Joseph P. Fleskes

Avian influenza at both ends of a migratory flyway: characterizing viral genomic diversity to optimize surveillance plans for North America

Although continental populations of avian influenza viruses are genetically distinct, transcontinental reassortment in low pathogenic avian influenza (LPAI) viruses has been detected in migratory birds. Thus, genomic analyses of LPAI viruses could serve as an approach to prioritize species and regions targeted by North American surveillance activities for foreign origin highly pathogenic avian influenza (HPAI). To assess the applicability of this approach, we conducted a phylogenetic and population genetic analysis of 68 viral genomes isolated from the northern pintail (Anas acuta) at opposite ends of the Pacific migratory flyway in North America. We found limited evidence for Asian LPAI lineages on wintering areas used by northern pintails in California in contrast to a higher frequency on breeding locales of Alaska. Our results indicate that the number of Asian LPAI lineages observed in Alaskan northern pintails, and the nucleotide composition of LPAI lineages, is not maintained through fall migration. Accordingly, our data indicate that surveillance of Pacific Flyway northern pintails to detect foreign avian influenza viruses would be most effective in Alaska. North American surveillance plans could be optimized through an analysis of LPAI genomics from species that demonstrate evolutionary linkages with European or Asian lineages and in regions that have overlapping migratory flyways with areas of HPAI outbreaks.

Spatial use by wintering greater white-fronted geese relative to a decade of habitat change in California's central valley

Abstract We investigated the effect of recent habitat changes in Californias Central Valley on wintering Pacific greater white-fronted geese (Anser albifrons frontalis) by comparing roost-to-feed distances, distributions, population range sizes, and habitat use during 1987–1990 and 1998–2000. These habitat changes included wetland restoration and agricultural land enhancement due to the 1990 implementation of the Central Valley Joint Venture, increased land area used for rice (Oryza sativa) production, and the practice of flooding, rather than burning, rice straw residues for decomposition because of burning restrictions enacted in 1991. Using radiotelemetry, we tracked 192 female geese and recorded 4,516 locations. Geese traveled shorter distances between roosting and feeding sites during 1998–2000 (24.2 ± 2.2 km) than during 1987–1990 (32.5 ± 3.4 km); distance traveled tended to decline throughout winter during both decades and varied among watershed basins. Population range size was smaller during 1998–2000 (3,367 km2) than during 1987–1990 (5,145 km2), despite a 2.2-fold increase in the size of the Pacific Flyway population of white-fronted geese during the same time period. The population range size also tended to increase throughout winter during both decades. Feeding and roosting distributions of geese also differed between decades; geese shifted into basins that had the greatest increases in the amount of area in rice production (i.e., American Basin) and out of other basins (i.e., Delta Basin). The use of rice habitat for roosting (1987–1990: 40%, 1998–2000: 54%) and feeding (1987–1990: 57%, 1998–2000: 72%) increased between decades, whereas use of wetlands declined for roosting (1987–1990: 36%, 1998–2000: 31%) and feeding (1987–1990: 22%, 1998–2000: 12%). Within postharvested rice habitats, geese roosted and fed primarily in burned rice fields during 1987–1990 (roost: 43%, feed: 34%), whereas they used flooded rice fields during 1998–2000 (roost: 78%, feed: 64%). Our results suggest that white-fronted geese have altered their spatial use of Californias Central Valley during the past decade in response to changing agricultural practices and the implementation of the Central Valley Joint Venture.

Pintail and mallard survival in California relative to habitat, abundance, and hunting

Abstract The influence of habitat, waterfowl abundance, and hunting on winter survival of waterfowl is not well understood. We studied late August–March survival of 163 after-hatch-year (AHY) and 128 hatch-year (HY) female mallards (Anas platyrhynchos) radiotagged in Sacramento Valley (SACV) and 885 AHY female northern pintails (A. acuta) radiotagged throughout the Central Valley of California, USA, relative to flooded habitat (HAB), January abundance of each species (JMAL or JPIN), hunter-days (HDY), and a hunting pressure index (HPI) that combined these variables. From EARLY (1987–1994) to LATE (1998–2000), HAB increased 39%, JPIN increased 45%, JMAL increased 53%, HDY increased 21%, duck-hunting season increased from 59 days to 100 days, and the female daily bag limit doubled to 2 for mallards but remained 1 for pintails. Survival (± SE) was greater during LATE versus EARLY for pintails radiotagged in each region (SACV: 93.2 ± 2.1% vs. 87.6 ± 3.0%; Suisun Marsh: 86.6 ± 3.2% vs. 77.0 ± 3.7%; San Joaquin Valley: 86.6 ± 3.1% vs. 76.9 ± 4.1%) but not for SACV mallards (AHY: 70.6 ± 7.2% to 74.4 ± 7.7% vs. 80.1 ± 7.2% to 82.8 ± 5.6%; HY: 48.7 ± 9.1% [1999–2000 only] vs. 63.5 ± 8.8% to 67.6 ± 8.0%). Most pintail (72%) and mallard (91%) deaths were from hunting, and lower HPI and higher JPIN or JMAL were associated with reduced mortality. Increased HAB was associated with reduced winter mortality for pintails but not for SACV mallards. Pintail survival rates that we measured were within the range reported for other North American wintering areas, and during LATE were higher than most, even though our study duration was 68–110 days longer. Winter survival rates of SACV mallards were also within the reported range. However, with higher bag limits and longer seasons, mallard survival during LATE was lower than in most other wintering areas, especially during 1999–2000, when high winds on opening weekend resulted in high hunting mortality. Habitat conservation and favorable agriculture practices helped create a Central Valley wintering environment where natural mortality of mallards and pintails was low and survival varied with hunting mortality. We recommend regulations and habitat management that continue to minimize natural mortality while allowing sustainable harvest at a level that helps maintain strong incentive for management of Central Valley waterfowl habitats, including the large portion that is privately owned.

Distribution and movements of female northern pintails radiotagged in San Joaquin Valley, California

To improve understanding of northern pintail (Anas acuta) distribution in central California (CCA), we radiotagged 191 Hatch-Year (HY) and 228 After-Hatch-Year (AHY) female northern pintails during late August-early October, 1991-1993, in the San Joaquin Valley (SJV) and studied their movements through March each year. Nearly all (94.3%) wintered in CCA, but 5.7% went to southern California, Mexico, or unknown areas; all that went south left before hunting season. Of the 395 radiotagged pintails that wintered in CCA, 83% flew from the SJV north to other CCA areas (i.e., Sacramento Valley [SACV], Sacramento-San Joaquin River Delta [Delta], Suisun Marsh, San Francisco Bay) during September-January; most went during December. Movements coincided with start of hunting seasons and were related to pintail age, mass, capture location, study year, and weather. Among pintails with less than average mass, AHY individuals tended to leave the SJV earlier than HY individuals. Weekly distribution was similar among capture locations and years but a greater percentage of pintails radiotagged in Tulare Basin (south part of SJV) were known to have (10.3% vs. 0.9%) or probably (13.8% vs. 4.6%) wintered south of CCA than pintails radiotagged in northern SJV areas (i.e., Grassland Ecological Area [EA] and Mendota Wildlife Area [WA]). Also, a greater percentage of SJV pintails went to other CCA areas before hunting season in the drought year of 1991-1992 than later years (10% vs. 3-5%). The percent of radiotagged pintails from Grassland EA known to have gone south of CCA also was greater during 1991-1992 than later years (2% vs. 0%), but both the known (19% vs. 4%) and probable (23% vs. 12%) percent from Tulare Basin that went south was greatest during 1993-1994, when availability of flooded fields there was lowest. The probability of pintails leaving the SJV was 57% (95% CI = 8-127%) greater on days with than without rain, and more movements per bird out of SJV occurred in years with more rain and fog but fewer days with southerly winds. Movements by pintails and changes in pintail distributions, direct recovery distributions, and harvest rates suggest the disproportionate decline of pintails in Tulare Basin was due to a lower percentage of pintails moving there in fall and a greater percentage or earlier movements north and south out of Tulare Basin. With fewer in Tulare Basin to replace Grasslands EA pintails going north in December, pintail abundance in the northern SJV declined during late winter. Changes in movement patterns correspond to habitat loss in Tulare Basin and increased habitats in SACV and western mainland Mexico. Habitat improvements, especially in Tulare Basin, that increase food, sanctuary, and winter survival would probably help restore pintails throughout the SJV.

Breeding-Season Sympatry Facilitates Genetic Exchange Among Allopatric Wintering Populations of Northern Pintails in Japan and California

Abstract. The global redistribution of pathogens, such as highly pathogenic avian influenza, has renewed interest in the connectivity of continental populations of birds. Populations of the Northern Pintail (Anas acuta) wintering in Japan and California are considered separate from a management perspective. We used data from band recoveries and population genetics to assess the degree of biological independence of these wintering populations. Distributions of recoveries in Russia of Northern Pintails originally banded during winter in North America overlapped with distributions of Northern Pintails banded during winter in Japan. Thus these allopatric wintering populations are partially sympatric during the breeding season. The primary areas of overlap were along the Chukotka and Kamchatka peninsulas in Russia. Furthermore, band recoveries demonstrated dispersal of individuals between wintering populations both from North America to Japan and vice versa. Genetic analyses of samples from both wintering populations showed little evidence of population differentiation. The combination of banding and genetic markers demonstrates that these two continental populations are linked by low levels of dispersal as well as likely interbreeding in eastern Russia. Although the levels of dispersal are inconsequential for population dynamics, the combination of dispersal and interbreeding represents a viable pathway for exchange of genes, diseases, and/or parasites.

Presence of avian influenza viruses in waterfowl and wetlands during summer 2010 in California: are resident birds a potential reservoir?

Although wild waterfowl are the main reservoir for low pathogenic avian influenza viruses (LPAIv), the environment plays a critical role for the circulation and persistence of AIv. LPAIv may persist for extended periods in cold environments, suggesting that waterfowl breeding areas in the northern hemisphere may be an important reservoir for AIv in contrast to the warmer southern wintering areas. We evaluated whether southern wetlands, with relatively small populations (thousands) of resident waterfowl, maintain AIv in the summer, prior to the arrival of millions of migratory birds. We collected water and fecal samples at ten wetlands in two regions (Yolo Bypass and Sacramento Valley) of the California Central Valley during three bi-weekly intervals beginning in late July, 2010. We detected AIv in 29/367 fecal samples (7.9%) and 12/597 water samples (2.0%) by matrix real time Reverse Transcription Polymerase Chain Reaction (rRT-PCR). We isolated two H3N8, two H2N3, and one H4N8 among rRT-PCR positive fecal samples but no live virus from water samples. Detection of AIv RNA in fecal samples was higher from wetlands in the Sacramento Valley (11.9%) than in the Yolo Bypass (0.0%), but no difference was found for water samples (2.7 vs. 1.7%, respectively). Our study showed that low densities of hosts and unfavorable environmental conditions did not prevent LPAIv circulation during summer in California wetlands. Our findings justify further investigations to understand AIv dynamics in resident waterfowl populations, compare AIv subtypes between migratory and resident waterfowl, and assess the importance of local AIv as a source of infection for migratory birds.

Survival of adult female northern pintails in Sacramento Valley, California

North American populations of northern pintails (Anas acuta) declined between 1979 and the early 1990s. To determine if low survival during winter contributed to declines, we estimated winter (last week of Aug-Feb 1987-90) survival for 190 adult (after hatching yr [AHY]) female radio-tagged pintails in late summer in Sacramento Valley (SACV), California. Survival rates did not vary by winter (P = 0.808), among preseason, hunting season, or postseason intervals (P = 0.579), or by body mass at time of capture (P = 0.127). Premolt (wing) pintails (n = 10) tended to survive at a lower rate (0.622, SE = 0.178) than pintails that had already replaced flight feathers (0.887, SE = 0.030) (P = 0.091). The pooled survival (all years) estimate for the 180-day winter was 0.874 (SE = 0.031). Hunting mortality rate (0.041-0.087) and nonhunting mortality rate (0.013-0.076) did not differ among years (P = 0.332) or within years (all P > 0.149). Legal hunting (n = 7), predation (n = 4), cholera (n = 2), illegal shooting (n = 2), botulism (n = 1), and unknown cause (n = 1) accounted for all mortality. Nonwintering survival (annu. survival/winter survival = 0.748) was lower than winter survival; thus, if gains in annual survival are desired for this population, managers should first examine the breeding-migration period for opportunities to achieve increases.

Mapping wintering waterfowl distributions using weather surveillance radar.

The current network of weather surveillance radars within the United States readily detects flying birds and has proven to be a useful remote-sensing tool for ornithological study. Radar reflectivity measures serve as an index to bird density and have been used to quantitatively map landbird distributions during migratory stopover by sampling birds aloft at the onset of nocturnal migratory flights. Our objective was to further develop and validate a similar approach for mapping wintering waterfowl distributions using weather surveillance radar observations at the onset of evening flights. We evaluated data from the Sacramento, CA radar (KDAX) during winters 1998–1999 and 1999–2000. We determined an optimal sampling time by evaluating the accuracy and precision of radar observations at different times during the onset of evening flight relative to observed diurnal distributions of radio-marked birds on the ground. The mean time of evening flight initiation occurred 23 min after sunset with the strongest correlations between reflectivity and waterfowl density on the ground occurring almost immediately after flight initiation. Radar measures became more spatially homogeneous as evening flight progressed because birds dispersed from their departure locations. Radars effectively detected birds to a mean maximum range of 83 km during the first 20 min of evening flight. Using a sun elevation angle of −5° (28 min after sunset) as our optimal sampling time, we validated our approach using KDAX data and additional data from the Beale Air Force Base, CA (KBBX) radar during winter 1998–1999. Bias-adjusted radar reflectivity of waterfowl aloft was positively related to the observed diurnal density of radio-marked waterfowl locations on the ground. Thus, weather radars provide accurate measures of relative wintering waterfowl density that can be used to comprehensively map their distributions over large spatial extents.

Spring migration of Northern Pintails from Texas and New Mexico, USA

Abstract We used satellite transmitters (platform transmitting terminals or PTTs) during 2002 and 2003 to document spring migration timing, routes, stopover sites, and nesting sites of adult female Northern Pintails (Anas acuta) from major wintering areas of the Gulf Coast (N = 20) and Playa Lakes Regions (PLR, N = 20) in Texas, and the Middle Rio Grande Valley, New Mexico (MRGV, N = 15). Some Pintails tagged in the MRGV continued movements into Mexico. Poor winter survival or PTT failure reduced sample size to 15 for PLR Pintails, 5 for Gulf Coast Pintails, and 11 for MRGV Pintails. Apparent winter survival was 66% lower for Texas Gulf Coast PTT-tagged Pintails than for those from the PLR and MRGV. Pintails from each area used different routes to their respective breeding grounds. PTT-tagged Pintails from the MRGV followed the Rio Grande Valley north to southern Colorado, before traveling on to the Dakotas and Canada or traveled northeast and joined the migration of PLR Pintails in Texas or Kansas. The latter made initial stops in Kansas, Nebraska, Colorado, or the Dakotas. Gulf Coast Pintails traveled through north-central Oklahoma or central Kansas. Pintails that had stopped first in Kansas or Nebraska tended to settle to nest in the United States. Wetland availability in the Prairie Pothole Region of the Northern Great Plains influenced nesting destinations of PTT-tagged Pintails, but individuals settled across a wide swath of northern North America. We did not detect any consistently-used spring staging areas. Therefore, negative impacts to any of the marked populations, or their wetland habitats, may have continental implications.

Genetic Diversity and Host Specificity Varies across Three Genera of Blood Parasites in Ducks of the Pacific Americas Flyway

Birds of the order Anseriformes, commonly referred to as waterfowl, are frequently infected by Haemosporidia of the genera Haemoproteus, Plasmodium, and Leucocytozoon via dipteran vectors. We analyzed nucleotide sequences of the Cytochrome b (Cytb) gene from parasites of these genera detected in six species of ducks from Alaska and California, USA to characterize the genetic diversity of Haemosporidia infecting waterfowl at two ends of the Pacific Americas Flyway. In addition, parasite Cytb sequences were compared to those available on a public database to investigate specificity of genetic lineages to hosts of the order Anseriformes. Haplotype and nucleotide diversity of Haemoproteus Cytb sequences was lower than was detected for Plasmodium and Leucocytozoon parasites. Although waterfowl are presumed to be infected by only a single species of Leucocytozoon, L. simondi, diversity indices were highest for haplotypes from this genus and sequences formed five distinct clades separated by genetic distances of 4.9%–7.6%, suggesting potential cryptic speciation. All Haemoproteus and Leucocytozoon haplotypes derived from waterfowl samples formed monophyletic clades in phylogenetic analyses and were unique to the order Anseriformes with few exceptions. In contrast, waterfowl-origin Plasmodium haplotypes were identical or closely related to lineages found in other avian orders. Our results suggest a more generalist strategy for Plasmodium parasites infecting North American waterfowl as compared to those of the genera Haemoproteus and Leucocytozoon.