SNAPSHOT USA 2019: a coordinated national camera trap survey of the United States.

With the accelerating pace of global change, it is imperative that we obtain rapid inventories of the status and distribution of wildlife for ecological inferences and conservation planning. To address this challenge, we launched the SNAPSHOT USA project, a collaborative survey of terrestrial wildlife populations using camera traps across the United States. For our first annual survey, we compiled data across all 50 states during a 14-week period (17 August-24 November of 2019). We sampled wildlife at 1,509 camera trap sites from 110 camera trap arrays covering 12 different ecoregions across four development zones. This effort resulted in 166,036 unique detections of 83 species of mammals and 17 species of birds. All images were processed through the Smithsonian's eMammal camera trap data repository and included an expert review phase to ensure taxonomic accuracy of data, resulting in each picture being reviewed at least twice. The results represent a timely and standardized camera trap survey of the United States. All of the 2019 survey data are made available herein. We are currently repeating surveys in fall 2020, opening up the opportunity to other institutions and cooperators to expand coverage of all the urban-wild gradients and ecophysiographic regions of the country. Future data will be available as the database is updated at eMammal.si.edu/snapshot-usa, as will future data paper submissions. These data will be useful for local and macroecological research including the examination of community assembly, effects of environmental and anthropogenic landscape variables, effects of fragmentation and extinction debt dynamics, as well as species-specific population dynamics and conservation action plans. There are no copyright restrictions; please cite this paper when using the data for publication.

Infectious Diseases, Livestock, and Climate: A Vicious Cycle?

Ruminant livestock are a significant contributor to global methane emissions. Infectious diseases have the potential to exacerbate these contributions by elevating methane outputs associated with animal production. With the increasing spread of many infectious diseases, the emergence of a vicious climate-livestock-disease cycle is a looming threat.

A framework and standardized terminology to facilitate the study of predation-risk effects.

The very presence of predators can strongly influence flexible prey traits such as behavior, morphology, life history, and physiology. In a rapidly growing body of literature representing diverse ecological systems, these trait (or "fear") responses have been shown to influence prey fitness components and density, and to have indirect effects on other species. However, this broad and exciting literature is burdened with inconsistent terminology that is likely hindering the development of inclusive frameworks and general advances in ecology. We examine the diverse terminology used in the literature, and discuss pros and cons of the many terms used. Common problems include the same term being used for different processes, and many different terms being used for the same process. To mitigate terminological barriers, we developed a conceptual framework that explicitly distinguishes the multiple predation-risk effects studied. These multiple effects, along with suggested standardized terminology, are risk-induced trait responses (i.e., effects on prey traits), interaction modifications (i.e., effects on prey-other-species interactions), nonconsumptive effects (i.e., effects on the fitness and density of the prey), and trait-mediated indirect effects (i.e., the effects on the fitness and density of other species). We apply the framework to three well studied systems to highlight how it can illuminate commonalities and differences among study systems. By clarifying and elucidating conceptually similar processes, the framework and standardized terminology can facilitate communication of insights and methodologies across systems and foster cross-disciplinary perspectives.

An efficient single-cell transcriptomics workflow for microbial eukaryotes benchmarked on Giardia intestinalis cells.

BACKGROUND: Most diversity in the eukaryotic tree of life is represented by microbial eukaryotes, which is a polyphyletic group also referred to as protists. Among the protists, currently sequenced genomes and transcriptomes give a biased view of the actual diversity. This biased view is partly caused by the scientific community, which has prioritized certain microbes of biomedical and agricultural importance. Additionally, some protists remain difficult to maintain in cultures, which further influences what has been studied. It is now possible to bypass the time-consuming process of cultivation and directly analyze the gene content of single protist cells. Single-cell genomics was used in the first experiments where individual protists cells were genomically explored. Unfortunately, single-cell genomics for protists is often associated with low genome recovery and the assembly process can be complicated because of repetitive intergenic regions. Sequencing repetitive sequences can be avoided if single-cell transcriptomics is used, which only targets the part of the genome that is transcribed. RESULTS: In this study we test different modifications of Smart-seq2, a single-cell RNA sequencing protocol originally developed for mammalian cells, to establish a robust and more cost-efficient workflow for protists. The diplomonad Giardia intestinalis was used in all experiments and the available genome for this species allowed us to benchmark our results. We could observe increased transcript recovery when freeze-thaw cycles were added as an extra step to the Smart-seq2 protocol. Further we reduced the reaction volume and purified the amplified cDNA with alternative beads to test different cost-reducing changes of Smart-seq2. Neither improved the procedure, and reducing the volumes by half led to significantly fewer genes detected. We also added a 5' biotin modification to our primers and reduced the concentration of oligo-dT, to potentially reduce generation of artifacts. Except adding freeze-thaw cycles and reducing the volume, no other modifications lead to a significant change in gene detection. Therefore, we suggest adding freeze-thaw cycles to Smart-seq2 when working with protists and further consider our other modification described to improve cost and time-efficiency. CONCLUSIONS: The presented single-cell RNA sequencing workflow represents an efficient method to explore the diversity and cell biology of individual protist cells.

Warmer nights offer no respite for a defensive mutualism.

Ecologically relevant symbioses are widespread in terrestrial arthropods but based on recent findings these specialized interactions are likely to be especially vulnerable to climate warming. Importantly, empirical data and climate models indicate that warming is occurring asynchronously, with night-time temperatures increasing faster than daytime temperatures. Daytime (DTW) and night-time warming (NTW) may impact ectothermic animals and their interactions differently as DTW results in greater daily temperature variation and moves organisms nearer to their thermal limits, while NTW avoids thermal limits and may relieve constraints of cooler night-time temperatures; a nuance that has largely been ignored in the literature. In laboratory experiments, we investigated how the timing of warming influences a widespread defensive mutualism involving the pea aphid Acyrthosiphon pisum, and its heritable symbiont, Hamiltonella defensa, which protects against an important natural enemy, the parasitic wasp Aphidius ervi. Three aphid sublines were experimentally created from single aphid genotype susceptible to A. ervi: one line infected with a highly protective H. defensa strain, one infected with a moderately protective strain and one without any facultative symbiont. We examined aphid fitness in the presence and absence of parasitoids and when exposed to an average 2.5°C increase occurring across three warming scenarios (night-time vs. daytime vs. uniform) relative to no-warming controls. An increase of 2.5°C, as predicted to occur by the IPCC before 2100, was sufficient to disable the aphid defensive mutualism regardless of the timing of warming; a surprising result given that the daily maxima for control and NTW scenarios were identical. We also found that warming negatively impacted (a) symbiont-mediated interactions between host and parasitoid more than symbiont-free ones; (b) species interactions (host-parasitoid) more than each participant independently and (c) aphids more than parasitoids even though higher trophic levels are generally predicted to be more affected by warming. Here we show that 2.5°C warming, regardless of timing, negatively impacted a common microbe-mediated defensive mutualism. While this was a laboratory-based study, results suggest that temperature increases predicted in the near-term may disrupt the many ecological symbioses present in terrestrial ecosystems.

Self-perpetuating ecological-evolutionary dynamics in an agricultural host-parasite system.

Ecological and evolutionary processes may become intertwined when they operate on similar time scales. Here we show ecological-evolutionary dynamics between parasitoids and aphids containing heritable symbionts that confer resistance against parasitism. In a large-scale field experiment, we manipulated the aphid's host plant to create ecological conditions that either favoured or disfavoured the parasitoid. The result was rapid evolutionary divergence of aphid resistance between treatment populations. Consistent with ecological-evolutionary dynamics, the resistant aphid populations then had reduced parasitism and increased population growth rates. We fit a model to quantify costs (reduced intrinsic rates of increase) and benefits of resistance. We also performed genetic assays on 5 years of field samples that showed persistent but highly variable frequencies of aphid clones containing protective symbionts; these patterns were consistent with simulations from the model. Our results show (1) rapid evolution that is intertwined with ecological dynamics and (2) variation in selection that prevents traits from becoming fixed, which together generate self-perpetuating ecological-evolutionary dynamics.

Behavioral plasticity mitigates the effect of warming on white-tailed deer.

Climate change is expected to create novel environments in which extant species cannot persist, therefore leading to the loss of them and their associated ecological functions within the ecosystem. However, animals may employ behavioral mechanisms in response to warming that could allow them to maintain their functional roles in an ecosystem despite changed temperatures. Specifically, animals may shift their activity in space or time to make use of thermal heterogeneity on the landscape. However, few studies consider the role of behavioral plasticity and spatial or temporal heterogeneity in mitigating the effects of climate change. We conducted experiments to evaluate the potential importance of behavior in mediating the net effects of warming on white-tailed deer (Odocoileus virginianus). We used shade structures to manipulate the thermal environment around feeding stations to monitor deer feeding activity and measure total consumption. In individual experiments where deer only had access to unshaded feeders, deer fed less during the day but compensated by increasing feeding during times when temperature was lower. In group experiments where deer had access to both shaded and unshaded feeders, deer often fed during the day but disproportionally preferred the cooler, shaded feeders. Our results suggest that deer can capitalize on temporal and spatial heterogeneity in the thermal environment to meet nutritional and thermal requirements, demonstrating the importance of behavioral plasticity when predicting the net effects of climate change.

Why and How to Create Nighttime Warming Treatments for Ecological Field Experiments.

While average global temperatures are increasing, a disproportionate amount of warming can be attributed to increasing nighttime temperatures rather than increasing daytime temperatures. Theory predicts that the timing of warming can generate different effects on organisms and their interactions within ecosystems. This occurs because an organism's response to warming depends on the current temperature. For example, warming when temperatures are low may have positive effects on an organism, while warming when temperatures are already high may have negative effects on an organism. Most field experiments that examine the ecological effects of climate warming employ warming methodologies that disproportionately elevate daytime warming treatments. The bias towards daytime warming treatments may arise because daytime temperatures can be manipulated with relatively simple and inexpensive technology that capitalizes on solar energy, such as open-top chambers that create a "greenhouse effect" or shade structures that reduce temperatures. However, these popular methods are ineffective when solar radiation is absent, and thus do not create warming treatments that accurately mimic the temporal patterns of climate warming. To encourage the investigation of nighttime warming's effect on ecosystems, we discuss why daytime and nighttime warming may have different effects on organisms, then present a review of methods that can be employed to elevate nighttime temperature in terrestrial field experiments. For each method, we offer a brief explanation, an evaluation of its pros and cons, and citations for further reference, as well as empirical data when possible. While some are impractical, we attempt to provide a comprehensive list of potential nighttime warming methods in hopes of stimulating ideas and discussions.

Testing the AC/DC hypothesis: Rock and roll is noise pollution and weakens a trophic cascade.

Anthropogenic sound is increasingly considered a major environmental issue, but its effects are relatively unstudied. Organisms may be directly affected by anthropogenic sound in many ways, including interference with their ability to detect mates, predators, or food, and disturbances that directly affect one organism may in turn have indirect effects on others. Thus, to fully appreciate the net effect of anthropogenic sound, it may be important to consider both direct and indirect effects. We report here on a series of experiments to test the hypothesis that anthropogenic sound can generate cascading indirect effects within a community. We used a study system of lady beetles, soybean aphids, and soybean plants, which are a useful model for studying the direct and indirect effects of global change on food webs. For sound treatments, we used several types of music, as well as a mix of urban sounds (e.g., sirens, vehicles, and construction equipment), each at volumes comparable to a busy city street or farm tractor. In 18-hr feeding trials, rock music and urban sounds caused lady beetles to consume fewer aphids, but other types of music had no effect even at the same volume. We then tested the effect of rock music on the strength of trophic cascades in a 2-week experiment in plant growth chambers. When exposed to music by AC/DC, who articulated the null hypothesis that "rock and roll ain't noise pollution" in a song of the same name, lady beetles were less effective predators, resulting in higher aphid density and reduced final plant biomass relative to control (no music) treatments. While it is unclear what characteristics of sound generate these effects, our results reject the AC/DC hypothesis and demonstrate that altered interspecific interactions can transmit the indirect effects of anthropogenic noise through a community.

Covariance between predation risk and nutritional preferences confounds interpretations of giving-up density experiments.

Giving-up density (GUD) experiments have been a foundational method to evaluate perceived predation risk, but rely on the assumption that food preferences are absolute, so that areas with higher GUDs can be interpreted as having higher risk. However, nutritional preferences are context dependent and can change with risk. We used spiders and grasshoppers to test the hypothesis that covariance in nutritional preferences and risk may confound the interpretation of GUD experiments. We presented grasshoppers with carbohydrate-rich and protein-rich diets, in the presence and absence of spider predators. Predators reduced grasshopper preference for the protein-rich food, but increased their preference for the carbohydrate-rich food. We then measured GUDs with both food types under different levels of risk (spider density, 0-5). As expected, GUDs increased with spider density indicating increasing risk, but only when using protein-rich food. With carbohydrate-rich food, GUD was independent of predation risk. Our results demonstrate that predation risk and nutritional preferences covary and can confound interpretation of GUD experiments.

Opposite effects of daytime and nighttime warming on top-down control of plant diversity.

Ecological analyses of climate warming explore how rising mean temperature will affect the species composition of communities and their associated functioning. Experimentation usually presumes that warming arises from simultaneous increase in daily maximum (daytime) and minimum (nighttime) temperatures. Yet evidence shows that mean warming arises largely from increasing nighttime temperatures. We report on a 3-yr experiment that compared the effects of daytime and nighttime warming on a community comprising herbaceous plants, grasshopper herbivores and predatory spiders. We warmed experimental mesocosms 3-4°C above ambient control treatments during the daytime (06:00-18:00 h) or nighttime (18:00-06:00 h). Daytime warming caused spiders to seek a thermal refuge low in the plant canopy and away from grasshopper prey, which allowed grasshoppers to spend more time feeding on a competitively dominant plant species. Nighttime had the opposite effect, where spider activity increased causing grasshoppers to reduce feeding. Two consecutive years of daytime warming resulted in a suppression of the competitive dominant plant and increased the diversity and evenness of the plant community, whereas nighttime warming had opposite effects. These results show that ignoring the nuanced effects of asymmetrical warming may lead to inaccurate conclusions about the net effects of climate change on ecosystems.

Contrasting the potential effects of daytime versus nighttime warming on insects.

Mean increases in temperatures associated with climate change are largely driven by increases in minimum (nighttime) temperatures; however, most climate change studies disproportionately increase maximum (daytime) temperatures. We review current literature to compare the potential effects of increasing daytime and nighttime temperatures on insects and their interactions within ecological communities. Although few studies have explicitly addressed the effects of nighttime warming, we draw from broader literature on how insects are affected by temperature to identify possible mechanisms that the timing (day or night) of warming may affect insects. Specifically, we discuss daily temperature variation, thermal performance curves, behaviour and activity patterns, nighttime recovery from hot days, and bottom-up effects mediated by plants. Although limited, the existing evidence suggests nighttime and daytime warming can have different effects, and thus we encourage scientists to use the most realistic warming treatments possible to truly understand how insects and their communities will be affected by climate change.

Mass mortality events and the role of necrophagous invertebrates.

Scale is important in understanding and applying concepts in ecology. Historically, the mechanisms regulating necrophagous arthropod community structure have been well explored on a single vertebrate carcass. However, practically nothing is known of whether such findings can be extrapolated to cases where large numbers of carcasses have been introduced into an ecosystem at a single time point. With the increasing incidences of mass mortality events (MMEs), understanding how scale effects community assembly of necrophagous insects and the resulting bottom-up or top-down effects on the impacted ecosystem are of utmost importance. Unfortunately, MMEs are unpredictable, making their study nearly impossible within a robust experimental framework. The objectives of this paper are to provide a brief overview of what is known with regards to ecological responses to carrion, opine on the ramifications of MMEs on local communities, and provide a brief overview of knowledge gaps, avenues for future research, and a potential study systems for rigorous MME experiments.

Combined effects of night warming and light pollution on predator-prey interactions.

Interactions between multiple anthropogenic environmental changes can drive non-additive effects in ecological systems, and the non-additive effects can in turn be amplified or dampened by spatial covariation among environmental changes. We investigated the combined effects of night-time warming and light pollution on pea aphids and two predatory ladybeetle species. As expected, neither night-time warming nor light pollution changed the suppression of aphids by the ladybeetle species that forages effectively in darkness. However, for the more-visual predator, warming and light had non-additive effects in which together they caused much lower aphid abundances. These results are particularly relevant for agriculture near urban areas that experience both light pollution and warming from urban heat islands. Because warming and light pollution can have non-additive effects, predicting their possible combined consequences over broad spatial scales requires knowing how they co-occur. We found that night-time temperature change since 1949 covaried positively with light pollution, which has the potential to increase their non-additive effects on pea aphid control by 70% in US alfalfa. Our results highlight the importance of non-additive effects of multiple environmental factors on species and food webs, especially when these factors co-occur.

A spatial theory for emergent multiple predator-prey interactions in food webs.

Predator-prey interaction is inherently spatial because animals move through landscapes to search for and consume food resources and to avoid being consumed by other species. The spatial nature of species interactions necessitates integrating spatial processes into food web theory and evaluating how predators combine to impact their prey. Here, we present a spatial modeling approach that examines emergent multiple predator effects on prey within landscapes. The modeling is inspired by the habitat domain concept derived from empirical synthesis of spatial movement and interactions studies. Because these principles are motivated by synthesis of short-term experiments, it remains uncertain whether spatial contingency principles hold in dynamical systems. We address this uncertainty by formulating dynamical systems models, guided by core habitat domain principles, to examine long-term multiple predator-prey spatial dynamics. To describe habitat domains, we use classical niche concepts describing resource utilization distributions, and assume species interactions emerge from the degree of overlap between species. The analytical results generally align with those from empirical synthesis and present a theoretical framework capable of demonstrating multiple predator effects that does not depend on the small spatial or temporal scales typical of mesocosm experiments, and help bridge between empirical experiments and long-term dynamics in natural systems.