The ecology and behaviour of pumas (Puma concolor) in northern California, U.S.A.

Large carnivores are important components of many ecosystems and play an integral role in determining the composition and structure of ecological communities. The influences of pumas (Puma concolor) on other species, including prey and competitors, vary across their range and among individuals. I used novel methodologies, including intensive real-time GPS investigations of potential kill sites using ARGOS satellite collars, and motion-triggered video cameras to study the intra- and inter-specific interactions of pumas and understand their influences on ecological communities. Results from my dissertation support previous findings that pumas play an integral role in shaping their respective ecosystem, but that pumas are also influenced substantially by their local environment. Overall, my dissertation highlights the importance of understanding intra- and inter-specific interactions of large carnivores when attempting to understand their influences on ecological communities. I tested whether pumas exhibited sexual variation in their use of communication behaviours at community scrape areas, and what factors influenced their mating strategies. I found that males more frequently exhibited and spent longer durations on ‘producing’ behaviours (scraping and body rubbing), while females more frequently exhibited and spent longer durations on ‘consuming’ behaviours (olfactory investigation and flehmen response behaviours). This suggests that male reproductive strategy is based on advertisement for possible mates, while female reproductive strategy is based on assessment of potential mates. Pumas also exhibited sexual variation in their patterns of visitation. Males were regular visitors, while females were irregular visitors whose visitation cycles were apparently correlated with oestrus. Mate selection by females was complex and based on multiple cues, the two most important of which were the visitation rate and mass of males. The frequency of male visits and the display of some behaviours were influenced most by visits from female pumas, but were also influenced by visits from competing males. I used real-time and fine-scale GPS location data to find prey killed by individual pumas, and analysed seasonal patterns to understand local influences on puma behaviour and feeding ecology. I found that black-tailed deer (Odocoileus hemionus columbianus) were the main prey of pumas, constituting 98.6% of their diet by mass, and that the elevations at which pumas killed black-tailed deer correlated significantly with seasonal elevations used by black-tailed deer. I found pumas had relatively high ungulate kill rates ( ̅ = 1.07 ungulates/week, and ̅ = 5.78 kg/day), and that kill rates in ungulates/week varied among seasons and were highest in summer and autumn. Importantly, the handling times of black-tailed deer >1 year old showed an inverse seasonal relationship with kill rates in ungulates/week, and the lower handling times may have been due to black bear kleptoparasitism. These findings suggest that puma feeding ecology can be strongly influenced by seasonal behaviour of their prey and dominant scavengers. Given the potential for large carnivores to influence scavengers, I studied the influences of both pumas and black bears on the scavenger community. I found that pumas and black bears were a source of limitation for scavengers, both on the species richness and sum feeding times of the scavenger community, as well as the occurrence, total feeding times, and mean feeding bout durations of scavenger species. However, pumas had some positive influences, for example they facilitated the acquisition of carrion by scavengers, and they apparently initiated a cascading pattern that led to an increase in the acquisition of carrion by small carnivores. In contrast, black bears, as dominant scavengers, monopolized carrion resources and substantially limited the acquisition of carrion by other scavengers, and in fact they had larger limitations for scavengers than pumas as top-level predators. The influences on carrion acquisition suggest that large carnivores have important influences on the scavenger community, and their influences could be a mechanism for the effects large carnivores have on community composition

Detection rates and diel activity patterns of four understudied felids from Borneo

Carnivore guilds are charismatic and have vital and irreplaceable roles in their native ecosystems, yet many of these species are threatened and remain understudied. Borneo is a biodiversity hotspot that hosts a rich diversity of endemic wildlife but is threatened by deforestation and habitat loss. Using cameras placed by the Smithsonian Institution in Sabah, Borneo, we assessed the detection rates and diel activity patterns of the native felid species. Across 51 camera trap sites between 2016 and 2019, felids were detected 55 times across a combined 9958 trap nights, including 20 independent detection events for Sunda leopard cats, 15 for Sunda clouded leopards, 12 for Borneo bay cats, and 5 for marbled cats, with no detections of flat‐headed cats. Collectively, this demonstrates the challenge of sampling cryptic species that have declined due to habitat loss and conflict with humans. Despite this, we show that Borneo bay cats and marbled cats exhibited different diel activity patterns than Sunda cloud leopards, suggesting the smaller species use temporal displacement to avoid competition and predation. Sunda leopard cats exhibited broadly similar activity patterns to Sunda clouded leopard, potentially because the two species typically occupy different dietary and habitat niches. These results demonstrate the importance of devoting future research towards monitoring these species and understanding the mechanisms by which they co‐exist

BOC is a modifier gene in holoprosencephaly

Holoprosencephaly (HPE), a common developmental defect of the forebrain and midface, has a complex etiology. Heterozygous, loss‐of‐function mutations in the sonic hedgehog (SHH) pathway are associated with HPE. However, mutation carriers display highly variable clinical presentation, leading to an “autosomal dominant with modifier” model, in which the penetrance and expressivity of a predisposing mutation is graded by genetic or environmental modifiers. Such modifiers have not been identified. Boc encodes a SHH coreceptor and is a silent HPE modifier gene in mice. Here, we report the identification of missense BOC variants in HPE patients. Consistent with these alleles functioning as HPE modifiers, individual variant BOC proteins had either loss‐ or gain‐of‐function properties in cell‐based SHH signaling assays. Therefore, in addition to heterozygous loss‐of‐function mutations in specific SHH pathway genes and an ill‐defined environmental component, our findings identify a third variable in HPE: low‐frequency modifier genes, BOC being the first identified.Holoprosencephaly (HPE), the most developmental common defect of the forebrain, is best explained by a “mutation with modifier” model. However, HPE modifier genes have not been identified. Here, we report HPE‐associated missense variants within the Hedgehog coreceptor BOC (arrows). Functional analyses of these variants, along with previous work in mouse models, are consistent with the conclusion that these variants act as phenotypic modifiers of a driver mutation or environmental insult.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138902/1/humu23286-sup-0001-text.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138902/2/humu23286_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138902/3/humu23286.pd

Keystone Individuals - Linking Predator Traits to Community Ecology

Individual behavioral plasticity enables animals to adjust to different scenarios. Yet, personality traits limit this flexibility, leading to consistent inter-individual differences in behavior. These individual behavioral traits have the potential to govern community interactions, although testing this is difficult in complex natural systems. For large predators who often exert strong effects on ecosystem functioning, this behavioral diversity may be especially important and lead to individualized ecosystem roles. We present a framework for quantifying individual behavioral plasticity and personality traits of large wild predators, revealing the extent to which certain natural behaviors are governed by these latent traits. The outcomes will reveal how the innate characteristics of wildlife can scale up to affect community interactions

Best Practices for Alchemical Free Energy Calculations

Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another. The hallmark of these methods is the use of "bridging" potential energy functions representing \emph{alchemical} intermediate states that cannot exist as real chemical species. The data collected from these bridging alchemical thermodynamic states allows the efficient computation of transfer free energies (or differences in transfer free energies) with orders of magnitude less simulation time than simulating the transfer process directly. While these methods are highly flexible, care must be taken in avoiding common pitfalls to ensure that computed free energy differences can be robust and reproducible for the chosen force field, and that appropriate corrections are included to permit direct comparison with experimental data. In this paper, we review current best practices for several popular application domains of alchemical free energy calculations, including relative and absolute small molecule binding free energy calculations to biomolecular targets.Comment: 48 pages, 14 figure

Atmospheric Acetaldehyde: Importance of Air-Sea Exchange and a Missing Source in the Remote Troposphere.

We report airborne measurements of acetaldehyde (CH3CHO) during the first and second deployments of the National Aeronautics and Space Administration (NASA) Atmospheric Tomography Mission (ATom). The budget of CH3CHO is examined using the Community Atmospheric Model with chemistry (CAM-chem), with a newly-developed online air-sea exchange module. The upper limit of the global ocean net emission of CH3CHO is estimated to be 34 Tg a-1 (42 Tg a-1 if considering bubble-mediated transfer), and the ocean impacts on tropospheric CH3CHO are mostly confined to the marine boundary layer. Our analysis suggests that there is an unaccounted CH3CHO source in the remote troposphere and that organic aerosols can only provide a fraction of this missing source. We propose that peroxyacetic acid (PAA) is an ideal indicator of the rapid CH3CHO production in the remote troposphere. The higher-than-expected CH3CHO measurements represent a missing sink of hydroxyl radicals (and halogen radical) in current chemistry-climate models