Find research datasets worth reusing

Eat or be eaten: Implications of potential exploitative competition between wolves and humans across predator- savvy and -naive deer populations

Recolonization of predators to their former ranges is becoming increasingly prevalent. Such recolonization places predators amongst their prey once again; the latter having lived without predation (from such predators) for considerable time. This renewed coexistence creates opportunities to explore predation ecology at both fundamental and applied levels. We used a paired experimental design to investigate white-tailed deer risk allocation in the Upper and Lower Peninsulas (UP and LP) in Michigan, USA. Wolves are functionally absent in the LP, while deer in the UP coexist with a re-established wolf population. We treated 15 sites each in UP and LP with wolf olfactory cues and observed deer vigilance, activity, and visitation rates at the interface of habitat covariates using remote cameras. Such a paired design across wolf versus no-wolf areas allowed us to examine indirect predation effects while accounting for confounding parameters such as the presence of other predators and human activity. While wolf urine had no effect across most metrics in both UP and LP, we observed differences in deer activity in areas with versus without wolves. Sites treated with wolf urine in the UP showed a reduction in crepuscular deer activity, compared to control/novel-scent treated sites. Further, we observed a strong positive effect of vegetation cover on deer vigilance in these sites. This indicates that simulated predator cues likely affect deer vigilance more acutely in denser habitats, which presumably facilitates predation success. Such responses were however absent among deer in the LP that are presumably naïve towards wolf predation. Where human and non-human predators hunt shared prey, such as in Michigan, predators may constrain human hunting success by increasing deer vigilance. Hunters may avoid such exploitative competition by choosing hunting/bait sites located in open areas. Our results pertaining to fundamental predation ecology have strong applied implications that can promote human-predator coexistence.

Of Mojave milkweed and mirrors: The population genomic structure of a species impacted by solar energy development

A rapid renewable energy transition has facilitated the development of large, ground‐mounted solar energy facilities worldwide. Deserts, and other sensitive aridland ecosystems, are the second most common land‐cover type for solar energy development globally. Thus, it is necessary to understand existing diversity within environmentally sensitive desert plant populations to understand spatiotemporal effects of solar energy siting and design. Overall, few population genomic studies of desert plants exist, and much of their biology is unknown. To help fill this knowledge gap, we sampled Mojave milkweed (Asclepias nyctaginifolia) in and around the Ivanpah Solar Electric Generating Station (ISEGS) in the Mojave Desert of California to understand the species' population structure, standing genetic variation, and how that intersects with solar development. We performed Restriction‐site Associated Sequencing (RADseq) and discovered 9942 single nucleotide polymorphisms (SNPs). Using these data, we found clear population structure over small spatial scales, suggesting each site sampled comprised a genetically distinct population of Mojave milkweed. While mowing, in lieu of blading, the vegetation across the solar energy facility's footprint prevented the immediate loss of the ISEGS Mojave milkweed population, we show that the effects of land‐cover change, especially those impacting desert washes, may impact long‐term genetic diversity and persistence. Potential implications of this include a risk of overall loss of genetic diversity, or even hastened extirpation. These findings highlight the need to consider the genetic diversity of impacted species when predicting the impact and necessary conservation measures of large‐scale land‐cover changes on species with small population sizes.

Applying genomic approaches to identify historic population declines in European forest bats

<ol> <li>Anthropogenically-driven environmental changes over the past two centuries have led to severe biodiversity loss, most prominently in the form of loss of populations and individuals. Better tools are needed to assess the magnitude of these wildlife population declines. Anecdotal evidence suggests European bat populations have suffered substantial declines in the past few centuries. However, there is little empirical evidence of these declines that can be used to put more recent population changes into historic context and set appropriate targets for species recovery. </li> <li>This study is a collaboration between academics and conservation practitioners to develop molecular approaches capable of providing quantitative evidence of historic population changes and their drivers that can inform the assessment of conservation status and conservation management. We generated a genomic dataset for the Western barbastelle, Barbastella barbastellus, a globally Near Threatened and regionally Vulnerable bat species, including colonies from across the species' British and Iberian ranges. We used a combination of landscape genetics and approximate Bayesian computation model-based inference of demographic history to identify both evidence of population size changes and possible drivers of these changes. </li> <li>We found that levels of genetic diversity and inbreeding were related to broadleaf woodland cover around the colony location. Genetic connectivity was impeded by artificial lights and facilitated by the combination of rivers and broadleaf woodland cover. </li> <li>The demographic history analysis showed that both the northern and southern British barbastelle populations have declined by 99% over the past 330–548 years. These declines may have been triggered by loss of large oak trees and native woodlands due to shipbuilding during the early colonial period.</li> <li> Synthesis and applications. Genomic approaches can be applied to provide a better understanding of the conservation status of threatened species, within historic and contemporary context, and inform their conservation management. This study shows how we can bridge the implementation gap and promote the application of genomics in conservation management through co-designing studies with conservation practitioners and co-developing applied management targets and recommendations.</li> </ol>

Code and data for: Shining a light on elusive lynx: density estimation of three Eurasian lynx populations in Ukraine and Belarus

The Eurasian lynx is a large carnivore widely distributed across Eurasia. However, our understanding of population status is heterogeneous across their range, with some populations isolated that are at risk of reduced genetic variation and a complete lack of information about others. In many European countries, Eurasian lynx are monitored through demographic studies crucial for their conservation and management. Even so, there are only rough and fragmented population assessments from Ukraine and Belarus, despite strict protection in both countries and their importance for lynx connectivity across Europe. We monitored lynx from October 2020 to March 2021 and used camera-trapping in combination with spatial capture-recapture (SCR) methods in a Bayesian Framework to provide the first SCR density estimation of three lynx populations across Ukraine and Belarus, including the Ukrainian Chornobyl Exclusion Zone, Southern Belarus, and the Ukrainian Carpathians. Our density estimates varied within our study areas ranging from 0.45 to 1.54 individuals/100 km2. This work provides a substantial scientific component to the overall understanding of lynx conservation for a region where only broad information is available and opens the doors for further large-scale monitoring and trend assessments. The crucial information we provide can greatly enhance the range-wide assessments of the status of this protected species. We also discuss the implications for Eurasian lynx conservation, despite the geopolitical realities impacting species monitoring in the region. Our work serves as a baseline, not only for future conservation interventions but also to evaluate the effects of disturbance and threats to these protected populations.

Data and code from: Disentangling the drivers of decadal body size decline in an insect population

While climate warming is widely predicted to reduce body size of ectotherms, evidence for this trend is mixed. Body size depends not only on temperature but also on other factors, such as food quality and intraspecific competition. Because temperature trends or other long-term environmental factors may affect population size and food sources, attributing trends in average body size to temperature requires the separation of potentially confounding effects. We evaluated trends in the body size of the midge Tanytarsus gracilentus and potential drivers (water temperature, population size, and food quality) between 1977 and 2015 at Lake Mývatn, Iceland. Although temperatures increased at Mývatn over this period, there was only a slight (non-significant) decrease in midge adult body size, contrary to theoretical expectations. Using a state-space model including multiple predictors, body size was negatively associated with both water temperature and midge population abundance, and it was positively associated with 13C enrichment of midges (an indicator of favorable food conditions). The magnitude of these effects were similar, such that simultaneous changes in temperature, abundance, and carbon stable isotopic signature could counteract each other in the long-term body size trend. Our results illustrate how multiple factors, all of which could be influenced by global change, interact to affect average ectotherm body size.

Highland islands: assessing gene flow among populations of an aquatic highland endemic

A variety of hierarchical gene flow models have been proposed to explain the distribution of genetic variation in aquatic environments. These models, including the Stream Hierarchy (SH), Death Valley (DV), Headwater (HW), and Widespread Gene flow (WG) models, provide testable hypotheses that focus on the degree of within-basin or within-stream network connectivity and an organism's dispersal abilities. We tested these models using Tlaloc hildebrandi (Profundulidae, Cyprinodontiformes), a freshwater fish endemic to the highlands of the Grijalva and Usumacinta River basins in southern Mexico. Data from ultraconserved elements (UCEs) showed that although T. hildebrandi was recovered as monophyletic, the sub-basins were not. We generated single nucleotide polymorphisms from the UCEs to analyse the data in a population genetic framework. These results differed between analyses such that two (STRUCTURE analysis) or three (DAPC analysis) genetic groupings were recovered. Overall, the results of this study provide support for the SH model. Some individuals from the Jataté sub-basin, however, conformed to the HW model, due to historical connections among headwater streams and rivers of the Jataté and Amarillo–Chenalhó clades/clusters. The greatest degree of gene flow has occurred from the Grijlava to the Usumacinta basins, two geographically proximate basins that have been hypothesized to have had previous connections.

opencc-by-4.0Nov 2023View details →

Pattern of Using Semaglutide Injection among the Population in Saudi Arabia

Semaglutide injection with lifestyle intervention has been shown to be more effective than lifestyle modification alone. However, pharmacological intervention shows fewer side effects than bariatric surgery. This cross-sectional study was conducted among the general population in Saudi Arabia. A self-administered questionnaire was sent among the targeted population using an online survey. The questionnaire includes socio-demographic data (e.g., age, gender, marital status, etc.), general awareness about Semaglutide injection, and a 4-item questionnaire to measure the knowledge about Semaglutide. Of the 382 participants, 52.4% were males, and 44.8% were aged between 18 to 30  years old. The level of knowledge about Semaglutide injection was poor among 69.4%, while the rest had good knowledge (30.6%). The overall mean knowledge score was 1.62 (SD 1.26) out of 4 points. Younger participants, gender female, unmarried, unemployed, normal or underweight, aware of Semaglutide injection, previous usage of Semaglutide, satisfaction with Semaglutide, and knowledge about combined benefits (diabetes control and weight loss) of Semaglutide injections were the factors associated with increased knowledge score. The knowledge of the general population regarding Semaglutide injection was lacking. Younger female participants with normal body weight who were satisfied with Semaglutide were identified as the most significant users of Semaglutide injections. Further investigations are needed to extract more data about the general population's knowledge of Semaglutide injections.

Data from: Relict stands of Central European oaks: unravelling autochthony and genetic structure based on a multi-population study

Central European white oaks expanded rapidly after the last glacial period and reached their current distribution range during the early Holocene. They have been an important resource of timber, fuelwood and animal feed for humans, who actively promoted their presence in forests and other landscape types at least since the early historical times. Besides stands with intensive management, putatively relict populations of three native oak species can be found on unproductive sites with restricted accessibility. Here, we apply chloroplast and nuclear microsatellite markers in order to address the autochthony of relict and managed stands and compare the spatial distribution of genetic variation between them. Based on data from more than 150 populations, we demonstrate that oak autochthony was preserved throughout historical times which is likely the result of traditional silvicultural treatment. This is supported by the fact that the spatial pattern of chloroplast haplotype distribution still reflects the post-glacial recolonization in both relict and old managed stands. We observed significant admixture of haplotypes only in stands established after the Second World War, which is attributable to the transfer of reproductive material used for afforestation. In terms of nuclear genetic variation, we observed marked differences among species. Quercus pubescens exhibited a pronounced genetic structure. Genetic drift and limited gene flow among its small and isolated populations in our study area might have contributed to this pattern. Varying extent of genetic introgression with other sympatric oak species could offer an additional explanation. On the contrary, the gene pools of Q. petraea and Q. robur are highly homogenous, displaying only weak isolation-by-distance. We found no significant differences of genetic diversity and differentiation between relict and managed stands. This suggests that seed transfer mostly occurred within our study area, even in those stands established in post-war times, verifying previous findings that point out limited human interference. We recommend consideration of population genetic structure for gene conservation, with a finer resolution of gene conservation units needed for Q. pubescens due to its spatial genetic structure. Both relict and old managed stands, species-pure or mixed, are suitable for conservation, as they host autochthonous gene pools. Coppice-with-standard management could contribute to preservation of autochthony. In the face of climate change, it is also important to maintain the evolutionary potential of the stands, by facilitating generative reproduction and allowing for hybridization in mixed stands.

opencc-by-4.0Oct 2006View details →

Figure 1 in Otolith characteristics of species, subspecies, and populations of Aphanius Nardo, 1827 (Teleostei, Cyprinodontiformes) from Anatolia (Turkey)

Figure 1. Map of Turkey showing the sample sites (after Wildekamp 1993, modified).

opencc-by-4.0Dec 2023View details →

Targeted DNA-seq analysis was performed on sorted population of CD45+/CD34+ HSPCs from control or FLI-1 modified mRNA treated mPB after co-culture with vascular niche cells

Human mPB HSPCs were harvested isolated and transduced with either control or FLI-1 modified mRNA. HSPCs were introduced into co-culture with vascular niche ECs. Cultures were harvested and CD45+/CD34+ HSPCs were resoerted and processed for trageted DNA-seq analysis. Contains raw FASTQ sequencing files, unfiltered VCFs, and curated results in an excel.

QTL mapping for seedling and adult plant resistance to stripe and leaf rust in two winter wheat populations

The two recombinant inbred lines (RIL) populations developed by crossing Almaly × Avocet S (206 RILs) and Almaly × Anza (162 RILs) were used to detect the novel genomic regions associated with adult plant resistance (APR) and seedling or all-stage resistance (ASR) to yellow rust (YR) and leaf rust (LR). Both the populations were evaluated for YR APR in two environments (2018 and 2019) and LR APR in three environments (2018, 2019, and 2020) in the Anza population and two environments (2018 and 2019) in the Avocet population; both the populations were phenotyped for one environment during 2020 for LR and YR ASR and genotyped using high throughput DArTseq technology. A set of 51 QTLs including 22 for YR APR, nine for LR APR, nine for YR ASR, and 11 for LR ASR were identified. Also, a set of 13 stable QTLs including nine QTLs (QYR-APR-2A.1, QYR-APR-2A.2, QYR-APR-4D.2, QYR-APR-1B, QYR-APR-2B.1, QYR-APR-2B.2, QYR-APR-3D, QYR-APR-4D.1, and QYR-APR-4D.2) for YR APR and four QTLs (QLR-APR-4A, QLR-APR-2B, QLR-APR-3B, and QLR-APR-5A.2) for LR APR were identified. In silico analysis revealed that the key putative candidate genes such as Cytochrome P450, Protein kinase-like domain superfamily, Zinc-binding ribosomal protein, SANT/Myb domain, WRKY transcription factor, Nucleotide-sugar transporter, and NAC domain superfamily were in the QTL regions and involved in the regulation of host response towards the pathogen infection. The stable QTLs identified in this study are useful for developing rust-resistant varieties through marker-assisted selection (MAS).

opencc-by-4.0Aug 2023View details →

Data from: Prioritizing global land protection for population persistence can double the efficiency of habitat protection for reducing mammal extinction risk

Halting the alarming rate of species extinction, driven primarily by habitat destruction, motivated the international community to adopt (2022) the Global Biodiversity Framework and it’s 23 targets aimed at reversing habitat and species loss. Due to urgency and resource constraints, a key challenge is meeting targets effectively and efficiently. Here we conduct a global prioritization linking 70,492 unique population maps and life history characteristics for 861 threatened terrestrial mammal species. Incorporating individual population data boosted viability for 84% more populations compared to using a more typical approach that uses species distributions alone, nearly doubling the security of long-term species persistence. We map and rank global mammal persistence priority areas and assess how well the current protected areas (PA) system captures these important regions. Our results will provide conservation actors a more direct and quantifiable linkage between conservation action and extinction risk than has previously been possible at a global scale.

opencc-by-4.0Nov 2022View details →

Population impact of fine particulate matter on tuberculosis risk in China: A causal inference

Supplementary to "Population impact of fine particulate matter on tuberculosis risk in China: A causal inference"

opencc-by-4.0Nov 2023View details →

Population Genomics Analysis of 30 Samples from Each of Multiple Populations Reveals Signatures of Selection from Breeding for Rapid Growth and Apical Dominance in Paulownia fortunei

Paulownia fortunei is an ecologically and economically valuable tree cultivated for its rapid growth and high-quality timber. To enhance Paulownia germplasm, we have developed the elite variety QingT with patented advantages in growth rate and apical dominance. To illuminate the genetic basis of QingT's superior traits, here we harness comparative population genomics to analyze genomic variation patterns between QingT and common Paulownia. We performed whole-genome re-sequencing of 30 QingT and 30 common samples, detecting 15.6 million SNPs and 2.6 million indels. Phylogeny and population structure analyses robustly partitioned common and QingT into distinct groups which indicate robust genome stabilization. QingT exhibited reduced heterozygosity and linkage disequilibrium decay compared to common Paulownia, reflecting high recombination, indicating hybridizing effects with common white-flowered string is the source of its patented advantages. Genome selection scans uncovered 25 regions of 169 genes with elevated nucleotide diversity, indicating selection sweeps among groups. Functional analysis of sweep genes revealed upregulation of ribosomal, biosynthesis and growth pathways in QingT, implicating enhanced protein production and developmental processes in its rapid growth phenotype. This study's insights comprehensively chart genomic variation during Paulownia breeding, localizing candidate loci governing agronomic traits, and underpinnings of future molecular breeding efforts to boost productivity.

Data from: Genetic signatures of lineage fusion closely resemble population decline

Accurate interpretation of the genetic signatures of past demographic events is crucial for reconstructing evolutionary history. Lineage fusion (complete merging, resulting in a single panmictic population) is a special case of secondary contact that is seldom considered. Here, the circumstances under which lineage fusion can be distinguished from population size constancy, growth, bottleneck, and decline were investigated. Multi-locus haplotype data were simulated under models of lineage fusion with different divergence versus sampling lag times (D:L ratios). These pseudo-observed datasets also differed in their allocation of a fixed amount of sequencing resources (number of sampled alleles, haplotype length, number of loci). Distinguishability of lineage fusion versus each of 10 untrue non-fusion scenarios was quantified based on six summary statistics (neutrality tests). Some datasets were also analyzed using extended Bayesian skyline plots. Results showed that signatures of lineage fusion very closely resemble those of decline—high distinguishability was generally limited to the most favorable scenario (D:L = 9), using the most sensitive summary statistics (FS and ZnS), coupled with the optimal sequencing resource allocation (maximizing number of loci). Also, extended Bayesian skyline plots often erroneously inferred population decline. Awareness of the potential for lineage fusion to carry the hallmarks of population decline is critical.

Data from: Quantifying the impacts of management and herbicide resistance on regional plant population dynamics in the face of missing data

A key challenge in the management of populations is to quantify the impact of interven-tions in the face of environmental and phenotypic variability. However, accurate estima-tion of the effects of management and environment, in large-scale ecological research is often limited by the expense of data collection, the inherent trade-off between quality and quantity, and missing data. In this paper we develop a novel modelling framework, and demographically informed imputation scheme, to comprehensively account for the uncertainty generated by miss-ing population, management, and herbicide resistance data. Using this framework and a large dataset (178 sites over 3 years) on the densities of a destructive arable weed (Alo-pecurus myosuroides) we investigate the effects of environment, management, and evolved herbicide resistance, on weed population dynamics. In this study we quantify the marginal effects of a suite of common management prac-tices, including cropping, cultivation, and herbicide pressure, and evolved herbicide re-sistance, on weed population dynamics. Using this framework, we provide the first empirically backed demonstration that herbi-cide resistance is a key driver of population dynamics in arable weeds at regional scales. Whilst cultivation type had minimal impact on weed density, crop rotation, and earlier cultivation and drill dates consistently reduced infestation severity. Synthesis and applications: As we demonstrate that high herbicide resistance levels can produce extremely severe weed infestations, monitoring of herbicide resistance is a pri-ority for famers across western Europe. Furthermore, developing non chemical control methods is essential to control current weed populations, and prevent further resistance evolution. We recommend that planning interventions that center on crop rotation and incorporate spring sewing and cultivation to provide the best reductions in weed densi-ties. More generally, by directly accounting for missing data our framework permits the analysis of management practices with data that would otherwise be severely compro-mised.

Functional traits and related environmental variables of 28 populations of Nuphar lutea

This dataset includes 31 leaf functional traits, 2 genetic diversity metrics and 4 leaf reflectance measures on 28 wild populations of yellow water lily (Nuphar lutea). For each population (plot) coordinates, water depth, specific conductivity, nitrate, sediment organic matter and sediment total phosphorus contents are provided as well. The populations were located in 4 different lake systems in central and northern Italy. All the information on the methodology used to collect the data and can be found in the related paper.

opencc-by-4.0Oct 2023View details →

ChromoPhyloGen: characterizing copy number alteration patterns in heterogeneous tumor cell populations at Single-Cell Resolution

The human liver cancer cell line Huh7 was obtained from the American Type Culture Collection (ATCC). Huh7 cells were cultivated in Dulbecco's Modified Eagle Medium (DMEM, Gibco, C11995), supplemented with 1% penicillin/streptomycin (Gibco, 15140122), and 10% fetal bovine serum (FBS, Excell, FSP500). Huh7 cell line was maintained under a 95% O2 and 5% CO2 humidified atmosphere in an incubator at 37˚C.  The scDNA-seq library was performed using the Chromium Single cell DNA Library & Gel Bead kit (10x Genomics, PN1000040) in combination with the Chromium instrument. The samples were processed on Chromium Single cell Chip C and D (10x Genomics, 1000022 and 1000042, respectively) according to the manufacturer's user guide and subsequently run on a thermocycler. The barcoded libraries were sequenced using the Novaseq 6000 300 cycle high-output flow cells. The scRNA-seq library was generated using the 10x Genomics Chromium Single Cell 3' & Gel Bead Kit v3 (10x Genomics, PN100075) in combination with the Chromium instrument. The samples were processed on Chromium Single cell Chip B (10x Genomics,1000154) according to the manufacturer's protocol and subsequently run on a thermocycler. The 3' gene expression libraries were sequenced using the Novaseq 6000 300 cycle high-output flow cells.

opencc-zeroDec 2023View details →

Population size shapes trade-off dilution and adaptation to a marginal niche unconstrained by sympatric habitual conditions

How does niche expansion occur when the habitual (high-productivity) and marginal (low-productivity) niches are simultaneously available? Without spatial structuring, such conditions should impose fitness maintenance in the former while adapting to the latter. Hence, adaptation to a given marginal niche should be influenced by the identity of the simultaneously available habitual niche. This hypothesis remains untested. Similarly, it is unknown if larger populations, which can access greater variation and undergo more efficient selection, are generally better at niche expansion. We tested these hypotheses using a large-scale evolution experiment with Escherichia coli. While we observed widespread niche expansion, larger populations consistently adapted to a greater extent to both marginal and habitual niches. Owing to diverse selection pressures in different habitual niches (constant versus fluctuating environments; environmental fluctuations varying in both predictability and speed), fitness in habitual niches was significantly shaped by their identities. Surprisingly, despite this diversity in habitual selection pressures, adaptation to the marginal niche was unconstrained by the habitual niche's identity. We show that in terms of fitness, two negatively correlated habitual niches can still have positive correlations with the marginal niche. This allows the marginal niche to dilute fitness trade-offs across habitual niches, thereby allowing costless niche expansion. Our results provide fundamental insights into sympatric niche expansion.