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opencc-by-4.0Dec 2018View details →

Experimental data for "Virtual Reality as a Tool for Promoting Reading via Enhanced Narrative Absorption and Empathy"

This dataset contains data of the publication "Virtual Reality as a Tool for Promoting Reading via Enhanced Narrative Absorption and Empathy". It includes measure for the Story World Absorption Scale and the State Empathy Scale used to compare subjective experiences while reading on paper and reading in a virtual reality environment. Original paper: Pianzola, F., Bálint, K., and Weller, J. (2019). Virtual Reality as a Tool for Promoting Reading via Enhanced Narrative Absorption and Empathy. Scientific Study of Literature 9(2). https://doi.org/10.1075/ssol.19013.pia

opencc-by-4.0Dec 2019View details →

SN4741 Promoter Capture HiC - HiCUP/CHiCAGO Analysis

Promoter capture HiC data generated from SN4741 cells. The HiCUP/CHiCAGO analysis was run five total times, and the most (liberal) and least (conservative) number of interactions was identified. Data is provided in the washU_text format which consolidates peaks and maintains only the higher rated score. See CHiCAGO Vignette for more information.

opencc-by-4.0May 2020View details →

Promotional Scheduling Software Price For Supermarkets

Supermarket chains and independent grocers use Demo Wizard <a href="http://https//www.demo-wizard.com/pricing.html">promotional Scheduling Software</a> Price to maximize utilization of their floor space for in store demos and improve their customer experience.

Data from: Foundation species promote local adaptation and fine-scale distribution of herbaceous plants

1) Interactions among neighbors can alter demography and traits of commingled species via adaptation or plasticity in phenotypic expression and understanding these two mechanisms in diverse communities is important for determining the ecological and evolutionary consequences of plant–plant interactions. 2) We reciprocally transplanted perennial species (Arenaria armerina and Festuca indigesta) among patches of two foundation shrub species and open ground to assess whether origin microsite (defined as the spatially distinct abiotic and biotic conditions associated with the two shrubs and open ground) determines germination, recruitment and growth that, in turn, promotes fine-scale distribution of species among microsites. In addition, we tested the effect of origin microsite on traits, competitive ability, drought tolerance and outlier loci to assess whether origin microsite conditions drove differences in traits, strategies and adaptive loci. 3) Germination was consistently greater for seeds planted back into their origin microsite relative to seeds sourced from foreign microsites, although this effect was weakened for recruitment. Plant growth was best in open sites regardless of origin microsite. In the greenhouse, A. armerina had conserved traits within origin microsite but distinct trait values among microsite conditions, specifically for plants originating from the most productive microsite (e.g. sufficient light and high nutrients and water availability). Festuca indigesta had conserved trait responses among microsites while within microsite, individuals had significant trait plasticity to different environmental conditions. The combined field and greenhouse results suggest that fine-scale distributions are supported by local adaptation among microsites of A. armerina and phenotypic plasticity of F. indigesta. Synthesis Adaptation or plasticity in phenotypic expression have different implications for demographic rate and persistence of species in changing environments. Local adaptation to neighbors suggests that reductions in foundation species diversity could concomitantly lead to reduced genetic diversity of commingled species while a plastic response indicates a more robust and broad response to changing climatic and biotic conditions.

Data from: Does migration promote or inhibit diversification? A case study involving the dominant radiation of temperate Southern Hemisphere freshwater fishes

While theory predicts that dispersal is a pivotal influence on speciation and extinction rates, it can have contradictory effects on each, such that empirical studies are needed to quantify its role. In many studies, dispersal reduction appears to promote diversification, although some analyses of migratory species suggest otherwise. Here we test for a relationship between migratory status and diversification rate within the dominant radiation of temperate Southern Hemisphere freshwater fishes, the Galaxiidae. We reconstructed a molecular phylogeny for the group, comprising >95% of extant lineages, and applied State-dependent Speciation Extinction models to estimate speciation, extinction, and diversification rates. In contrast to some previous studies, we revealed higher diversification rates in non-migratory lineages. The reduced gene flow experienced by non-migratory galaxiids appears to have increased diversification under conditions of allopatry or local adaptation. Migratory galaxiid lineages, by contrast, are genetically homogeneous within landmasses, but may also be rarely able to colonise other landmasses in the temperate Southern Hemisphere. The life history state exhibiting higher diversification likely reflects the spatial context of the study system relative to species dispersal abilities, by means of the intermediate dispersal model; the accurate quantification of dispersal abilities will aid in our understanding of these likely interactions.

Data from: The effectiveness of pseudomagic traits in promoting divergence and enhancing local adaptation

The first file contains the code necessary to generate figures in the style of Fig 1 of the associated manuscript. These figures show the divergence between both ecological traits and mating traits by the strength of mating preference. Different panels correspond to different rates of recombination between these loci that control these types of traits. Files S1 and S2 are Mathematica versions of the corresponding files in the Supplementary Information of the paper.

Data from: Habitat deterioration promotes the evolution of direct development in metamorphosing species

Although metamorphosis is widespread in the animal kingdom, several species have evolved life cycle modifications to avoid complete metamorphosis. Some species, e.g., many salamanders and newts, have deleted the adult stage via a process called paedomorphosis. Others, e.g., some frog species and marine invertebrates, no longer have a distinct larval stage and reach maturation via direct development. Here we study which ecological conditions can lead to the loss of metamorphosis via the evolution of direct development. To do so, we use size-structured consumer-resource models in conjunction with the adaptive-dynamics approach. In case the larval habitat deteriorates, individuals will produce larger offspring and in concert accelerate metamorphosis. While this leads to the evolutionary transition from metamorphosis to direct development when the adult habitat is highly favourable, the population will go extinct in case the adult habitat does not provide sufficient food in order to escape metamorphosis. With a phylogenetic approach we furthermore show that among amphibians the transition of metamorphosis to direct development is indeed, in line with model predictions, conditional on and preceded by the evolution of larger egg sizes.

opencc-zeroAug 2020View details →

Data from: An experimental investigation of how intraspecific competition and phenotypic plasticity can promote the evolution of novel, complex phenotypes

Intraspecific competition has long been considered a key driver of evolutionary diversification, but whether it can also promote evolutionary innovation is less clear. We examined the interplay between competition and phenotypic plasticity in fueling the origins of a novel, complex phenotype––a distinctive carnivore morph found in spadefoot toad tadpoles (genus Spea) that specializes on fairy shrimp. We specifically sought to explore the possible origins of this phenotype by providing shrimp to Scaphiopus holbrookii tadpoles (the sister genus to Spea that does not produce carnivores) while subjecting them to competition for their standard diet of detritus. Previous research had shown that this species will eat shrimp when detritus is limited, and that these shrimp-fed individuals produce features that are redolent of a rudimentary Spea carnivore. In this study, we found that: 1) behavioral and morphological plasticity enabled some individuals to expand their diet to include shrimp; 2) there was heritable variation in this plasticity; and 3) individuals received a growth and development benefit by eating shrimp. Thus, novel resource use can arise via plasticity as an adaptive response to intraspecific competition. More generally, our results show how competition and plasticity may interact to pave the way for the evolution of complex, novel phenotypes, such as the distinctive carnivore morph in present-day Spea.

opencc-zeroAug 2020View details →

Code for individual-based simulations in "Environmental fluctuations can promote evolutionary rescue in high-extinction-risk scenarios"

Substantial environmental change can force a population onto a path towards extinction, but under some conditions, adaptation by natural selection can rescue the population and allow it to persist. This process, known as evolutionary rescue, is believed to be less likely to occur with greater magnitudes of random environmental fluctuations because environmental variation decreases expected population size, increases variance in population size, and increases evolutionary lag. However, previous studies of evolutionary rescue in fluctuating environments have only considered scenarios in which evolutionary rescue was likely to occur. We extend these studies to assess how baseline extinction risk (which we manipulated via changes in the initial population size, degree of environmental change, or mutation rate) influences the effects of environmental variation on evolutionary rescue following an abrupt environmental change. Using a combination of analytical models and stochastic simulations, we show that autocorrelated environmental variation hinders evolutionary rescue in low-extinction-risk scenarios but facilitates rescue in high-risk scenarios. In these high-risk cases, the chance of a run of good years counteracts the otherwise negative effects of environmental variation on evolutionary demography. These findings can inform the development of effective conservation practices that consider evolutionary responses to abrupt environmental changes.

opencc-zeroOct 2020View details →

Interspecific social dominance networks reveal mechanisms promoting coexistence in sympatric charrs in Hokkaido, Japan

1. Coexistence of species requires equalizing mechanisms that minimize fitness differences, which are balanced by stabilizing mechanisms that enhance negative intraspecific interactions versus interspecific ones. Here, we develop a simple theoretical framework that allows measuring the relative strength of intraspecific versus interspecific competition in dominance hierarchies. We use it to evaluate mechanisms promoting coexistence between congeneric charrs that compete for foraging positions, which strongly influence density-dependent growth and survival. 2. Agonistic interactions (n = 761) among 71 Dolly Varden Salvelinus malma and whitespotted charr S. leucomaenis were measured by snorkeling in two pools in the sympatric zone of a Hokkaido stream during two summers. Interspecific dominance hierarchies, analyzed using three methods, were closely correlated with fish length but the species treated each other equally. Ranks for the most dominant fish in each pool, determined directly by knockout experiments, were also virtually identical to ranks by length. 3. Similarly, exponential random graph modeling of the social networks provided no evidence that either species was dominant over the other. Instead, larger fish were more likely to win contests, especially over fish of the next lower ranks. 4. These results demonstrated that the two species were nearly ecological equivalents in accessing key resources in this sympatric zone. Nearly identical growth and stable densities over 4 years further supported this inference, although Dolly Varden were a minority (29% of the assemblage), a sign of some fitness difference. 5. Detailed foraging observations coupled with two concurrent studies revealed an effective stabilizing mechanism. Dolly Varden shifted to feeding directly from the benthos when drifting invertebrates declined, a behavior enhanced by morphological character displacement, thereby partitioning food resources and enhancing intraspecific competition while avoiding agonistic encounters with whitespotted charr. 6. The plurality of evidence indicates that fitness differences between these ecologically equivalent species are small in this local assemblage, and balanced by resource partitioning, a modest stabilizing mechanism that promotes coexistence. The theoretical framework presented here is a useful tool to evaluate the strength of interspecific versus intraspecific competition, which combined with information on tradeoffs in ecological performance can contribute to a mechanistic understanding of species coexistence. 26-Oct-2020

opencc-by-4.0Nov 2013View details →

Genetic architecture promotes the evolution and maintenance of cooperation

Code and data for Frenoy et al 2013 ("Genetic Architecture Promotes the Evolution and Maintenance of Cooperation" in PLoS Computational Biology)

opencc-zeroJan 2021View details →

Species redistribution combined with invasive dominance but not species turnover promotes biotic homogenization following invasion

Disentangling the processes lead to biotic homogenization is important and will guide conservation efforts. Temporal turnover in species composition (i.e., β-diversity) and changes in local α-diversity are two distinct processes drive biotic homogenization, but these effects may be masked by invasive dominance. After removing invasive dominance, we compared the changes in species diversity and species distribution patterns before and after invasion aims to measure the relative contribution of species turnover and local diversity changes to biological homogenization. Invasive dominance indeed had an important contribution to biotic homogenization, and the effects increased with an increase in the invasive species number. Species composition of native plots was not significantly different from invaded plots when removing invasive species. Invasion changed native species distribution patterns and promoted the wide spread of most species, which causes an increase in local richness and community evenness. We highlight that species redistribution combined with invasive dominance but not species turnover promotes biotic homogenization, especially at early invasion stages. Avoiding the ecological impacts of biotic homogenization following invasion will require much stronger proactive management to prevent invasive dominance as well as increase monitoring at the early stages of invasion.

opencc-zeroDec 2017View details →

Data from: Hybridization and postzygotic isolation promote reinforcement of male mating preferences in a diverse group of fishes with traditional sex roles

Behavioral isolation is thought to arise early in speciation due to differential sexual and/or natural selection favoring different preferences and traits in different lineages. Alternatively, behavioral isolation can arise due to reinforcement favoring traits and preferences that prevent maladaptive hybridization. In darters, female preference for male coloration has been hypothesized to drive speciation, because behavioral isolation evolves before F1 inviability. However, as with many long-lived organisms, the fitness of second generation hybrids has not been assessed because raising animals to adulthood in the lab is challenging. Recently, reinforcement of male preferences has been implicated in darters because male preference for conspecific females is high in sympatry but absent in allopatry in multiple species pairs. The hypothesis that reinforcement accounts for behavioral isolation in sympatry assumes that hybridization and postzygotic isolation are present. Here, we used genomic and morphological data to demonstrate that hybridization is ongoing between orangethroat and rainbow darters and used hybrids collected from nature to measure postzygotic barriers across two hybrid generations. We observed sex ratio distortion in adult F1s and a dramatic reduction in backcross survival. Our findings indicate that selection to avoid hybridization promotes the evolution of male-driven behavioral isolation via reinforcement in this system.

opencc-zeroApr 2020View details →

Data from: Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene

Species that evolved in temperate regions during the Pleistocene experienced periods of extreme climatic transitions. Consequent population fragmentation and dynamics had the potential to generate small, isolated populations where the influence of genetic drift would be expected to be strong. We use comparative genomics to assess the evolutionary influence of historical demographics and natural selection through a series of transitions associated with the formation of the genus Capreolus, speciation within this genus during the Quaternary and during divergence among European roe deer (C. capreolus) populations. Our analyses were facilitated by the generation of a new high-coverage reference genome for the Siberian roe deer (Capreolus pygargus). We find progressive reductions in effective population size (Ne), despite very large census sizes in modern C. capreolus populations and show that low Ne has impacted the C. capreolus genome, reducing diversity and increasing linkage disequilibrium. Even so, we find evidence for natural selection shared among C. capreolus populations, including a population that has been through a severe bottleneck. During each period of transition there is evidence for selection, including at loci associated with diapause (delayed embryonic development), a phenotype restricted to this genus among the even-toed ungulates. Together these data allow us to assess expectations for the origin and diversification of a mammalian genus during a period of extreme environmental change.

opencc-zeroDec 2016View details →

Data from: Fast life history traits promote invasion success in amphibians and reptiles

Competing theoretical models make different predictions on which life history strategies facilitate growth of small populations. While 'fast' strategies allow for rapid increase in population size and limit vulnerability to stochastic events, 'slow' strategies and bet-hedging may reduce variance in vital rates in response to stochasticity. We test these predictions using biological invasions since founder alien populations start small, compiling the largest dataset yet of global herpetological introductions and life history traits. Using state-of-the-art phylogenetic comparative methods, we show that successful invaders have fast traits, such as large and frequent clutches, at both establishment and spread stages. These results, together with recent findings in mammals and plants, support 'fast advantage' models and the importance of high potential population growth rate. Conversely, successful alien birds are bet-hedgers. We propose that transient population dynamics and differences in longevity and behavioural flexibility can help reconcile apparently contrasting results across terrestrial vertebrate classes.

opencc-zeroMar 2020View details →

Neural ensemble reactivation in REM and SWS coordinate with muscle activity to promote rapid motor skill learning

Neural activity patterns of recent experiences are reactivated during sleep in structures critical for memory storage, including hippocampus and neocortex. This reactivation process is thought to aid memory consolidation. Although synaptic rearrangement dynamics following learning involve an interplay between slow-wave sleep (SWS) and rapid eye movement sleep (REM), most physiological evidence implicates SWS directly following experience as a preferred window for reactivation. Here we show that reactivation occurs in both REM and SWS, and that coordination of REM and SWS activation on the same day is associated with rapid learning of a motor skill. We performed 6-hour recordings from cells in rats' motor cortex as they were trained daily on a skilled reaching task. In addition to SWS following training, reactivation occurred in REM, primarily during the pre-task rest period, and REM and SWS reactivation occurred on the same day in rats that acquired the skill rapidly. Both pre-task REM and posttask SWS activation were coordinated with muscle activity during sleep, suggesting a functional role for reactivation in skill learning. Our results provide the first demonstration that reactivation in REM sleep occurs during motor skill learning, and that coordinated reactivation in both sleep states on the same day, although at different times, is beneficial for skill learning.

opencc-zeroApr 2020View details →

Decoupled jaws promote trophic diversity in Cichlid fishes

Functional decoupling of oral and pharyngeal jaws is widely considered to have expanded the ecological repertoire of cichlid fishes. But, the degree to which the evolution of these jaw systems is decoupled and whether decoupling has impacted trophic diversification remains unknown. Focusing on the large Neotropical radiation of cichlids, we ask whether oral and pharyngeal jaw evolution is correlated and how their evolutionary rates respond to feeding ecology. In support of decoupling, we find relaxed evolutionary integration between the two jaw systems, resulting in novel trait combinations that potentially facilitate feeding mode diversification. These outcomes are made possible by escaping the mechanical trade-off between force transmission and mobility, which characterizes a single jaw system that functions in isolation. In spite of the structural independence of the two jaw systems, results using a Bayesian, state-dependent, relaxed-clock model of multivariate Brownian motion indicate strongly aligned evolutionary responses to feeding ecology. So, while decoupling of prey capture and processing functions released constraints on jaw evolution and promoted trophic diversity in cichlids, the natural diversity of consumed prey has also induced a moderate degree of evolutionary integration between the jaw systems, reminiscent of the original mechanical trade-off between force and mobility.

opencc-zeroJan 2020View details →

Competition for resources can promote the divergence of social learning phenotypes

Social learning occurs when animals acquire knowledge or skills by observing or interacting with others, and is the fundamental building block of culture. Within populations, some individuals use social learning more frequently than others, but why social learning phenotypes differ among individuals is poorly understood. We modelled the evolution of social learning frequency in a system where foragers compete for resources and there are many different foraging options to learn about. Social learning phenotypes diverged when some options offered much better rewards than others and expected rewards changed moderately quickly over time. When options offered similar rewards or when rewards changed slowly, a single social learning phenotype evolved. This held for fixed and simple conditional social learning rules. Sufficiently complex conditional social learning rules prevented the divergence of social learning phenotypes under all conditions. Our results explain how competition can promote the divergence of social learning phenotypes.

opencc-zeroDec 2017View details →

Data from: Farmer preferences for conservation incentives that promote voluntary phosphorus abatement in agricultural watersheds

Financial incentives are commonly used to promote voluntary adoption of agricultural best management practices (BMPs), but little is known about farmer preferences among alternative incentives. Using experimental procurement auctions, we evaluate how different conservation incentives affect farmer willingness to adopt BMPs that reduce phosphorus (P) runoff, a major driver of harmful algal blooms in Lake Erie. We rank incentives (e.g., payment, BMP insurance, tax credit, and certification price premium) by the cost per pound of P runoff reduction. Payments and tax credits that target high impact areas of the watershed are more cost-effective than untargeted price premiums for product certification. Farmers demand higher payments for contracts offering BMP insurance (i.e., protection against yield loss from BMP use) due to uncertainty about how the program will be implemented and the reliability of indemnities, as well as anticipated transaction costs associated with the program. Understanding farmer preferences for different types of conservation incentives is critical to design agri-environmental programs that engage more farmers and cost-effectively enhance ecosystem services.