Summary 1.We considered the impact of an emerging pathogen ( Mycoplasma gallisepticum Edward and Kanarek) on apparent survival, encounter and transition rates in a population of a novel host (the house finch, Carpodacus mexicanus Müller). We used a multistate analysis of mark-encounter data from individually marked birds. Individual birds were categorized to a particular disease 'state'; transition rates among states, conditional on apparent survival, were analogous to rates of new infection and recovery from infection. We hypothesized that M. gallisepticum infection would reduce the apparent survival of infected individuals, and that the magnitude of this reduction would vary as a function of the physiological condition of the host (which was characterized in our analyses by including a demographic and an environmental surrogate as covariates). 2. We found consistent support for the hypothesis that M. gallisepticum infection resulted in lower apparent survival among infected individuals, and that recovery rates (from infected to non-infected) were greater than infection rates in this population. We also found strong evidence indicating that infected individuals were less likely to be encountered than were non-infected individuals. Although we predicted that both sex and temperature (proxies for physiological condition) would explain a significant proportion of the variation in our data, only marginal influences of both factors on apparent survival, encounter and state transition rates were detected. 3. Our analyses identified several factors that may be important to studies of disease in the wild. First, disease state assignment may be uncertain, which can complicate parameter estimation. Secondly, encounter rate for infected individuals in our study was low relative to that for non-infected individuals, reflecting possible behavioural changes in infected individuals. Low encounter rates reduces precision of estimated parameters, especially for multistate models. Finally, our results (and mark-recapture models in general) assume independence among individual birds. However, we are aware that there is a social structuring in house finches (and in general for many bird species). Accounting for such non-independence may be especially important for situations where the state transitions are directly related to the pattern of social contact.

Investigations of disease dynamics in wild animal populations often use estimated prevalence or incidence as a measure of true disease frequency. Such indices, almost always based solely on raw counts of infected and uninfected individuals, are often used as the basis for analysis of temporal and spatial dynamics of diseases. Generally, such studies do not account for potential differences in observer detection probabilities of host individuals stratified by biotic and/or abiotic factors. We demonstrate the potential effects of heterogeneity in state-specific detection probabilities on estimated disease prevalence using mark-recapture data from previous work in a House Finch (Carpodacus mexicanus) and Mycoplasma gallisepticum system. In this system, detection probabilities of uninfected finches were generally higher than infected individuals. We show that the magnitude and seasonal pattern of variation in estimated prevalence, corrected for differences in detection probabilities, differed markedly from uncorrected (apparent) prevalence. When the detection probability of uninfected individuals is higher than infected individuals (as in our study), apparent prevalence is negatively biased, and vice versa. In situations where state-specific detection probabilities strongly interact over time, we show that the magnitude and pattern of apparent prevalence can change dramatically; in such cases, observed variations in prevalence may be completely spurious artifacts of variation in detection probability, rather than changes in underlying disease dynamics. Accounting for differential detection probabilities in estimates of disease frequency removes a potentially confounding factor in studies seeking to identify biotic and/or abiotic drivers of disease dynamics. Given that detection probabilities of different groups of individuals are likely to change temporally and spatially in most field studies, our results underscore the importance of estimating and incorporating detection probabilities in estimated disease prevalence (specifically), and more generally, any ecological index used to estimate some parameter of interest. While a mark-recapture approach makes it possible to estimate detection probabilities, it is not always practical, especially at large scales. We discuss several alternative approaches and categorize the assumptions under which analysis of uncorrected prevalence may be acceptable.

Few studies have evaluated the rate of infection or mode of transmission for wildlife diseases, and the implications of alternative management strategies. We used hunter harvest data from 2002 to 2013 to investigate chronic wasting disease (CWD) infection rate and transmission modes, and address how alternative management approaches affect disease dynamics in a Wisconsin white-tailed deer population. Uncertainty regarding demographic impacts of CWD on cervid populations, human and domestic animal health concerns, and potential economic consequences underscore the need for strategies to control CWD distribution and prevalence. Using maximum-likelihood methods to evaluate alternative multi-state deterministic models of CWD transmission, harvest data strongly supports a frequency-dependent transmission structure with sex-specific infection rates that are two times higher in males than females. As transmissible spongiform encephalopathies are an important and difficult-to-study class of diseases with major economic and ecological implications, our work supports the hypothesis of frequency-dependent transmission in wild deer at a broad spatial scale and indicates that effective harvest management can be implemented to control CWD prevalence. Specifically, we show that harvest focused on the greater-affected sex (males) can result in stable population dynamics and control of CWD within the next 50 years, given the constraints of the model. We also provide a quantitative estimate of geographic disease spread in southern Wisconsin, validating qualitative assessments that CWD spreads relatively slowly. Given increased discovery and distribution of CWD throughout North America, insights from our study are valuable to management agencies and to the general public concerned about the impacts of CWD on white-tailed deer populations.

Summary1. The global growth of wind energy has outpaced our assessment of possible impacts on wildlife. There is a pressing need for studies with pre-and post-construction data to determine whether wind facilities will have detrimental effects on susceptible avian groups such as raptors. 2. A pre-and post-construction study was conducted to determine the impact of a windfarm on the abundance and behaviour of raptors in Wisconsin, USA. Variation in abundance and behaviour was examined both within and among years and relative to selected spatial, temporal and weather covariates. Raptor avoidance rates and indices of collision risk were calculated. 3. Raptor abundance post-construction was reduced by 47% compared to pre-construction levels. Flight behaviour varied by species, but most individuals remained at a distance of at least 100 m from turbines and above the height of the rotor zone. 4. Turkey vultures Cathartes aura and red-tailed hawks Buteo jamaicensis displayed high-risk flight behaviours more often than all other raptor species, but also showed signs of avoidance. Red-tailed hawks were the only raptor species found dead beneath turbines during mortality searches. There were few observed mortalities and corrected mortality estimates were comparable to those from other windfarm studies. 5. Synthesis and applications. The decline in raptor abundance post-construction together with other lines of evidence suggests some displacement from the windfarm project area. While certain species may be at risk, flight behaviour data and mortality estimates indicate that the majority of raptors may not be directly affected by the presence of turbines. The avoidance rates recorded in this study should be used to improve collision risk models, and both current and future windfarms should investigate avoidance behaviour post-construction.

The search for easy‐to‐use indices that substitute for direct estimation of animal density is a common theme in wildlife and conservation science, but one fraught with well‐known perils (Nichols & Conroy, 1996; Yoccoz, Nichols & Boulinier, 2001; Pollock et al., 2002). To establish the utility of an index as a substitute for an estimate of density, one must: (1) demonstrate a functional relationship between the index and density that is invariant over the desired scope of inference; (2) calibrate the functional relationship by obtaining independent measures of the index and the animal density; (3) evaluate the precision of the calibration (Diefenbach et al., 1994). Carbone et al. (2001) argue that the number of camera‐days per photograph is a useful index of density for large, cryptic, forest‐dwelling animals, and proceed to calibrate this index for tigers (Panthera tigris). We agree that a properly calibrated index may be useful for rapid assessments in conservation planning. However, Carbone et al. (2001), who desire to use their index as a substitute for density, do not adequately address the three elements noted above. Thus, we are concerned that others may view their methods as justification for not attempting directly to estimate animal densities, without due regard for the shortcomings of their approach.

Ever since Mycoplasma gallisepticum emerged among house finches in North America, it has been suggested that bird aggregations at feeders are an important cause of the epidemic of mycoplasmal conjunctivitis because diseased birds could deposit droplets of pathogen onto the feeders and thereby promote indirect transmission by fomites. In this paper we bring the first experimental evidence that such transmission (bird-to-feeder-to-bird) does actually take place. House finches infected via this route, however, developed only mild disease and recovered much more rapidly than birds infected from the same source birds but directly into the conjunctiva. While it is certainly probable that house finch aggregations at artificial feeders enhance pathogen transmission, to some degree transmission of M. gallisepticum by fomites may serve to immunize birds against developing more severe infections. Some such birds develop M. gallisepticum antibodies, providing indication of an immune response, although no direct evidence of protection.

The use of controlled, horizontal-transmission experiments provides detailed information on the spread of disease within fixed social groups, which informs our understanding of disease dynamics both in an empirical and theoretical context. For that reason, we characterized in 2002, horizontal transmission of Mycoplasma gallisepticum (MG) in two flocks of 11 wild-caught house finches housed in outdoor aviaries over a 6-mo period. All birds were initially free of MG by a polymerase chain reaction (PCR)-based test, rapid plate agglutination (RPA), and the scoring of physical signs. We inoculated one flock member bilaterally in the palpebral conjunctiva and reintroduced it into its cage. Index birds developed conjunctivitis within 3 to 5 days but died 13 and 20 days postinfection (PI) possibly because of very severe weather. The proportion of birds with physical signs increased gradually, reached 40% at 6 wk PI, and fluctuated around 40% until 21 wk PI. By the time our experiment ended at 24.5 wk PI, 28% of the birds still exhibited physical signs. Across both flocks, 80% of the birds developed unilateral or bilateral conjunctivitis, and several birds relapsed. The appearance of physical signs in new individuals occurred between 10 and 144 days PI (median 41 days PI). Physical signs lasted 1-172 days (median 42 days). Birds that became infected earlier during the experiment developed more severe conjunctivitis, and there was a tendency for birds that developed bilateral conjunctivitis to develop physical signs earlier. Most birds that developed physical signs of MG were also PCR- and RPA-positive, although we detected a single asymptomatic carrier and a single symptomatic false negative. No birds died as a result of secondary MG infection.

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