Find research datasets worth reusing

opencc-zeroJan 2023View details →

Whole genome demographic models indicate divergent effective population size histories shape contemporary genetic diversity gradients in a montane bumble bee

Understanding historical range shifts and population size variation provides important context for interpreting contemporary genetic diversity. Methods to predict changes in species distributions and model changes in effective population size (Ne) using whole genomes make it feasible to examine how temporal dynamics influence diversity across populations. We investigate Ne variation and climate-associated range shifts to examine the origins of a previously observed latitudinal heterozygosity gradient in the bumble bee Bombus vancouverensis Cresson (Hymenoptera: Apidae: Bombus Latreille) in western North America. We analyze whole genomes from a latitude-elevation cline using sequentially Markovian coalescent models of Ne through time to test whether relatively low diversity in southern high-elevation populations is a result of long-term differences in Ne. We use Maxent models of the species range over the last 130,000 years to evaluate range shifts and stability. Ne fluctuates with climate across populations, but more genetically diverse northern populations have maintained greater Ne over the late Pleistocene and experienced larger expansions with climatically favorable time periods. Northern populations also experienced larger bottlenecks during the last glacial period which matched the loss of range area near these sites, however, bottlenecks were not sufficient to erode diversity maintained during periods of large Ne. A genome sampled from an island population indicated a severe postglacial bottleneck, indicating that large recent post-glacial declines are detectable if they have occurred. Genetic diversity was not related to niche stability or glacial-period bottleneck size. Instead, spatial expansions and increased connectivity during favorable climates likely maintain diversity in the north while restriction to high elevations maintains relatively low diversity despite greater stability in southern regions. Results suggest genetic diversity gradients reflect long-term differences in Ne dynamics and also emphasize the unique effects of isolation on insular habitats for bumble bees. Patterns are discussed in the context of conservation under climate change.

opencc-by-4.0Feb 2023View details →

Data and code for paper "Freihardt (2024): Perceptions of environmental changes among a climate-vulnerable population from Bangladesh. Climatic Change. DOI 10.1007/s10584-024-03678-6"

This dataset contains the temperature, precipitation, erosion, and perception data, as well as the analysis code in R necessary to replicate the results of the paper: Freihardt, J. (2024): Perceptions of environmental changes among a climate-vulnerable population from Bangladesh. Climatic Change, 177, 25. DOI: 10.1007/s10584-024-03678-6.

Data from: Genomics reveals the role of admixture in the evolution of structure among sperm whale populations within the Mediterranean Sea

In oceanic ecosystems, the nature of barriers to gene flow, and the processes by which populations may become isolated are different from the terrestrial environment, and less well understood. In this study, we investigate a highly mobile species (the sperm whale, Physeter macrocephalus) that is genetically differentiated between an open North Atlantic population and the populations in the Mediterranean Sea. We apply high-resolution single nucleotide polymorphisms (SNP) analysis to study the nature of barriers to gene flow in this system, comparing gene flow across the putative boundary into the Mediterranean (Strait of Gibraltar and Alboran Sea region) with novel analyses on structuring among sperm whale populations within the Mediterranean basin. Our data support a recent founding of the Mediterranean, around the time of the last glacial maximum, and shows concerted historical demographic profiles in both the Atlantic and the Mediterranean. In each region, there is evidence for a population decline around the time of the founder event, more extreme within the Mediterranean Sea where effective population size is substantially lower. While differentiation is strongest at the Atlantic/Mediterranean boundary, there is also significant differentiation between the Eastern and Western basins of the Mediterranean Sea. We propose, however, that the mechanisms are different. While post-founding gene flow was reduced between the Mediterranean and Atlantic populations, within the Mediterranean an important factor differentiating the basins is likely a greater degree of admixture between the Western basin and the North Atlantic.

Using DNA metabarcoding to explore spatial variation in diet across European Hawfinch populations

The investigation of diet in avian species is essential to an understanding of their ecology and local adaptations, as well as long-term conservation. This can be particularly challenging due to the wide distribution and high ecological plasticity of many bird species. Dietary richness and variation are under-studied in woodland bird species, due primarily to challenges in accurately identifying plant and invertebrate taxa consumed. Within Europe, Hawfinch (Coccothraustes coccothraustes) have shown variation in population trends, with moderate declines across central and eastern Europe, while western European populations have shown moderate increases. Ecological drivers behind this differing trend are still unknown; one possibility is differences in diet, yet little research has been conducted into Hawfinch diet in mainland Europe or elsewhere. This study aimed to present the first molecular dietary analysis of Hawfinch populations across two European countries. Faecal samples were collected between January and July of 2019 from Hawfinch caught at six artificial feed sites: two in Denmark and four in Germany. DNA was successfully extracted from 80 samples and plant Internal Transcribed Spacer 2 (ITS2) and invertebrate Cytochrome Oxidase Subunit 1 (COI) barcodes were amplified. A total of 35 plant and 37 invertebrate taxa were found across the 80 Hawfinch faecal samples, with plant and insect orders Fagales and Lepidoptera respectively the most frequently detected. Hawfinch dietary composition differed significantly between European countries, suggesting Hawfinch can make use of available food resources which are likely to differ spatially. Our study shows how DNA metabarcoding can be used to provide novel ecological information associated with under-studied bird species, thus providing essential information for future management and conservation of Hawfinch and their habitats.

opencc-by-4.0Feb 2023View details →

Supplementary material for Metabolic constraints on the body size scaling of extreme population densities

Data for the analysis of the paper entitled Metabolic constraints on the body size scaling of extreme population densities. Ecology letters. <a href="https://zenodo.org/api/files/a60c335d-e6ca-4bd9-a17f-fc98ca9703e2/air_sea_outputs_L4_nsw.txt?versionId=1416dceb-47d0-45b1-99a8-baa833df8f76">air_sea_outputs_L4_nsw.txt </a> This data set contains 8693 rows and 13 variables From colum 1 to 13 the following names apply: Julian- Day of the year (1rst January =1) day- Day number month- Month number year- Year number lat- Latitude lon- Longitude wind_speed_m_s- 1m wind speed in meters per second  presure_mB- Air pressure in milibars Temp_°C- Air temperature in degrees Celsius  Temp_algo- Other temperature Cloud_cover%- Percentage of cloud cover SST_°C- sea surface temperature in degree Celsius SW_Radiation_W_m2- Short wave radiation in Watts per square meter. <a href="https://zenodo.org/api/files/a60c335d-e6ca-4bd9-a17f-fc98ca9703e2/SurfaceTemperature_L4_Merged.csv?versionId=9738e9d6-53ed-49c4-ab0d-136b74ddb16e">SurfaceTemperature_L4_Merged.csv </a> This data set has 1064 rows and two columns Fechas_tempAll is the date of measurement formated as (Year-Month-Day Hour) e.g. 2013-05-20 09:00:00 TEMP_EC- Surface water Temperature in degree Celsius <a href="https://zenodo.org/record/7374166/files/Nutrients.csv?download=1">Nutrients.csv</a> The data set sas 445 rows and 8 Variables Sample.Date- Date when surface water sample was taken. NITRITE.µM, - Nitrite (NO2) concentration in micromolar NITRATE.NITRITE.µM"- Nitrate (NO3) concentration in micromolar AMMONIA.µM, - Ammonia (NH4) concentration in micromolar SILICATE.µM, - Silica (Si) concentration in micromolar PHOSPHATE.µM- - Posphate (PO4) concentration in micromolar FLAG- Quality flag (TRUE/FALSE).

Data for: Amazonian birds in more dynamic habitats have less population genetic structure and higher gene flow

Understanding the factors that govern variation in genetic structure across species is key to the study of speciation and population genetics. Genetic structure has been linked to several aspects of life history, such as foraging strategy, habitat association, migration distance, and dispersal ability, all of which might influence dispersal and gene flow. Comparative studies of population genetic data from species with differing life histories provide opportunities to tease apart the role of dispersal in shaping gene flow and population genetic structure. Here, we examine population genetic data from sets of bird species specialized on a series of Amazonian habitat types hypothesized to filter for species with dramatically different dispersal abilities: stable upland forest, dynamic floodplain forest, and highly dynamic riverine islands. Using genome-wide markers, we show that habitat type has a significant effect on population genetic structure, with species in upland forest, floodplain forest, and riverine islands exhibiting progressively lower levels of structure. Although morphological traits used as proxies for individual-level dispersal ability did not explain this pattern, population genetic measures of gene flow are elevated in species from more dynamic riverine habitats. Our results suggest that the habitat in which a species occurs drives the degree of population genetic structuring via its impact on long-term fluctuations in levels of gene flow, with species in highly dynamic habitats having particularly elevated gene flow. These differences in genetic variation across taxa specialized in distinct habitats may lead to disparate responses to environmental change or habitat-specific diversification dynamics over evolutionary time scales.

opencc-by-4.0Aug 2003View details →

Figs 1–2 in The population structure of Leptoiulus proximus (Nĕmec, 1896) (Diplopoda, Julidae) in floodplain forests after summer flooding

Figs 1–2. Changes in abundance of individual stadia in the population of L. proximus. 1. Changes in epigeic activity (numbers of individuals per 18 pitfall traps) at four-week intervals over the four years after flooding. 2. Changes in density (individuals/m2) at four-week intervals over the four years after flooding (animals extracted from soil samples by Tullgren funnels).

opencc-by-4.0Jan 2023View details →

[Dataset] Data for the course "Population Genomics" at Aarhus University

Datasets, conda environments and Softwares for the course "Population Genomics" of Prof Kasper Munch. This course material is maintained by the <a href="https://hds-sandbox.github.io/">health data science sandbox</a>. This <a href="https://hds-sandbox.github.io/PopulationGenomicsCourse/">webpage</a> shows the latest version of the course material. <ol> <li> Data.tar.gz Contains the datasets and executable files for some of the softwares You can unpack by simply doing tar -zxf Data.tar.gz -C ./ This will create a folder called Data with the uncompressed material inside</li> <li>Course_Env.packed.tar.gz Contains the conda environment used for the course. This needs to be unpacked to adjust all the prefixes (Note this environment is created on Ubuntu 22.10). You do this in the command line by <ol> <li>creating the folder Course_Env:  mkdir Course_Env</li> <li>untar the file: tar -zxf Course_Env.packed.tar.gz -C Course_Env</li> <li>Activate the environment: conda activate ./Course_Env</li> <li>Run the unpacking script (it can take quite some time to get it done): conda-unpack</li> </ol> </li> <li>Course_Env.unpacked.tar.gz The same environment as above, but will work only if untarred into the folder /usr/Material - so use the version above if you are using it in another folder. This file is mostly to execute the course in our own cloud environment.</li> <li>environment_with_args.yml The file needed to generate the conda environment. Create and activate the environment with the following commands: <ol> <li>conda env create -f environment_with_args.yml -p ./Course_Env</li> <li>conda activate ./Course_Env</li> </ol> </li> </ol>   The data is connected to the following repository:<a href="https:// github.com/hds-sandbox/Popgen_course_aarhus."> https://github.com/hds-sandbox/Popgen_course_aarhus.</a> The original course material from Prof Kasper Munch is at <a href="https://github.com/kaspermunch/PopulationGenomicsCourse">https://github.com/kaspermunch/PopulationGenomicsCourse</a>.   Description The participants will after the course have detailed knowledge of the methods and applications required to perform a typical population genomic study. The participants must at the end of the course be able to: <ul> <li>Identify an experimental platform relevant to a population genomic analysis.</li> <li>Apply commonly used population genomic methods.</li> <li>Explain the theory behind common population genomic methods.</li> <li>Reflect on strengths and limitations of population genomic methods.</li> <li>Interpret and analyze results of population genomic inference.</li> <li>Formulate population genetics hypotheses based on data</li> </ul> The course introduces key concepts in population genomics from generation of population genetic data sets to the most common population genetic analyses and association studies. The first part of the course focuses on generation of population genetic data sets. The second part introduces the most common population genetic analyses and their theoretical background. Here topics include analysis of demography, population structure, recombination and selection. The last part of the course focus on applications of population genetic data sets for association studies in relation to human health. Curriculum The curriculum for each week is listed below. "Coop" refers to a set of <a href="https://github.com/cooplab/popgen-notes/releases/download/v1.2/minicoop.pdf">lecture notes by Graham Coop</a> that we will use throughout the course. Course plan <ol> <li>Course intro and overview: <ul> <li>Coop chapters 1, 2, 3, <a href="https://www.nature.com/articles/nature18964">Paper: Genome Diversity Project</a></li> </ul> </li> <li>Drift and the coalescent: <ul> <li>Coop chapter 4; <a href="https://www.nature.com/articles/ng.3036">Paper: Platypus</a></li> <li>Exercise: Read mapping and base calling</li> </ul> </li> <li>Recombination: <ul> <li>Lecture: <a href="https://royalsocietypublishing.org/doi/10.1098/rstb.2016.0455">Review: Recombination in eukaryotes</a>, <a href="https://www.nature.com/articles/s41576-020-0240-1">Review: Recombination rate estimation</a></li> <li>Exercise: Phasing and recombination rate</li> </ul> </li> <li>Population strucure and incomplete lineage sorting: <ul> <li>Lecture: Coop chapter 6, <a href="https://doi.org/10.1146/annurev-genet-120213-092532">Review: Incomplete lineage sorting</a></li> <li>Exercise: Working with VCF files</li> </ul> </li> <li>Hidden Markov models: <ul> <li>Lecture: Durbin chapter 3, <a href="https://www.nature.com/articles/nature07331">Paper: population structure</a></li> <li>Exercise: Inference of population structure and admixture</li> </ul> </li> <li>Ancestral recombination graphs: <ul> <li>Lecture: <a href="https://bmcgenomdata.biomedcentral.com/articles/10.1186/1471-2156-7-16">Paper: Approximating the ARG</a>, <a href="https://www.nature.com/articles/s41588-019-0484-x">Paper: Tree inference</a></li> <li>Exercise: ARG dashboard exercises + Inference of trees along sequence</li> </ul> </li> <li>Past population demography: <ul> <li>Lecture: Coop chapter 4, <a href="https://www.nature.com/articles/nature10231">Paper: PSMC</a>, revisit <a href="https://www.nature.com/articles/s41588-019-0484-x">Paper: Tree inference</a></li> <li>Exercise: Inferring historical populations</li> </ul> </li> <li>Direct and linked selection: <ul> <li>Lecture: Coop chapters 12, 13, revisit <a href="https://www.nature.com/articles/s41588-019-0484-x">Paper: Tree inference</a></li> </ul> </li> <li>Admixture: <ul> <li>Lecture: <a href="https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007349">Review: Admixture</a>, <a href="https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007641">Paper: Admixture inference</a></li> <li>Exercise: Detecting archaic ancestry in modern humans</li> </ul> </li> <li>Genome-wide association study (GWAS): <ul> <li>Lecture: <a href="https://github.com/cooplab/popgen-notes/releases/download/v1.2/release_popgen_notes.pdf">Coop lecture notes</a> 99-120</li> <li>Exercise: GWAS quality control</li> </ul> </li> <li>Heritability: <ul> <li>Lecture: Coop Lecture notes Sec. 2.2 (p23-36) + Chap. 7 (p119-142)</li> <li>Exercise: Association testing</li> </ul> </li> <li>Evolution and disease: <ul> <li>Lecture:  Coop Lecture notes Sec. 11.0.1 (p217-221)</li> <li>Exercise: Estimating heritability</li> </ul> </li> </ol>

Phenological mismatch affects individual fitness and population growth in the winter moth

Climate change can severely impact species that depend on temporary resources by inducing phenological mismatches between consumer and resource seasonal timing. In the winter moth, warmer winters caused eggs to hatch before their food source, young oak leaves, became available. This phenological mismatch changed the selection on the temperature sensitivity of egg development rate. However, we know little about the fine-scale fitness consequences of phenological mismatch at the individual level and how this mismatch affects population dynamics in the winter moth. To determine the fitness consequences of mistimed egg hatching relative to timing of oak budburst, we quantified survival and pupation weight in a feeding experiment. We found that mismatch greatly increased mortality rates of freshly hatched caterpillars, as well as affecting caterpillar growth and development time. We then investigated whether these individual fitness consequences have population-level impacts by estimating the effect of phenological mismatch on population dynamics, using our long-term data (1994–2021) on relative winter moth population densities at four locations in the Netherlands. We found a significant effect of mismatch on population density with higher population growth rates in years with a smaller phenological mismatch. Our results indicate that climate change-induced phenological mismatch can incur severe individual fitness consequences that can impact population density in the wild.

Transgenerational effect on sexual reproduction in rotifer populations in relation to the environmental predictability of their habitats

Understanding the processes that enable adaptation of organisms to time-varying environments is critically relevant in evolutionary ecology. A way to cope with environmental fluctuations where predictable conditions affect several generations of individuals is through non-genetic transgenerational effects. The phenotype of ancestors affects the phenotype of their descendants matching it with the expected environment of the latter. Facultatively sexual rotifers inhabiting water bodies that cover a wide gradient of environmental predictability in Eastern Spain are a good study model for this topic. In their life cycle sex is linked to diapausing-egg production that enables survival between growing seasons. In several rotifer species, sexual reproduction is inhibited in several generations after diapausing-egg hatching. We hypothesized that in ponds where the growing season length is more predictable, rotifer clones proliferate asexually longer, hence allowing a fuller exploitation of the growing season and therefore maximize diapausing-egg production by the end of the season. We tested this prediction by estimating the proportion of sexual females produced by eight clones of the rotifer Brachionus plicatilis inhabiting eight ponds (8x8= 64 clones) from our study system. Here, we present the raw data gathered from the experiment.

Barcoding populations of Pseudomonas fluorescens SBW25

In recent years evolutionary biologists have developed increasing interest in the use of barcoding strategies to study eco-evolutionary dynamics of lineages within evolving populations and communities. Although barcoded populations can deliver unprecedented insight into evolutionary change, barcoding microbes presents specific technical challenges. Here, strategies are described for barcoding populations of the model bacterium Pseudomonas fluorescens SBW25, including the design and cloning of barcoded regions, preparation of libraries for amplicon sequencing, and quantification of resulting barcoded lineages. In so doing, we hope to aid the design and implementation of barcoding methodologies in a broad range of model and non-model organisms. In here we deposit, the raw and processed data we have used during our study.

Datasets and codes for De Lorm et al. 2023: Optimising the automated recognition of individual animals to support population monitoring

Reliable estimates of population size and demographic rates are central to assessing the status of threatened species. However, obtaining individual-based demographic rates requires long-term data, which is often costly and difficult to collect. Photographic data offer an inexpensive, non-invasive method for individual-based monitoring of species with unique markings, and could therefore increase available demographic data for many species. However, selecting suitable images and identifying individuals from photographic catalogues is prohibitively time-consuming. Automated identification software can significantly speed up this process. Nevertheless, automated methods for selecting suitable images are lacking, as are studies comparing the performance of the most prominent identification software packages.   In this study, we develop a framework that automatically selects images suitable for individual identification, and compare the performance of three commonly used identification software packages; Hotspotter, I3S-Pattern, and WildID. As a case study, we consider the African wild dog Lycaon pictus, a species whose conservation is limited by a lack of cost-effective large-scale monitoring. To evaluate intra-specific variation in the performance of software packages, we compare identification accuracy between two populations (in Kenya and Zimbabwe) that have markedly different coat colouration patterns.     The process of selecting suitable images was automated using Convolutional Neural Nets that crop individuals from images, filter out unsuitable images, separate left and right flanks, and remove image backgrounds. Hotspotter had the highest image-matching accuracy for both populations. However, the accuracy was significantly lower for the Kenyan population (62%), compared to the Zimbabwean population (88%).    Our automated image pre-processing has immediate application for expanding monitoring based on image-matching. However, the difference in accuracy between populations highlights that population-specific detection rates are likely and may influence certainty in derived statistics. For species such as the African wild dog, where monitoring is both challenging and expensive, automated individual recognition could greatly expand and expedite conservation efforts.

opencc-zeroDec 2022View details →

Sponge diversification in marine lakes: implications for phylogeography and population genomic studies on sponges

The relative influence of geography, currents and environment on gene flow within sessile marine species remains an open question. Detecting subtle genetic differentiation at small scales is challenging in benthic populations due to large effective population sizes, general lack of resolution in genetic markers, and because barriers to dispersal often remain elusive. Marine lakes can circumvent confounding factors by providing discrete and replicated ecosystems. Using high-resolution double digest restriction-site associated DNA sequencing (4,826 Single Nucleotide Polymorphisms, SNPs), we genotyped populations of the sponge Suberites diversicolor (n=125) to test the relative importance of spatial scales (1-1,400km), local environmental regimes, and permeability of seascape barriers in shaping population genomic structure. With the SNP dataset we show strong intra-lineage population structure, even at scales <10km (average FST = 0.63), that was not detected previously using single markers. Most variation was explained by differentiation between populations (AMOVA: 48.8%) with signatures of population size declines and bottlenecks per lake. Though the populations were strongly structured, we did not detect significant effects of geographic distance, local environments, or degree of connection to the sea on population structure, suggesting mechanisms such as founder events with subsequent priority effects may be at play. We show that the inclusion of morphologically cryptic lineages that can be detected with the COI marker can reduce the obtained SNP set by almost 90%. Future work on sponge genomics should confirm that only one lineage is included. Our results call for a reassessment of poorly dispersing benthic organisms that were previously assumed to be highly connected based on low-resolution markers.

opencc-zeroDec 2022View details →

Global burden of non-tuberculous mycobacteria in the cystic fibrosis population: A systematic review and meta-analysis

Background: People living with cystic fibrosis have an increased risk of lung infection with non-tuberculous mycobacteria (NTM), which is reportedly increasing. We conducted a systematic review of the literature to estimate the burden (prevalence and incidence) of non-tuberculous mycobacteria in the cystic fibrosis population. Methods: Electronic databases, registries, and grey literature sources were searched for cohort and cross-sectional studies reporting epidemiological measures (incidence and prevalence) of NTM infection or NTM pulmonary disease (NTM-PD) in cystic fibrosis. The last search was conducted in September 2021; we included reports since database creation and registry reports published since 2010. The methodological quality of studies was appraised with the Joanna Briggs Institute tool. A random-effects meta-analysis was conducted to summarize the prevalence of NTM infection, and the remaining results are presented in a narrative synthesis. Results: Ninety-five studies were included in this review. All 95 studies reported on NTM infection, and 14 of these also reported on NTM-PD. The pooled estimate for the point prevalence of NTM infection was 7.9% (CI 95%, 5.1–12.0%). In meta-regression, sample size and geographical location of the study modified the estimate. Longitudinal analysis of registry reports showed an increasing trend in NTM infection prevalence between 2010 and 2019. Conclusions: The overall prevalence of NTM infection in CF is 7.9% and is increasing over time based on international registry reports. Future studies should report screening frequency, microbial identification methods, and incidence rates of progression from NTM infection to pulmonary disease.

Pylake tutorial dataset: Population dynamics

A dataset of force data measured on a LUMICKS C-Trap. The system consists of a DNA hairpin construct tethered between two polystyrene beads held at a constant distance with the optical traps.

VCF file from: Signatures of local adaptation to current and future climate in phenology-related genes in natural populations of Quercus robur

Qrob_seqcap_87_18799.vcf - containing 18,799 single nucleotide variants (SNPs) in phenology-related genes in 87 individuals of Quercus robur from 6 populations, described in Meger et al.

opencc-zeroMar 2023View details →

Data and code for: Failure to purge: Population and individual inbreeding effects on fitness across generations of wild Impatiens capensis

Inbreeding exposes deleterious recessive alleles in homozygotes, lowering fitness and generating inbreeding depression (ID). Both purging (via selection) and fixation (via drift) should reduce segregating deleterious mutations and ID in more inbred populations. These theoretical predictions are not well-tested in wild populations, which is concerning given purging/fixation have opposite fitness outcomes. We examined how individual- and population-level inbreeding and genomic heterozygosity affected maternal and progeny fitness within and among 12 wild populations of Impatiens capensis. We quantified maternal fitness in home sites, maternal multilocus heterozygosity (using 12,560 SNPs), and lifetime fitness of selfed and predominantly outcrossed progeny in a common garden. These populations spanned a broad range of individual- (fi = -0.17–0.98) and population-level inbreeding (FIS = 0.25–0.87). More inbred populations contained fewer polymorphic loci, less fecund mothers, and smaller progeny, suggesting higher fixed loads. However, despite appreciable ID (mean: 8.8 lethal equivalents per gamete), ID did not systematically decline in more inbred population. More heterozygous mothers were more fecund and produced fitter progeny in outcrossed populations, but this pattern unexpectedly reversed in highly inbred populations. These observations suggest that persistent overdominance or some other force acts to forestall purging and fixation in these populations.

openmit-licenseMar 2023View details →

Celluloepidemiology: a novel paradigm for quantifying infectious disease dynamics through T-cell modelling on a population level

T-cell receptor sequencing (TCR-seq) was performed on enriched CD8+ T-cells. TCR clonotype annotation was performed using MiXCR v.3.0.13 with the default input parameters. Full origin and method description available in: Celluloepidemiology: a novel paradigm for quantifying infectious disease dynamics through T-cell modelling on a population level

opencc-by-4.0Apr 2023View details →

Virus infections in 20 Plantago lanceolata populations in the Aland Island (2017)

Virus occurrences from individual Plantago lanceolata plant leaves. The methods of collection as well as sample processing, including virus sequencing, are described in <a href="https://doi.org/10.1016/j.cub.2023.03.022">Norberg, Susi, et al. (2023) Current Biology</a>.