Find research datasets worth reusing

opencc-by-4.0Nov 2017View details →

ASreml code and Data from the study "Between-population differences in the genetic and maternal components of body mass in roe deer"

This repository contains the source code (ASremL input files) and the data used to perform the QG analyses (univariate, bivariate, random regression animal models) in the study "Between-population differences in the genetic and maternal components of body mass in roe deer". Quéméré E et al.

opencc-zeroApr 2024View details →

Data from: Maternal diet influences fecundity in a freshwater turtle undergoing population decline

Food availability determines the amount of energy animals can acquire and allocate to reproduction and other necessary functions. Female animals that are food-limited thus experience reduced energy available for reproduction. When this occurs, females may reduce frequency of reproductive events or the number or size of offspring per reproductive bout. We assessed how maternal diet affects reproductive output in adult female Murray River short-necked turtles, Emydura macquarii, from four wetlands in Victoria. We previously found that turtle diets differ in the composition of plants and animals between our study wetlands. In this study, we tested whether differences in turtle diet composition (i.e plants and animals) at these wetlands were associated with differences in clutch mass, individual egg mass, bulk egg composition, and hatching success. We found total clutch mass increased with maternal body size at each site. At sites where filamentous green algae were scarce and E. macquarii were carnivorous, females produced smaller clutches relative to body size compared to females from sites where algae were abundant, and turtles were more herbivorous. Individual egg mass, bulk egg composition, and hatching success did not differ across wetlands. Isotopic analysis revealed a significant positive relationships between the carbon and nitrogen isotopes (δ13C, δ15N) of the eggs and those of the mothers, indicating that mothers allocated ratios of carbon and nitrogen isotopes to their eggs similar to those present in their tissues. Our study suggests that at sites where females are more carnivorous due to a relative absence of algae, females produce smaller clutches but other aspects of their reproduction are not significantly impacted. The reduction in clutch size associated with differences in the availability of dietary plants and animals may have long-term consequences for E. macquarii and other freshwater turtle species that are experiencing population declines.

SNP data (DArTseq) for population genomics of Araucaria bidwillii

We took Araucaria bidwillii leaf DNA samples from a total of 31 sites and 171 samples, representing 3 sites from a northern population in the Australian Wet Tropics and 28 sites from a southern population in Southeast Queensland, Australia. SNP data was obtained from genotyping-by-sequencing platform Divesity Arrays Technology (DArTseq) and the resultant dataset has not been processed for quality control.

Data from: Genome-wide scans reveal selection signatures and cross-population variation in South African and European beef cattle breeds

In genetics and evolutionary biology, the concept of selection signatures is used to describe specific patterns in the genome that are associated with the process of natural selection. These selection signatures provide insights into how evolutionary forces have shaped a population over time.In this study, a total of 96 samples were collected in several farms from four different cattle breeds, namely South African indigenous Nguni (n = 28) and Bonsmara (n = 21), Scottish Angus (n = 22), and Swedish Simmental (n = 25). Genotyped samples were subjected to quality control, and a total of 105,675 SNPs from 78 individuals remained for further analysis. Genomic signatures of positive selection within each breed were identified using the Integrated Haplotype Score (iHS) method, and cross-population comparison analysis using cross-population extended haplotype homozygosity ( XP-EHH), relative extended haplotype homozygosity (Rsb), and fixation index (Fst) methods, to assess the genetic differences between breeds. The results from the iHS method revealed selection signatures in two genomic regions for Bonsmara, six for Simmental, four for Nguni, and one for Angus cattle. Ten regions were found to be under selection, with BTA 12 being shared between Nguni and Bonsmara. Comparisons across populations using Rsb, and Fst methods performed better and revealed the most specific genomic regions that varied in selection between breeds. Gene annotation analyses linked candidate genes to several Quantitative Trait Loci (QTL). For example, in Simmental cattle's FAM110B gene was linked to carcass weight and body confirmation score. Bonsmara showed fewer candidate genes, such as CDK8 and FLT1, whereas Angus had none on BTA 18. Nguni identified potential genes such as CRB1, PLAG2GA, and VASH2, with CDK8 shared by Bonsmara and Nguni on BTA 12. Further cross-population studies revealed candidate genes associated with certain traits, genes including as PLCXD3, FAM149B1, and GRIK2 for Bonsmara versus Nguni, and SLIT2 and TSPAN9 for Simmental vs Angus. The study also emphasised gene related to meat quality, reproduction, health, illnesses, fertility, and body conformation score. Gene interaction study with the STRING database revealed a network of 63 candidate genes, demonstrating the structure of genetic connections, some biological processes. The study found that iHS performed well in population analysis with Nguni cattle, having exhibited the highest number of signatures across the genome, and significant signatures were also seen in comparisons between Nguni and Bonsmara using the Fst and Rsb methods. Furthermore, the study discovered that a bigger number of genes were connected with various traits, including sperm count and insemination per conception, sensitivity to bovine respiratory disease, and ease of calving. This genomic analysis underlined the relevance of the genetic relying which distinguishes distinct breeds. This understanding has the potential to significantly enhance selective breeding and increase desirable traits in cattle herds. This genomic analysis underlined the significance of the genetic basis for breed-specific traits. This understanding has the potential to drastically improve selective breeding and increase desirable traits in cattle herds.

Data from: Small but connected islands can maintain populations and genetic diversity under climate change

In response to the striking effects of environmental change, conservation strategies often include the identification of conservation areas that can effectively maintain vulnerable species. Consequently, identifying system-specific conditions that maintain the demographic and genetic viability of species of conservation concern is essential. Connectivity plays a critical role in the persistence of populations. Islands have been model systems to understand connectivity and metapopulation processes and have emerged as particularly favorable targets for conservation. While islands can be isolated from mainland disturbances, it is unknown what degree of isolation is necessary to avoid unfavorable changes but remain sufficiently connected to maintain population viability. To test this question, we explored connectivity within the Apostle Islands, an archipelago of 22 islands within Lake Superior, by comparing historical and contemporary trends in ice bridge connectivity and by simulating the effect of reduced connectivity within this system. We developed a demographically informed individual-based model to explicitly test the role of connectivity to influence the persistence and genetic diversity of American marten (Martes americana), a forest carnivore at risk across its southern range boundary. We found that genetic diversity was resilient to moderate changes in ice cover, but a complete loss of connectivity resulted in rapid genetic erosion. Despite genetic erosion, populations persisted as long as nominal connectivity occurred between islands. Our work suggests that connectivity will decline, but martens would be resilient to moderate changes, and, in the short term, the Apostle Islands can act as a refuge along this species' southern range boundary. Identifying thresholds in connectivity that maintain populations but allow for isolation from disturbance will be necessary to identify suitable areas for species conservation across space and time.

opencc-by-nc-4.0Dec 2023View details →

Data from: Versatile MRI Acquisition and Processing Protocol for Population-Based Neuroimaging

This data repository contains an example of the acquired MRI sequences and the output of the post-processing pipelines in the Rhineland Study. An overview and information about the MRI sequences and post-processing pipelines can be found in our work 'Versatile MRI Acquisition and Processing Protocol for Population-Based Neuroimaging.' (under-submission)

Data from: The basic-reproduction number of infectious diseases in spatially structured host populations

The spatial structure of a host population has a profound effect on the dynamics of infectious diseases. The basic reproduction number, a central quantity in the study of epidemic dynamics, is affected by host clustering as well as host density. Several authors have developed methods to quantify the basic reproduction number in a spatially structured host population. The methods used and the expressions derived are however difficult to apply to real life spatial host structures. In this paper we introduce an explicit expression for the basic reproduction number using the O-ring statistic, developed in spatial statistics, that quantifies the host density as a function of the distance from a randomly selected host individual. The O-ring statistic is frequently used in the study of the ecology of spatially structured plant populations, being a convenient summary of the properties of a landscape by way of a single function. The connection we develop between spatial statistics and epidemic dynamics can be used to study the effect of host spatial pattern on the basic reproduction number of infectious diseases. As well as showing how explicit expressions for the basic reproduction number can be derived for landscapes with standard structures, our expression for the basic reproduction number is tested against a simulation model. The model structure in our simulation is motivated by the spread of a plant disease epidemic, although it is applicable more broadly. The agreement between our analytic expression for the basic reproduction number and the corresponding numeric quantity extracted from simulations is close to perfect across a wide range of landscape structures and model parameterisations, and including cases in which more than one species of host is at risk of infection.

Data from: Population and community consequences of perceived risk from humans in wildlife

Human activities catalyze risk avoidance behaviors in wildlife across taxa and systems. However, the broader ecological significance of human-induced risk perception remains unclear, with a limited understanding of how phenotypic responses scale up to affect population or community dynamics. We conducted a comprehensive literature review of non-consumptive effects (NCE; population effects) and trait-mediated indirect effects (TMIE; community effects) of anthropogenic disturbances. This dataset includes all papers identified from the comprehensive review of the different types of human-induced behavioral and physiological phenotypic change and their influence on vital rates and population parameters in wildlife. All papers in this database tested for a human-induced NCE or TMIE in wildlife but not all found evidence for an effect. Many of the papers did not explicitly measure the presumed phenotypic change linking human activity to vital rates or population parameters. The authors, paper title, journal, publication year, type of human disturbance, species, system, phenotypic response measured, demographic response measured, if a demographic effect was found, and whether an NCE or TMIE was tested are all included in the dataset. In addition, we include the source of the paper in our dataset (i.e. whether it came up in our Web of Science search, as a citing paper of Frid and Dill (2002), or in a review paper on human-induced fear in wildlife; column A). The papers in which multiple NCE or TMIE pathways were tested may have multiple values in a single cell. Papers are sorted alphabetically by author. Evidence for human-induced NCEs and TMIEs is mixed, with half of published studies finding a relationship between human activities, phenotypic change, and population outcomes. Strong research biases in taxa, systems, human disturbance type, and demographic measures prevent unified inference about the prevalence of population responses to human activities. Coexistence with and conservation of wildlife requires additional research linking human-induced phenotypic change to population and community outcomes.

opencc-zeroJun 2024View details →

Data from: Density matters: How population dynamics of house mice (Mus musculus) inform the epidemiology of Leptospira

Rodents are maintenance hosts of numerous pathogens, and both their density and the pathogen prevalence determine the risk they pose to other animals or humans. However, density is often overlooked. We investigated a capture-mark-recapture-sampling strategy to study introduced mice (Mus musculus) and Leptospira as a model and demonstrate the advantages of a combined approach. We estimated population density and Leptospira prevalence in mice in a replicated longitudinal survey conducted between 2016 and 2018. Capture-mark-recapture sessions were undertaken at two sites in Spring and Autumn and blood and kidney samples were collected at the end of each session. Mouse density and areas of activity were estimated using spatially explicit capture-recapture (SECR) models and both were compared between Leptospira positive and negative mice. Leptospira exposure and shedding status were estimated using Microscopic Agglutination Test, and a combination of culture and lipL32 PCR on kidneys. Leptospira prevalence was higher in spring (83% to 86%) than in autumn (31% to 37%) and mouse densities simultaneously varied from 3.6 to 55.9/ha. However, despite these variations in prevalence and density, the density of infected animals remained relatively constant over time (3 to 8/ha). Shedding or being seropositive was also associated with the activity of mice. Shedding or seropositive mice had a larger activity area, and seropositive mice were trapped on average one day earlier than seronegative mice. Synthesis and applications. Our results show how understanding the population dynamics of pathogen-carrying rodents is critical in epidemiology. The wider movement patterns and easier encounters of positive mice highlight the possibility of biases in classical prevalence surveys and have implications for disease transmission within and between species. Importantly, and quite counter-intuitively, Leptospira prevalence was negatively associated with mouse density, resulting in a constant density of shedders that contradicts the conventional view of higher exposure risk at high rodent density. More broadly, such hybrid sampling designs can improve animal and disease control policies and better inform modelling studies by providing more parameter estimates than classical prevalence surveys.

opencc-zeroJun 2024View details →

Data from: Consequences of repeated sarcoptic mange outbreaks in an endangered mammal population

Diseases and parasites are important drivers of population dynamics in wild mammal populations. Small and endangered populations that overlap with larger, reservoir populations are particularly vulnerable to diseases and parasites, especially in ecosystems highly influenced by climate change. Sarcoptic mange, caused by a parasitic mite (Sarcoptes scabiei), constitutes a severe threat to many wildlife populations and is today considered a panzootic. The Scandinavian arctic fox (Vulpes lagopus) is endangered with a fragmented distribution and is threatened by e.g., red fox (Vulpes vulpes) expansion, prey scarcity and inbreeding depression. Moreover, one of the subpopulations in Scandinavia has suffered from repeated outbreaks of sarcoptic mange during the past decade, most likely spread by red foxes. This was first documented in 2013 and then again 2014, 2017, 2019, 2020 and 2021. We used field inventories and wildlife cameras to follow the development of sarcoptic mange outbreaks in this arctic fox subpopulation with specific focus on disease transmission and consequences for reproductive output. In 2013-14, we documented visual symptoms of sarcoptic mange in about 30% of the total population. Despite medical treatment, we demonstrate demographic consequences where the number of arctic fox litters plateaued and litter size was reduced after the introduction of S. scaibei. Furthermore, we found indications that mange likely was transmitted by a few arctic foxes travelling between several dens, i.e., "super-spreaders". This study highlights sarcoptic mange as a severe threat to small populations and can put the persistence of the entire Scandinavian arctic fox population at risk.

opencc-by-4.0Apr 2024View details →

Data: Approaching a population level assessment of body size in pinnipeds using drones, an early warning of environmental degradation.

Data and R sctipts for measuring harbour seal body sizes and estimating mass based on .shp files containing outlines. Associated with the manusctipt currently titled "Approaching a population level assessment of body size in pinnipeds using drones, an early warning of environmental degradation." 1_Seal_Volume_Function.R: A function for the estimation of length, width, and ellipsoid volume of harbour seals from georeferenced polygons representing individual outlines 2_Polygon_Process.R: This script uses the curved_length_vol function (1_Seal_Volume_Function.R) to process a folder full of .shp file subfolders containing georeferenced polygons representing individual outlines and outputs a .csv with estimates of length, width, and ellipsoid volume for each individual. 3_Calibration.R: This script processes and calibrates summarized harbor seal measurements based on reference to known individuals CSV_Files: Folder containing data files Known_Seals.csv: True measurments of length and mass for known seals with derived estimates of 'true' width and volume. Drone based estimates of length, width, simple and complex volume for the same individuals, information on pose. measurments.csv: Drone based estimates of length, width, simple and complex volume for all individuals. Pup_growth.csv: Data on pup mass by age from Harding et al. 2005 (<a href="https://doi.org/10.1111/j.0269-8463.2005.00945.x" rel="nofollow">https://doi.org/10.1111/j.0269-8463.2005.00945.x</a>). Slottsskogen_Data.csv: True and drone based measurments for individual captive harbour seals taken on two seperate occasions. Summarised_Weights.csv: True measurments of length, girth, and mass for harbour seals.

opencc-zeroJun 2024View details →

Data from: Responses of population structure and genomic diversity to climate change and fishing pressure in a pelagic fish

The responses of marine species to environmental changes and anthropogenic pressures (e.g. fishing) interact with ecological and evolutionary processes that are not well understood. Knowledge of changes in the distribution range and genetic diversity of species and their populations into the future is essential for the conservation and sustainable management of resources. Almaco jack (Seriola rivoliana) is a pelagic fish with high importance to fisheries and aquaculture in the Pacific Ocean. In this study, we assessed contemporary genomic diversity and structure in loci that are putatively under selection (outlier loci) and determined their potential functions. Utilizing a combination of genotype-environment association, spatial distribution models, and demogenetic simulations, we modeled the effects of climate change (under three different RCP scenarios) and fishing pressure on the species' geographic distribution and genomic diversity and structure to 2050 and 2100. Our results show that most of the outlier loci identified were related to biological and metabolic processes that may be associated with temperature and salinity. Contemporary genomic structure showed three populations—two in the Eastern Pacific (Cabo San Lucas and Eastern Pacific) and one in the Central Pacific (Hawaii). Future projections suggest a loss of suitable habitat and potential range contractions for most scenarios, while fishing pressure decreased population connectivity. Our results suggest that future climate change scenarios and fishing pressure will affect the genomic structure and genotypic composition of S. rivoliana and lead to loss of genomic diversity in populations distributed in the eastern-central Pacific Ocean, which could have profound effects in fisheries that depend on this resource.

opencc-by-4.0Feb 2024View details →

Data from: A genome-guided strategy for climate resilience in American chestnut restoration populations

The American chestnut (Castanea dentata) is a functionally extinct tree species that was decimated by an invasive fungal pathogen in the early 20th century. An understanding of the genomic architecture of local adaptation in wild American chestnut was necessary in order to deploy locally adapted, disease-resistant American chestnut populations. Here, we characterize the genomic basis of climate adaptation in remnant wild American chestnut, develop new computational methods, and evaluate the adaptive genomic content captured within backcross breeding populations. Whole genome re-sequencing data of 356 trees from Sandercock et al. (2022) coupled with genotype-environment association methods identified 18483 climate associated loci.

opencc-zeroJul 2024View details →

Remote camera monitoring and arboreal trapping data for a reintroduced population of red-tailed phascogales (Phascogale calura)

Effective monitoring methods are required to evaluate the success of wildlife reintroduction programs. To improve the threat status of the Vulnerable red-tailed phascogale (Phascogale calura), the Australian Wildlife Conservancy reintroduced the species to a fenced reserve at Mt. Gibson Wildlife Sanctuary. After trialing a variety of post-release monitoring methods, remote camera monitoring and arboreal trapping with an extensive period of pre-luring provided the most information with which to evaluate the success of the reintroduction. To date, reintroduced red-tailed phascogales have increased in both occupancy and population size following releases which began at Mt. Gibson in 2017. Other managers of red-tailed phascogale populations may find the described methods useful, particularly in the context of multi-species reintroductions where trap saturation can reduce capture rates of smaller species, such as phascogales.

opencc-zeroJul 2024View details →

Data from: Phenotypic selection on an ornamental trait is not modulated by breeding density in a pied flycatcher population

Most studies of phenotypic selection in the wild have focused on morphological and life-history traits and looked at abiotic (climatic) variation as the main driver of selection. Consequently, our knowledge of the effects of biotic environmental variation on phenotypic selection on sexual traits is scarce. Population density can be considered a proxy for the intensity of intra- and inter-sexual competition and could therefore be a key factor influencing the covariation between individual fitness and the expression of sexual traits. Here, we used an individual-based data set from a population of pied flycatchers (Ficedula hypoleuca) monitored over 24 years to analyse the effect of breeding density on phenotypic selection on dorsal plumage colouration, a heritable and sexually selected ornament in males of this species. Using the number of recruits as a fitness proxy, our results show overall stabilizing selection on male dorsal colouration, with intermediate phenotypes being favoured over extremely dark and dull individuals. However, our results did not support the hypothesis that breeding density mediates phenotypic selection on this sexual trait. We discuss the possible role of other biotic factors influencing selection on ornamental plumage.

opencc-zeroJul 2024View details →

Data from: Drivers of population dynamics of at-risk populations change with pathogen arrival

Successful wildlife conservation in an era of global change requires understanding determinants of species population growth. However, when populations are faced with novel stressors, factors associated with healthy populations can change, necessitating shifting conservation strategies. For example, emerging infectious diseases can cause conditions previously beneficial to host populations to increase disease impacts. Here, we paired a population dataset of 265 colonies of the federally endangered Indiana bat (Myotis sodalis) with 50.7 logger-years of environmental data to explore factors that affected colony response to white-nose syndrome (WNS), an emerging fungal disease. We found variation in colony responses to WNS, ranging from extirpation to stabilization. The severity of WNS impacts was associated with hibernaculum temperature, as colonies of cold hibernacula declined more severely than those in relatively warm hibernacula, an association that arose following pathogen emergence. Interestingly, this association was opposite that of a sympatric bat species, the little brown bat (Myotis lucifugus), illustrating that environmental dependence of disease can vary by species in a multi-host community. Simulating future colony dynamics suggests that most extirpations have already occurred, as the pathogen has been present for several years in most colonies, and that relatively small colonies are more susceptible to extirpation. Overall, this study illustrates that emerging infectious diseases can change the factors associated with host population growth, including through novel environmental associations that vary by host species. Consideration of these shifting associations and differences between impacted species will be essential to the conservation of host communities challenged by emerging infectious disease.

opencc-by-4.0Dec 2019View details →

Figure 4 in First data on population estimates and dispersal of Montenegrina subcristata - a field study at Virpazar, Montenegro

Figure 4. Sum of individuals counted at each observation date at site A (above) and site B (below).

opencc-by-4.0Dec 2017View details →

Supporting data and script for "Productivity, biodiversity, and pathogens influence the global hunter-gatherer population density" (Tallavaara et al.)

This submission contains data and R-script that enable to reproduce the data manipulations and analyses in the paper “Productivity, biodiversity, and pathogens influence the global hunter-gatherer population density” by Miikka Tallavaara, Jussi T. Eronen, and Miska Luoto (PNAS 2018 115 (6) 1232-1237, doi/10.1073/pnas.1715638115). Please, cite the above paper, if you use the files included in this Zenodo record in your work. Included in the submission are R-script as a pdf-file (Tallavaara_Data_analyses.pdf), global net primary productivity data (Tallavaara_Dataset_1.tif), global biodiversity data (Tallavaara_Dataset_2.tif), and global pathogen stress data (Tallavaara_Dataset_3.tif) as GeoTIFF-files. In addition, submission contain global hunter-gatherer data (Tallavaara_Dataset_4.xls) as xls-file. If these datasets are saved in the working directory they can be read in to the R using the included R-script (Tallavaara_Data_analyses).

opencc-by-nc-4.0Dec 2017View details →

Data from a field plot experiment with the canola pathogen Leptosphaeria maculans including disease severity at the leaf spot and canker stages of the epidemic, and population composition as isolates infectivity pathotypes.

Data set Data are from an experiment simulating how differences in Brassica napus resistance deployment strategies and landscape connectivity influence epidemic severity and pathogen population composition of the fungus Leptosphaeria maculans on field plots inoculated with combinations of stubble in 2016 at CSIRO Canberra, ACT, Australia. Disease severity was assessed on the 60 field plots [Data_severity.csv] and 1490 isolates were sampled and assessed for infectivity [Data_infectivity.csv]. This dataset is described and analyzed in Bousset et al. (2018). Treatments were factorial combination of Resistance, Genetic Connectivity and Spatial Connectivity, replicated in 4 blocks (B1 to B4). Resistance has 3 categories (Rlm4, Rlm6 LepR1) differing by the resistance genes in oilseed rape varieties. Genetic Connectivity has 2 levels (HighGC, LowGC) differing by the pre-adaptation of the stubble populations to the host variety. Spatial Connectivity has two levels (HighSC, LowSC) differing by the stubble load. Control plots had NoStubble. Data files [Data_severity.csv] Disease severity was assessed on the 60 field plots at leaf spot and canker stages of the epidemic. Leaf spots data are counts. Canker data are numbers of stems in 12 categories defined by the cankered area on cross section (0 = no canker to 100 = fully cankered). [Data_infectivity.csv] Two types of isolates (122 from 3 stubble sources with contrasting preadaptation and 1368 from leaves sampled on 50 field plots) were tested for infectivity response (V = infective; A = non-infective) on the three host varieties (Rlm4, Rlm6 LepR1), at the seedling stage in greenhouse. Associated publication Bousset L, Sprague S, Thrall PH, Barrett LG (2018). Spatio-temporal connectivity and host resistance influence evolutionary and epidemiological dynamics of the canola pathogen Leptosphaeria maculans. Evolutionary Applications [ DOI: 10.1111/eva.12630 ]. Funding information This work benefited from the financial support of INRA – the French National Institute for Agronomical Research, a CSIRO Sir Frederick McMaster fellowship to L. Bousset (Impact of inoculum carry-over on landscape dynamics of the blackleg canola pathogen) and the Grains Research & Development Corporation (GRDC Grant CSP00192)