Mark-recapture estimators assume no loss of marks to provide unbiased estimates of population parameters. We describe a hidden Markov model (HMM) framework that integrates a mark loss model with a Cormack-Jolly-Seber model for survival estimation. Mark loss can be estimated with single-marked animals as long as a sub-sample of animals has a permanent mark. Double-marking provides an estimate of mark loss assuming independence but dependence can be modeled with a permanently marked sub-sample. We use a log-linear approach to include covariates for mark loss and dependence which is more flexible than existing published methods for integrated models. The HMM approach is demonstrated with a dataset of black bears (Ursus americanus) with two ear tags and a subset of which were permanently marked with tattoos. The data were analyzed with and without the tattoo. Dropping the tattoos resulted in estimates of survival that were reduced by 0.005-0.035 due to tag loss dependence that could not be modeled. We also analyzed the data with and without the tattoo using a single tag. By not using.Supplementary materials accompanying this paper appear on-line.

State and federal natural resource management agencies often collect age-structured harvest data. These data represent finite realizations of stochastic demographic and sampling processes and have long been used by biologists to infer population trends. However, different sources of data have been combined in ad hoc ways and these methods usually failed to incorporate sampling error. In this article, we propose a "hidden process" (or state-space) model for estimating abundance, survival, recovery rate, and recruitment from age-at-harvest data that incorporate both demographic and sampling stochasticity. To this end, a likelihood for age-at-harvest data is developed by embedding a population dynamics model within a model for the sampling process. Under this framework, the identification of abundance parameters can be achieved by conducting a joint analysis with an auxiliary data set. We illustrate this approach by conducting a Bayesian analysis of age-at-harvest and mark-recovery data from black bears (Ursus americanus) in Pennsylvania. Using a set of reasonable prior distributions, we demonstrate a substantial increase in precision when posterior summaries of abundance are compared to a bias-corrected Lincoln-Petersen estimator. Because demographic processes link consecutive abundance estimates, we also obtain a more realistic biological picture of annual changes in abundance. Because age-at-harvest data are often readily obtained, we argue that this type of analysis provides a valuable strategy for wildlife population monitoring.

1. Perceived predation risk and the resulting antipredator behaviour varies across space, time and predator identity. Communities with multiple predators that interact and differ in their use of space, time of activity and hunting mode create a complex landscape for prey to avoid predation. Anthropogenic presence and disturbance have the potential to shift interactions among predators and prey and the where and when encounters occur.2. We examined how white-tailed deer Odocoileus virginianus fawn spatiotemporal antipredator behaviour differed along an anthropogenic disturbance gradient that had black bears Ursus americanus, coyotes Canis latrans, bobcats Lynx rufus and humans present.3. We quantified (a) spatial co-occurrence in species distributions, (b) temporal overlap across the diel cycle and (c) spatiotemporal associations between humans, bears, coyotes, bobcats, adult male deer and fawns. We also examined how deer vigilance behaviour changed across the anthropogenic disturbance gradient and survey duration. Anthropogenic disturbance influenced spatiotemporal co-occurrence across multiplescales, often increasing spatiotemporal overlap among species. In general, species' spatial co-occurrence was neutral or positive in anthropogenically disturbed environments. Bears and fawns, coyotes and adult male deer, and bobcats and fawns all had higher temporal overlap in the agriculture-development matrix sites. In addition, factors that influenced deer vigilance (e.g. distance to forest edge and predator relative abundance) in the agriculture-development matrix sites did not in the forest matrix site. 5. By taking into account the different antipredator behaviours that can be detected and the different scales these behaviours might occur, we were able to gain a more comprehensive picture of how humans reduce available niche space for wildlife, creating the neutral and positive spatiotemporal associations between species that studies have been seeing in more disturbed areas.

Since the early 1990s there has been an increase in the number of cases and geographic expansion of severe mange in the black bear (Ursus americanus) population in Pennsylvania. Although there are 3 species of mites associated with mange in bears, Sarcoptes scabiei has been identified as the etiologic agent in these Pennsylvania cases. Historically, S. scabiei-associated mange in bears has been uncommon and sporadic, although it is widespread and relatively common in canid populations. To better understand this recent emergence of sarcoptic mange in bears in Pennsylvania and nearby states, we genetically characterized S. scabiei samples from black bears in the eastern United States. These sequences were compared with newly acquired S. scabiei sequences from wild canids (red fox [Vulpes vulpes] and coyote [Canis latrans]) and a porcupine (Erethizon dorsatum) from Pennsylvania and Kentucky and also existing sequences in GenBank. The internal transcribed spacer (ITS)-2 region and cytochrome c oxidase subunit 1 (cox1) gene were amplified and sequenced. Twenty-four ITS-2 sequences were obtained from mites from bears (n = 16), red fox (n = 5), coyote (n = 2), and a porcupine. The sequences from bear samples were identical to each other or differed only at polymorphic bases, whereas S. scabiei from canids were more variable, but 2 were identical to S. scabiei sequences from bears. Eighteen cox1 sequences obtained from mites from bears represented 6 novel haplotypes. Phylogenetic analysis of cox1 sequences revealed 4 clades: 2 clades of mites of human origin from Panama or Australia, a clade of mites from rabbits from China, and a large unresolved clade that included the remaining S. scabiei sequences from various hosts and regions, including sequences from the bears from the current study. Although the cox1 gene was more variable than the ITS-2, phylogenetic analyses failed to detect any clustering of S. scabiei from eastern U.S. hosts. Rather, sequences from black bears grouped into a large clade that included S. scabiei from numerous hosts from Europe, Asia, Africa, and Australia. Collectively, these data suggest that the increasing number of S. scabiei cases in northeastern black bears is not due to the emergence and expansion of a single parasite strain.

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