Find research datasets worth reusing

Individual variability and versatility in an eco-evolutionary model of avian migration

Seasonal migration is a complex and variable behavior with the potential to promote reproductive isolation. In Eurasian blackcaps (Sylvia atricapilla), a migratory divide in central Europe separating populations with southwest and southeast autumn routes may facilitate isolation, and individuals using new wintering areas in Britain show divergence from Mediterranean winterers. We tracked 100 blackcaps in the wild to characterize these strategies. Blackcaps to the west and east of the divide used predominantly SW and SE directions, respectively, but close to the contact zone many individuals took intermediate (S) routes. At 14.0ºE, we documented a sharp transition from SW to SE migratory directions across only 27 (10–86) km, implying a strong selection gradient across the divide. Blackcaps wintering in Britain took northwesterly migration routes from continental European breeding grounds. They originated from a surprisingly extensive area, spanning 2000 km of the breeding range. British winterers bred in sympatry with SW-bound migrants but arrived 9.8 days earlier on the breeding grounds, suggesting some potential for assortative mating by timing. Overall, our data reveal complex variation in songbird migration and suggest that selection can maintain variation in migration direction across short distances while enabling the spread of a novel strategy across a wide range.

Data from: Integration and harmonization of trait data from plant individuals across heterogeneous sources

Trait data represent the basis for ecological and evolutionary research and have relevance for biodiversity conservation, ecosystem management and earth system modelling. The collection and mobilization of trait data has strongly increased over the last decade, but many trait databases still provide only species-level, aggregated trait values (e.g. ranges, means) and lack the direct observations on which those data are based. Thus, the vast majority of trait data measured directly from individuals remains hidden and highly heterogeneous, impeding their discoverability, semantic interoperability, digital accessibility and (re-)use. Here, we integrate quantitative measurements of verbatim trait information from plant individuals (e.g. lengths, widths, counts and angles of stems, leaves, fruits and inflorescence parts) from multiple sources such as field observations and herbarium collections. We develop a workflow to harmonize heterogeneous trait measurements (e.g. trait names and their values and units) as well as additional information related to taxonomy, measurement or fact and occurrence. This data integration and harmonization builds on vocabularies and terminology from existing metadata standards and ontologies such as the Ecological Trait-data Standard (ETS), the Darwin Core (DwC), the Thesaurus Of Plant characteristics (TOP) and the Plant Trait Ontology (TO). A metadata form filled out by data providers enables the automated integration of trait information from heterogeneous datasets. We illustrate our tools with data from palms (family Arecaceae), a globally distributed (pantropical), diverse plant family that is considered a good model system for understanding the ecology and evolution of tropical rainforests. We mobilize nearly 140,000 individual palm trait measurements in an interoperable format, identify semantic gaps in existing plant trait terminology and provide suggestions for the future development of a thesaurus of plant characteristics. Our work thereby promotes the semantic integration of plant trait data in a machine-readable way and shows how large amounts of small trait data sets and their metadata can be integrated into standardized data products.

Selection on individuals of introduced species starts before introduction

Biological invasion is a global problem with large negative impacts on ecosystems and human societies. When a species is introduced, individuals will first have to pass through the invasion stages of uptake and transport, before actual introduction in a non-native range. Selection is predicted to act during these earliest stages of biological invasion, potentially influencing the invasiveness and/or impact of introduced populations. Despite this potential impact of pre-introduction selection, empirical tests are virtually lacking. To test the hypothesis of pre-introduction selection, we followed the fate of individuals during capture, initial acclimation, and captivity in two bird species with several invasive populations originating from the international trade in wild-caught pets (the weavers Ploceus melanocephalus and Euplectes afer). We confirm that pre-introduction selection acts on a wide range of physiological, morphological, behavioral and demographic traits (incl. sex, age, size of body/brain/bill, bill shape, body mass, corticosterone levels, and escape behavior); these are all traits which likely affect invasion success. Our study thus comprehensively demonstrates the existence of hitherto ignored selection acting before the actual introduction into non-native ranges. This could ultimately change the composition and functioning of introduced populations, and therefore warrants greater attention. More knowledge on pre-introduction selection also might provide novel targets for the management of invasive species, if pre-introduction filters can be adjusted to change the quality and/or quantity of individuals passing through such that invasion probability and/or impacts are reduced.

opencc-by-4.0Oct 2020View details →

Individualized Nutritional Support versus Usual Care in Medical Inpatients at Risk of Malnutrition: Randomized Trial

Dataset for analysis of the trial "Individualized Nutritional Support versus Usual Care in Medical Inpatients at Risk of Malnutrition"

SARS-CoV-2 transmission and control in a hospital setting: an individual-based modelling study

Background: Development of strategies for mitigating the severity of COVID-19 is now a top public health priority. We sought to assess strategies for mitigating the COVID-19 outbreak in a hospital setting via the use of non-pharmaceutical interventions. Methods: We developed an individual-based model for COVID-19 transmission in a hospital setting. We calibrated the model using data of a COVID-19 outbreak in a hospital unit in Wuhan. The calibrated model was used to simulate different intervention scenarios and estimate the impact of different interventions on outbreak size and workday loss. Findings: The use of high efficacy facial masks was shown to be able to reduce infection cases and workday loss by 80% (90% CrI: 73.1% - 85.7%) and 87% (CrI: 80.0% - 92.5%), respectively. The use of social distancing alone, through reduced contacts between healthcare workers, had a marginal impact on the outbreak. Our results also indicated that a quarantine policy should be coupled with other interventions to achieve its effect. The effectiveness of all these interventions was shown to increase with their early implementation. Conclusions: Our analysis shows that a COVID-19 outbreak in a hospital's non-COVID-19 unit can be controlled or mitigated by the use of existing non-pharmaceutical measures.

Data from: Fitness outcomes in relation to individual variation in constitutive innate immune function

Although crucial for host survival when facing persistent parasite pressure, costly immune functions will inevitably compete for resources with other energetically expensive traits such as reproduction. Optimising, but not necessarily maximising, immune function might therefore provide net benefit to overall host fitness. Evidence for associations between fitness and immune function is relatively rare, limiting our potential to understand ultimate fitness costs of immune investment. Here, we assess how measures of constitutive immune function (haptoglobin, natural antibodies, complement activity) relate to subsequent fitness outcomes (survival, reproductive success, dominance acquisition) in a wild passerine (Malurus coronatus). Surprisingly, survival probability was not positively linearly predicted by any immune index. Instead, both low and high values of complement activity (quadratic effect) were associated with higher survival, suggesting that different immune investment strategies might reflect a dynamic disease environment. Positive linear relationships between immune indices and reproductive success suggest that individual heterogeneity overrides potential resource reallocation trade-offs within individuals. Controlling for body condition (size-adjusted body mass) and chronic stress (heterophil-lymphocyte ratio) did not alter our findings in a sample subset with available data. Overall, our results suggest that constitutive immune components have limited net costs for fitness and that variation in immune maintenance relates to individual differences more closely.

Male fairy-wrens produce and maintain vibrant breeding colours irrespective of individual quality

Conspicuous colours may signal individual quality if high-quality individuals produce more elaborate colours or have a greater capacity to invest in colour maintenance. We investigate these hypotheses using repeated within-individual observations and experimentally-induced colour production in a wild bird, the superb fairy-wren (Malurus cyaneus). Male superb fairy-wrens undergo an annual moult from brown, non-breeding plumage to an ultraviolet-blue and black breeding plumage. Colour maintenance is especially relevant for this species because structural, ultraviolet-blue plumage colours are particularly susceptible to fading. Further, only the most sexually attractive males moult to breeding plumage early (before spring) and thereby keep their colours for an extended time before the breeding season. Our results show that (i) sexually attractive, early-moulting males do not have higher quality breeding colours and (ii) breeding colours are not impacted by experimentally inducing males to moult early and while in low body condition. We found that (iii) breeding colours do not fade but remain consistent or become more saturated within individuals over time. Despite this, (iv) males do not spend more time preening while in breeding plumage. Instead, males keep their colours in pristine condition by re-moulting parts of their breeding plumage throughout the breeding season, suggesting an alternative, potential cost of maintaining ornamental colours. We conclude that variation in structural breeding colours is unlikely to indicate individual quality in superb fairy-wrens.

opencc-zeroAug 2021View details →

Hare's affairs: lessons learnt from a noninvasive genetic monitoring for tracking mountain hare individuals

Systematic monitoring of individuals and their abundance over time has become an important tool to provide information for conservation. For genetic monitoring studies, noninvasive sampling has emerged as a valuable approach, particularly so for elusive or rare animals. Here, we present the five-year results of an ongoing noninvasive genetic monitoring of mountain hares (Lepus timidus) in a protected area in the Swiss Alps. We used nuclear microsatellites and a sex marker to identify individuals and assign species to noninvasively collected feces samples. Through including a marker for sex identification, we were able to assess sex-ratio changes and sex-specific demographic parameters over time. Male abundance in the area showed high fluctuations and apparent survival for males was lower than for females. Generally, males and females showed only little temporary migration into and out of the study area. Additionally, using genotyped tissue samples from mountain hares, European hares (Lepus europaeus) and their hybrids, we were able to provide evidence for the first occurrence of a European hare in the study area at an elevation of 2300 m a.s.l. in spring 2016. For future monitoring studies, we suggest to include complementary analysis methods to reliably infer species identities of the individuals analyzed and thus, not only monitor mountain hare individual abundance, but also assess the potential threats given through competitive exclusion by and hybridization with the European hare.

opencc-by-4.0Nov 2020View details →

DATS 6103 - Individual Project 2 - Graham Hulsey

Hello! This page contains the results from a Data Mining project I completed for DATS 6103. For this project, I web scraped headlines from 12 major news outlets:   1. <a href="https://www.nytimes.com/">New York Times</a> 2. <a href="https://www.washingtonpost.com/">Washington Post</a> 3. <a href="https://www.cnbc.com">CNBC</a> 4. <a href="https://www.aljazeera.com/">Al-Jazeera</a> 5. <a href="https://bbc.com/news">BBC</a> 6. <a href="https://global.chinadaily.com.cn/">China Daily</a> 7. <a href="https://www.foxnews.com/">Fox News</a> 8. <a href="https://en.mehrnews.com/">Mehr News</a> 9. <a href="https://www.theatlantic.com/">The Atlantic</a> 10. <a href="https://www.buzzfeed.com/">Buzzfeed</a> 11. <a href="https://www.newyorker.com/">New Yorker</a> 12. <a href="https://www.motherjones.com/">Mother Jones</a> Using the text data, I wanted to analyze which issues got covered by which outlets, and how news coverage changed in response to major events surround this US election. All graphs and analysis are uploaded with this page. If you would like to download the raw data and code, you can visit my Github page <a href="https://github.com/grahamh39/DATS6103-Project-2-Graham-Hulsey-">here</a>. You can visit my <a href="https://grahamh39.github.io/">github.io page</a> site to view the analysis as well.

Colorful traits in avian females, individual condition, reproductive performance, and male mate preferences: A meta-analytic approach

Colorful ornaments in females are suggested to have evolved and be maintained by sexual selection. Although several studies have evaluated this idea evidence is still equivocal. Results from empirical studies have been compilated in reviews, but quantitative analyses have seldom been performed. Here, using a meta-analytic approach, we show that evidence from empirical studies conducted in birds, supports the ideas that colorful female ornaments are positively associated with individual condition, reproductive performance, and male-mate preferences. Hence, females' colorful traits, in birds, likely evolved and are maintained by sexual selection.

opencc-by-4.0Nov 2020View details →

EPSRC HEED Data Repository: Individual Appliance Monitoring System

The dataset deposited here was prepared under the EPSRC-funded <a href="http://heed-refugee.coventry.ac.uk/">Humanitarian Engineering and Energy for Displacement</a> research project (EP/P029531/1). The project aimed to understand energy needs of displaced communities, create an evidence base on the usage of different energy interventions and provide recommendations for improved design of future energy interventions to better meet the needs of people.  As part of the project, we deployed an Individual Appliance Monitoring (IAM) System in the Uttargaya settlement in Nepal. The Individual Appliance Monitoring System provides a simple, cost-effective and unobtrusive method of collecting data on the energy usage of connected appliances with the aim to: Evaluate energy consumption of different appliances and Evaluate usage patterns for different appliances. The monitoring system comprises of 2 types of devices – Energenie MiHome Smart Plugs MIHO005 (i.e. Individual Appliance Monitors (IAM)) to sense data relating to power and voltage drawn by the connected appliance, and gateway nodes to collect data from IAM. The unit cost of a MIHO005 adaptor and Raspberry Pi-based gateway is £34.99 and £74.17 respectively. The main component of the gateway node is a Raspberry Pi fitted with an Energenie ENER314-RT (receiver-transmitter) add-on board to allow the Pi to communicate with the smart plugs. The data collected by the gateway is stored locally in an SD card as well as sent to the heed-data server hosted in Coventry University. Post Deployment Challenges: ·         Power outages: These are common in the camp. Data is lost during this time as the devices have no access to power. ·         Internet connectivity: The availability and reliability of Wi-Fi continue to be an issue for the transmission of data to heed-data server.

Quantifying capital vs. income breeding: new promise with stable isotope measurements of individual amino acids

1. Capital breeders accumulate nutrients prior to egg development, then use these stores to support offspring. In contrast, income breeders rely on local nutrients consumed contemporaneously with offspring development. Understanding such nutrient allocations is critical to assessing wildlife reliance on different habitats. 2. Despite the contrast between these strategies, it remains challenging to trace nutrients from endogenous stores or exogenous food intake into offspring. Here, we tested a new solution to this problem. 3. Using tissue samples collected opportunistically from wild emperor penguins (Aptenodytes forsteri), which exemplify capital breeding, we hypothesized that the stable carbon (δ13C) and nitrogen (δ15N) isotope values of individual amino acids (AA) in endogenous stores (e.g., muscle) and in egg yolk and albumen reflect the nutrient sourcing that distinguishes capital versus income breeding. Unlike other methods, this approach does not require untested assumptions or diet sampling. 4. We found that over half of essential AA had δ13C values that did not differ between muscle and yolk or albumen, suggesting that most of these AA were directly routed from muscle into eggs. In contrast, almost all non-essential AA differed in δ13C values between muscle and yolk or between muscle and albumen, suggesting de novo synthesis. Over half of AA that have labile nitrogen atoms (i.e., "trophic" AA) had higher δ15N values in yolk and albumen than in muscle, suggesting that they were transaminated during their routing into egg tissue. This effect was smaller for AA with less labile nitrogen atoms (i.e., "source" AA). 5. Our results indicate that the δ15N offset between trophic-source AA (Δ15Ntrophic-source) may provide an index of the extent of capital breeding. The value of emperor penguin Δ15NPro-Phe was higher in yolk and albumen than in muscle, reflecting the mobilization of endogenous stores; in comparison, the value of Δ15NPro-Phe was similar across muscle and egg tissue in previously-published data for income-breeding herring gulls (Larus argentatus smithsonianus). Our results provide a quantitative basis for using AA δ13C and δ15N, and isotopic offsets among AA (e.g., Δ15NPro-Phe), to explore the allocation of endogenous versus exogenous nutrients across the capital versus income spectrum of avian reproduction.

Color scores, COI haplotypes and SNP data for Phelotrupes auratus individuals

We studied the population genetic structure underlying the geographic variation in the structural color of the geotrupid dung beetle, Phelotrupes auratus, which exhibits metallic body colors of different reflectance wavelengths perceived as red, green, and indigo. These forms occur parapatrically in an area of Japan. The color variation was not related to variation in climatic factors. Using single-nucleotide polymorphisms (SNPs) from restriction-site associated DNA sequences, we discriminated five groups of populations (west/red, south/green, south/indigo, south/red, and east/red) by a combination of genetic clusters (west, south, and east) and three color forms. There were three transition zones for the color forms: two between the red and green forms were hybrid zones with steep genetic clines, which implies the existence of barriers to gene flow between regions with different colors. The remaining transition zone between the green and indigo forms lacked genetic differentiation, despite the evident color changes, which implies regionally specific selection on the different colors. In a genome-wide association study, we identified four SNPs that were associated with the red/green or indigo color and were not linked with one another, which implies that the coloration was controlled by multiple loci, each affecting the expression of a different color range. These loci may have controlled the transitions between different combinations of colors. Our study demonstrates that geographic color variation within a species can be maintained by nonuniform interactions among barriers to gene flow, locally specific selection on different colors, and the effects of different color loci.

opencc-zeroDec 2020View details →

Seasonal isotopic niche of a rodent: High between-individual variation but no changes in individual niche width during the rich-resource period

The dynamics of trophic niche width in animals at both population- and individual-level is potentially influenced by temporal variation of food resources, by between-individual differences in food-resource rank preferences, and also by competition. Using stable isotope of carbon and nitrogen (δ13C and δ15N) of fecal samples, we investigated the trophic niche dynamics and individual variation in food-resource use by the arboreal rat Rhipidomys macrurus, in the highly seasonal Brazilian savanna (Cerrado). We tested the hypothesis that dietary niche expansion during the rich-resource period (wet season) occurs via individual specialization and consequently lower individual niche overlap in contrast with niche retraction during the low-resource period (dry season) via increase in niche overlap and expansion of individual niches. The results indicated that R. macrurus is primarily frugivorous and presents a wider isotopic niche in the rich-resource period in comparison to the low-resource period. The increase in niche width was achieved by individual specialization (decrease in niche overlap), as expected. During the low-resource period, however, individual niche widths were not wider than during the rich-resource period. Additionally, individual body condition was lower in the wet season than in the dry season, suggesting higher competition in this period. We conclude that an increase in the population niche may involve only between-individual variation and not necessarily requiring changes in individual niche width. We propose that the combination of ecological opportunity (high resource diversity) in addition to a greater competition in the warm-wet season leads to expansion of the population trophic niche width via individual specialization.

opencc-by-4.0Dec 2020View details →

Dataset associated with "Thermoelectric signature of individual skyrmions"

Dataset for the article: A. Fernández Scarioni, C. Barton, H. Corte-León, S. Sievers, X. Hu, F. Ajejas, W. Legrand, N. Reyren, V. Cros, O. Kazakova, H. W. Schumacher, “Thermoelectric signature of individual skyrmions,” Phys. Rev. Lett. The data is divided in figures and for each figure we report the raw data. For more information follow the Readme.txt file .

opencc-zeroDec 2020View details →

Data from: The sources of variation for individual prey-to-predator size ratios

The relative body size at which predators are willing to attack prey, a key trait for predator-prey interactions, is usually considered invariant. However, this ratio can vary widely among individuals or populations. Identifying the range and origin of such variation is key to understanding the strength and constraints on selection in both predators and prey. Still, these sources of variation remain largely unknown. We filled this gap by measuring the genetic, maternal and environmental variation of the maximum prey-to-predator size ratio (PPSRmax) in juveniles of the wolf spider Lycosa fasciiventris using a paternal half-sib split brood design, in which each male was paired with two different females and the offspring reared in two different food environments: poor and rich. Each juvenile spider was then sequentially offered crickets of decreasing size and the maximum prey size killed was determined. We also measured body size and body condition of spiders upon emergence and just before the trial. We found low, but significant heritability (h2=0.069) and dominance and common environmental variance (d2+4c2=0.056). PPSRmax was also partially explained by body condition (during trial) but there was no effect of the rearing food environment. Finally, a maternal correlation between body size early in life and PPSRmax indicated that offspring born larger were less predisposed to feed on larger prey later in life. Therefore, PPSRmax, a central trait in ecosystems, can vary widely and this variation is due to different sources, with important consequences for changes in this trait in the short and long terms.

opencc-by-4.0Dec 2020View details →

Replication package for: Improving Management with Individual and Group-Based Consulting: Results from a Randomized Experiment in Colombia

This package contains the data and code needed to reproduce tables and figures in Iacovone, Maloney and McKenzie (forthcoming) " Improving Management with Individual and Group-Based Consulting: Results from a Randomized Experiment in Colombia"., Review of Economic Studies.  Anonymized firm data are provided for analyzing impacts on management and employment. Authorized log files and output files are provided for analysis that uses the confidential EAM data, along with instructions for applying to access these data if required.

opencc-zeroJan 2021View details →

Sequential organization of birdsong: Relationships with individual quality and fitness

Many vocalizing animals produce the discrete elements of their acoustic signals in a specific sequential order, but we know little about the biological relevance of this ordering. For that, we must characterize the degree by which individuals differ in how they organize their signals sequentially and relate these differences to variation in quality and fitness. In this study, we fulfilled these tasks in male collared flycatchers (Ficedula albicollis). We characterized the sequential order of syllables with a network analysis approach and studied the consistency of network variables on distinct time-scales (within-day, between-day, and between-year), and assessed their relationship with such quality indicators as age, body condition, arrival date, and fitness-related proxies like survival to the next year and pairing success. We found that the syllables were associated non-randomly with one another and both the frequency differences of consecutive syllables and the number of motif types were higher in the original than in randomized syllable sequences. Average degree and small-worldness showed considerable among-individual differences and decreasing repeatability with increasing time-scale. Furthermore, we found relationships between male age and average degree among and within individuals. Accordingly, older males produce syllable sequences by using common syllables less often than younger individuals. However, the network variables showed no relationship with fitness-related variables. In conclusion, the sequential organization of birdsong has the potential to encode individual-specific characteristics, which thus could be used as signals in social interactions and thus potentially could be subject to sexual selection.

opencc-by-4.0Jan 2021View details →

Estimating individual level plant traits at scale: input data

This dataset includes the input data to ensure replicability of the results. This dataset include the (1) reflectance for individual tree crowns, extracted from field and algorithmically delineated crowns in 2 NEON sites (OSBS and TALL); (2) the associated measures of tree traits (N%, C%, P%, LMA). The folder should be decompressed inside of the root directory of the project in https://github.com/MarconiS/Estimating-individual-level-plant-traits-at-scale/ for correctly replicate the analysis.