Find research datasets worth reusing

Soil composition, phenotypic and genetic data to: Adaptive differentiation on serpentine soil in diploid versus autotetraploid populations of Biscutella laevigata (Brassicaceae)

Serpentine soils exhibit extreme properties (e.g. high magnesium content) influencing plant growth and survival and have been repeatedly documented to promote adaptive edaphic differentiation in plants. Individuals from four pairs of nearby diploid and autotetraploid populations of Biscutella laevigata sampled on serpentine vs non-serpentine soils in a factorial design are used to assess the genetic and phenotypic changes associated with edaphic origin and ploidy level. Individual samples from natural populations were subjected to soil elemental analysis and genotyping using restriction site-associated DNA sequences (RAD-seq) to link genetic variation with contrasting soils and ploidy levels. In diploids, genetic variation was consistent with demographic contraction and a pattern of isolation by environment with respect to the ratio of calcium / magnesium concentrations, whereas tetraploids presented evidence of expansion with limited edaphic differentiation. The genetic basis of tolerance and adaptation to serpentine was further assessed experimentally on seed-grown individuals from all populations subjected to high (serpentine-like) vs low (control) concentrations of magnesium in hydropony. Fitness-related phenotypic traits under experimental cultivation were consistent with adaptive differentiation among diploid ecotypes but not among the tetraploids that similarly grow in both habitats and consistently present higher investment in roots. Further work comparing experimentally resynthesized polyploids to natural diploids and polyploids has to tease the role of whole genome duplication apart from the impact of post-polyploidy evolution.

Data from: Evolutionarily labile dispersal behavior and discontinuous habitats enhance population differentiation in island vs continentally distributed swallows

The causes of population divergence in vagile groups remain a paradox in evolutionary biology: dispersive species should be able to colonize new areas, a prerequisite for allopatric speciation, but dispersal also facilitates gene flow, which erodes population differentiation. Strong dispersal ability has been suggested to enhance divergence in patchy habitats and inhibit divergence in continuous landscapes, but empirical support for this hypothesis is lacking. Here we compared patterns of population divergence in a dispersive clade of swallows distributed across both patchy and continuous habitats. The Pacific Swallow (Hirundo tahitica) has an insular distribution throughout Southeast Asia and the Pacific, while its sister species, the Welcome Swallow (H. neoxena), has a continental distribution in Australia. We used whole-genome data to demonstrate strong genetic structure and limited introgression among insular populations, but not among continental populations. Demographic models show that historic changes in habitat connectivity have contributed to population structure within the clade. Swallows appear to exhibit evolutionarily labile dispersal behavior in which they reduce dispersal propensity after island colonization despite retaining strong flight ability. Our data support the hypothesis that fragmented habitats enhance population differentiation in vagile groups, and suggest that labile dispersal behavior is a key mechanism underlying this pattern.

Data from: Genomic architecture drives population structuring in Amazonian birds

Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on the spatial and temporal origins of population variation have been largely limited to evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known as genomic architecture in producing heterogeneity in differentiation across the genome. To test how genomic architecture impacts our ability to reconstruct general patterns of diversification in species that co-occur across geographic barriers, we sequenced the whole genomes of multiple bird populations that are distributed across rivers in southeastern Amazonia. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with species tree support. Gene flow was less pervasive in regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection, skewing genome-wide estimates of effective population sizes and gene flow between populations towards lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from neutral processes to elucidate how inferring spatial patterns of diversification are sensitive to genomic architecture.

Reference genome resources associated with the project: Functional genetic diversity is correlated with intensity of genetic drift in populations of an endangered rattlesnake

Theory predicts that genetic erosion in small, isolated populations of endangered species can be assessed using estimates of neutral genetic variation reflecting long-term impacts of genetic drift, yet this widely used approach has been questioned in the genomics era. Here we leverage a chromosome-level assembly and whole genome resequencing data (N=110 individuals) from an endangered rattlesnake (Sistrurus catenatus) to evaluate the relationship between genome-wide neutral and functional diversity over long- and short-term timescales. As predicted for populations at long-term equilibrium, we found a positive correlation between population-level estimates of neutral genetic diversity (π) and the mean number of highly detrimental loss-of-function mutations, and a negative relationship between neutral genetic diversity and an estimate of genetic load. In contrast, we found only a weak, non-significant positive correlation between levels of neutral and adaptive variation. Additional analyses using estimates of drift at more recent time scales (> 100 generations) show expected correlations between both measures of genetic load, but a lack of a significant correlation with levels of adaptive variation. Individual-based demographic metrics that capture drift impacts over recent time scales confirm these results. Broadly, our results confirm that estimates of diversity and demography based on neutral genetic variation provide an accurate measure of a key component of genetic erosion – genetic load – in populations of a threatened vertebrate. Our findings also provide nuance to the neutral-functional diversity controversy by demonstrating that neutral genetic diversity is useful in predicting some, but not all, components of functional genetic diversity.

Evaluating the use of non‐invasive hair sampling and ddRAD to characterize populations of endangered species: Application to a peripheral population of the European mink

The application of next‐generation sequencing (NGS) to non‐invasive samples is one of the most promising methods in conservation genomics, but these types of samples present significant challenges for NGS. The European mink (Mustela lutreola) is critically endangered throughout its range. However, important aspects such as census size and inbreeding remain still unknown in many populations, so it is crucial to develop new methods to monitor this species. In this work, we placed hair tubes along riverbanks in a border area of the Iberian population, which allowed the genetic identification of 76 European mink hair samples. We then applied a reduced representation genomic sequencing (ddRAD) technique to a subset of these samples to test whether we could extract sufficient genomic information from them. We show that several problems with the DNA, including contamination, fragmentation, oxidation, and possibly sample mixing, affected the samples. Using various bioinformatic techniques to reduce these problems, we were able to unambiguously genotype 19 hair samples belonging to six individuals. This small number of individuals showed that the demographic status of the species in this peripheral population is worse than expected. The data obtained also allowed us to perform preliminary analyses of relatedness and inbreeding. Although further improvements in sampling and analysis are needed, the application of the ddRAD technique to non‐invasively obtained hairs represents a significant advance in the genomic study of endangered species.

Data from: Clinical antibiotic-resistance plasmids have small effects on biofilm formation and population growth in Escherichia coli in vitro

<div> <div> <div> Antimicrobial resistance (AR) mechanisms encoded on plasmids can affect other phenotypic traits in bacteria, including biofilm formation. These effects may be important contributors to the spread of AR and the evolutionary success of plasmids, but it is not yet clear how common such effects are for clinical plasmids/bacteria, and how they vary among different plasmids and host strains. Here, we used a combinatorial approach to test the effects of clinical AR plasmids on biofilm formation and population growth in clinical and laboratory Escherichia coli strains. In most of the 25 plasmid-bacterium combinations tested, we observed no significant change in biofilm formation upon plasmid introduction, contrary to the notion that plasmids frequently alter biofilm formation. In a few cases we detected altered biofilm formation, and these effects were specific to particular plasmid-bacterium combinations. By contrast, we found a relatively strong effect of a chromosomal streptomycin-resistance mutation (in rpsL) on biofilm formation. Further supporting weak and host-strain- dependent effects of clinical plasmids on bacterial phenotypes in the combinations we tested, we found growth costs associated with plasmid carriage (measured in the absence of antibiotics) were moderate and varied among bacterial strains. These findings suggest some key clinical resistance plasmids cause only mild phenotypic disruption to their host bacteria, which may contribute to the persistence of plasmids in the absence of antibiotics. </div> </div> </div>

A whole-genome reference panel of 14,393 individuals for East Asian populations accelerates discovery of rare functional variants

Underrepresentation of non-European populations hinders growth of global precision medicine. Resources such as imputation reference panels that match the study population are necessary to find low-frequency variants with substantial effects. We created a reference panel consisting of 14,393 whole-genome sequences including more than 11,000 Asian individuals. Genome-wide association studies were conducted using the reference panel and a population-specific genotype array of 72K subjects for eight phenotypes. This panel yields improved imputation accuracy of rare and low-frequency variants within East Asian populations compared with the largest reference panel. Thirty-nine previously unidentified associations were found, and more than half of the variants were East-Asian-specific. We discovered genes with rare protein-altering variants, including LTBP1 for height and GPR75 for body mass index, as well as putative regulatory mechanisms for rare noncoding variants with cell-type-specific effects. We suggest this data set will add to the potential value of Asian precision medicine.

opencc-by-4.0Oct 2023View details →

Supplement: In situ spatial reconstruction of distinct normal and pathological cell populations within the human adrenal gland

Supplemental legends, figure, and table for  In situ spatial reconstruction of distinct normal and pathological cell populations within the human adrenal gland.

opencc-by-4.0Sep 2020View details →

Figure 2 in Protandrous Arrival in a Population of the Periodical Cicada Magicicada septendecim (Linnaeus) (Hemiptera: Cicadidae) in Montgomery County, Maryland

Figure 2. Magicicada septendecim: newly eclosed teneral. (Maryland, Michael J. Raupp, 16 May 2004)

Population genetics of Daphnimorpha species

A climate relict is of particular importance in evolutionary biology because of its long-term survival in the face of climatic oscillations. However, because their current distributions are usually restricted and fragmented, many climatic relicts have extinction risks. Daphnimorpha (Thymelaeaceae) is a Japanese endemic genus that comprises two species (D. capitellata and D. kudoi) showing a disjunct distribution in the southern part of Japan. These two species are endemic to a single mountain range. In this study, we conducted population genetic analyses using genome-wide single nucleotide polymorphism obtained from multiplexed inter-simple sequence repeat genotyping by sequencing to reveal the phylogeographic history and obtain conservation implications for the two species. The results showed these two species may have been isolated since the Tertiary period, indicating that they are climate relicts. In addition, D. kudoi showed clear genetic differentiation between two mountains (Mt. Nagata and Mt. Kuromi), with a decline in effective population sizes during the last glacial period. In contrast, D. capitellata showed no clear intraspecific genetic structure and its effective population size was relatively stable. These differences could be a result of differences in habitat preferences between the species. For conservation, we should manage the two species based on the three evolutionary significant units (ETUs; D. capitellata, D. kudoi population on Mt. Nagata, and D. kudoi population on Mt. Kuromi). Considering the limited gene flows among subpopulations and their small population sizes, all ETUs require conservative attention to maintain or increase their effective population sizes.

Understanding habitat selection of range-expanding populations of large carnivores: 20 years of grey wolves (Canis lupus) recolonizing Germany

Aim: The non-stationarity in habitat selection of expanding populations poses a significant challenge for spatial forecasting. Focusing on the grey wolf (Canis lupus) natural recolonization of Germany, we compared the performance of different distribution modelling approaches for predicting habitat suitability in unoccupied areas. Furthermore, we analysed whether grey wolf showed non-stationarity in habitat selection in newly colonized areas, which will impact the predictions for potential habitat. Location: Germany Methods: Using telemetry data as presence points, we compared the predictive performance of five modelling approaches based on combinations of distribution modelling algorithms –GLMM, MaxEnt, and ensemble modelling– and two background point selection strategies. We used a homogeneous Poisson point process to draw background points from either the minimum convex polygons derived from telemetry or the whole area known to be occupied by wolves. Models were fit to the data of the first years and validated against independent data representing the expansion of the species. The best-performing approach was then used to further investigate non-stationarity in the species' response in spatiotemporal restricted datasets that represented different colonization steps. Results: Whilst all approaches performed similarly when evaluated against a subset of the data used to fit the models, the ensemble model based on integrated data performed best when predicting range expansion. Models for subsequent colonization steps differed substantially from the global model, highlighting the non-stationarity of wolf habitat selection towards human disturbance during the colonization process. Main conclusions: While telemetry-only data overfitted the models, using all available datasets increased the reliability of the range expansion forecasts. The non-stationarity in habitat selection pointed to wolves settling in the best areas first, and filling in nearby lower-quality habitat as the population increases. Our results caution against spatial extrapolation and space-for-time substitutions in habitat models, at least with expanding species.

opencc-by-4.0May 2023View details →

Data From: Dynamic environments generate geographic fluctuations in population structure of an inland shorebird

Data From: Dynamic environments generate geographic fluctuations in population structure of an inland shorebird. Table S2: δ2H values in breast feathers sampled from 352 pre-fledged young mountain plovers from across the breeding range used for isoscape calibration. The table provides the latitude and longitude coordinates for each δ2H feather sample.

opencc-by-4.0Oct 2023View details →

Population links between an insectivorous bird and moths disentangled through national scale monitoring data

Code in support of "Population links between an insectivorous bird and moths disentangled through national scale monitoring data" Luke Christopher Evans, Malcolm D. Burgess, Simon G. Potts, William E. Kunin, Tom H. Oliver

opencc-zeroMay 2024View details →

Population genetics and comparative morphology of two serpentine Phlox species

Hybridization between rare and widespread species can result in loss of genetic integrity for the rarer species, which can have management and conservation implications. One rare species, Phlox hirsuta, is a serpentine endemic in northern California, and it frequently co-occurs with a widespread congener, P. speciosa. Putative hybrids were recognized based on intermediate morphology, so the possibility of hybridization was explored using floral morphological and molecular data. Ninety-eight individuals of P. hirsuta and P. speciosa were collected from each of three populations, and floral features were measured and compared. Eleven microsatellite loci were amplified for species and putative hybrids, and inter- and intraspecific genetic diversity and relationships were investigated with multiple methods. Variation in morphological and molecular data was recognized. Floral variation was greater for P. hirsuta than P. speciosa. Putative hybrids were genetically allied with P. speciosa, but two individuals of P. hirsuta were resolved to have genetic similarity with P. speciosa. While hybridization is possible between the species, it is uncommon and appears to be primarily unidirectional, with P. speciosa as the hypothesized male parent and P. hirsuta as the hypothesized female parent. The small number of recognized hybrids may be due to ineffective interspecific pollination, early acting inbreeding depression, hybrids being less fit than parents, and/or small sample sizes. Reinforcement does not appear to play a role in secondary contact between species. Both microsatellite loci and floral morphology varied across the small geographic range of P. hirsuta, suggesting local differentiation and adaptation are possible over short distances.

opencc-by-4.0Dec 2017View details →

Figure 4 in Otolith shape analysis of three gobiid species of the Northwestern Black Sea and characterization of local populations of Neogobius melanostomus

Figure 4. – Discrimination of the three species by otolith shape analysis.

opencc-by-4.0May 2019View details →

Analysis of genome-wide DNA arrays reveals the genomic population structure and diversity in autochthonous Greek goat breeds

Genotyping data in ped and map format (ped/map) for 72 goats and 53,347 genotypes.

closedIPD-NOFeb 2026View details →

Assessment and Augmentation of Lip Appearance in Specific Study Populations

ClinicalTrials.gov study NCT04839692. IPD Sharing: NO. Countries: 1. Publications: 13.

restrictedIPD-UNDECIDEDFeb 2026View details →

Brief Interventions for Short-Term Suicide Risk Reduction in Military Populations

ClinicalTrials.gov study NCT02042131. IPD Sharing: Not stated. Countries: 1. Publications: 2.

restrictedIPD-UNDECIDEDFeb 2026View details →

Tolerability of a Foaming Facial Cleanser and Moisturizer SPF 30 in a Pediatric Population (7-11) With Acne Prone Skin.

ClinicalTrials.gov study NCT01909713. IPD Sharing: Not stated. Countries: 1. Publications: 1.