Integrated modeling of bilateral photo-identification data in mark-recapture analyses.

When natural marks provide sufficient resolution to identify individual animals, noninvasive sampling using cameras has a number of distinct advantages relative to "traditional" mark-recapture methods. However, analyses from photo-identification records often pose additional challenges. For example, it is often unclear how to link left- and right-side photos to the same individual, and previous studies have primarily used data from just one side for statistical inference. Here we describe how a recently developed statistical method can be adapted for integrated mark-recapture analyses using bilateral photo-identification records. The approach works by assuming that the true encounter history for each animal is a latent (unobserved) realization from a multinomial distribution. Based on the type of photo encounter (e.g., right, left, or both sides), the recorded (observed) encounter histories can only arise from certain combinations of these latent histories. In this manner, the approach properly accounts for uncertainty about the true number of distinct animals observed in the study. Using a Markov chain Monte Carlo sampling procedure, we conduct a small simulation study to show that this approach has reasonable properties and outperforms other methods. We further illustrate our approach by estimating population size from bobcat photo-identification records. Although motivated by bilateral photo-identification records, we note that the proposed methodology can be used to combine and jointly analyze other types of mark-recapture data (e.g., photo and DNA records).

Gene flow and pathogen transmission among bobcats (Lynx rufus) in a fragmented urban landscape.

Urbanization can result in the fragmentation of once contiguous natural landscapes into a patchy habitat interspersed within a growing urban matrix. Animals living in fragmented landscapes often have reduced movement among habitat patches because of avoidance of intervening human development, which potentially leads to both reduced gene flow and pathogen transmission between patches. Mammalian carnivores with large home ranges, such as bobcats (Lynx rufus), may be particularly sensitive to habitat fragmentation. We performed genetic analyses on bobcats and their directly transmitted viral pathogen, feline immunodeficiency virus (FIV), to investigate the effects of urbanization on bobcat movement. We predicted that urban development, including major freeways, would limit bobcat movement and result in genetically structured host and pathogen populations. We analysed molecular markers from 106 bobcats and 19 FIV isolates from seropositive animals in urban southern California. Our findings indicate that reduced gene flow between two primary habitat patches has resulted in genetically distinct bobcat subpopulations separated by urban development including a major highway. However, the distribution of genetic diversity among FIV isolates determined through phylogenetic analyses indicates that pathogen genotypes are less spatially structured-exhibiting a more even distribution between habitat fragments. We conclude that the types of movement and contact sufficient for disease transmission occur with enough frequency to preclude structuring among the viral population, but that the bobcat population is structured owing to low levels of effective bobcat migration resulting in gene flow. We illustrate the utility in using multiple molecular markers that differentially detect movement and gene flow between subpopulations when assessing connectivity.

Sex-specific effects of reproductive season on bobcat space use, movement, and resource selection in the Appalachian Mountains of Virginia.

Across taxa, sex-specific demands vary temporally in accordance with reproductive investments. In solitary carnivores, females must provision and protect young independently while meeting increased energetic demands. Males seek to monopolize access to females by maintaining large territories and defending them from other males. For many species, it is poorly understood how these demands relate to broad-scale animal movements. To investigate predictions surrounding the reproductive strategies of solitary carnivores and effects of local conditions on bobcat (Lynx rufus) spatial ecology, we examined the effects of sex and reproductive season on home range size, movement rate, and resource selection of bobcats in the central Appalachian Mountains. Male seasonal home ranges were approximately 3 times larger than those of females (33.9 ± 2.6 vs. 12.1 ± 2.4 km2, x±SE), and male movement rates were 1.4 times greater than females (212.6 ± 3.6 vs. 155 ± 8.2 m/hr), likely reflecting male efforts to maximize access to females. Both sexes appear to maintain relatively stable seasonal home ranges despite temporally varying reproductive investments, instead adjusting movements within home ranges. Males increased movements during the dispersal period, potentially reflecting increased territoriality prior to breeding. Females increased movements during the kitten-rearing period, when foraging more intensively, and frequently returning to den sites. Both sexes selected home ranges at higher elevations. However, females selected deciduous forest and avoided fields, whereas males selected fields and avoided deciduous forest, perhaps explained by male pressure to access multiple females across several mountain ridges and higher risk tolerance. Seasonal changes in home range selection likely reflect changes in home range shape. Increased female avoidance of fields during kitten rearing may indicate female avoidance of presumably resource rich, yet risky, fields at the time when kittens are most vulnerable. Our results indicate that while reproductive chronology influences the spatial ecology of solitary carnivores, effects may be constrained by territoriality.

Mark-recapture and mark-resight methods for estimating abundance with remote cameras: a carnivore case study.

Abundance estimation of carnivore populations is difficult and has prompted the use of non-invasive detection methods, such as remotely-triggered cameras, to collect data. To analyze photo data, studies focusing on carnivores with unique pelage patterns have utilized a mark-recapture framework and studies of carnivores without unique pelage patterns have used a mark-resight framework. We compared mark-resight and mark-recapture estimation methods to estimate bobcat (Lynx rufus) population sizes, which motivated the development of a new "hybrid" mark-resight model as an alternative to traditional methods. We deployed a sampling grid of 30 cameras throughout the urban southern California study area. Additionally, we physically captured and marked a subset of the bobcat population with GPS telemetry collars. Since we could identify individual bobcats with photos of unique pelage patterns and a subset of the population was physically marked, we were able to use traditional mark-recapture and mark-resight methods, as well as the new "hybrid" mark-resight model we developed to estimate bobcat abundance. We recorded 109 bobcat photos during 4,669 camera nights and physically marked 27 bobcats with GPS telemetry collars. Abundance estimates produced by the traditional mark-recapture, traditional mark-resight, and "hybrid" mark-resight methods were similar, however precision differed depending on the models used. Traditional mark-recapture and mark-resight estimates were relatively imprecise with percent confidence interval lengths exceeding 100% of point estimates. Hybrid mark-resight models produced better precision with percent confidence intervals not exceeding 57%. The increased precision of the hybrid mark-resight method stems from utilizing the complete encounter histories of physically marked individuals (including those never detected by a camera trap) and the encounter histories of naturally marked individuals detected at camera traps. This new estimator may be particularly useful for estimating abundance of uniquely identifiable species that are difficult to sample using camera traps alone.