally, and increased in size from the smallest forms on the Kanin and Taimyr peninsulas in western Eurasia to the largest forms breeding in the Anadyr Lowlands of eastern Chukotka. Clinal variation was less apparent in the Nearctic, as both the smallest form in the Nearctic and the largest form overall (the Tule Goose) were from different breeding areas in Alaska. The Tule Goose was 25% larger than the smallest form. Birds from Greenland (A. a. flavirostris) were the second largest, although only slightly larger than geese from several North American populations. Body size was not correlated with breeding latitude but was positively correlated with temperature on the breeding grounds, breeding habitat, and migration distance. Body mass of Greater White-fronted Geese from all populations remained relatively constant during the period of wing moult. Morphological distinctness of eastern and western Palearctic forms concurs with earlier findings of complete range disjunction. Conclusions: Patterns of morphological variation in Greater White-fronted Geese across the Holarctic can be generally attributed to adaptation to variable breeding environments, migration requirements, and phylo-geographical histories.

Bird Study↗

USGS2010

Measuring sediment accretion in early tidal marsh restoration

Sediment accretion is a critical indicator of initial progress in tidal marsh restoration. However, it is often difficult to measure early deposition rates, because the bottom surface is usually obscured under turbid, tidally-influenced waters. To accurately measure early sediment deposition in marshes, we developed an echosounder system consisting of a specialized acoustic profiler, differential global positioning system unit, and laptop computer mounted on a shallow-draft boat. We conducted a bathymetry at the Tubbs Setback tidal restoration site on San Pablo Bay, California, along north–south transects at 25-m intervals. Horizontal position was recorded within 1 m each second and water depth to 1 cm every 0.05 s. Bottom elevations were adjusted for tidal height with surveyed tide gages. We created detailed bathymetric maps (grid cell size: 12.5 m x 12.5 m) by interpolation with inverse distance weighting. During the third year after restoration, sediment accretion averaged 57.1 ± 1.1 cm and the estimated sediment gain was 132,900 m3. The mean difference between the elevations from the bathymetry system and the 9 sediment pins was 2.0 ± 1.0 cm. The mean difference of the intersection points of east–west and north–south survey transects was 2.1 ± 0.2 cm, which provided a measure of repeatability with changing water levels. Our echosounder system provided accurate and repeatable measurements of sediment accretion of a recently restored tidal wetland, and this system proved to be a viable tool for determining sediment deposition in marshes and assessing early restoration progress.

California↗

USGS2010

Field detection of avian influenza virus in wild birds: evaluation of a portable rRT-PCR system and freeze-dried reagents

Wild birds have been implicated in the spread of highly pathogenic avian influenza (HPAIV) of the H5N1 subtype, prompting surveillance along migratory flyways. Sampling of wild birds is often conducted in remote regions, but results are often delayed because of limited local analytical capabilities, difficulties with sample transportation and permitting, or problems keeping samples cold in the field. In response to these challenges, the performance of a portable real-time, reverse transcriptase-polymerase chain reaction (rRT-PCR) unit (RAPID(Registered), Idaho Technologies, Salt Lake City, UT) that employed lyophilized reagents (Influenza A Target 1 Taqman; ASAY-ASY-0109, Idaho Technologies) was compared to virus isolation combined with real-time RT-PCR conducted in a laboratory. This study included both field and experimental-based sampling. Field samples were collected from migratory shorebirds captured in northern California, while experimental samples were prepared by spiking fecal material with an H6N2 AIV isolate. Results indicated that the portable rRT-PCR unit had equivalent specificity to virus isolation with no false positives, but sensitivity was compromised at low viral titers. Use of portable rRT-PCR with lyophilized reagents may expedite surveillance results, paving the way to a better understanding of wild bird involvement in HPAIV H5N1 transmission.

Journal of Virological Methods↗

USGS2010

Factors influencing the at-sea distribution of Cassin's Auklets (Ptychoramphus aleuticus) that breed in the Channel Islands, California

We used radiotelemetry to evaluate at-sea habitat use by Cassin's Auklets ( Ptychoramphus aleuticus ) that bred at Prince Island, off southern California, from 1999 through 2001. We used logistic regression to compare paired radiotelemetry (presence) with random (pseudo-absence) location-associated habitat variables derived from (1) satellite remote-sensing of sea surface temperature and chlorophyll- a concentration and (2) bathymetry. Compared with random locations within their foraging area and after controlling for distance to colony, odds ratios indicated that Cassin's Auklets with dependent young occurred in relatively shallower, warmer, and chlorophyll-rich water associated with chlorophyll fronts near the insular shelf break. These oceanographic features characterize habitats that support key euphausiid prey (e.g., Thysanoessa spinifera ) and also other krill predators. Radiotelemetry combined with satellite remote-sensing of the ocean provides an alternative to vessel-based surveys for evaluating seabird foraging habitats. In the absence of information on the actual distribution, abundance, and, hence, availability of Zooplankton prey for seabirds, environmental factors can serve as proxies to help elucidate distributional patterns of seabirds at sea.

California↗

USGS2010

Space use and habitat selection of migrant and resident American Avocets in San Francisco Bay

San Francisco Bay is a wintering area for shorebirds, including American Avocets (Recurvirostra americana). Recently, a new resident population of avocets has emerged, presumably because of the development of tidal marshes into salt-evaporation ponds. In habitat restoration now underway, as many as 90% of salt ponds will be restored to tidal marsh. However, it is unknown if wintering and resident avocets coexist and if their requirements for space and habitat differ, necessitating different management for their populations to be maintained during restoration. We captured and radio-marked wintering avocets at a salt pond and a tidal flat to determine their population status (migrant or resident) and examine their space use and habitat selection. Of the radio-marked avocets, 79% were migrants and 21% were residents. At the salt pond, residents' fidelity to their location of capture was higher, and residents moved less than did migrants from the same site. Conversely, on the tidal flat, fidelity of residents to their site of capture was lower, and residents' home ranges were larger than those of migrants from the same site. Habitat selection of migrants and residents differed little; however, capture site influenced habitat selection far more than the birds' status as migrants or residents. Our study suggests that individual avocets have high site fidelity while wintering in San Francisco Bay, although the avocet as a species is plastic in its space use and habitat selection. This plasticity may allow wintering migrant and resident avocets to adapt to habitat change in San Francisco Bay. ?? The Cooper Ornithological Society 2010.

Condor↗

USGS2010

Waterfowl ecology and avian influenza in california: Do host traits inform us about viral occurrence?

We examined whether host traits influenced the occurrence of avian influenza virus (AIV) in Anatidae (ducks, geese, swans) at wintering sites in California's Central Valley. In total, 3487 individuals were sampled at Sacramento National Wildlife Refuge and Conaway Ranch Duck Club during the hunting season of 2007-08. Of the 19 Anatidae species sampled, prevalence was highest in the northern shoveler (5.09%), followed by the ring-necked duck (2.63%), American wigeon (2.57%), bufflehead (2.50%), greater white-fronted goose (2.44%), and cinnamon teal (1.72%). Among host traits, density of lamellae (filtering plates) of dabbling ducks was significantly associated with AIV prevalence and the number of subtypes shed by the host, suggesting that feeding methods may influence exposure to viral particles. ?? 2010 American Association of Avian Pathologists.

Avian Diseases↗

USGS2010

Migration of waterfowl in the east asian flyway and spatial relationship to HPAI H5N1 outbreaks

Poyang Lake is situated within the East Asian Flyway, a migratory corridor for waterfowl that also encompasses Guangdong Province, China, the epicenter of highly pathogenic avian influenza (HPAI) H5N1. The lake is the largest freshwater body in China and a significant congregation site for waterfowl; however, surrounding rice fields and poultry grazing have created an overlap with wild waterbirds, a situation conducive to avian influenza transmission. Reports of HPAI H5N1 in healthy wild ducks at Poyang Lake have raised concerns about the potential of resilient free-ranging birds to disseminate the virus. Yet the role wild ducks play in connecting regions of HPAI H5N1 outbreak in Asia is hindered by a lack of information about their migratory ecology. During 2007-08 we marked wild ducks at Poyang Lake with satellite transmitters to examine the location and timing of spring migration and identify any spatiotemporal relationship with HPAI H5N1 outbreaks. Species included the Eurasian wigeon ( Anas penelope ), northern pintail ( Anas acuta ), common teal ( Anas crecca ), falcated teal ( Anas falcata ), Baikal teal ( Anas formosa ), mallard ( Anas platyrhynchos ), garganey ( Anas querquedula ), and Chinese spotbill ( Anas poecilohyncha ). These wild ducks (excluding the resident mallard and Chinese spotbill ducks) followed the East Asian Flyway along the coast to breeding areas in northern China, eastern Mongolia, and eastern Russia. None migrated west toward Qinghai Lake (site of the largest wild bird epizootic), thus failing to demonstrate any migratory connection to the Central Asian Flyway. A newly developed Brownian bridge spatial analysis indicated that HPAI H5N1 outbreaks reported in the flyway were related to latitude and poultry density but not to the core migration corridor or to wetland habitats. Also, we found a temporal mismatch between timing of outbreaks and wild duck movements. These analyses depend on complete or representative reporting of outbreaks, but by documenting movements of wild waterfowl, we present ecological knowledge that better informs epidemiological investigations seeking to explain and predict the spread of avian influenza viruses. ?? 2010 American Association of Avian Pathologists.

Avian Diseases↗

USGS2010

Sexing California gulls using morphometrics and discriminant function analysis

A discriminant function analysis (DFA) model was developed with DNA sex verification so that external morphology could be used to sex 203 adult California Gulls (Larus californicus) in San Francisco Bay (SFB). The best model was 97% accurate and included head-to-bill length, culmen depth at the gonys, and wing length. Using an iterative process, the model was simplified to a single measurement (head-to-bill length) that still assigned sex correctly 94% of the time. A previous California Gull sex determination model developed for a population in Wyoming was then assessed by fitting SFB California Gull measurement data to the Wyoming model; this new model failed to converge on the same measurements as those originally used by the Wyoming model. Results from the SFB discriminant function model were compared to the Wyoming model results (by using SFB data with the Wyoming model); the SFB model was 7% more accurate for SFB California gulls. The simplified DFA model (head-to-bill length only) provided highly accurate results (94%) and minimized the measurements and time required to accurately sex California Gulls.

Waterbirds↗

USGS2010

Rice production systems and avian influenza: Interactions between mixed-farming systems, poultry and wild birds

Wild waterfowl are the reservoir for avian influenza viruses (AIVs), a family of RNA viruses that may cause mild sickness in waterbirds. Emergence of H5N1, a highly pathogenic avian influenza (HPAI) strain, causing severe disease and mortality in wild birds, poultry and humans, had raised concerns about the role of wild birds in possible transmission of the disease. In this review, the link between rice production systems, poultry production systems, and wild bird ecology is examined to assess the extent to which these interactions could contribute towards the persistence and evolution of HPAI H5N1. The rice (Oryza sativa) and poultry production systems in Asia described, and then migration and movements of wild birds discussed. Mixed farming systems in Asia and wild bird movement and migration patterns create opportunities for the persistence of low pathogenic AIVs in these systems. Nonetheless, there is no evidence of long-term persistence of HPAI viruses (including the H5N1 subtype) in the wild. There are still significant gaps in the understanding of how AIVs circulate in rice systems. A better understanding of persistence of AIVs in rice farms, particularly of poultry origins, is essential in limiting exchange of AIVs between mixed-farming systems, poultry and wild birds.

Waterbirds↗

USGS2010

Spring migration and summer destinations of northern pintails from the coast of southern California

To examine pathways, timing, and destinations during migration in spring, we attached satellite-monitored transmitters (platform transmitting terminals) to 10 northern pintails ( Anas acuta ) during February 2001, at Point Mugu, Ventura County, California. This is a wintering area on the southern coast of California. We obtained locations from five adult males and three adult females every 3rd day through August. Average date of departure from the wintering area was 15 March ( SE = 3 days). We documented extended stopovers of ≥30 days for several northern pintails that could have accommodated nesting attempts (San Joaquin Valley, southwestern Montana, southern Alberta, north-central Nevada) or post-nesting molt (eastern Oregon, south-central Saskatchewan, northern Alaska, central Alberta). Wintering northern pintails from the southern coast of California used a wide range of routes, nesting areas, and schedules during migration in spring, which was consistent with the larger, wintering population in the Central Valley of California. Therefore, conservation of habitat that is targeted at stopover, nesting, and molting areas will benefit survival and management of both wintering populations.

California↗

USGS2010

Mapping elevations of tidal wetland restoration sites in San Francisco Bay: Comparing accuracy of aerial lidar with a singlebeam echosounder

The southern edge of San Francisco Bay is surrounded by former salt evaporation ponds, where tidal flow has been restricted since the mid to late 1890s. These ponds are now the focus of a large wetland restoration project, and accurate measurement of current pond bathymetry and adjacent mud flats has been critical to restoration planning. Aerial light detection and ranging (lidar) has become a tool for mapping surface elevations, but its accuracy had rarely been assessed for wetland habitats. We used a singlebeam echosounder system we developed for surveying shallow wetlands to map submerged pond bathymetry in January of 2004 and compared those results with aerial lidar surveys in two ponds that were dry in May of 2004. From those data sets, we compared elevations for 5164 (Pond E9, 154 ha) and 2628 (Pond E14, 69 ha) echosounder and lidar points within a 0.375-m radius of each other (0.750-m diameter lidar spot size). We found that mean elevations of the lidar points were lower than the echosounder results by 5 ?? 0.1 cm in Pond E9 and 2 ?? 0.2 cm in Pond E14. Only a few points (5% in Pond E9, 2% in Pond E14) differed by more than 20 cm, and some of these values may be explained by residual water in the ponds during the lidar survey or elevation changes that occurred between surveys. Our results suggest that aerial lidar may be a very accurate and rapid way to assess terrain elevations for wetland restoration projects. ?? 2010 Coastal Education and Research Foundation.

Journal of Coastal Research↗

USGS2010

Colony attendance patterns by mated Forster's Terns Sterna forsteri using an automated data-logging receiver system

In order to examine 24-hour colony attendance patterns by mated Forster's Terns Sterna forsteri in South San Francisco Bay, California, during incubation and chick-rearing stages, we radio-marked 10 individuals consisting of five pairs and recorded colony attendance using an automated data-logging receiver system. We calculated and analyzed five variables: the total attendance time by pairs and individuals, the duration of individual attendance bouts, and the duration both members of a pair either overlapped in colony attendance or were both absent from the colony. The percentage of time spent on the colony by at least one individual of a pair was highest during incubation and declined during chick rearing. Overall, male terns spent a greater proportion of time diurnally attending the colony than females. Females spent a greater proportion of time on colony at night, and without these nocturnal records, we would have reported overall female colony attendance rates as being much lower. Despite sex-specific differences in attendance rates, the length of attendance bouts did not differ between the sexes. Simultaneous colony attendance by both members of a pair was high at night, but during the day, pairs infrequently overlapped in their colony attendance and both members were frequently absent. Our datalogging system functioned well, and our data illustrates the importance of collecting 24-hour records when considering attendance rates.

Ardea↗

USGS2010

Potential spread of highly pathogenic avian influenza H5N1 by wildfowl: dispersal ranges and rates determined from large-scale satellite telemetry

1. Migratory birds are major candidates for long-distance dispersal of zoonotic pathogens. In recent years, wildfowl have been suspected of contributing to the rapid geographic spread of the highly pathogenic avian influenza (HPAI) H5N1 virus. Experimental infection studies reveal that some wild ducks, geese and swans shed this virus asymptomatically and hence have the potential to spread it as they move. 2. We evaluate the dispersive potential of HPAI H5N1 viruses by wildfowl through an analysis of the movement range and movement rate of birds monitored by satellite telemetry in relation to the apparent asymptomatic infection duration (AID) measured in experimental studies. We analysed the first large-scale data set of wildfowl movements, including 228 birds from 19 species monitored by satellite telemetry in 2006–2009, over HPAI H5N1 affected regions of Asia, Europe and Africa. 3. Our results indicate that individual migratory wildfowl have the potential to disperse HPAI H5N1 over extensive distances, being able to perform movements of up to 2900 km within timeframes compatible with the duration of asymptomatic infection. 4. However, the likelihood of such virus dispersal over long distances by individual wildfowl is low: we estimate that for an individual migratory bird there are, on average, only 5–15 days per year when infection could result in the dispersal of HPAI H5N1 virus over 500 km. 5. Staging at stopover sites during migration is typically longer than the period of infection and viral shedding, preventing birds from dispersing a virus over several consecutive but interrupted long-distance movements. Intercontinental virus dispersion would therefore probably require relay transmission between a series of successively infected migratory birds. 6. Synthesis and applications . Our results provide a detailed quantitative assessment of the dispersive potential of HPAI H5N1 virus by selected migratory birds. Such dispersive potential rests on the assumption that free-living wildfowl will respond analogously to captive, experimentally-infected birds, and that asymptomatic infection will not alter their movement abilities. Our approach of combining experimental exposure data and telemetry information provides an analytical framework for quantifying the risk of spread of avian-borne diseases.

Journal of Applied Ecology↗

USGS2010

Spatial dynamics of bar-headed geese migration in the context of H5N1

Virulent outbreaks of highly pathogenic avian influenza (HPAI) since 2005 have raised the question about the roles of migratory and wild birds in the transmission of HPAI. Despite increased monitoring, the role of wild waterfowl as the primary source of the highly pathogenic H5N1 has not been clearly established. The impact of outbreaks of HPAI among species of wild birds which are already endangered can nevertheless have devastating consequences for the local and non-local ecology where migratory species are established. Understanding the entangled dynamics of migration and the disease dynamics will be key to prevention and control measures for humans, migratory birds and poultry. Here, we present a spatial dynamic model of seasonal migration derived from first principles and linking the local dynamics during migratory stopovers to the larger scale migratory routes. We discuss the effect of repeated epizootic at specific migratory stopovers for bar-headed geese ( Anser indicus ). We find that repeated deadly outbreaks of H5N1 on stopovers during the autumn migration of bar-headed geese could lead to a larger reduction in the size of the equilibrium bird population compared with that obtained after repeated outbreaks during the spring migration. However, the opposite is true during the first few years of transition to such an equilibrium. The age-maturation process of juvenile birds which are more susceptible to H5N1 reinforces this result.

Journal of the Royal Society Interface↗

USGS2010

Understanding the potential dispersal of HPAI H5N1 virus by migratory wildfowl

We analysed wildfowl movements between 2006-2009, including 228 birds from 19 species, part of a larger international programme (see Figure 1) coordinated by the Food and Agricultural Organisation (FAO) of the United Nations aimed at understanding if there are temporal or spatial relationships between HPAI H5N1 outbreaks and movements of migratory wildfowl, the first large scale data set available for such an analysis.

Argos Forum↗