Most bulk cloud microphysics schemes predict up to three standard properties of hydrometeor size distributions, namely, the mass mixing ratio, number concentration, and reflectivity factor in order of increasing scheme complexity. However, it is unclear whether this combination of properties is optimal for obtaining the best simulation of clouds and precipitation in models. In this study, a bin microphysics scheme has been modified to act like a bulk microphysics scheme. The new scheme can predict...

Hot-iron disbudding, a routine procedure that prevents horn bud growth through cauterization, is painful for calves. The resulting burns remain sensitive to touch for weeks, but it is unknown whether calves experience ongoing, non-evoked pain. We evaluated conditioned place preference for analgesia in 44 calves disbudded or sham-disbudded 6 hours (Day 0) or 20 days (Day 20) before testing (n = 11/treatment). Calves were conditioned to associate the effects of a lidocaine cornual nerve block...

In plant-pathogen relations, disease symptoms arise from the interaction of the host and pathogen genomes. Host-pathogen functional gene interactions are well described while little is known about how the pathogen genetic variation modulates both organisms’ transcriptomes. To model and generate hypotheses on a generalist pathogen control of gene expression regulation, we used the Botrytis cinerea - Arabidopsis thaliana pathosystem and the genetic diversity of a collection of 96 B. cinerea isolates. We performed expression-based genome-wide...

Fungi in the marine environment are often neglected, despite that they having critical roles on land as decomposers, pathogens or beneficial endophytes. We used culture-dependent methods to survey the fungi associated with the seagrass, Zostera marina, and then placed these sequences in the fungal tree of life. Four different sequence alignments were generated, (1) an alignment to investigate seagrass isolates in the Basidiomycota and Zygomycota phyla, (2) an alignment to investigate seagrass isolates in the...

The potential for automated vehicles (AVs) to reduce parking to allow for the conversion of on-and off-street parking to new uses, such as new space for walk, bike, and shared -micro-mobility services, and housing), has sparked significant interest among urban planners. AVs could drop-off and pick-up passengers in areas where parking costs are high or limited. Personal AVs could return home or park in less expensive locations and shared AVs could serve other passengers. However,...

Wild ungulates can recognize certain predators without previous experience, but this innate ability may be relaxed under domestication. Using naïve dairy calves, Bos taurus, we examined the effects of exposure to a predator odour (coyote, Canis latrans, urine) and two control odours (deer urine and water) on (1) latency to approach a milk food reward, (2) exploration, vigilance and locomotor play, (3) magnitude of the startle response to a sudden noise delivered upon arrival at...

There has been general trend to shift the location of warehouses and distribution facilities away from consumer markets (logistics sprawl) in Southern California. This shift has a negative impact on cost and the environment because freight vehicles have to travel longer to reach their destinations. However, during the last decade, this trend has not continued at the same pace, and it may have even reversed. Two main factors potentially explain this phenomenon: the 2008-2009 economic...

Pair-living is a common social system found across animal taxa, and the relationship between pair-living and reproduction varies greatly among species. Siphonaria gigas, hermaphroditic pulmonate gastropods, often live in pairs in the rocky intertidal zone of the tropical Eastern Pacific. Combining genetic parentage analysis using four polymorphic microsatellite loci with behavioral observations from a 10-week field study, we provide the first description of the mating system of a Siphonaria species incorporating genetic data. S. gigas...

Leading up to the 2020 Convention on Biological Diversity there is momentum around setting bold conservation targets. Yet it remains unclear how much of Earth’s land area remains without significant human influence and where this land is located. We compare four recent global maps of human influences across Earth’s land, Anthromes, Global Human Modification, Human Footprint, and Low Impact Areas, to answer these questions. Despite using various methodologies and data, these different spatial assessments independently...

The data and code provided in this repository are associated with the technical report on the "Multiple Benefits from Agricultural and Natural Land Covers" project and were prepared by the authors for the Migratory Bird Conservation Partnership. MBCP partner organizations include The Nature Conservancy, California Audubon, and Point Blue Conservation Science. Executive Summary The Central Valley of California is one of the most heavily modified landscapes in the world, with millions of acres of semi-arid...

Genetic approaches in model organisms have consistently demonstrated that molecular traits such as gene expression are under genetic regulation, similar to clinical traits. The resulting expression quantitative trait loci (eQTL) have revolutionized our understanding of genetic regulation and identified numerous candidate genes for clinically-relevant traits. More recently, these analyses have been extended to other molecular traits such as protein abundance, metabolite levels, and miRNA expression. Here we performed global hepatic eQTL and miRNA expression quantitative...

This dataset contains the R and JAGS code underlying the simulation study, as well as the data and code underlying the case study on bird occurrence in Murchison Falls National Park, presented in the paper "A Bayesian Dirichlet process community occupancy model to estimate community structure and species similarity".

Regional-scale groundwater quality degradation from nonpoint source pollution threatens the long-term sustainability of major alluvial aquifer-aquitard systems worldwide. Upscaled models can efficient represent nonpoint source transport, but fail to accurately characterize non-Fickian (anomalous) transport caused by mean flow direction transience. In this study, we demonstrate that hydrogeologic factors explain this failure. Specifically, vertical anisotropy in K and seasonal pumping and recharge in typical alluvial aquifer systems can fundamentally change hydraulic gradients and shift the mean...

Ocean acidification (OA) poses a major threat to marine ecosystems and shellfish aquaculture. A promising mitigation strategy is the identification and breeding of shellfish varieties exhibiting resilience to acidification stress. We experimentally compared the effects of OA on two populations of red abalone (Haliotis rufescens), a marine mollusck important to fisheries and global aquaculture. Results from our experiments simulating captive aquaculture conditions demonstrated that abalone sourced from a strong upwelling region were tolerant of ongoing...

Honey bee wing lengths and vein patterns differ between major genetic lineages. In this dataset we publish forewing images for 276 individual honey bees with mixtures of African and European genetic ancestry of varying proportions. In the associated population genomics study, we compared evolutionary outcomes of the Africanized honey bee invasion in North and South America (California and Argentina). Samples from Argentina were provided by the National Institute of Agricultural Technology (INTA), Argentina.

Bees and other beneficial insects experience multiple stressors within agricultural landscapes that act together to impact their health and diminish their ability to deliver the ecosystem services on which human food supplies depend. Disentangling the effects of coupled stressors is a primary challenge for understanding how to promote their populations and ensure robust pollination and other ecosystem services. We used a crossed design to quantify the individual and combined effects of food resource limitation and...

Blossom-end rot is a physiological disorder causing significant losses in the produce industry each year. Accumulation of reactive oxygen species has been established as a key characteristic of blossom-end rot development. An increase in peroxidase activity and lignin precursor content are also associated with blossom-end rot symptoms, leading to the hypothesis that lignification may be occurring during blossom-end rot development. To investigate the potential involvement of lignification, hydrogen peroxide content, catalase activity, and peroxidase activity...

Migratory animals exhibit traits that allow them to exploit seasonally variable habitats. In environments where migration is no longer beneficial, such as oceanic islands, migration-association traits may be selected against or be under relaxed selection. Monarch butterflies are best known for their continent-scale migration in North America but have repeatedly become established as non-migrants in the tropical Americas and on Atlantic and Pacific Islands. These replicated non-migratory populations provide natural laboratories for understanding the rate...

Injury can produce long-lasting motivational changes that may alter decisions made under risk. Our objective was to determine whether a routine painful husbandry procedure, hot-iron disbudding, affects how calves trade off risk avoidance against a competing motivation (i.e., feeding), and whether this response depends on time since injury. We used a startle test to evaluate this trade-off in calves disbudded 0 or 21 days previously and non-injured control calves. For 3 days, calves were individually...

Epifaunal invertebrates play an important role in seagrass systems, both by grazing epiphytic algae from seagrass blades and by acting as a major food source for higher trophic levels. However, while many studies have described epifaunal community properties at small spatial scales (1 – 10 m2) and across very large gradients (from continental coastlines to the entire globe), few have examined regional-scale (100 ­– 1000 km2) patterns or, more importantly, disentangled the drivers of these...

Developmental plasticity influences the size of adult tissues in insects. Tissues can have unique responses to environmental perturbation during development, however, the prevalence of within species evolution of tissue-specific developmental plasticity remains unclear. To address this, we studied the effects of temperature and nutrition on wing and femur size in D. melanogaster populations from a temperate and tropical region. Wings were more sensitive to temperature, while wings and femurs were equally responsive to nutrition in...

Leptonetidae are rarely encountered spiders, usually associated with caves and mesic habitats, and are disjunctly distributed across the Holarctic. Data from ultraconserved elements (UCEs) were used in concatenated and coalescent-based analyses to estimate the phylogenetic history of the family. Our taxon sample included close outgroups, and 90% of described leptonetid genera, with denser sampling in North America and Mediterranean Europe. Two data matrices were assembled and analysed; the first ‘relaxed’ matrix includes the maximum number...

The outcomes of predator-prey interactions between endotherms and ectotherms can be heavily influenced by environmental temperature, owing to the difference in how body temperature affects locomotor performance. However, as elastic energy storage mechanisms can allow ectotherms to maintain high levels of performance at cooler body temperatures, detailed analyses of kinematics are necessary to fully understand how changes in temperature might alter endotherm-ectotherm predator-prey interactions. Viperid snakes are widely distributed ectothermic mesopredators that interact with endotherms...

Interval timing is a fundamental component of action, and is interestingly susceptible to motor-related temporal distortions. Several experiments have shown that temporal expansion and compression can occur in systematic ways with modifications of movement direction, speed, and length. These studies have largely shown that movement biases temporal estimates, but have primarily considered self-modulated movement only. However, real-world encounters often include situations in which movement is restricted or perturbed by environmental factors. Thus, in the following...

The members of the Temnothorax salvini species group are rarely collected, arboreally nesting ants of Central American forests. Previously thought to consist of two broadly dispersed species, recent collections have revealed a diversity of specimens that defy the two-species salvini group concept, but these are difficult to distinguish from each other based solely on morphology. I contrast several model-based approaches to species delimitation based on target-enriched genomic data. With molecular data from thousands of ultraconserved...