Susan A. Shriner

SPATIAL AUTOCORRELATION AND AUTOREGRESSIVE MODELS IN ECOLOGY

Recognition and analysis of spatial autocorrelation has defined a new par- adigm in ecology. Attention to spatial pattern can lead to insights that would have been otherwise overlooked, while ignoring space may lead to false conclusions about ecological relationships. We used Gaussian spatial autoregressive models, fit with widely available software, to examine breeding habitat relationships for three common Neotropical migrant songbirds in the southern Appalachian Mountains of North Carolina and Tennessee, USA. In preliminary models that ignored space, the abundance of all three species was cor- related with both local- and landscape-scale habitat variables. These models were then modified to account for broadscale spatial trend (via trend surface analysis) and fine-scale autocorrelation (via an autoregressive spatial covariance matrix). Residuals from ordinary least squares regression models were autocorrelated, indicating that the assumption of independent errors was violated. In contrast, residuals from autoregressive models showed little spatial pattern, suggesting that these models were appropriate. The magnitude of habitat effects tended to decrease, and the relative importance of different habitat variables shifted when we incorporated broadscale and then fine-scale space into the analysis. The degree to which habitat effects changed when space was added to the models was roughly correlated with the amount of spatial structure in the habitat variables. Spatial pattern in the residuals from ordinary least squares models may result from failure to include or adequately measure autocorrelated habitat variables. In addition, con- tagious processes, such as conspecific attraction, may generate spatial patterns in species abundance that cannot be explained by habitat models. For our study species, spatial patterns in the ordinary least squares residuals suggest that a scale of 500-1000 m would be ap- propriate for investigating possible contagious processes.

TIME-OF-DETECTION METHOD FOR ESTIMATING ABUNDANCE FROM POINT-COUNT SURVEYS

Abstract Point-count surveys are often used to collect data on the abundance and distribution of birds, generally as an index of relative abundance. Valid comparison of these indices assumes that the detection process is comparable over space and time. These restrictive assumptions can be eliminated by estimating detection probabilities directly. We generalize a recently proposed removal model for estimating detection probabilities using a time-of-detection approach, which can account for more sources of variation in point-count data. This method is specifically designed to account for variation in detection probabilities associated with singing rates of birds. Our model accounts for both availability bias and detection bias by modeling the combined probability that a bird sings during the count, and the probability that it is detected given that it sings. The model requires dividing the count into several intervals and recording detections of individual birds in each interval. We develop maximum-likelihood estimators for this approach and provide a full suite of models based on capture-recapture models, including covariate models. We present two examples of this method: one for four species of songbirds surveyed in Great Smoky Mountains National Park using three unequal intervals, and one for the Pearly-eyed Thrasher (Margarops fuscatus) surveyed in Puerto Rico using four equal intervals. Models incorporating individual heterogeneity were selected for all data sets using information-theoretic model-selection techniques. Detection probabilities varied among count-time intervals, which suggests that birds may be responding to observers. We recommend applying this method to surveys with four or more equal intervals to reduce assumptions and to take full advantage of standard capture-recapture software. The time-of-detection approach provides a better understanding of the detection process, especially when singing rates of individual birds affect detection probabilities. Estimación de la Abundancia en Puntos de Conteo Mediante el Método del Tiempo de Detección

When fur and feather occur together: interclass transmission of avian influenza A virus from mammals to birds through common resources.

The potential role of wild mammals in avian influenza A virus (IAV) transmission cycles has received some attention in recent years and cases where birds have transmitted IAV to mammals have been documented. However, the contrasting cycle, wherein a mammal could transmit an avian IAV to birds, has been largely overlooked. We experimentally tested the abilities of two mammalian species to transmit avian IAV to mallards (Anas platyrhynchos) in simulated natural environments. Results suggested that striped skunks (Mephitis mephitis) can successfully transmit avian IAV to mallards through indirect contact with shared resources, as transmission was noted in 1 of 4 of the mallards tested. Cottontail rabbits (Sylvilagus sp.) exhibited a similar pattern, as one of five cottontail rabbits successfully transmitted IAV to a mallard, likely through environmental contamination. For each mammalian species tested, the mallards that became infected were those paired with the individual mammals with the lowest shedding levels but were anecdotally observed to be the most active animals. Mammals associated with and around poultry rearing facilities should be taken into consideration in biosecurity plans.

Geographic approaches to biodiversity conservation: implications of scale and error to landscape planning

This chapter reviews the implications of scale and error effects on conservation design, and provides an overview of geographic-based conservation approaches before examining scale and error effects in detail using data from the work on biodiversity patterns in the southwestern United States. The fundamental datum for any geographic approach is a spatial location for a given species. Although there may be other attributes of species or areas brought along in the datum record, “knowing” where each species occurs on the landscape is the minimum prerequisite needed to characterize biodiversity across some area of interest. There are four broad classes of data types or sources for such information. First, are survey-based data providing spatially explicit empirical observations of species occupancy. A second data type that is often used is that generated by expert judgment, and the third data type is predicted occurrence of species. Spatial interpolation that is based only on the geometry of location records is the simplest form of filling in species occupancy gaps. Data of this type start with empirical observations of species that are then linked geographically with environmental predictors that allow the planner to extrapolate occupancy across a region of interest.

Surveillance for highly pathogenic H5 avian influenza virus in synanthropic wildlife associated with poultry farms during an acute outbreak

In November 2014, a Eurasian strain H5N8 highly pathogenic avian influenza virus was detected in poultry in Canada. Introduced viruses were soon detected in the United States and within six months had spread to 21 states with more than 48 million poultry affected. In an effort to study potential mechanisms of spread of the Eurasian H5 virus, the United States Department of Agriculture coordinated several epidemiologic investigations at poultry farms. As part of those efforts, we sampled synanthropic birds and mammals at five infected and five uninfected poultry farms in northwest Iowa for exposure to avian influenza viruses. Across all farms, we collected 2,627 samples from 648 individual birds and mammals. House mice were the most common mammal species captured while house sparrows, European starlings, rock pigeons, swallows, and American robins were the most commonly captured birds. A single European starling was positive for Eurasian H5 viral RNA and seropositive for antibodies reactive to the Eurasian H5 virus. Two American robins were also seropositive. No mammal species showed evidence of infection. These results indicate synanthropic species merit further scrutiny to better understand potential biosecurity risks. We propose a set of management practices aimed at reducing wildlife incursions.

Impact of body condition on influenza A virus infection dynamics in mallards following a secondary exposure

Migratory waterfowl are often viewed as vehicles for the global spread of influenza A viruses (IAVs), with mallards (Anas platyrhynchos) implicated as particularly important reservoir hosts. The physical demands and energetic costs of migration have been shown to influence birds’ body condition; poorer body condition may suppress immune function and affect the course of IAV infection. Our study evaluated the impact of body condition on immune function and viral shedding dynamics in mallards naturally exposed to an H9 IAV, and then secondarily exposed to an H4N6 IAV. Mallards were divided into three treatment groups of 10 birds per group, with each bird’s body condition manipulated as a function of body weight by restricting food availability to achieve either a -10%, -20%, or control body weight class. We found that mallards exhibit moderate heterosubtypic immunity against an H4N6 IAV infection after an infection from an H9 IAV, and that body condition did not have an impact on shedding dynamics in response to a secondary exposure. Furthermore, body condition did not affect aspects of the innate and adaptive immune system, including the acute phase protein haptoglobin, heterophil/lymphocyte ratios, and antibody production. Contrary to recently proposed hypotheses and some experimental evidence, our data do not support relationships between body condition, infection and immunocompetence following a second exposure to IAV in mallards. Consequently, while annual migration may be a driver in the maintenance and spread of IAVs, the energetic demands of migration may not affect susceptibility in mallards.

Detection of Viruses from Bioaerosols Using Anion Exchange Resin

This protocol demonstrates a customized bioaerosol sampling method for viruses. In this system, anion exchange resin is coupled with liquid impingement-based air sampling devices for efficacious concentration of negatively-charged viruses from bioaerosols. Thus, the resin serves as an additional concentration step in the bioaerosol sampling workflow. Nucleic acid extraction of the viral particles is then performed directly from the anion exchange resin, with the resulting sample suitable for molecular analyses. Further, this protocol describes a custom-built bioaerosol chamber capable of generating virus-laden bioaerosols under a variety of environmental conditions and allowing for continuous monitoring of environmental variables such as temperature, humidity, wind speed, and aerosol mass concentration. The main advantage of using this protocol is increased sensitivity of viral detection, as assessed via direct comparison to an unmodified conventional liquid impinger. Other advantages include the potential to concentrate diverse negatively-charged viruses, the low cost of anion exchange resin (~

Transmission of H6N2 wild bird-origin influenza A virus among multiple bird species in a stacked-cage setting

0.14 per sample), and ease of use. Disadvantages include the inability of this protocol to assess infectivity of resin-adsorbed viral particles, and potentially the need for the optimization of the liquid sampling buffer used within the impinger.

Multiple‐species analysis of point count data: a more parsimonious modelling framework

Live bird markets are common in certain regions of the U.S. and in other regions of the world. We experimentally tested the ability of a wild bird influenza A virus to transmit from index animals to naïve animals at varying animal densities in stacked cages in a simulated live bird market. Two and six mallards, five and twelve quail, and six and nine pheasants were used in the low-density and high-density stacks of cages, respectively. Transmission did not occur in the high-density stack of cages likely due to the short duration and relatively low levels of shedding, a dominance of oral shedding, and the lack of transmission to other mallards in the index cage. In the low-density stack of cages, transmission occurred among all species tested, but not among all birds present. Oral and cloacal shedding was detected in waterfowl but only oral shedding was identified in the gallinaceous birds tested. Overall, transmission was patchy among the stacked cages, thereby suggesting that chance was involved in the deposition of shed virus in key locations (e.g., food or water bowls), which facilitated transmission to some birds.