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opencc-by-3.0-usOct 2022View details →

Dataset for "Polyploidy impacts population growth and competition with diploids: Multigenerational experiments reveal key life history tradeoffs"

Datasets associated with the manuscript "Polyploidy impacts population growth and competition with diploids: Multigenerational experiments reveal key life history tradeoffs".

Runs of homozygosity reveal past bottlenecks and contemporary inbreeding across diverging populations of an island-colonizing bird

Genomes retain evidence of the demographic history and evolutionary forces that have shaped populations. Across island systems, contemporary patterns of genetic diversity reflect complex population demography, including colonisation events, bottlenecks, gene flow and genetic drift. Here, we investigate whether island founder events have prolonged effects on genome-wide diversity and runs of homozygosity (ROH) distributions, using whole genome resequencing from six populations across three archipelagos of Berthelot's pipit (Anthus berthelotii) – a passerine which has undergone island speciation relatively recently. Pairwise sequential Markovian coalescent (PSMC) analyses estimated divergence from its sister species approximately two million years ago. Results indicate that all Berthelot's pipit populations had shared ancestry until approximately 50,000 years ago, when the Madeiran archipelago populations were founded, while the Selvagens were colonised within the last 8,000 years. We identify extensive long ROH (>1 Mb) in genomes in the most recently colonised populations of Madeira and Selvagens which have experienced sequential island founder events and population crashes. Population expansion within the last 100 years may have eroded long ROH in the Madeiran archipelago, resulting in a prevalence of short ROH (<1 Mb). Extensive long and short ROH in the Selvagens reflects strong recent inbreeding, small contemporary effective population size and past bottleneck effects, with as much as 37.7% of the autosomes comprised of ROH >250 kb in length. These findings highlight the importance of demographic history, as well as selection and genetic drift, in shaping contemporary patterns of genomic diversity across diverging populations.

Data from: Demographic histories shape population genomics of the common coral grouper (Plectropomus leopardus)

Many coral reef fishes display remarkable genetic and phenotypic variation across their geographic ranges. Understanding how historical and contemporary processes have shaped these patterns remains a focal question in evolutionary biology since they reveal how diversity is generated and how it may respond to future environmental change. Here we compare the population genomics and demographic histories of a commercially and ecologically important coral reef fish, the common coral grouper (Plectropomus leopardus [Lacépède 1802]), across two adjoining regions (the Great Barrier Reef; GBR, and the Coral Sea, Australia) spanning approximately 14 degrees of latitude and 9 degrees of longitude. We analysed 4,548 single nucleotide polymorphism (SNP) markers across 11 sites and show that genetic connectivity between regions is low, despite their relative proximity (~ 100 km) and an absence of any obvious geographic barrier. Inferred demographic histories using 10,479 markers suggest that the Coral Sea population was founded by a small number of GBR individuals and that divergence occurred ~ 190 kya under a model of isolation with asymmetric migration. We detected population expansions in both regions, but estimates of contemporary effective population sizes were approximately 50 % smaller in Coral Sea sites, which also had lower genetic diversity. Our results suggest that P. leopardus in the Coral Sea have experienced a long period of isolation that precedes the recent glacial period (~ 10–120 kya) and may be vulnerable to localised disturbances due to their relative reliance on local larval replenishment. While it is difficult to determine the underlying events that led to the divergence of Coral Sea and GBR lineages, we show that even geographically proximate populations of a widely dispersed coral reef fish can have vastly different evolutionary histories.

Personality and temporal plasticity in fish populations along a gradient of evolutionary divergence

Personality is now recognized as an ecologically and evolutionarily significant phenomenon because it can affect fitness directly. However, empirical studies specifically tackling the importance of personality in the processes of adaptive divergence and speciation are scarce. Whether selection favours plasticity or canalization of personality traits in specific contexts and how ecological conditions affect the presence and the structure of personalities remain to be elucidated. We used five populations of Arctic charr, Salvelinus alpinus, chosen along a gradient of genetic and phenotypic divergence: an anadromous population supposedly close to the ancestral population and two pairs of sympatric lake morphs. Fish were raised individually from eggs in a common-garden experiment to specifically assess the genetic bases of the boldness trait in these populations. Thirty-two individuals per morph were repeatedly tested at 11 months old in an open field test with a shelter to assess boldness. The repeatability of the boldness trait (i.e. personality), within- and among-individual variation and temporal variation were assessed within each population. Then, the temporal plasticity in boldness and boldness mean score were assessed among populations. The results show differences between populations for the three variables, with the highest repeatability in the most diverged population, an increase in boldness over time and a lower mean value (especially the first time they were exposed to the novel environment) in the anadromous population. This suggests that boldness and temporal plasticity differ between the anadromous population and the more diverged lake populations under a controlled embryonic/juvenile environment. Further research is needed to verify the contribution of temporal plasticity for personality traits in the context of rapid adaptive radiation such as that seen in Arctic charr.

opencc-by-4.0Nov 2022View details →

Source Data: No evidence for a common blood microbiome based on a population study of 9,770 healthy humans

Source data for manuscript titled: 'No evidence for a common blood microbiome based on a population study of 9,770 healthy humans' (https://www.biorxiv.org/content/10.1101/2022.07.29.502098v1)

opencc-by-4.0Feb 2023View details →

On the seed population of solar energetic particles in the inner heliosphere : simulation data

Figures and simulation data of the paper titled 'On the seed population of solar energetic particles in the inner heliosphere', which is submitted to the Journal of Geophysical Research: Space Physics.  The simulation data consist of all the output from the EUHFORIA model and the PARADISE model that was used in the paper. The abstract of the paper is: Particles measured in large gradual solar energetic particle (SEP) events are believed to be predominantly accelerated at shocks driven by coronal mass ejections (CMEs).  Ion charge state and composition analyses suggest that the origin of the seed particle population for the mechanisms of particle acceleration at CME-driven shocks is not the bulk solar wind thermal material, but rather a suprathermal population present in the solar wind. This suprathermal population could result from remnant material accelerated in prior solar flares and/or preceding CME-driven shocks. In this work, we examine the distribution of this suprathermal particle population in the inner heliosphere by combining a magnetohydrodynamic (MHD) simulation of the solar wind and a Monte-Carlo simulation of particle acceleration and transport. Assuming that the seed particles are uniformly distributed near the Sun by solar flares of various magnitudes, we study the longitudinal distribution of the seed population at multiple heliocentric distances. We consider a non-uniform background solar wind, consisting of fast and slow streams that lead to compression and rarefaction regions within the solar wind. Our simulation shows that the seed population at a particular location (e.g., 1 au) is strongly modulated by the underlying solar wind configuration. Corotating interaction regions (CIRs) and merged interactions regions (MIRs) can strongly alter the energy spectra of the seed particle populations. In addition, cross-field diffusion plays an important role in mitigating strong  variations of the seed population in both space and energy.

Data for: Sex-biased infections scale to population impacts for an emerging wildlife disease

Demographic factors are fundamental in shaping infectious disease dynamics. Aspects of populations that create structure, like age and sex, can affect patterns of transmission, infection intensity and population outcomes. However, studies rarely link these processes from individual to population-scale effects. Moreover, the mechanisms underlying demographic differences in disease are frequently unclear. Here, we explore sex-biased infections for a multi-host fungal disease of bats, white-nose syndrome, and link disease-associated mortality between sexes, the distortion of sex ratios, and the potential mechanisms underlying sex differences in infection. We collected data on host traits, infection intensity, and survival of five bat species at 42 sites across seven years. We found females were more infected than males for all five species. Females also had lower apparent survival over winter and accounted for a smaller proportion of populations over time. Notably, female-biased infections were evident by early hibernation and likely driven by sex-based differences in autumn mating behavior. Male bats were more active during autumn which likely reduced replication of the cool-growing fungus. Higher disease impacts in female bats may have cascading effects on bat populations beyond the hibernation season by limiting recruitment and increasing the risk of Allee effects.

Population regulation and density‐dependent demography in the Trinidadian guppy

Classic theory for density-dependent selection for delayed maturation requires that a population be regulated through some combination of adult fecundity and/or juvenile survival. We tested whether those demographic conditions were met in four experimental populations of Trinidadian guppies in which delayed maturation of males evolved when the densities of those populations became high. We used monthly mark-recapture data to examine population dynamics and demography in these populations. Three of the four populations displayed clear evidence of regulation. In all four populations, monthly adult survival rates were independent of biomass density or actually increased with increased biomass density. Juvenile recruitment, which is a combination of adult fecundity and juvenile survival, decreased as biomass density increased in all four populations. Demography showed marked seasonality, with greater survival and higher recruitment in the dry season than the wet season. Population regulation via juvenile recruitment supports the hypothesis that density-dependent selection was responsible for the evolution of delayed maturity in males. This body of work represents one of the few complete tests of density-dependent selection theory.

Distinct responses and range shifts of lizards populations across an elevational gradient under climate change

Ongoing climate change has profoundly affected global biodiversity, but its impacts on populations across elevations remain understudied. Using a mechanistic niche model incorporating species traits, we predicted ecophysiological responses (activity times, oxygen consumption and evaporative water loss) for lizard populations at high-elevation (< 3600 m asl) and extra-high-elevation (> 3600 m asl) under recent (1970–2000) and future (2081–2100) climates. Compared with their high-elevation counterparts, lizards from extra-high-elevations are predicted to experience a greater increase in activity time and oxygen consumption but a similar increase in evaporative water loss. By integrating these ecophysiological traits into a hybrid species distribution model (HSDM), we were able to make the following predictions under two warming scenarios (SSP1-2.6, SSP5-8.5). By 2081–2100, we predict that lizards at both high- and extra-high-elevations will shift upslope; lizards at extra-high-elevations will gain more and lose less habitat than will their high-elevation congeners. We therefore advocate the conservation of high-elevation species in the context of climate change, especially for those populations living close to their lower elevational range limits. In addition, by comparing the results from HSDM and traditional species distribution models, we highlight the importance of considering intraspecific variation and local adaptation in physiological traits along elevational gradients when forecasting species' future distributions under climate change.

opencc-zeroFeb 2022View details →

Data on range-wide breeding habitat use of the critically endangered Yellow-breasted Bunting Emberiza aureola after population collapse

The population of the Yellow-breasted Bunting Emberiza aureola, a formerly widely distributed and abundant songbird of northern Eurasia, suffered a catastrophic decline and a strong range contraction between 1980 and 2013. There is evidence that the decline was driven by illegal trapping during migration, but potential contributions of other factors to the decline, such as land-use change, have not yet been evaluated. Before effects of land-use change can be evaluated, a basic understanding of the ecological requirements of the species is needed. We therefore compared habitat use in ten remaining breeding regions across the range, from European Russia to Japan and the Russian Far East. We also assessed large-scale variation in habitat parameters across the breeding range. We found large variation in habitat use, within and between populations. Differences were related to the cover and height of trees and shrubs at Yellow-breasted Bunting territories. In many regions, Yellow-breasted Buntings occupied early successional stages, including anthropogenic habitats characterized by mowing, grazing or fire regimes. We found that the probability of presence can be best predicted with the cover of shrubs, herbs and grasses. Highest probabilities were found at shrub cover values of 40 to 70 %. Differences in habitat use along a longitudinal gradient were small, but we found strong differences across latitudes, possibly related to habitat availability. We conclude that the remaining Yellow-breasted Bunting populations are not limited to specific habitat types. Our results provide important baseline information to model the range-wide distribution of this critically endangered species and to guide targeted conservation measures.

Genetic diversity and population structure from a Peruvian nucleus cattle herd using SNP data

New-generation sequencing technologies, among them SNP chips for massive genotyping, have proven to be useful for the effective management of genetic resources. Also, developing nucleus herds is an effective method for genetic improvement work. To date, molecular studies in Peruvian cattle are still in their infancy. To close this gap, we here employed two SNP panels (BovineHD and Bovine100K) to determine for the first time the Peruvian nucleus herd's genetic diversity and population structure that belong to INIA. This nucleus comprises Brahman (N=16), Braunvieh (N=14), Gyr (N=11), and Fleckvieh (N=22) breeds. Additionally, samples from a locally adapted creole cattle, the Arequipa Fighting Bull (AFB, N=12), were incorporated into the study. The genetic diversity indices in all breeds showed a high proportion of polymorphic SNPs, varying from 69.37% in Gyr to 80.81% in Braunvieh. Also, Braunvieh possessed the highest observed heterozygosity (0.53±0.17), while Brahman possessed the lowest (0.44±0.10), indicating that the former is more diverse compared to the other cattle breed groups. According to the molecular variance analysis, 83.92% of the variance occurs within individuals, whereas 16.0% occurs between populations. The pairwise FST estimates between breeds showed values that ranged from 0.054 (Braunvieh vs AFB) to 0.266 (Brahman vs AFB). Pairwise Reynold's distance showed a pattern similar to the one obtained with the FST statistics, with values ranging from 0.058 to 0.309. A dendrogram was constructed using the Neighbor-Joining clustering algorithm, and similar to the principal coordinate analysis, three groups were identified. Results showed a clear separation between Bos indicus (Brahman and Gyr) and B. taurus breeds (Braunvieh and Fleckvieh). For Fleckvieh and Braunvieh, there were two subgroups each one of them grouping with the AFB group. Similar results were obtained with ADMIXTURE analysis with K= 3 as the most optimal number for the inferred genetic structure of the populations. The results from the current study would contribute to the appropriate management avoiding loss of genetic variability in these breeds and to future improvements for this nucleus. Additional work is needed to speed up the breeding process in the Peruvian cattle system.

Multiplex imaging of breast cancer lymph node metastases identifies prognostic single-cell populations independent of clinical classifiers

This repository contains the raw IMC data of ZTMA 26 as continuation of dataset 10.5281/zenodo.7494413. The zip files starting with ZTMA contain the raw IMC measurements (mcd and txt) of those parts of the TMA. The TMA measurements are split up into parts in order to avoid huge files. Additionally, this repository contains the metadata of the patients analyzed in this study, the panel information and the single-cell data that was extracted from the multiplexed images together with the associated metadata in SingleCellExperiment format for analysis in R. The analysis.zip folder contains files that were written out during the analysis according to the scripts in https://github.com/BodenmillerGroup/BC_LN_metastses. The single-cell and other data outputs from CellProfiler can be found in the cpout.zip file. The IF_whole_sections.zip file contains the IF images of the primary breast cancer sections (czi files) and the extracted single-cell data.

Multiplex imaging of breast cancer lymph node metastases identifies prognostic single-cell populations independent of clinical classifiers

This repository contains the raw IMC data of ZTMA 21 and 25 of the matched primary breast cancer and lymph node metastasis study presented in Fischer and Jackson et al., 2023. The code that was used to process and analyze this data can be found at https://github.com/BodenmillerGroup/BC_LN_metastses. The zip files starting with ZTMA contain the raw IMC measurements (mcd and txt) of the respective parts of the TMA. The TMA measurements are split up into parts in order to avoid huge files.

Data for: Breeding honey bees (Apis mellifera L.) for low and high Varroa destructor population growth: gene expression of bees performing grooming behavior

Background Social organisms, including honey bees (Apis mellifera L.), have defense mechanisms to control the multiplication and transmission of parasites and pathogens within their colonies. Self-grooming, a mechanism of behavioral immunity, seems to contribute to restraining the population growth of the ectoparasitic mite Varroa destructor in honey bee colonies. Because V. destructor is the most damaging parasite of honey bees, breeding them for resistance against the mite is a high priority of the beekeeping industry. We conducted a bidirectional breeding program to select honey bee colonies with low and high varroa population growth (LVG and HVG, respectively). Having high and low lines of bees allowed the study of genetic mechanisms underlying self-grooming behavior between the extreme genotypes. Worker bees were classified into two categories: 'light groomers' and 'intense groomers'. The brains of bees from the different categories (LVG-intense, LVG-light, HVG-intense, and HVG-light) were used for gene expression and viral quantification analyses. Results Differentially expressed genes (DEGs) associated with the LVG and HVG lines were identified, including four odorant-binding proteins and a gustatory receptor. A functional enrichment analysis showed 19 enriched pathways from a list of 219 down-regulated DEGs in HVG bees, including the Kyoto Encyclopedia of Genes and Genomes (KEGG) term of oxidative phosphorylation. Additionally, bees from the HVG line showed higher levels of Apis rhabdovirus 1 and 2, Varroa destructor virus -1 (VDV-1), and Deformed wing virus-A (DWV-A) compared to bees of the LVG line. Conclusions The difference in expression of odorant-binding protein genes and a gustatory receptor between bee lines suggests a possible link between them and the perception of irritants to trigger rapid self-grooming instances that require the activation of energy metabolic pathways. Therefore, our results provide new insights into the molecular mechanisms involved in honey bee grooming behavior. Differences in viral levels in the brains of LVG and HVG bees showed the importance of investigating the pathogenicity and potential impacts of neurotropic viruses on behavioral immunity. The results of this study advance the understanding of a trait used for selective breeding, self-grooming, and the potential of using genomic-assisted selection to improve breeding programs.

opencc-by-4.0Feb 2023View details →

Fig. 1 in Main Functions Of Loud Vocalization In Populations Of Edible Dormouse Glis Glis

Fig. 1. Mean number of "performances" (a) and loud calls (b) found in all studied edible

Drivers of strong isolation and small effective population size at a leading range edge of a widespread plant

Climate change has influenced species distributions worldwide with upward elevational shifts observed in many systems. Leading range edge populations, like those at upper elevation limits, are crucial for climate change responses but can exhibit low genetic diversity due to founder effects, isolation, or limited outbreeding. These factors can hamper local adaptation at range limits. Using the widespread herb, Argentina anserina, we measured ecological attributes (population density on the landscape, area of population occupancy, and plant and flower density) spanning a 1000m elevation gradient, with high elevation populations at the range limit. We measured vegetative clonal potential in the greenhouse for populations spanning the gradient. We combined these data with a ddRAD-seq dataset to test the hypotheses that high-elevation populations would exhibit ecological and genomic signatures of leading range edge populations. We found that population density on the landscape declined towards the high elevation limit, as is expected towards range edges. However, plant density was elevated within edge populations. In the greenhouse, high-elevation plants exhibited stronger clonal potential than low-elevation plants, likely explaining increased plant density in the field. Phylogeographic analysis supported more recent colonization of high-elevation populations which were also more genetically isolated, had more extreme heterozygote excess, and had smaller effective population size than low. Results support that colonization of high elevations was likely accompanied by increased asexuality, contributing to a decline in effective population size. Despite high plant density in leading-edge populations, their small effective size, isolation, and clonality could constrain adaptive potential.

Survival analysis after vertebral compression fractures in population over 65 years old

Background: Mortality in vertebral compression fractures (VCF) is rarely directly associated with the fracture. Lower mortality has been demonstrated when fractures are treated surgically (vertebral augmentation) versus conservatively. However, the exact mechanism that justifies this increased survival is unknown. This study aims to analyze overall survival in elderly patients who have suffered a non-pathological VCF, its causes, and the relationship with different factors. Methods: All patients over 65 years old diagnosed with acute, non-pathologic thoracic or lumbar VCF, treated consecutively in our center from January 2017 to December 2020, were retrospectively selected for analysis. Those patients with follow-ups under two years or who required arthrodesis due to poor fracture evolution were excluded. Only the first process was considered for patients who presented a second VCF in the first three months. Results: A total of 509 consecutive fractures were registered. Seventeen were excluded, leaving 492 cases for final analysis. The mean age was 78.9 years old. Overall mortality was 36.2%. Survival rate at 1-, 12-, 24-, 48-, and 60-month follow-up was 97.4%, 86.6%, 78.0%, 64.4%, and 59.4%, respectively. The independent factors associated with a higher mortality risk were age, male, oncologic history, non-traumatic mechanism, and co-morbidity during hospitalization. No statistical differences were found when comparing the two survival curves by treatment (vertebral augmentation vs. conservative management) over time. No benefit was observed in those patients with comprehensive outpatient geriatric care.  Conclusion: Age, male sex, history of oncological disease, non-traumatic mechanism of the fracture, and any comorbidity during hospitalization were identified as variables independently associated with a higher risk of mortality following a VCF in the elderly. Vertebral augmentation and comprehensive outpatient geriatric care showed no benefit in overall survival.

Assessment of the Genetic Diversity and Population Structure of the Peruvian Andean Legume, Tarwi (Lupinus mutabilis), with High Quality SNPs

Lupinus mutabilis Sweet (Fabaceae), “tarwi” or “chocho”, is an important grain legume in the Andean region. In Peru, studies on tarwi have mainly focused on morphological features; however, they have not been molecularly characterized. Currently, it is possible to explore the genetic parameters of plants with reliable and modern methods such as genotyping by sequencing (GBS). Here, for the first time, we used single nucleotide polymorphism (SNP) markers to infer the genetic diversity and population structure of 89 accessions of tarwi from nine Andean regions of Peru. A total of 5922 SNPs distributed along all chromosomes of tarwi were identified. STRUCTURE analysis revealed that this crop is grouped into two clusters. A dendrogram was generated using the UPGMA clustering algorithm and, like the principal coordinate analysis (PCoA), it showed two groups that correspond to the geographic origin of the tarwi samples. AMOVA showed a reduced variation between clusters (7.59%) and indicated that variability within populations is 92.41%. Population divergence (Fst) between clusters 1 and 2 revealed low genetic difference (0.019). We also detected a negative Fis for both populations, demonstrating that, like other Lupinus species, tarwi also depends on cross-pollination. SNP markers were powerful and effective for the genotyping process in this germplasm. We hope that this information is the beginning of the path towards a modern genetic improvement and conservation strategies of this important Andean legume.

Seasonal ecosystem linkages contribute to the maintenance of migratory polymorphism in a salmonid population

The influence of resource subsidies on animal growth, survival, and reproduction is well understood, but their ultimate effects on life history have been less explored. Some wild species have a partially migratory life history, wherein migration is dictated based upon threshold traits regulated in part by the seasonal availability of resources. We conducted a large-scale field manipulation experiment where we provided a terrestrial invertebrate subsidy to red-spotted masu salmon. Individuals in stream reaches that received a subsidy had, on average, a 53% increase in growth rate relative to those in control reaches. This increased growth resulted in a greater proportion of individuals reaching the threshold body size and smolting in the autumn. Consequently, 19–55% of females in subsidized reaches became migratory, whereas 0–14% became migratory in the control reaches. Our findings highlight seasonal ecosystem linkage as a key ecosystem property for maintaining migratory polymorphism in partially migratory animals.

QGIS Data for Canadian Population, PM2.5, Nighttime lights.

This is the dataset for the QGIS analysis for Canadian Population, PM2.5, Nighttime lights.