Population dynamics of tundra swans on the lower Alaska Peninsula

Thesis (M.S.) University of Alaska Fairbanks, 2007This study was initiated in response to concerns regarding apparent declines in abundance and breeding pair density of tundra swans on and adjacent to Izembek National Wildlife Refuge (NWR) on the lower Alaska Peninsula. I conducted an analysis of long-term data (1978-1996) to estimate demographic parameters and assess the relationship between survival probabilities and a number of environmental and ecological factors. Rates of productivity (egg, nest, cygnet survival) and annual rates of apparent adult survival were lower and more variable than previously observed for other swan populations and species. A negative relationship between nesting success and brown bear density indicates that depredation by bears is a primary determinant of tundra swan reproductive success. Changes in apparent survival probability were primarily influenced by high and variable rates of permanent emigration. Because of low rates of production and apparent survival, immigration by swans from other breeding areas may be important for sustaining a breeding population of tundra swans on and adjacent to Izembek NWR.Productivity of tundra swans breeding on the lower Alaska Peninsula -- Age-specific survival of tundra swans along the lower Alaska Peninsula

Detection, prevalence, and transmission of avian hematozoa in waterfowl at the Arctic/sub-Arctic interface: co-infections, viral interactions, and sources of variation

Background The epidemiology of avian hematozoa at high latitudes is still not well understood, particularly in sub-Arctic and Arctic habitats, where information is limited regarding seasonality and range of transmission, co-infection dynamics with parasitic and viral agents, and possible fitness consequences of infection. Such information is important as climate warming may lead to northward expansion of hematozoa with unknown consequences to northern-breeding avian taxa, particularly populations that may be previously unexposed to blood parasites. Methods We used molecular methods to screen blood samples and cloacal/oropharyngeal swabs collected from 1347 ducks of five species during May-August 2010, in interior Alaska, for the presence of hematozoa, Influenza A Virus (IAV), and IAV antibodies. Using models to account for imperfect detection of parasites, we estimated seasonal variation in prevalence of three parasite genera (Haemoproteus, Plasmodium, Leucocytozoon) and investigated how co-infection with parasites and viruses were related to the probability of infection. Results We detected parasites from each hematozoan genus in adult and juvenile ducks of all species sampled. Seasonal patterns in detection and prevalence varied by parasite genus and species, age, and sex of duck hosts. The probabilities of infection for Haemoproteus and Leucocytozoon parasites were strongly positively correlated, but hematozoa infection was not correlated with IAV infection or serostatus. The probability of Haemoproteus infection was negatively related to body condition in juvenile ducks; relationships between Leucocytozoon infection and body condition varied among host species. Conclusions We present prevalence estimates for Haemoproteus, Leucocytozoon, and Plasmodium infections in waterfowl at the interface of the sub-Arctic and Arctic and provide evidence for local transmission of all three parasite genera. Variation in prevalence and molecular detection of hematozoa parasites in wild ducks is influenced by seasonal timing and a number of host traits. A positive correlation in co-infection of Leucocytozoon and Haemoproteus suggests that infection probability by parasites in one or both genera is enhanced by infection with the other, or that encounter rates of hosts and genus-specific vectors are correlated. Using size-adjusted mass as an index of host condition, we did not find evidence for strong deleterious consequences of hematozoa infection in wild ducks.Geological Survey (U.S.) (Wildlife Program of the Ecosystem Mission Area)U.S. Fish and Wildlife ServiceDelta Waterfowl FoundationInstitute for Wetland and Waterfowl ResearchIcahn School of Medicine at Mount Sinai (Center for Research on Influenza Pathogenesis)Center of Excellence for Influenza Research and Surveillance (contracts HHSN272201400008C and HHSN266200700010C

Effects of Industrial and Investigator Disturbance on Arctic-Nesting Geese

Oil and gas development on the Arctic Coastal Plain (ACP) of Alaska, USA may have effects on Arctic-nesting birds. To estimate effects of industrial activity and investigator disturbance on avian productivity, we monitored nests of greater white-fronted geese (Anser albifrons) with digital cameras and periodic nest visits during 2013–2014 at 2 sites on the ACP. A disturbed site was adjacent to human-made infrastructure and industrial clean-up activities initiated at the onset of the study and a control site was \u3e2 km from sources of industrial disturbance. We assessed variation in estimates of incubation constancy, nest survival, and predator behavior relative to site, year, and distance from industrial activity using nest photographs obtained at 1-minute intervals. We compared analysis of hourly nest survival informed by intensive monitoring with cameras to analysis of daily nest survival informed by traditional nest visit data obtained at intervals of 5–7 days to assess how method and time scale of sampling affect ecological inference. Geese in both sites exhibited high levels of nest attendance and initiated incubation breaks less than once per day. Observer-caused incubation breaks associated with nest visits (_x¼37.8 min) were longer than other types of incubation breaks (_x¼8.7 min), demonstrating a differential response by nesting geese to direct human encroachment versus indirect vehicular and aircraft traffic. During both years, geese were absent from nests more frequently in the disturbed (_x¼0.9 breaks/day) than control (_x¼0.6 breaks/day) site, and this break frequency was slightly higher for nests closer to industrial activity. In the year with high rates of depredation, nest survival was positively related to distance from industrial activity and abandoned infrastructure, consistent with predictions of industry-caused effects. This relationship, however, was not evident in the year with reduced predation pressure, likely because of annual variation in arctic fox (Vulpes lagopus) behavior. Analysis of nest survival probability informed by camera data allowed for detection of detailed patterns of variation that were not supported when using only visit data for the same nests. Observer visits were responsible for reductions of 7–35% in nest survival probability, highlighting the importance of minimizing, and controlling for, observer effects in studies of avian productivity. Indirect vehicular and aircraft disturbance posed less risk to nest survival than direct encroachment by observers at nest sites. Therefore, effects of industrial activities on avian productivity in the Arctic can be minimized through practices that limit direct encounters with nests

Inundation, sedimentation, and subsidence creates goose habitat along the Arctic coast of Alaska

The Arctic Coastal Plain of Alaska is characterized by thermokarst lakes and drained lake basins, and the rate of coastal erosion has increased during the last half-century. Portions of the coast are <1 m above sea level for kilometers inland, and are underlain by ice-rich permafrost. Increased storm surges or terrestrial subsidence would therefore expand the area subject to marine inundation. Since 1976, the distribution of molting Black Brant ( Branta bernicla nigricans ) on the Arctic Coastal Plain has shifted from inland freshwater lakes to coastal marshes, such as those occupying the Smith River and Garry Creek estuaries. We hypothesized that the movement of geese from inland lakes was caused by an expansion of high quality goose forage in coastal areas. We examined the recent history of vegetation and geomorphological changes in coastal goose habitat by combining analysis of time series imagery between 1948 and 2010 with soil stratigraphy dated using bomb-curve radiocarbon. Time series of vertical imagery and in situ verification showed permafrost thaw and subsidence of polygonal tundra. Soil stratigraphy and dating within coastal estuaries showed that non-saline vegetation communities were buried by multiple sedimentation episodes between 1948 and 1995, accompanying a shift toward salt-tolerant vegetation. This sedimentation allowed high quality goose forage plants to expand, thus facilitating the shift in goose distribution. Declining sea ice and the increasing rate of terrestrial inundation, sedimentation, and subsidence in coastal estuaries of Alaska may portend a ‘tipping point’ whereby inland areas would be transformed into salt marshes

Normalized Difference Vegetation Index as an Estimator for Abundance and Quality of Avian Herbivore Forage in Arctic Alaska

Tools that can monitor biomass and nutritional quality of forage plants are needed to understand how arctic herbivores may respond to the rapidly changing environment at high latitudes. The Normalized Difference Vegetation Index (NDVI) has been widely used to assess changes in abundance and distribution of terrestrial vegetative communities. However, the efficacy of NDVI to measure seasonal changes in biomass and nutritional quality of forage plants in the Arctic remains largely un-evaluated at landscape and fine-scale levels. We modeled the relationships between NDVI and seasonal changes in aboveground biomass and nitrogen concentration in halophytic graminoids, a key food source for arctic-nesting geese. The model was calibrated based on data collected at one site and validated using data from another site. Effects of spatial scale on model accuracy were determined by comparing model predictions between NDVI derived from moderate resolution (250 × 250 m pixels) satellite data and high resolution (20 cm diameter area) handheld spectrometer data. NDVI derived from the handheld spectrometer was a superior estimator (R2 ≥ 0.67) of seasonal changes in aboveground biomass compared to satellite-derived NDVI (R2 ≤ 0.40). The addition of temperature and precipitation variables to the model for biomass improved fit, but provided minor gains in predictive power beyond that of the NDVI-only model. This model, however, was only a moderately accurate estimator of biomass in an ecologically-similar halophytic graminoid wetland located 100 km away, indicating the necessity for site-specific validation. In contrast to assessments of biomass, satellite-derived NDVI was a better estimator for the timing of peak percent of nitrogen than NDVI derived from the handheld spectrometer. We confirmed that the date when NDVI reached 50% of its seasonal maximum was a reasonable approximation of the period of peak spring vegetative green-up and peak percent nitrogen. This study demonstrates the importance of matching the scale of NDVI measurements to the vegetation properties of biomass and nitrogen phenology

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

<div><p>Birds of the order Anseriformes, commonly referred to as waterfowl, are frequently infected by Haemosporidia of the genera <i>Haemoproteus</i>, <i>Plasmodium</i>, and <i>Leucocytozoon</i> via dipteran vectors. We analyzed nucleotide sequences of the Cytochrome <i>b</i> (Cyt<i>b</i>) 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 Cyt<i>b</i> 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 <i>Haemoproteus</i> Cyt<i>b</i> sequences was lower than was detected for <i>Plasmodium</i> and <i>Leucocytozoon</i> parasites. Although waterfowl are presumed to be infected by only a single species of <i>Leucocytozoon</i>, <i>L</i>. <i>simondi</i>, 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 <i>Haemoproteus</i> and <i>Leucocytozoon</i> 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 <i>Plasmodium</i> haplotypes were identical or closely related to lineages found in other avian orders. Our results suggest a more generalist strategy for <i>Plasmodium</i> parasites infecting North American waterfowl as compared to those of the genera <i>Haemoproteus</i> and <i>Leucocytozoon</i>.</p></div

A point mutation in the polymerase protein PB2 allows a reassortant H9N2 influenza isolate of wild-bird origin to replicate in human cells

© 2016. H9N2 influenza A viruses are on the list of potentially pandemic subtypes. Therefore, it is important to understand how genomic reassortment and genetic polymorphisms affect phenotypes of H9N2 viruses circulating in the wild bird reservoir. A comparative genetic analysis of North American H9N2 isolates of wild bird origin identified a naturally occurring reassortant virus containing gene segments derived from both North American and Eurasian lineage ancestors. The PB2 segment of this virus encodes 10 amino acid changes that distinguish it from other H9 strains circulating in North America. G590S, one of the 10 amino acid substitutions observed, was present in ~12% of H9 viruses worldwide. This mutation combined with R591 has been reported as a marker of pathogenicity for human pandemic 2009 H1N1 viruses. Screening by polymerase reporter assay of all the natural polymorphisms at these two positions identified G590/K591 and S590/K591 as the most active, with the highest polymerase activity recorded for the SK polymorphism. Rescued viruses containing these two polymorphic combinations replicated more efficiently in MDCK cells and they were the only ones tested that were capable of establishing productive infection in NHBE cells. A global analysis of all PB2 sequences identified the K591 signature in six viral HA/NA subtypes isolated from several hosts in seven geographic locations. Interestingly, introducing the K591 mutation into the PB2 of a human-adapted H3N2 virus did not affect its polymerase activity. Our findings demonstrate that a single point mutation in the PB2 of a low pathogenic H9N2 isolate could have a significant effect on viral phenotype and increase its propensity to infect mammals. However, this effect is not universal, warranting caution in interpreting point mutations without considering protein sequence context

Haplotype and nucleotide diversity values (H and π respectively) and their 95% confidence intervals for all haplotypes belonging to each genus of haemosporidian identified in this study.

<p>Haplotype and nucleotide diversity values (H and π respectively) and their 95% confidence intervals for all haplotypes belonging to each genus of haemosporidian identified in this study.</p