cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1c59zw3zs
title: Data from: Two for the price of one: eDNA metabarcoding reveals temporal and spatial variability of mussel and fish co-distributions in Michigan riverine systems

description: Freshwater mussels (family Unionidae) are among the world’s most
 endangered taxa, with almost 75% of North American taxa classified as a
 species of concern, threatened, or endangered. Despite the critical
 importance of comprehensive distributional data for the conservation of
 unionids and fishes, these data are often lacking because of the labor and
 resources associated with traditional survey methods. During their larval
 stage, unionid mussels use various fish species as obligate hosts, making
 native fish species vital to unionid persistence and an understanding of
 host distribution similarly important. Here, we utilized an eDNA
 metabarcoding approach to evaluate patterns of co-distribution of unionid
 mussels and fishes along ~362 km of the densely sampled Grand River
 network as well as the outlets of 19 tributaries along the eastern shore
 of Lake Michigan, USA. We detected a total of 21 mussel and 40 fish taxa,
 with distinctive composition of both mussel and fish assemblages across
 tributaries and differences in fish taxa between sampling periods.
 Notably, we detected more mussel taxa within the Grand River watershed
 than at the outlets of all 20 rivers combined. Within the Grand River
 network, two fish taxa (Pylodictus olivaris and Cyprinella) were found
 more frequently in areas of high mussel diversity, and three fish taxa
 more frequently in areas of low mussel diversity (Umbra, Leuciscidae, and
 Etheostoma). There was little difference between eDNA detections of
 mussels from samples collected in June versus August, but we detected
 significantly more fish taxa in August compared to June. Taken together,
 our findings demonstrate the value of eDNA metabarcoding for evaluating
 co-distribution of ecologically connected taxa. The use of eDNA as a tool
 for determining distributions of mussels and their obligate hosts may
 facilitate conservation efforts for these imperiled taxa.
description: See manuscript.
description: See manuscript.
DOI: 10.5061/dryad.tb2rbp043
title: Data from: Conservation of Chinese Theaceae species under future climate and land use changes

description: Aim: Climate and land use changes are two major pervasive and growing
 global causes of rapid changes in the distribution patterns of
 biodiversity, challenging the future effectiveness of protected areas
 (PAs), which were mainly designed based on a static view of biodiversity.
 Therefore, evaluating the effectiveness of protected areas for protecting
 the species threatened by climate and land use change is critical for
 future biodiversity conservation. Location: China Methods: Here, using
 distributions of 200 Chinese Theaceae species and ensemble species
 distribution models, we identified species threatened by future climate
 and land use change (i.e. species with predicted loss of suitable habitat
 ≥ 30%) under scenarios incorporating climate change, land use change and
 dispersal. We then estimate the richness distribution patterns of
 threatened species and identify priority conservation areas and
 conservation gaps of the current PA network. Results: Our results suggest
 that 36.30%-51.85% of Theaceae species will be threatened by future
 climate and land use conditions, and that although the threatened species
 are mainly distributed at low latitudes in China under both current and
 future periods, the mean richness of the threatened species per grid cell
 will decline by 0.826-3.188 species by the 2070s. Moreover, we found that
 these priority conservation areas are highly fragmented and that the
 current PA network only covers 14.21%-20.87% of the ‘areas worth
 exploring’ and 6.91%-7.91% of the ‘areas worth attention’. Main
 conclusions: Our findings highlight the necessity of establishing new
 protected areas and ecological corridors in priority conservation areas to
 protect the threatened species. Moreover, our findings also highlight the
 importance of taking into consideration the potential threatened species
 under future climate and land use conditions when designating priority
 areas for biodiversity conservation.
DOI: 10.5061/dryad.0rxwdbs4b
title: The effectiveness and safety of intensive lipid-lowering with different Rosuvastatin-based regimens in patients at high risk: A nonblind, randomized, controlled trial

description: Background: Statin alone or nonstatins as add-ons have been introduced to
 intensive low-density lipoprotein cholesterol (LDL-C) lowering therapy in
 patients at high cardiovascular disease (CVD) risk. The purpose of this
 study was to evaluate the effectiveness and safety of different
 statin-based regimens for patients at high risk. Methods: Three hundred
 patients at high CVD risk were randomly assigned to the statin group
 (Rosuvastatin 20mg/d), statin_EZ group (Rosuvastatin 10mg/d +
 ezetimibe 10mg/d),  statin_pcsk group
 (Rosuvastatin 10mg/d + alirocumab 75mg/2weeks) or combine3 group
 (Rosuvastatin 10mg/d + ezetimibe 10mg/d + alirocumab
 75mg/2weeks). The primary outcome measure was cholesterol levels (LDL-C,
 total cholesterol (TC) triglycerides (TGs), and high-density lipoprotein
 cholesterol (HDL-C)) after 24 weeks of follow-up. The secondary outcome
 measures were safety markers and the proportion of patients who achieved
 the &lt; 70 mg/dL (1.8 mmol/L) LDL-C target. A logistic regression
 model was performed to explore the factors affecting lipid target
 achievement. Results: The TC and LDL-C levels after treatment were
 significantly different among the four groups (p &lt; 0.05). The
 levels in both the combine3 group and the statin_pcsk9 group were
 significantly lower than those in the statin group and the statin_EZ group
 (p &lt; 0.05), but there was no significant difference between the
 combine3 group and the statin_pcsk9 group. The incidence of adverse events
 in the four groups was low. Body mass index (BMI) and hypertensive status
 were related to target achievement. Conclusion: The combination of a
 statin and a PCSK9 inhibitor was safe and more effective for the treatment
 of high-risk CVD patients, while the addition of ezetimibe was unable to
 significantly lower lipid levels any further. The rate of achieving the
 target was higher in patients with hypertension and a low BMI.
description: Laboratory tests,
 including tests for lipid
 levels (LDL-C, total cholesterol (TC) triglycerides (TGs), and
 high-density lipoprotein cholesterol (HDL-C)), liver and renal function tests, and creatine
 kinase (CK) tests, were
 conducted prior to the treatment and at the 12<sup>th</sup>
 week and 24<sup>th</sup> week. Information on sex, age, smoking history,
 hypertension, diabetes history, body mass index (BMI) and other related
 medical history was collected. The patients were followed up for 24
 weeks.
DOI: 10.5061/dryad.ffbg79czp
title: Enhanced foliar 15N enrichment with increasing nitrogen addition rates: Role of plant species and nitrogen compounds

description: Determining the abundance of N isotope (δ15N) in natural environments is a
 simple but powerful method for providing integrated information on the N
 cycling dynamics and status in an ecosystem under exogenous N inputs.
 However, whether the input of different N compounds could differently
 impact plant growth and their 15N signatures remains unclear. Here, the
 response of δ15N signatures and growth of three dominant plants (Leymus
 chinensis, Carex duriuscula, and Thermopsis lanceolata) to the addition of
 three N compounds (NH4HCO3, urea, and NH4NO3) at multiple N addition rates
 were assessed in a meadow steppe in Inner Mongolia. The three plants
 showed different initial foliar δ15N values because of differences in
 their N acquisition strategies. Particularly, T. lanceolata (N2-fixing
 species) showed significantly lower 15N signatures than L. chinensis
 (associated with arbuscular mycorrhizal fungi, AMF) and C. duriuscula
 (associated with AMF). Moreover, the foliar δ15N of all three species
 increased with increasing N addition rates, with a sharp increase above an
 N addition rate of ~10 g N m-2yr-1. Foliar δ15N values were significantly
 higher when NH4HCO3 and urea were added than when NH4NO3 was added,
 suggesting that adding weakly acidifying N compounds could result in a
 more open N cycle. Overall, our results imply that assessing the N
 transformation processes in the context of increasing global N deposition
 necessitates the consideration of N deposition rates, forms of the
 deposited N compounds, and N utilization strategies of the co-existing
 plant species in the ecosystem.
DOI: 10.5061/dryad.9p8cz8wkz
title: Data for: Modeling the transition of death assemblages through the mixed layer predicts a downcore increase in time averaging

description: Understanding how time averaging changes during the burial is essential
 for using Holocene and Anthropocene cores to analyze ecosystem change,
 given the many ways in which the time averaging affects biodiversity
 measures. Here, we use transition-rate matrices to explore how time
 averaging changes downcore when shells transit through a
 taphonomically-complex mixed layer into permanently-buried historical
 layers: this is a null model, without any temporal changes in rates of
 sedimentation or bioturbation, to contrast with downcore patterns that
 might be produced by human activity. Assuming stochastic burial and
 exhumation movements of shells between increments within the mixed layer
 and stochastic disintegration within increments, almost all combinations
 of net sedimentation, mixing, and disintegration produce a downcore
 increase in time averaging (interquartile range, IQR), typically
 associated with a decrease in kurtosis and skewness and with a shift from
 right-skewed to symmetrical age distributions. A downcore increase in time
 averaging is a null expectation wherever bioturbation generates an
 internally-structured mixed layer (i.e., a surface well-mixed layer is
 underlain by an incompletely-mixed layer), so that shells are mixed
 throughout the entire mixed layer at slower rate than they are buried
 below it by sedimentation. This downcore trend created by mixing is
 further amplified by the downcore decline in disintegration rate. Using
 data from the southern California shelf, we find that transition-rate
 matrices accurately reproduce the downcore changes in IQR, skewness, and
 kurtosis observed in sediment cores. The right-skewed distributions
 typical of surface death assemblages – the focus of most actualistic
 research – might be fossilized under exceptional conditions of
 episodic anoxia or sudden burial. However, such right-skewed assemblages
 will not typically transfer into subsurface historical layers and thus
 will be geologically transient. The deep-time fossil record will be
 dominated instead by more time-averaged assemblages with weakly skewed age
 distributions that form in the lower parts of the mixed layer.
description: Functions for forward and inverse modeling of age distributions.
 Data used to estimate transition rates – radiocarbon-calibrated amino acid
 racemization age data of two bivalve species from the southern California
 shelf. Collection and dating details: Tomašových, A.,
 Kidwell, S.M., Alexander, C.R. and Kaufman, D.S., 2019. Millennial‐scale
 age offsets within fossil assemblages: Result of bioturbation below the
 taphonomic active zone and out‐of‐phase production. Paleoceanography and
 Paleoclimatology, 34, 954-977.
description: Data is in R language.
DOI: 10.5061/dryad.d2547d85q
title: Forest gaps around wind turbines attract bat species with high collision risk

description: Globally, renewable energy is highly demanded, leading to a recent
 increase in the number of wind turbines at forested sites. For the
 deployment of turbines, forest areas must be cleared, which results in
 significant habitat changes. To assess the ecological consequences of
 these changes for forest-associated bats, we quantified the activity of
 three bat foraging guilds at turbine clearings, adjacent forest edges, and
 nearby forest canopies. Specifically, open-space and edge-space foraging
 bats were more active at turbine clearings and forest edges than at forest
 canopies. Narrow-space foragers were also more often recorded at turbine
 clearings than at forest canopies. An increased activity of open- and
 edge-space foragers at turbine clearings may increase the risk for
 casualties. Therefore, if turbines need to be placed in forests, strict
 curtailment schemes should be practiced to mitigate collision risk for
 these bats. This may impair the efficacy of wind energy production at
 forested sites.
description: Please check description in the paper.
description: RMD-files can be opened with R or RStudio (scripts were written
 in R version 4.1.3). xlsx-files can be opened with
 Microsoft Excel or alternative spreadsheet.
description: # Title of Dataset: Forest gaps around wind turbines attract bat species
 with high collision risk --- Provided tables assembly data from a study at
 wind turbine sites within forests. We sampled acoustic bat data at wind
 turbine clearings, clearing edges and the adjacent forest and
 environmental variables on plot level. echolocation_bat_data.xlsx contains
 the number of minutes with bat activity for each bat foraging guild,
 habitat, plot, and moth of sampling. foraging_bat_data.xlsx additionally
 contains the number of feeding buzzes as indicators for foraging activity.
 site_parameters.xlsx compiles for each plot the forest type (deciduous,
 coniferous), age, rotor diameter and tower height of wind turbines as well
 as clearing size. Effects of habitat and a selection of environmental
 variables on bat echolocation and foraging activity was assessed with
 generalized linear mixed effect models (GLMM). Results show, that
 especially bats of the open-space and edge-space foraging guild are more
 active at turbine clearings or clearing edge. Narrow-space foraging bats
 are rather influenced by size of wind turbine rotors. ## Description of
 the Data and file structure Explanations for the names of variables are
 given in the Excel-sheets. RDM-files contain an annotated R-script for
 analysing the effect of turbine and environmental variables on
 echolocation activity (echolocation_analysis_for dryad.Rmd) and foraging
 activity (foraging_analysis_for_dryad.Rmd). ## Sharing/access Information
 Wind turbine related information was retrieved from: Hessisches Landesamt
 fr Naturschutz, Umwelt und Geologie (HLNUG) (2019). Windenergie in Hessen.
 Retrieved from
DOI: 10.5061/dryad.kkwh70s7j
title: Code to find the cost-effective treatments to stop a propagating front

description: Invasive species propagation is a common phenomenon, and a major question
 is how humans would stop its propagation in the most cost-effective
 manner. This package includes software and simulation results to find the
 optimal shape of the suppression function under certain conditions. This
 package accompanies the paper "Optimizing the use of suppression
 zones for containment of invasive species" by Adam Lampert and Andrew
 Liebhold. In particular, it includes the complete code for generating
 Figs. 2-4 in the paper. The file front_complete_code.zip includes the
 entire code. The file simulation_results.zip includes the results.
description: The code was written by Adam Lampert.
description: Opening and running the code requires an installation of Matlab
 (2021b for Windows or similar).
DOI: 10.5061/dryad.0k6djhb3m
title: Can regime shifts in reproduction be explained by changing climate and food availability?

description: Marine populations often show considerable variation in their
 productivity, including regime shifts. Of special interest are prolonged
 shifts to low recruitment and low abundance which occur in many fish
 populations despite reductions in fishing pressure. One of the possible
 causes for the lack of recovery has been suggested to be the Allee effect
 (depensation). Nonetheless, both regime shifts and the Allee effect are
 empirically emerging patterns but provide no explanation about the
 underlying mechanisms. Environmental forcing, on the other hand, is known
 to induce population fluctuations and has also been suggested as one of
 the primary challenges for recovery. Yet, traditional stock-recruitment
 models used in fisheries management have been time-invariant and
 considered only density-dependence. In the present study, we build upon
 recently developed Bayesian change-point models to explore the
 contribution of food and climate as external drivers in recruitment regime
 shifts, while accounting for density-dependent mechanisms (compensation
 and depensation). Food availability is approximated by the copepod
 community. Temperature is included as a climatic driver. Three demersal
 fish populations in the Irish Sea are studied: Atlantic cod (Gadus
 morhua), whiting (Merlangius merlangus), and common sole (Solea solea). We
 demonstrate that while spawning stock biomass undoubtedly impacts
 recruitment, abiotic and biotic drivers can have substantial additional
 impacts, which can explain regime shifts in recruitment dynamics or low
 recruitment at low population abundances. Our results stress the fact that
 traditional abundance-based stock-recruitment models are not sufficient to
 capture variability in fish recruitment.
description: The recruitment models were fitted to the empirical data using
 the Bayesian online change-point detection method (BOCPD), combined with
 simulation-based filtering. The data were divided into segments by
 calculating their most likely segmentation (MLS). The methods are
 described more in detail in the article and its supporting
 material.
description: The file environmental_predictors.Rmd describes data
 pre-processing. The folder BOCPD provides scripts for
 fitting the change point models to the empirical data. Consider parallel
 computing for efficiency. The empirical data are not adjusted, consider
 lags, when needed (see the article and its supplementary
 material). The results data enable model comparison
 based on the negative log marginal likelihood (nlml).
DOI: 10.5061/dryad.j0zpc86j4
title: Genome mining reveals the prevalence and extensive diversity of toxin-antitoxin systems in Staphylococcus aureus

description: Staphylococcus aureus (S. aureus) is a ubiquitous Gram-positive bacterium
 that is highly pathogenic and adaptive, showing great persistence in the
 environment. The toxin-antitoxin (TA) system is considered a valuable
 strategy for bacterial pathogens to survive in stressed environments and
 plays a crucial role in the defense system. Numerous studies have wildly
 explored the distribution and function of TA systems in clinical
 pathogens. However, little is known about the diversity of the TA
 systems and their evolutionary dynamics in S. aureus. In
 this study, we performed a comprehensive in silico screening of
 621 isolates recovered from public databases. We identified 44 TA groups
 belonging in S. aureus genomes using bioinformatic
 search and prediction tools, including SLING, TADB2.0 and
 TASmania. There was a median of 7 TA systems in each genome, and
 3 type II TA groups which were found in more than 80% of the strains,
 including HD, HD_3, and YoeB, others were more sporadic. The
 majority of predicted TA genes are chromosomally encoded. The
 Staphylococcal cassette chromosome mec (SCCmec) genomic
 islands also harbored TA genes. Further functional
 characterization of the putative TA system could reveal how these
 widespread prevalent gene modules potentially influence the ecology,
 virulence, and disease management practices of S. aureus. Our study opens
 the prospect of characterizing these putative TA genes and the design of
 more targeted antimicrobial agents in the future.
description: S. aureus genome assemblies (FASTA), annotated genomes (GBK and
 GFF) and protein sequence (FAA) for each corresponding isolate record were
 gathered from the NCBI database (https://www.ncbi.nlm.nih.gov/) as of
 August 31, 2021. Isolate background information was obtained by retrieving
 relevant literature and BioSample database
 (http://www.ebi.ac.uk/biosamples) with a self-written Python
 script.
DOI: 10.5061/dryad.63xsj3v5r
title: Data for: Repeated genetic divergence plays a minor role in repeated phenotypic divergence of lake-stream stickleback

description: Recent studies have shown that the repeated evolution of similar
 phenotypes in response to similar ecological conditions (here ‘parallel
 evolution’) often occurs through mutations in the same genes. However,
 many previous studies have focused on known candidate genes in a limited
 number of systems. Thus, the question of how often parallel phenotypic
 evolution is due to parallel genetic changes remains open. Here, we used
 quantitative trait locus (QTL) mapping in F2 intercrosses between lake and
 stream threespine stickleback (Gasterosteus aculeatus) from four
 independent watersheds on Vancouver Island, Canada to determine whether
 the same QTL underlie divergence in the same phenotypes across, between,
 and within watersheds. We find few parallel QTL, even in independent
 crosses from the same watershed or for phenotypes that have diverged in
 parallel. These findings suggest that different mutations can lead to
 similar phenotypes. The low genetic repeatability observed in these
 lake-stream systems contrasts with the higher genetic repeatability
 observed in other stickleback systems. We speculate that differences in
 evolutionary history, gene flow, and/or the strength and direction of
 selection might explain these differences in genetic parallelism and
 emphasize that more work is needed to move beyond documenting genetic
 parallelism to identifying the underlying causes.
description: All methods are described in the accompanying manuscript: Hilary
 A. Poore, Yoel E. Stuart, Diana J. Rennison, Marius Roesti, Andrew P.
 Hendry, Daniel I. Bolnick, Catherine L. Peichel (2022) Repeated genetic
 divergence plays a minor role in repeated phenotypic divergence of
 lake-stream stickleback. Evolution, in press. All
 datasets and scripts are described in the README file.
description: All datasets are provided as .csv, .txt, or .tab files. Analyses
 were conducted in R (script files are indicated as .r), bash (script files
 are indicated as .sh), and PERL (script files are indicated as
 .pl).