Bayesian model-based age classification using small mammal body mass and capture dates

Accurate age determination is a fundamental prerequisite for demographic studies as well as population monitoring efforts that provide information for management and conservation. Yet, common age determination methods suffer from low accuracy rates, impose additional handling and time costs on animals and biologists, or rely on invasive techniques such as tooth extraction. We introduce an alternative, mixture modeling approach for age determination that exploits mammalian growth patterns to classify newly encountered animals as juveniles or adults, and present an example analysis that classifies Allegheny woodrats based solely on their capture dates and mass at capture, in combination with data from known adults. We also introduce and validate a simulation-based heuristic to evaluate potential classification accuracy when no known-age test cases are available. In the Allegheny woodrat example, the mixture model achieved a 90–92% accuracy rate (heuristic range: 89–94%), far better than the 36–43% achieved with a fixed mass criterion, and comparable to accuracies reported for other species using more data-intensive, multivariate classification techniques. The model can be extended to classify multiple age groups, estimate chronological age, or further improve accuracy by including additional morphometric measures

Performance benchmarks for scholarly metrics associated with fisheries and wildlife faculty

Research productivity and impact are often considered in professional evaluations of academics, and performance metrics based on publications and citations increasingly are used in such evaluations. To promote evidence-based and informed use of these metrics, we collected publication and citation data for 437 tenure-track faculty members at 33 research-extensive universities in the United States belonging to the National Association of University Fisheries and Wildlife Programs. For each faculty member, we computed 8 commonly used performance metrics based on numbers of publications and citations, and recorded covariates including academic age (time since Ph.D.), sex, percentage of appointment devoted to research, and the sub-disciplinary research focus. Standardized deviance residuals from regression models were used to compare faculty after accounting for variation in performance due to these covariates. We also aggregated residuals to enable comparison across universities. Finally, we tested for temporal trends in citation practices to assess whether the law of constant ratios , used to enable comparison of performance metrics between disciplines that differ in citation and publication practices, applied to fisheries and wildlife sub-disciplines when mapped to Web of Science Journal Citation Report categories. Our regression models reduced deviance by 1/4 to 1/2. Standardized residuals for each faculty member, when combined across metrics as a simple average or weighted via factor analysis, produced similar results in terms of performance based on percentile rankings. Significant variation was observed in scholarly performance across universities, after accounting for the influence of covariates. In contrast to findings for other disciplines, normalized citation ratios for fisheries and wildlife sub-disciplines increased across years. Increases were comparable for all sub-disciplines except ecology. We discuss the advantages and limitations of our methods, illustrate their use when applied to new data, and suggest future improvements. Our benchmarking approach may provide a useful tool to augment detailed, qualitative assessment of performance. © 2016 Swihart et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Development and validation of an eDNA protocol for monitoring endemic Asian spiny frogs in the Himalayan region of Pakistan

Wildlife monitoring programs are instrumental for the assessment of species, habitat status, and for the management of factors affecting them. This is particularly important for species found in freshwater ecosystems, such as amphibians, as they have higher estimated extinction rates than terrestrial species. We developed and validated two species-specific environmental DNA (eDNA) protocols and applied them in the field to detect the Hazara Torrent Frog (Allopaa hazarensis) and Murree Hills Frog (Nanorana vicina). Additionally, we compared eDNA surveys with visual encounter surveys and estimated site occupancy. eDNA surveys resulted in higher occurrence probabilities for both A. hazarensis and N. vicina than for visual encounter surveys. Detection probability using eDNA was greater for both species, particularly for A. hazarensis. The top-ranked detection model for visual encounter surveys included effects of both year and temperature on both species, and the top-ranked occupancy model included effects of elevation and year. The top-ranked detection model for eDNA data was the null model, and the top-ranked occupancy model included effects of elevation, year, and wetland type. To our knowledge, this is the first time an eDNA survey has been used to monitor amphibian species in the Himalayan region

Landscape transformations produce favorable roosting conditions for turkey vultures and black vultures

Recent increases in turkey vulture (Cathartes aura) and black vulture (Coragyps atratus) populations in North America have been attributed in part to their success adapting to human-modified landscapes. However, the capacity for such landscapes to generate favorable roosting conditions for these species has not been thoroughly investigated. We assessed the role of anthropogenic and natural landscape elements on roosting habitat selection of 11 black and 7 turkey vultures in coastal South Carolina, USA using a GPS satellite transmitter dataset derived from previous research. Our dataset spanned 2006–2012 and contained data from 7916 nights of roosting. Landscape fragmentation, as measured by land cover richness, influenced roosting probability for both species in all seasons, showing either a positive relationship or peaking at intermediate values. Roosting probability of turkey vultures was maximized at intermediate road densities in three of four seasons, and black vultures showed a positive relationship with roads in fall, but no relationship throughout the rest of the year. Roosting probability of both species declined with increasing high density urban cover throughout most of the year. We suggest that landscape transformations lead to favorable roosting conditions for turkey vultures and black vultures, which has likely contributed to their recent proliferations across much of the Western Hemisphere

Reducing Baylisascaris procyonis Roundworm Larvae in Raccoon Latrines

Baylisascaris procyonis roundworms, a parasite of raccoons, can infect humans, sometimes fatally. Parasite eggs can remain viable in raccoon latrines for years. To develop a management technique for parasite eggs, we tested anthelmintic baiting. The prevalence of eggs decreased at latrines, and larval infections decreased among intermediate hosts, indicating that baiting is effective

Digital reconstruction of the inner ear of Leptictidium auderiense (Leptictida, Mammalia) and North American leptictids reveals new insight into leptictidan locomotor agility

Leptictida are basal Paleocene to Oligocene eutherians from Europe and North America comprising species with highly specialized postcranial features including elongated hind limbs. Among them, the European Leptictidium was probably a bipedal runner or jumper. Because the semicircular canals of the inner ear are involved in detecting angular acceleration of the head, their morphometry can be used as a proxy to elucidate the agility in fossil mammals. Here we provide the first insight into inner ear anatomy and morphometry of Leptictida based on high-resolution computed tomography of a new specimen of Leptictidium auderiense from the middle Eocene Messel Pit (Germany) and specimens of the North American Leptictis and Palaeictops. The general morphology of the bony labyrinth reveals several plesiomorphic mammalian features, such as a secondary crus commune. Leptictidium is derived from the leptictidan groundplan in lacking the secondary bony lamina and having proportionally larger semicircular canals than the leptictids under study. Our estimations reveal that Leptictidium was a very agile animal with agility score values (4.6 and 5.5, respectively) comparable to Macroscelidea and extant bipedal saltatory placentals. Leptictis and Palaeictops have lower agility scores (3.4 to 4.1), which correspond to the more generalized types of locomotion (e.g., terrestrial, cursorial) of most extant mammals. In contrast, the angular velocity magnitude predicted from semicircular canal angles supports a conflicting pattern of agility among leptictidans, but the significance of these differences might be challenged when more is known about intraspecific variation and the pattern of semicircular canal angles in non-primate mammals

Temporal dynamics of mast and small mammals: Short-term responses to silviculture

Oaks (Quercus) are a keystone species in eastern deciduous forests. One of their most important functions is the production of hard mast (acorns), a crucial food resource for many wildlife species. Oaks are relatively shade-intolerant and have been maintained as a dominant overstory species in many forests through a cycle of disturbance including fire and land clearing for agriculture. Recently, changing disturbance regimes have resulted in oak regeneration failure. Eventually, oak-dominated stands may instead be dominated by other tree species, such as maple (Acer). This shift may have important negative consequences for other forest species that rely on oak, especially those that consume hard mast. Forest managers have begun to use silviculture (i.e., timber harvest) as an artificial disturbance mechanism in an effort to promote oak regeneration and maintain oak dominance in deciduous forests, with mixed results. Understanding the effects of timber harvest on wildlife species is an important corollary to these efforts, particularly in the case of wildlife species that themselves affect successful oak regeneration (e.g., small mammals and acorn weevils (Curculio)). In this thesis, I examined the impact of two groups of acorn predators, small mammals and acorn weevils, on the survival of acorns prior to the implementation of timber harvest (Chapter 2). I then studied the effect of several methods of silviculture on common small mammal species, two of which (the white-footed mouse, Peromyscus leucopus, and the eastern chipmunk, Tamius straitus) are consumers of acorns (Chapters 3-4). I used two recently developed statistical techniques, an N-mixture model of abundance and a multi-species occupancy model, to make inferences about small mammal responses to harvest. Both models explicitly incorporated variability in detection probability, which if ignored can be a significant source of bias. I found that acorn mortality due to both weevils and removal by small mammals was maximized when mast production was lowest, reflecting the scarcity of this crucial food resource. In years when mast was abundant, small mammal predators preferred to remove more valuable acorns (e.g., acorns that were undamaged). Not surprisingly, abundance of granivorous small mammals were closely linked to mast availability throughout the study. Of the common small mammals that were the focus of the second portion of this thesis, one (the eastern chipmunk) generally responded positively to the creation of openings through timber harvest. A second, the generalist white-footed mouse, generally did not respond strongly to any type of silviculture. In contrast, the short-tailed shrew (Blarina brevicauda) and the pine vole (Microtus pinetorum) generally responded negatively to the creation of openings via harvest. In general, small mammals did not respond strongly to the first stage of a shelterwood harvest. Some of these shifts may have been due to changes in habitat variables following harvest; notably, the eastern chipmunk was associated with areas containing a large amount of coarse woody debris, which increased following the creation of openings. The results of this thesis will be useful in furthering our understanding of how silviculture affects insects and wildlife that play important roles in the oak life cycle. Successful oak regeneration depends on proper implementation of silviculture, but also on ensuring that potential sources of oak mortality, such as small mammals and weevils, do not create a bottleneck in the oak life cycle. My results lay the groundwork for future studies that examine the effects of animals and insects on the entire life cycle of oak in managed forests

Interactive effects of animals and silviculture on the early life history of oak

Oak (Quercus) is a dominant component of the forest canopy in many deciduous forests of the eastern United States. In the past century, a pattern of anthropogenic fire suppression throughout the eastern United States has created conditions that favor more shade-tolerant tree species at the expense of oak regeneration. Loss of oak as dominant canopy component would have a powerful impact on forest ecosystems; oak acorns are a keystone food resource for greater than 50 species of mammals and birds in these forests, due to their ubiquity and nutritional content. In response, forest managers have developed and applied silvicultural techniques, including timber harvesting, to emulate forest disturbance and regenerate oak. Timber harvesting can impact key trophic interactions with animals during early oak life history, thus potentially impacting the oak regeneration process indirectly; however, these impacts are not well understood. To address this research gap, I examined the effects of clearcut and shelterwood harvesting approaches on key early life history parameters involved in acorn predation, dispersal, seedling survival, and seedling growth for black oak (Q. velutina) and white oak (Q. alba) in southern Indiana. I found that the initial phase of shelterwood harvesting (midstory removal) resulted in increased acorn dispersal and reduced survival but that these changes were dependent on dispersal agent and acorn species. At the seedling life stage, growth was highest but survival was lowest (for black oak) in clearcut openings. The lower survival in clearcuts was likely due to drought during two consecutive growing seasons. Herbivory by white-tailed deer (Odocoileus virginianus) impacted seedling growth but not survival; rates of browsing were low throughout the study. With this field data, I developed an individual-based, spatially-explicit simulation model of early oak life history connecting early life history parameters with consequences for oak regeneration. Simulation results indicated that the observed differences in acorn predation and dispersal parameters in shelterwoods had a small, but significant, negative impact on accumulation of oak seedlings (\u3c1.4 m height) in the period following harvest. However, this effect was not carried through to density of oak saplings (?1.4 m). Greater disturbance in the second and third phases of the shelterwood harvest may result in stronger impacts on seed predation and dispersal. Increasing the frequency of drought years in the simulation model had a powerful negative effect on both oak seedlings and saplings, and the effect increased with intensity of harvest disturbance. The impact of drought is concerning given predictions that climate change will bring more frequent drought to the Midwestern United States; the ultimate impacts on oak regeneration success are unclear since drought may affect oak competitors even more strongly. The simulation model I developed is a flexible tool that could be used to examine a wide range of animal impacts on early oak life history and project their impacts on oak regeneration success