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opencc-zeroJul 2022View details →

The impact of species phylogenetic relatedness on invasion varies distinctly along resource versus nonresource environmental gradients

Understanding why certain plant communities are vulnerable to alien invasive species is essential to predicting and controlling invasion in a changing environment. Darwin's naturalization hypothesis suggests that non-native species should be more successful in communities where their close relatives are absent. Empirical tests of this hypothesis, however, have produced mixed results. Using plot-level data from natural forests along elevational transects covering strong environmental gradients, we examined whether the invasion of the globally invasive species Ageratina adenophora can be explained by environmental filtering and/or competition from closely related species linked to environmental gradients. Abundant precipitation, warm temperatures, open canopies, and postfire environments facilitated A. adenophora invasion, whereas resident taxonomic richness suppressed its invasion. Importantly, we found that invader-resident relatedness had a strong negative effect on invader cover under resource scarcity conditions (e.g., low water availability), but not under nonresource environmental stress conditions (e.g., low temperature). Our findings help reconcile the varied applicability of Darwin's naturalization hypothesis to biological invasions in a changing world.

opencc-by-4.0Jul 2022View details →

Supporting material for "Impact of gender on the formation and outcome of formal mentoring relationships in the life sciences"

This repository contains data and analysis code associated with the manuscript: L.P. Schwartz, J. Liénard, S. V. David. (2022) "Impact of gender on formation and outcome of formal mentoring relationships in the life sciences." Figures and tables in the manuscript can be produced by running the make_figures.ipynb notebook. Figures have been marked with headings indicating their position in the manuscript (Figure 1, Figure S1, etc.). In addition, the notebook contains code to reproduce regression analyses that are cited in the text but not directly associated with a figure. Data on mentoring relationships derives from Academic Family Tree (AFT, www.academictree.org) and public data sources on funding, publications, and awards. Inclusion criteria, public data sources, and procedures for linking across sources are described in the manuscript.  Personal identifiers for researchers have been anonymized, but remain consistent across all data in the repository. In other words, the personal identifier "1" refers to the same person in all dataframes in the repository. But, that person is *not* the same researcher identified as "1" on the public AFT website. Installation Requires Python 3.x. and Pandas. To load required libraries using Anaconda, run: `conda create --name aft -c conda-forge pandas numpy scipy ipython jupyterlab scipy scikit-learn pandas matplotlib numpy statsmodels seaborn pytables` Dataframes Data is stored as a series of Pandas dataframes within HDF5 or CSV files: * cng_tc: The primary dataset used in the analysis. The name is an acronym for "connections" (i.e. training relationships, "cn"), "gender" ("g"), and "trainee count" ("tc"). Each row contains data on the mentor and trainee in one training relationship. See manuscript for inclusion criteria. * mentors: Data on mentors. Each row contains data on one mentor. See manunscript for inclusion criteria. * mentors_grants, mentors_hindex, mentors_locs_ranked: Subset of mentors with data available for funding (mentors_grants), citation (mentors_hindex), and institution rank (mentors_locs_ranked). * mentors_nobel, mentors_hhmi, mentors_nas: Subsets of mentors that received a Nobel (mentors_nobel), Howard Hughes Medical Institute grants (mentors_hhmi), or membership in the National Academy of Sciences (mentors_nas). See manuscript for details of data sources and linking procedures. * cn, cng, first_names, gn, gn_all, locs: Partial data (connections only, inferred gender only, connections and gender only, location only, first names and inferred gender only) for more inclusive sets of researchers in AFT. They are generally not used used for analysis, but have been included here to calculate statistics on the total amount of data included and to screen for data from U.S. locations. * nsf_gender_phds, nsf_gender_pds: National Science Foundation survey data on gender and fraction PhDs conferred per year (nsf_gender_phds) or fraction postdocs employed per year (nsf_gender_pds). See manuscript for details of data source. * photo: Data for validation of gender inference method. Dataframe columns * amount: Mentor's total funding * amount_adj: Mentor's total funding (adjusted to 2020 dollars) * broad_field: Mentor's general research area (e.g., life sciences, engineering, based on National Science Foundation classifications) * continue: Whether trainee went on to become a mentor (i.e., has trainees listed in AFT) * country: Country in which mentor's current institution is located * firstname: First name of researcher (table of first names is not aligned with tables containing anonymized personal identifiers) * first_grant_year: Year of mentor's first grant * funding_rate: Mentor's annual funding rate (since first grant) * funding_rate_adj: Mentor's annual funding rate (since first grant) adjusted to 2020 dollars * hhmi: Whether mentor was granted HHMI funding * hindex: Mentor's hindex * location: Name of mentor's current institution * locid: Identifier for mentor's institution * locid_rank: Postion of mentor's institution in 2015 Quacquarelli-Symonds rankings (lower numbers are better) * locid_rank_rev: Reversed version of "locid_rank" (i.e., higher numbers are better) * majorarea: Mentor's specific research area (e.g, neuroscience) * male_mentor, male trainee: Whether the probability that a researcher's first name is used by a person identifying as a man meets threshold (see manuscript for details on gender inference using first names) * match_score: Score for string match between institution or name of awardee and researcher * mentor_career_start: The date at which the mentor's academic career began * mentor_continue_rate: Fraction of mentor's trainees that become mentors * mentor_continue_rate_ft: Fraction of mentor's woman trainees that become mentors * mentor_continue_rate_mt: Fraction of mentor's man trainees that become mentors * mentor_t_p_male0: Fraction of mentor's trainees that are men * mentor_t_p_male0_gs: Fraction of mentor's trainees that are men (graduate students only) * mentor_t_p_male0_pd: Fraction of mentor's trainees that are men (postdocs only) * mentor_tcount0: Mentor's total number of trainees * nas: Whether mentor is a member of the National Academy of Sciences * nobel: Whether mentor is a Nobel laureate * p_male_mentor, p_male_trainee: Probability that a researcher's first name is used by a person identifying as a man * pid: Anonymized identifier of researcher * pid_mentor: Anonymized identifier of mentor in training relationship * pid_trainee: Anonymized identifier of trainee in training relationship * pq: "1" if data on training relationship is drawn from ProQuest database and has not been manually edited a human AFT user * relation: Type of training relationship (1: graduate student, 2: postdoc) * scorer1, scorer2, scorer3: Results of photo validation of gender inference for each scorer * start: Training start year * stop: Training end year * trainee_tcount: Total people that the trainee has trained * triad: Whether trainee has participated in both a graduate-level and postdoctoral training relationship The cn dataframe follows slightly different naming conventions, but is not generally used in the analysis (pid1 = pid_trainee, pid2 = pid_mentor, startdate = start, stopdate = stop).

opencc-zeroJul 2022View details →

Impacts of abiotic and biotic factors on terrestrial leeches in

Haemadipsid leeches are ubiquitous inhabitants of tropical and sub-tropical forests in the Indo-Pacific region. They are increasingly used as indicator taxa for biomonitoring, yet very little is known about their basic ecology. For example, to date no study has assessed the occurrence and distribution of haemadipsid leeches across naturally occurring gradients within intact habitats. We analysed a long-term data set (2012-2020) on the closely related tiger (Haemadipsa picta) and brown (Haemadipsa spp.) leech species to investigate if and how abiotic and biotic factors influence their occurrence across a gradient of forest types at an undisturbed tropical rainforest site in Indonesian Borneo. We compared a series of negative binomial mixed models and found that, of the abiotic factors, soil moisture had the largest positive effect on encounter rates of both leech species. Among biotic factors, forest type had differential effects on counts of the two species: while tiger leech counts were greater in low elevation forest types, brown leech counts were greater in high elevation forest types. Additionally, we found that the presence of one species had a positive effect on the presence of the other species. Finally, our results show that the tiger leech has a narrower distribution, being restricted to lower elevation forest types with higher water retention, suggesting that the tiger leech could be more sensitive to lower soil moisture levels.

opencc-zeroJul 2022View details →

Long-term experimental drought alters floral scent and pollinator visits in a Mediterranean plant community despite overall limited impacts on plant phenotype and reproduction

Pollinators are declining globally, with climate change implicated as an important driver. Climate change can induce phenological shifts and reduce floral resources for pollinators, but little is known about its effects on floral attractiveness and how this might cascade to affect pollinators, pollination functions and plant fitness. We used an in situ long-term drought experiment to investigate multiple impacts of reduced precipitation in a natural Mediterranean shrubland, a habitat where climate change is predicted to increase the frequency and intensity of droughts. Focusing on three insect-pollinated plant species that provide abundant rewards and support a diversity of pollinators (Cistus albidus, Salvia rosmarinus and Thymus vulgaris), we investigated the effects of drought on a suite of floral traits including nectar production and floral scent. We also measured the impact of reduced rainfall on pollinator visits, fruit set and germination in S. rosmarinus and C. albidus. Drought altered floral emissions of all three plant species qualitatively, and reduced nectar production in T. vulgaris only. Apis mellifera and Bombus gr. terrestris visited more flowers in control plots than drought plots, while small wild bees visited more flowers in drought plots than control plots. Pollinator species richness did not differ significantly between treatments. Fruit set and seed set in S. rosmarinus and C. albidus did not differ significantly between control and drought plots, but seeds from drought plots had slower germination for S. rosmarinus and marginally lower germination success in C. albidus. Synthesis. Overall, we found limited but consistent impacts of a moderate experimental drought on floral phenotype, plant reproduction and pollinator visits. Increased aridity under climate change is predicted to be stronger than the level assessed in the present study. Drought impacts will likely be stronger and this could profoundly affect the structure and functioning of plant-pollinator networks in Mediterranean ecosystems.

opencc-by-4.0Jun 2022View details →

Data for "Measurement Report: A Multi-Year Study on the Impacts of Chinese New Year Celebrations on Air 1 Quality in Beijing, China."

These are the datasets that have been used for the article "Measurement Report: A Multi-Year Study on the Impacts of Chinese New Year Celebrations on Air 1 Quality in Beijing, China," which is published in the journal Atmospheric Chemistry and Physics, by Foreback et al. (2022).

opencc-by-4.0Jun 2022View details →

Evolution of ocean circulation in the North Atlantic Ocean during the Miocene: impact of the Greenland Ice Sheet and the Eastern Tethys Seaway

This dataset contains atmosphere and ocean outputs (NetCDF files) from modeling experiments with realistic early Miocene paleogeography as well as sensitivity to Greenland Ice Sheet and Eastern Tethys Seaway. The set of simulation targets the evolution of the North Atlantic Deep Water during the Miocene. The simulations have been run using the IPSL-CM5A2 General Circulation Model (Sepulchre et al. 2020 - IPSL-CM5A2 – an Earth system model designed for multi-millennial climate simulations, GMD). It includes 3 ocean-atmosphere simulations. Data are monthly averages over the last 100 years of the simulations.

opencc-by-4.0Jul 2022View details →

The impact of cerebellar transcranial direct current stimulation (tDCS) on sensorimotor and inter-sensory temporal recalibration

Data related to the study "The impact of cerebellar transcranial direct current stimulation (tDCS) on sensorimotor and inter-sensory temporal recalibration".

opencc-zeroAug 2022View details →

Data from: Worldwide impacts of landscape anthropization on mosquito abundance and diversity: a meta-analysis

In recent decades, the emergence and resurgence of vector-borne diseases have been well documented worldwide, especially in tropical regions where protection and defence tools for human populations are still very limited. In this context, the dynamics of pathogens are influenced by landscape anthropization (i.e., urbanization, deforestation, and agricultural development), and one of the mechanisms through which this occurs is a change in the abundance and/or diversity of the vectors. An increasing number of empirical studies have described heterogeneous effects of landscape anthropization on vector communities; therefore, it is difficult to have an overall picture of these effects on a global scale. Here, we performed a meta-analysis to quantify the impacts of landscape anthropization on a global scale on the presence/abundance and diversity of mosquitoes, the most important arthropods affecting human health. We obtained 338 effect sizes on 132 mosquito species, compiled from 107 studies in 52 countries that covered almost every part of the world. The results of the meta-analysis showed an overall decline of mosquito presence/abundance and diversity in response to urbanization, deforestation, and agricultural development, except for a few mosquito species that have been able to exploit landscape anthropization well. Our results highlighted that these few favoured mosquito species are those of global concern. They thus provide a better understanding of the overall effect of landscape anthropization on vector communities and, more importantly, suggest a greater risk of emergence and transmission of vector-borne diseases in human-modified landscapes.

The impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip, supplementary table 3

Supplementary table 3: Summary statistics from an EWAS assessing the relationship between variance in DNA methylation value and DNA input level.

Combined_ST_SM_Changes_Impacts SH LE observations

Here the data were used to evaluate latent and sensible heat flux data of ERA5-Land, along with the other evaluations against in situ observations.

opencc-zeroAug 2022View details →

Quantifying the ecological impacts of alien aquatic macrophytes: A global meta‐analysis of effects on fish, macroinvertebrate and macrophyte assemblages

Biological invasions constitute a pervasive and growing threat to the biodiversity and functioning of freshwater ecosystems. Macrophytes are key primary producers and ecosystem engineers in freshwaters, meaning that alien macrophyte invasions have the capacity to alter the structure and function of recipient aquatic ecosystems profoundly. Although prevailing wisdom holds that alien macrophyte invasions tend to compromise freshwater ecosystem structure and function, the ecological impacts of alien macrophyte invasion have not been quantitatively reviewed to date. Here we present a global meta-analysis of 202 cases from 53 research articles, exploring the impacts of alien macrophyte invasion on the abundance and diversity of three ubiquitous and ecologically important focal groups, which together comprise the bulk of non-microbial freshwater biodiversity: resident macrophytes, macroinvertebrates and fish. Our synthesis includes data from all continents except Antarctica and Asia, covering 25 alien macrophyte species, but reveals considerable taxonomic and geographical biases in knowledge. Meta-analysis results reveal that invasion by alien macrophytes has an overall negative impact on taxonomic diversity of the three focal groups, but no consistent effect on abundance. At a finer resolution, we detect a strong negative effect of alien macrophyte invasion on resident macrophyte abundance and diversity, and a significant but smaller positive effect of submerged alien macrophyte invasion on macroinvertebrates. Effects on fish appear inconsistent. Our findings emphasise the importance of context- and taxon-specific ecological research in informing appropriate and proportionate management of alien macrophyte invasions, since alien macrophyte impacts are not consistently negative. We also identify significant geographical and taxonomic limitations in existing studies, quantitative data being lacking for many alien taxa.

Combined_ST_SM_Changes_Impacts Soil moisture observations

There are 956 observational soil moisture data files with detailed information about the files in ReadMe.txt.

Cross-boundary effects of human impacts on animal assemblages

Data describing the abundance of coastal vertebrates and fish across 100 sites surveyed twice over two years on the Sunshine coast in eastern Australia.

opencc-zeroAug 2022View details →

Home and hub: pet trade and traditional medicine impact reptile populations in source locations and destinations

The pet trade and Traditional Chinese Medicine (TCM) consumption are major drivers of global biodiversity loss. Tokay geckos (Gekko gecko) are among the most traded reptile species worldwide. In Hong Kong, pet and TCM markets sell tokay geckos while wild populations also persist. To clarify connections between trade sources and destinations, we compared genetics and stable isotopes of wild tokays in local and nonlocal populations to dried individuals from TCM markets across Hong Kong. We found that TCM tokays are likely not of local origin. Most wild tokays were related to individuals in South China, indicating a probable natural origin. However, two populations contained individuals more similar to distant populations, indicating pet trade origins. Our results highlight the complexity of wildlife trade impacts within trade hubs. Such trade dynamics complicate local legal regulation when endangered species are protected, but the same species might also be non-native and possibly damaging to the environment.

opencc-zeroSep 2022View details →

IMPACT

Annotations produced by IMPACT (Inference and Modeling of Phenotype-related ACtive Transcription) to predict functional impact of genome sequence variation. <a href="https://github.com/immunogenomics/IMPACT">https://github.com/immunogenomics/IMPACT</a> These annotations have been reformatted as <a href="http://www.htslib.org/doc/tabix.html">tabix</a>-indexed files for rapid queries, and are used by echolocatoR to perform in silico validation analyses. Data has been reprocessed to enable API access and querying of files using tabix. <a href="https://github.com/RajLabMSSM/echolocatoR">https://github.com/RajLabMSSM/echolocatoR</a> If you use these annotations, please cite the following: <ul> <li> Amariuta T, Luo Y, Gazal S, et al. IMPACT: Genomic Annotation of Cell-State-Specific Regulatory Elements Inferred from the Epigenome of Bound Transcription Factors. Am J Hum Genet. 2019;104(5):879-895. doi:10.1016/j.ajhg.2019.03.012 </li> <li> Amariuta T, Ishigaki K, Sugishita H, et al. Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements. Nat Genet. 2020;52(12):1346-1354. doi:10.1038/s41588-020-00740-8 </li> <li> Schilder BM, Humphrey J, Raj T. echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline. Bioinformatics. 2021;btab658. doi:10.1093/bioinformatics/btab658 </li> <li> Schilder, Brian. (2022). IMPACT [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7062238 </li> </ul>

opencc-by-4.0Sep 2022View details →

Impacts of pressure, temperature, and rel. humidity on NDIR CO2 sensors (DATA)

These files support the experiments demonstrated in the peer-reviewed article "Low-complexity methods to mitigate the impact of environmental variables on low-cost UAS-based atmospheric carbon dioxide measurements", available via open access at the European Geophysical Union's Atmospheric Measurements Techniques journal.

opencc-by-4.0Sep 2022View details →

Economic impacts of melting of the Antarctic Ice Sheet

Dataset supporting figures and tables in Dietz, Simon and Koninx, Felix (forthcoming), "Economic impacts of melting of the Antarctic Ice Sheet", Nature Communications

opencc-zeroSep 2022View details →

Data from: Grazing by non-native ungulates negatively impacts vegetation important to a native species of concern

Non-native grazers compete with native species across the globe. In the northwestern Great Basin of the western United States competition among livestock, feral horses, and Greater Sage-grouse has been the subject of numerous legal actions and management policies, yet spatially explicit temporal data documenting the details of this competition are lacking. We present a novel approach to studying the composition of the herbaceous understory across three study areas within the Great Basin with different historic and contemporary grazing regimes. We surveyed the landscape using distance sampling for livestock and horse feces as an index of use. In addition, we surveyed the herbaceous understory of random sites as well as sites chosen by female Greater Sage-grouse to nest and brood their chicks. We used a novel Bayesian hierarchical modeling framework to link vegetation metrics with the spatial-temporal distribution of horses and livestock while accounting for observation error. When livestock and feral horses were not present, we found that Greater Sage-grouse chose sites with higher percentages of perennial grasses and forbs to build their nests and brood their chicks compared to what was available to them. As livestock increased, we found evidence for decreases in the percentage of perennial grasses, forbs, cheatgrass (Bromus tectorum), and increases in the amount of bare ground. These effects were consistent at available sites and brood sites, however, we found less evidence for an impact of livestock at nest sites. As feral horses increased, we observed similar results at available sites, but at sites chosen by females to nest and brood their chicks, we observed increases in the amount of invasive cheatgrass as feral horses increased, which could reflect attempts by Greater Sage-grouse to compensate for reductions in protective cover. We present a noninvasive approach to assess space use that can be applied to other species. More importantly, we document that grazing by non-native ungulates impacts components of the plant community important to Greater Sage-grouse reproduction. We provide spatial-temporal maps of livestock and feral horse use to aid managers attempting to balance the needs of livestock producers, feral horses, Greater Sage-grouse, and ecosystem function.

Global aquatic biodiversity impacts of nitrogen and phosphorus fertiliser use for major crops

Abstract Purpose The intensive application of nitrogen and phosphorus fertilisers on agricultural land to fertilise crops has caused eutrophication, the nutrient enrichment of waterbodies leading to excessive growth of algae, deoxygenation and loss of aquatic biodiversity. Life cycle impact assessments (LCIA) are often used to determine the environmental impacts of fertiliser use. However, the lack of suitable methodologies to estimate the fate and transport of nutrients from soils makes crop and regional impact comparisons challenging. Using a newly devised, spatially explicit nutrient fate and transport model (fate factor, FF) within an LCIA framework, this study estimates the global spatial-variability of nutrient loss from fertilisation of crops and their relative impact on aquatic biodiversity, specifically species richness. Method The newly devised FFs are based on the global spatially explicit nutrient model IMAGE-GNM. The FF’s enable us to assess N and P’s fate and transport from indirect soil emissions (arable land, grassland and natural land) to freshwater environments. We additionally improve the spatial resolution of existing soil FFs for N within marine environments from basin scale to 5 arcmin resolution. We applied our FF’s within current LCIA methodologies to assess the nutrient loading (midpoint indicator) and final aquatic biodiversity impact (endpoint indicator) from 17 crops. Results and discussion Our results identify strong variability in inputs, loadings and impacts due to differences in the fate, transport and impact of nutrients within the local environmental context. Such variability is translated into large differences between the popularly used nutrient use efficiency (NUE) indicator and final aquatic impacts caused by specific crops. Heavily produced crops (maize, rice, wheat, sugarcane and soybean) with the highest loading rates to receptors did not necessarily have the highest aquatic impacts. We identified rank variability existed at different metric stages (fertiliser inputs, receptor loadings, aquatic impacts) specifically for wheat and sugarcane. Our results showed high spatial variability in high aquatic impacts with significant biodiversity loss outside of the highest production regions. Conclusion Our study identified global hotspots for biodiversity impacts depend on the local context that exist beyond the field (e.g. the fate and transport of nutrients to receptor environments, and the receptor environment's vulnerability). Aquatic impacts from fertiliser use for specific crop commodities should be considered in strategic fertiliser pollution control decision-making and environmentally sustainable crop-commodity trade sourcing decisions. The development of the improved FFs should be used to aid spatially explicit and site-specific LCIA nutrient studies from soils. Here we provide the fate factors developed and used in our study to estimate biodiversity impacts from nitrogen and phosphorus fertiliser use.