Find research datasets worth reusing

opencc-by-4.0Oct 2024View details →

Low-intensity insect herbivory could have large effects on ecosystem productivity through reduced canopy photosynthesis. R code and data.

R code and data to reproduce analysis in the publication: Visakorpi K., Gripenberg S., Malhi Y. and Riutta T. Low-intensity insect herbivory could have large effects on ecosystem productivity through reduced canopy photosynthesis. Web Ecology, 2024.   File named "Visakorpietal2024_litteratureSurvey.csv" contains data collected from literature survey and to perform a meta-analysis. The columns contain the following data: Reference = unique identifier for each study group_id = if a study described several experiments or treatments, this column identifies them from each other. Plant_species = name of the plant species studied Herbivore_species = name of the herbivore species studies Plant_species_phylo and Plant_species_phylo2 = alternative ways to write the plant species name for phylogenetic analysis Plant_clade = Angiosperm or Gymnosperm Growth_form = seedling, sapling or tree Herbivore_order = phylogenetic order of the herbivore species Herbivore_family = phylogenetic family of the herbivore species Type_of_herbivory = chewing, sap-sucking, root-feeding, leafmining or bark-feeding Leaf_type = whether the leaf that was measured was damaged by herbivores, or intact Manipulation = whether herbivores were added (A) or removed (R) Year_published = year when the study was published PN_herb, SD_herb, se_herb, n_herb = photosynthetic rate, standard deviation, standard error, and sample size, of the treatment group (i.e. experiencing herbivory) PN_intact, SD_intact, se_intact, n_intact = photosynthetic rate, standard deviation, standard error, and sample size, of the control group (i.e. not experiencing herbivory) Indirect_effect, SD_indirect = the proportional difference in photosynthetic rates between the treatment and control values, and the standard deviation of the proportional difference

opencc-by-4.0Apr 2024View details →

Data and R code used in Hennecke et al. "Plant species richness and the root economics space drive soil fungal communities"

To investigate how plant diversity and root traits relate to soil fungal communities, in 2021 we collected trait data from plots in the Jena Experiment (https://the-jena-experiment.de; funded by the DFG FOR 5000) and characterized fungal communities by sequencing, respiration and lipid fatty acid quantification.

opencc-by-4.0Jun 2021View details →

Sample Raw (PPG, Accel, and Gyro) and Processed (steps, calories, sleep, HR, HRV, SPO2, Respiratory Rate, R-R) data over 24 hours

Over the course of 24 hours, we collected raw (Photoplethysmography (PPG), Acceleration, and Gyro) and processed (steps, calories, sleep, HR, HRV, SPO2, Respiratory Rate, R-R) data samples. Biostrap approaches health insights from a data-driven perspective. Our clinical-grade hardware enables users to accurately track SpO2, HRV, RHR, and a variety of other biometrics with confidence.

opencc-zeroSep 2021View details →

Compiled comparative data and the R code from: "Why do some primate mothers carry their infant's corpse? A cross-species comparative study"

Non-human primates respond to the death of a conspecific in diverse ways, some of which may present phylogenetic continuity with human thanatological responses. Of these responses, infant corpse carrying by mothers (ICC) is the most frequently reported. Despite its prevalence, quantitative analyses of this behaviour are scarce and inconclusive. We compiled a database of 409 published cases across 50 different primate species of mothers' responses to their infants' deaths and used Bayesian phylogenetic regressions with an information-theoretic approach to test hypotheses proposed to explain between- and within-species variation in ICC. We found that ICC was more likely when the infant's death was non-traumatic (e.g. illness) versus traumatic (e.g. infanticide), and when the mother was younger. These results support the death detection hypothesis, which proposes that ICC occurs when there are fewer contextual or sensory cues indicating death. Such an interpretation suggests that primates are able to attain an awareness of death. In addition, when carried, infant age affected ICC duration, with longer ICC observed for younger infants. This result suggests that ICC is a by-product of strong selection on maternal behaviour. The findings are discussed in the context of the evolution of emotion, and implications for evolutionary thanatology are proposed.

opencc-zeroSep 2021View details →

Data and R code from: Nature calls: intelligence and natural foraging style predict welfare problems in captive parrots

Around half of all parrots (a highly threatened order) live in captivity. Here, some species thrive. Others, however, breed poorly or display stereotypic behaviours indicating stress. Using data on the prevalence of three types of stereotypic behaviour in pet (50 species; 1,378 individuals) and aviculture hatch rates (115 species; 10,255 breeding pairs), we applied Phylogenetic Comparative Methods (PCMs) to test hypothesised causes of this variation (relating to species' rarity and constraints on natural behaviour). In the first empirical evidence that high intelligence increases vulnerability to poor captive welfare, species with large relative brain sizes were found to be most at risk of oral and whole-body stereotypic behaviour. This suggests that if they are to be kept in private homes, such parrots must be offered substantially more cognitive stimulation. Self-harming behaviours involving feather damage were predicted by naturally relying on food items that require substantial handling, highlighting inadequacies in captive diets (often highly processed); while relatively low hatch rates in aviculture were predicted by small captive population sizes, potentially due to genetic bottlenecks, inbreeding, and/or low availability of compatible mates. These novel findings should help advance captive parrot husbandry, and inspire further research applying PCMs to understand and improve animal welfare.

opencc-zeroSep 2021View details →

Data and R scripts from: Assemblage reorganisation of South African dragonflies due to climate change

Aim: Climate change is expected to cause large shifts in species assemblages such as dragonflies and damselflies (Insecta: Odonata). Here we assess the influence of environmental drivers of turnover on Odonata assemblages. Secondly, we map the predicted spatial variation in species composition, first as a gradient of assemblage similarity, and then as discrete bioregions delineating major areas of odonate endemism. Finally, we map the magnitude of expected change in species turnover in response to climate change under two emission scenarios. Location: South Africa Methods: We used a spatial database comprising of 164 species of odonates and 20 covariates, to explore changes in compositional turnover using generalised dissimilarity models. Bioregions were compiled through various clustering techniques. Results: Present-day odonate bioregions correspond to climatic zones and are clearly separated by transitional zones with rapid spatial turnover. Present odonate bioregions are projected to undergo extensive reorganisation by 2050 and 2070. Temporal turnover in species composition is expected to reach up to 80% in the large arid interior and 64% along the coast. Half of all South Africa's protected areas are likely to experience climate-induced changes to dragonfly bioregions in the near future. Main conclusions: Species assemblages are rapidly changing. This work highlights future shifts in climate will result in complex and non-linear responses in Odonata communities. With ongoing climate change, current odonate bioregions are predicted to expand while others will contract considerably in size within the next thirty years. The current demarcated protected areas may be inadequate to protect dragonflies as climates change. Odonata can be used to track forefronts of climate change, which will likely affect a larger array of taxa as well.

opencc-by-4.0Dec 2020View details →

Data and R-Scripts: Predicting hotspots for invasive species introduction in Europe

The .rar file comprises all data and R-scripts needed to replicate our study entitled "Predicting Hotspots for Invasive Species Introduction in Europe" published in Environmental Research Letters. The folder data holds all input data as well as the final datasets used for training the algorithms, in the subfolder A_ML_ready_datasets. The folder descriptives provides tables with descriptive statistics. The folder figures provides files for all figures displayed in the manuscript and the supplementary material as well as visualizations of descriptive statistics for all background approaches in the corresponding subfolders. The folder results holds all generated results. The folder scripts provides all R-scripts used for intermediate computations. The master and master_results scripts coordinate all computations and the generation of results, respectively. Notably, various spatial layers were used to extract point-values of features which subsequently were used to estimate the models and generate the predictions. Here, we only upload the extracted point-values in the data folder. If you are interested in using any of the raw spatial layers, please refer to section 2.1.3. of our publication to find the corresponding references. Alternatively, feel free to reach out to me and I will direct you to the original databases and/or send you the raw spatial layers.

opencc-zeroOct 2021View details →

Emergence and radiation of distemper viruses in terrestrial and marine mammals - Input files, bash and R codes for analysing PDV and CDV sequence data

Canine distemper virus (CDV) and phocine distemper virus (PDV) are major pathogens to terrestrial and marine mammals. Yet little is known about the timing and geographical origin of distemper viruses and to what extent it was influenced by environmental change and human activities. To address this, we i) performed the first comprehensive time-calibrated phylogenetic analysis of the two distemper viruses; ii) mapped distemper antibody and virus detection data from marine mammals collected between 1972-2018; iii) and compiled historical reports on distemper dating back to the 18th century. We find that CDV and PDV diverged in the early 17th century. Modern CDV strains last shared a common ancestor in the 19th century with a marked radiation during the 1930s-50s. Modern PDV strains are of more recent origin, diverging in the 1970s-80s. Based on the compiled information on distemper distribution, the diverse host range of CDV and basal phylogenetic placement of terrestrial morbilliviruses, we hypothesize a terrestrial CDV-like ancestor giving rise to PDV in the North Atlantic. Moreover, given the estimated timing of distemper origin and radiation, we hypothesize a prominent role of environmental change such as the Little Ice Age, and human activities like globalisation and war in distemper virus evolution.

opencc-by-4.0Nov 2022View details →

Data and R code for statistical analyses on trap experiments

Data and R code for statistical analyses related to trap experiments used in the article titled "Attractant activity of host-related chemical blends on the Poultry Red Mite at different spatial scales". Data are provided as two .csv files and codes as one .rmd file and one .R file as follows: - 6-trap laboratory experiments (data_PRM_lab_6-trap_experiments.csv and Lab_6-trap-experiments.rmd) - field experiments (data_PRM_field_trapping.csv and Field_trap_analyses.R).

Evaluating drivers of female dominance in the spotted hyena: R code and data

Introduction: Dominance relationships in which females dominate males are rare among mammals. Mechanistic hypotheses explaining the occurrence of female dominance suggest that females dominate males because 1) they are intrinsically more aggressive or less submissive than males, and/or 2) they have access to more social support than males. Methods: Here, we examine the determinants of female dominance across ontogenetic development in spotted hyenas (Crocuta crocuta) using 30 years of detailed behavioral observations from the Mara Hyena Project to evaluate these two hypotheses. Results: Among adult hyenas, we find that females spontaneously aggress at higher rates than males, whereas males spontaneously submit at higher rates than females. Once an aggressive interaction has been initiated, adult females are more likely than immigrant males to elicit submission from members of the opposite sex, and both adult natal and immigrant males are more likely than adult females to offer submission in response to an aggressive act. We also find that adult male aggressors are more likely to receive social support than adult female aggressors, and that both adult natal and immigrant males are 2-3 times more likely to receive support when attacking a female than when attacking another male. Across all age classes, females are more likely than males to be targets of aggressive acts that occur with support. Further, receiving social support does slightly help immigrant males elicit submission from adult females compared to immigrant males acting alone, and it also helps females elicit submission from other females. However, adult females can dominate immigrant males with or without support far more often than immigrant males can dominate females, even when the immigrants are supported against females. Discussion: Overall, we find evidence for both mechanisms hypothesized to mediate female dominance in this species: 1) male and female hyenas clearly differ in their aggressive and submissive tendencies, and 2) realized social support plays an important role in shaping dominance relationships within a clan. Nevertheless, our results suggest that social support alone cannot explain sex-biased dominance in spotted hyenas. Although realized social support can certainly influence fight outcomes among females, adult females can easily dominate immigrant males without any support at all.

Data, sample sizes, and R code for analysis of: Variation in mutation (co)variances

Because of pleiotropy, mutations affect the expression and inheritance of multiple traits and, together with selection, are expected to shape standing genetic covariances between traits and eventual phenotypic divergence between populations. It is therefore important to find if the M matrix, describing mutational variances of each trait and covariances between traits, varies between genotypes. We here estimate the M matrix for six locomotion behavior traits in lines of two genotypes of the nematode Caenorhabditis elegans that accumulated mutations in a nearly-neutral manner for 250 generations. We find significant mutational variance along at least one phenotypic dimension of the M matrices, but neither their size nor their orientation had detectable differences between genotypes. The number of generations of mutation accumulation, or the number of MA lines measured, was likely insufficient to sample enough mutations and detect potentially small differences between the two M matrices. We then tested if the M matrices were similar to one G matrix describing the standing genetic (co)variances of a population derived by the hybridization of several genotypes, including the two measured for M, and domesticated to a lab-defined environment for 140 generations. We found that the M and G were different because the genetic covariances caused by mutational pleiotropy in the two genotypes are smaller than those caused by linkage disequilibrium in the lab population. We further show that M matrices differed in their alignment with the lab population G matrix. If generalized to other founder genotypes of the lab population, these observations indicate that selection does not shape the evolution of the M matrix for locomotion behavior in the short-term of a few tens to hundreds of generations and suggests that the hybridization of C. elegans genotypes allows selection on new phenotypic dimensions of locomotion behavior.

Data and R scripts for: Effects of hunting on genetic diversity, inbreeding and dispersal in Finnish black grouse (Lyrurus tetrix)

While intensive hunting activities, such as commercial fishing and trophy hunting, can have profound influences on natural populations, less intensive recreational hunting can also have more subtle effects on animal behaviour, habitat use and movement, with implications for population persistence. Lekking species such as the black grouse (Lyrurus tetrix) may be especially prone to hunting as leks are temporally and spatially predictable, making them easy targets. Furthermore, inbreeding in black grouse is mainly avoided through female-biased dispersal, so any disruptions to dispersal caused by hunting could lead to changes in gene flow, leading to an increasing risk of inbreeding. We therefore investigated the impact of hunting on genetic diversity, inbreeding and dispersal on a metapopulation of black grouse in Central Finland. We genotyped 1,065 adult males and 813 adult females from twelve lekking sites (six hunted, six unhunted) and 200 unrelated chicks from seven sites (two hunted, five unhunted) at up to thirteen microsatellite loci. Our initial confirmatory analysis of sex-specific fine-scale population structure revealed little genetic structure in the metapopulation. Levels of inbreeding did not differ significantly between hunted and unhunted sites in both adults and chicks. However, immigration rates into hunted sites were significantly higher among adults compared to immigration into unhunted sites. We conclude that the influx of migrants into hunted sites may compensate for the loss of harvested individuals, thereby increasing gene flow and mitigating inbreeding. Given the absence of any obvious potential barriers to gene flow in Central Finland, a spatially heterogeneous matrix of hunted and unhunted regions may be crucial to ensure sustainable harvests into the future.

Data and R scripts for: Ant invasions is associated with lower root density and different root distribution of a foundational savanna tree species

Some invasive ants have worldwide distributions and impose substantial impacts on human society and native biodiversity. Yet we know little about how ants impact soil ecosystems in general, much less how soil ecosystems shift when invasive ants move in. We excavated the coarse roots of a monodominant savanna tree in invaded and uninvaded areas to test the hypothesis that the presence of invasive ants would be associated with changes in root distribution and biomass across the landscape. We found that in the presence of invasive ants, trees had a shifted distribution of lateral coarse roots, with proportionally less root biomass near the surface and far from tree stems. In addition, the density of lateral coarse-root biomass was ~20% lower for trees within invaded landscapes. Our results suggest that soil-nesting invasive ants can drive important changes in rooting strategy for a tree species that serves a foundational role in the biogeochemical cycles of vertisol savannas.

opencc-zeroMar 2023View details →

Data and R code for: Temperature-induced multispecies cohort effects in sympatric snakes

In reptiles, reproductive maturity is often determined by size rather than age. Consequently, growth early in life may influence population dynamics through effects on generation time and survival to reproduction. Because reproductive phenology and pre- and post-natal growth are temperature-dependent, environmental conditions may induce multi-species cohort effects on body size in sympatric reptiles. I present evidence of this using ten years of neonatal size data for three sympatric viviparous snakes, Dekay's Brownsnakes (Storeria dekayi), Red-bellied Snakes (S. occipitomaculata) and Common Gartersnakes (Thamnophis sirtalis). End-of-season neonatal size varied in parallel across species such that snout-vent length was 36-61% greater and mass was 65-223% greater in years when gestating females could achieve higher April-May (vs. June-July or August-September) operative temperatures. Thus, temperature had a larger impact during follicular enlargement and ovulation than during gestation or post-natal growth. Multi-species cohort effects like these may affect population dynamics and increase with climate change.

opencc-zeroMar 2023View details →

Data and R scripts from: Using conservation genetics to prioritise management options for an endangered songbird

Genetic data can be highly informative for answering questions relevant to practical conservation efforts but remain one of the most neglected aspects of species recovery plans. Framing genetic questions with reference to practical and tractable conservation objectives can help bypass this limitation of the application of genetics in conservation. Using a single-nucleotide polymorphism dataset from reduced-representation sequencing (DArTSeq), we conducted a genetic assessment of remnant populations of the endangered forty-spotted pardalote (Pardalotus quadragintus), a songbird endemic to Tasmania, Australia. Our objectives were to inform strategies for conservation of genetic diversity in the species and estimate effective population sizes and patterns of inter-population movement to identify management units relevant to population conservation and habitat restoration. We show population genetic structure and identify two small populations on mainland Tasmania as 'satellites' of larger Bruny Island populations connected by migration. Our data identify management units for conservation objectives relating to genetic diversity and habitat restoration. Although our results do not indicate the immediate need to genetically manage populations, the small effective population sizes we estimated for some populations indicate that they are vulnerable to genetic drift, highlighting the urgent need to implement habitat restoration to increase population size and to conduct genetic monitoring. We discuss how our genetic assessment can be used to inform management interventions for the forty-spotted pardalote, and show that by assessing contemporary genetic aspects, valuable information for conservation planning and decision-making can be produced to guide actions that account for genetic diversity and increase chances of recovery in species of conservation concern.

opencc-by-4.0Apr 2023View details →

Data and R codes from: Effects of human disturbance on risk-taking behavior in painted turtles

Animals are exposed to high levels of anthropogenic disturbance, which has profound consequences for population persistence. Individuals can adjust their behavior plastically when faced with perturbations in their environment and may show consistent differences in the way they perceive and respond to risky situations. Over time, this variability among individuals in response to risk can affect the dynamics of populations exposed to human disturbance. Thus, understanding how animals cope behaviorally with human disturbance is important, especially for species vulnerable to human perturbations, such as turtles. In this context, we evaluated whether risk-taking behaviors are consistent within individual painted turtles (Chrysemys picta) and assessed how these behaviors are related to the extent of human disturbance along the Rideau Canal, Ontario, Canada. Specifically, we conducted repeated measurements of the number of active defensive behaviors used during handling and the time taken to escape a floating platform for a total of 730 painted turtles (1117 observations) from 22 sites varying in human disturbance along the canal. We also quantified the emergence of the turtles from the water after escaping the platform. First, individual painted turtles showed consistent differences in all risk-taking behaviors. Second, painted turtles in areas with high boat activity displayed more active defensive behaviors, while turtles from sites in proximity to more houses with access to the canal used fewer. Our study highlights the importance of studying animal behavior to better understand the impact of human activities on animal populations.

opencc-zeroMay 2023View details →

DNA sequence data for two Roscoea species, R. stenophylla and R. australis (Zingiberaceae)

This dataset includes three genomic regions, nrITS (ITS1-5.8S–ITS2) and two chloroplast DNA (cpDNA) regions (psbA-trnH and trnL-F) for two Roscoea species R. stenophylla and R. australis (Zingiberaceae).

opencc-by-4.0May 2023View details →

Review data for: SnowQM 1.0: A fast R Package for bias-correcting spatial fields of snow water equivalent using quantile mapping

Climatology of snow water equivalent of Switzerland between winters 1962 and 2021. Obtained using quartile mapping between a model using data assimilation since 1998 and a model without data assimilation. This version of the dataset corresponds to the publication revision time. The publication has been submitted to GMD Copernicus journal as: SnowQM 1.0: A fast R Package for bias-correcting spatial fields of snow water equivalent using quantile mapping

opencc-zeroMay 2023View details →

Physiological constraints and cognitive chunking in Zebra Finch songs: Data and R script

Learned bird songs often have a hierarchical organization. In the case of zebra finches, each bird's song is made up of a string of notes delivered in a stereotyped sequence to form a "motif", and motifs are repeated to form a song bout. During song learning, young males copy "chunks" of two or more consecutive notes from their tutors' songs. These chunks are represented as distinct units within memory (during learning) and within motor systems (during song production). During song performance, motifs may deviate from the learned sequence by stopping short, starting late, or by skipping, inserting or repeating notes. We measured acoustic and temporal variables related to the respiratory and vocal physiology of song production and asked how they related to deviations from each bird's "canonical" sequence. The best predictor of deviations from that sequence was the duration of the silent interval between notes, when inspiration normally occurs. Deviations from the canonical motif occurred less often after higher-pitched notes, perhaps because a high-low sequence forms a prosodic unit. Premature stops often followed louder and longer notes, suggesting that respiratory and muscular physiology influence the location of such stops. Boundaries between the learned chunks of a male's motif predicted where and how often non-canonical starts occurred. Physiological and cognitive elements also interacted to define the segmentation of zebra finch song sequences. Long silent intervals between notes were associated both with physiology (inspirations) and with the cognitive boundaries of learned chunks – and hence with deviations from the canonical motif.