cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t1g1jwt5t
title: Microbial community composition of earthworm-invaded and earthworm-free soils of the Canadian boreal forest

description: Earthworm invasion in North American forests has the potential to greatly
 impact soil microbiomes by altering soil physicochemical properties. We
 characterized and compared microbial communities of earthworm-invaded and
 non-invaded soils in previously described sites across three major soil
 types found in the Canadian boreal forest using phospholipid fatty acid
 (PLFA) analysis and metabarcoding of the 16S rRNA gene (bacteria and
 archaea) and ITS2 region (fungi).
description: Samples of mineral soils, forest floors, and earthworm casts were
 collected in the summer of 2019 in multiple boreal forest sites across
 Canada. Phospholipid fatty acids were extracted from
 freeze-dried samples following a modified Bligh and Dyer extraction
 method. PLFA identification was performed using the Sherlock Microbial
 Identification System version 4.5 following standard nomenclature. All
 unsaturated PLFAs were in cis configuration. DNA was
 extracted from 250 mg of ground and freeze-dried soil sample using the
 DNeasy PowerSoil DNA Isolation Kit. For bacteria and archaea, primers 515F-Y
 (5’-GTGYCAGCMGCCGCGGTAA-3’) and 926R (5’-
 CCGYCAATTYMTTTRAGTTT-3’) were used for amplification of the V4-V5
 regions of the 16S rRNA gene with 30 PCR cycles and an
 annealing temperature of 55 ºC. For fungi, primers ITS9F (5’-GAACGCAGCRAAIIGYGA-3’)
 and ITS4R (5’- TCCTCCGCTTATTGATATGC-3’) were used for amplification of the internal
 transcriber spacer 2 (ITS2) region with 30 PCR cycles and an annealing
 temperature of 60 ºC. The
 pooled libraries were sequenced on an Illumina MiSeq platform using a
 MiSeq Reagent v3 600 cycles Kit (Illumina Inc., San Diego, CA, USA) at the
 University of Alberta Molecular Biological Sciences
 Unit. Sequence data were archived at NCBI-SRA (BioProject
 PRJNA850095). Raw sequence data were demultiplexed and quality
 filtered using the q2‐demux plugin followed by denoising with DADA2 in
 QIIME2. After trimming off
 the primers, the first 20 base pairs (bp) to remove primers, sequence
 reads were truncated where the average quality score dropped below 34 (at
 285 and 215 bp for forward and reverse 16S reads; at 260 and 225 bp for
 forward and reverse ITS reads), and dereplicated with paired end setting
 to generate amplicon sequence variants (ASVs) tables containing read
 counts. After training the
 naïve Bayes classifiers (q2‐feature‐classifier), taxonomy was assigned to
 ASVs using classify-sklearn with SILVA 138 SSURef NR99 full-length (99 %)
 and UNITE 8.3 (97 %) databases for 16S and ITS2,
 respectively. Fungal
 functional guilds were determined with FUNGuild database. Fungal ASVs
 associated with a unique guild ranked (highly) probable were grouped into
 ectomycorrhizal, pathogenic, and saprotrophic fungi. Additional ASVs were
 manually selected based on the literature and added when
 relevant.
DOI: 10.5061/dryad.tb2rbp042
title: Long-term fire and vegetation change in northwestern Amazonia

description: Amazonian forest plots are used to quantify biodiversity and carbon
 sequestration, and provide the foundation for much of what is known about
 tropical ecology. Many plots are assumed to be undisturbed, but recent
 work suggests that past fire, forest openings, and cultivation created
 vegetation changes that have persisted for decades to centuries
 (ecological legacies). The Yasuní Forest Dynamics plot is one of the most
 biodiverse places on earth, yet its human history remains unknown. Here,
 we use charcoal and phytolith analysis to investigate the fire and
 vegetation history of the Yasuní forest plot, and compare results with
 nearby forest plots in Colombia (Amacayacu) and Peru (Medio
 Putumayo-Algodón (MPA)) to explore the spatial variability of past
 disturbances and ecological legacies in northwestern Amazonia. Three 14C
 dated charcoal fragments provided evidence for a modern (1956 CE) and a
 past fire event ca. 750 years ago at Yasuní, compared with fire ages of
 1000-1600 years ago documented at Amacayacu and MPA. Small-scale
 disturbances and localized canopy-openings also occurred in the Yasuní
 plot. Phytolith assemblages from Yasuní and Amacayacu showed more
 variability in past vegetation change than MPA. Low-intensity,
 non-continuous disturbances occurred at all three plots in the past, and
 our results highlight the variability of past human activities both in
 space and time in northwestern Amazonia. Our data also suggest that
 post-Columbian human disturbances from the Rubber Boom (AD 1850-1920) and
 subsequent oil exploration have likely left stronger ecological legacies
 than those left by pre-Columbian peoples in our studied regions.
description: Samples were collected in Yasuní Forest Dynamics Plot and
 analyzed at the University of Amsterdam (see Heijink et al., (2022) for
 more details). Phytoliths were identified using published reference
 photographs (Huisman et al., 2018, Morcote-Ríos et al., 2016, Piperno,
 2006, Piperno and McMichael, 2020, Witteveen et al., 2022) and the
 phytolith reference collection of the University of Amsterdam.
DOI: 10.5061/dryad.4j0zpc8gb
title: Colonizing polar environments: thermal niche evolution in Collembola

description: Temperature is a primary driver in defining the ecophysiological activity
 and performance of ectotherms. Thus, thermal tolerance limits have a
 profound effect in determining geographic ranges. In regions with extreme
 cold temperatures, lower thermal limits of species are a key physiological
 trait for survival. Moreover, thermal niche breadth also plays an
 important role in allowing organisms to withstand climatic variability and
 confers species with broader potential to establish in new regions. Here
 we study the evolution of thermal tolerance limits among Collembola
 (Arthropoda) and explore how they are affected by the colonization of
 polar environments. In addition, we test the hypothesis that globally
 invasive species are more eurythermal than non-invasive ones. Critical
 thermal limits (CTmin and CTmax), classic measurements of thermal
 tolerance, were compiled from the literature and complemented with
 experimental assays for springtail species. Genetic data of the
 mitochondrial gene cytochrome oxidase subunit 1 (COI) was used to assemble
 a phylogeny. Our results show that polar springtails have lower CTmin and
 lower CTmax compared to species from temperate and tropical regions,
 consistent with the Polar pressure hypothesis. We found no phylogenetic
 signal for CTmax, but low values of phylogenetic signal for CTmin.
 Globally invasive species do not have significantly broader thermal
 tolerance breadth (CTrange) than non-invasive ones, thus not supporting
 the predictions of the Eurythermality hypothesis. We conclude that polar
 springtails have evolved their thermal niches in order to adapt to
 extremely cold environments, which has led to decreasing both upper and
 lower thermal tolerance limits.
description: # Colonizing polar environments: thermal niche evolution in Collembola ##
 Description of the Data and file structure * Sp: Species * n\_max: Number
 of individuals for CTmax * ctmax\_mean: Mean of CTmax * sd\_ctmax:
 Standard deviation of CTmax * n\_min: Number of individuals for CTmin *
 ctmin\_mean: Mean of CTmin * sd\_ctmin: Standard deviation of CTmin *
 ctrange: Range of CT (CTmax + CTmin) * locality: Region of collection *
 status: If the species is considered invasive or native *
 reference\_status: Reference of the invasive/native status *
 reference\_ct: Reference of the CT value * code\_COI: Code of the sequence
 * source: Website of the sequence * ramping\_rate: Experimental ramp in
 ºC/minute * acclimation\_temp\_ºC: Acclimation temperature in ºC *
 acclimation\_time: Acclimation time in hours, weeks or generations (F2) *
 cat\_acc\_time: Category attributed to acclimation time *
 arr\_mean\_ctmax: Mean of the acclimation response ratio for CTmax *
 arr\_mean\_ctmin: Mean of the acclimation response ratio for CTmin *
 ctmax\_duration\_trial: Duration trial for CTmax in minutes *
 ctmin\_duration\_tiral: Duration trial for CTmin in minutes NA: mean that
 we do not know the data ### Sharing/access Information:
 https://doi.org/10.1016/j.cris.2021.100023
DOI: 10.5061/dryad.dv41ns22j
title: Social-ecological cascade effects of land-use on vertebrate pest dynamics in arid agricultural communities

description: Extensive land conversion to agriculture in drylands and associated
 resource use have wide-ranging impacts on desert ecosystems globally.
 Incorporating the impacts of human-social aspects is thus imperative in
 examining ecological interactions. The provision of agricultural inputs in
 these resource-scarce regions supports invasive and pest species,
 negatively impacting both agricultural productivity and native desert
 ecosystems. Understanding the spatial dynamics of invasive and pest
 species requires analyzing both bottom-up resource availability factors
 underlying animal distributions and top-down biological controls. Here, we
 evaluate the social-ecological cascading effects of dryland agriculture on
 vertebrate pest communities in dryland agricultural communities of Israel.
 Our study region is characterized by 18 agricultural cooperatives with
 distinct crop regimes due to contrasting social decision-making and
 resource allocation schemes (i.e., communal Kibbutzim vs. privatized
 Moshavim). Crop choices further affect land management (e.g., enclosed vs.
 open farm systems) and resource intensity. This system is ideal to study
 trophic mechanisms underlying animal assemblages between agricultural
 regimes. We examine the role of agricultural land-use practices on pest
 spatial distributions based on multi-year vertebrate pest observations
 with agricultural datasets. We use structural equation modelling (SEM) to
 quantify the relative importance of added agricultural resources
 underlying bottom-up and top-down trophic processes regulating vertebrate
 pest assemblages. Results reveal that crop choices determine pest
 distributions through bottom-up processes directly, while simultaneously
 driving pest competitive interactions through indirect top-down cascades
 impacting pest communities. For example, due to the indirect negative
 effect of wolves on meso-predators (foxes and jackals) mediated by
 livestock, the total positive effect of livestock on the abundance of
 meso-predators is reduced. Our study illustrates the social-ecological
 cascading effects of agricultural regimes on pest community assemblages
 mediated by contrasting agricultural land-use practices. Considering the
 expansion of dryland agro-ecological systems globally, understanding the
 intricate cascading pathways of predator- and prey-pest communities has
 important implications for agricultural management, biological invasions
 in drylands and fragile desert environments.
DOI: 10.5281/zenodo.18402077
title: Financing Climate-Smart Agriculture: The effect of credit constraints on greenhouse technology adoption by smallholder tomato farmers in Kenya

description: This is data effect of credit constraints on adoption of greenhouse technology by smallholder tomato farmers in Kenya
DOI: 10.5281/zenodo.18402078
title: Financing Climate-Smart Agriculture: The effect of credit constraints on greenhouse technology adoption by smallholder tomato farmers in Kenya

description: This is data effect of credit constraints on adoption of greenhouse technology by smallholder tomato farmers in Kenya
DOI: 10.5061/dryad.jm63xsjfc
title: Data from: Dental health utilization in the Republic of Palau: A survey to determine feasibility of an oral cancer screening program

description: Cancer is the second leading cause of death in the Western Pacific region.
 The prevalent tradition of chewing betel nut in Palau, an island nation in
 this region, is a risk factor in the development of oral cancer. Oral
 cancer is the fifth most common cancer in Palau, and prognosis can be
 improved with early detection. The purpose of this study is to assess the
 feasibility of oral cancer screening using existing dental health
 infrastructure in Palau. A mixed methods approach was used to explore
 topics related to dental health and use of these resources in Palau.
 Quantitative measures of dental health utilization and qualitative
 assessment of barriers and facilitators to accessing dental care were the
 primary measures of this study. Knowledge, attitudes, and beliefs about
 betel nut use and oral cancer were secondary measures of this study.
 Open-ended survey questions were coded to develop emergent themes based in
 grounded theory. These themes are interpreted in the context of the Three
 Delays model. There was a total of 223 completed surveys. Mean age was
 43.7 years, 80% identified as female, and most (94.3%) reported ever
 having seen a dentist in Palau. Dental care was seen as important (mean
 score 82.3), and 57.9% reported it was easy to see a dentist. Themes
 regarding barriers to dental care addressed cost and availability of
 dentists/appointments. Themes regarding facilitators included multilevel
 resources and transportation. Approximately half of respondents were
 current users of betel nut, and the majority of these (64.1%) were daily
 users. Results suggest there are facilitators in place to promote seeking
 and obtaining dental care, however, existing infrastructure may not
 support an oral cancer screening program. These data provide important
 areas to address that can improve access and support the implementation of
 oral cancer screening through existing dental care in the future.
description: Informed consent was obtained (written). The survey was made
 available through Facebook Ads. Responses were stored in REDCap and
 analyzed using Excel and SPSS. Open-ended responses were open-coded by two
 of the authors and themes were generated using grounded theory. 
description: Microsoft Excel
DOI: 10.3886/e197845v1-198161
title: Data and Code for: Domestic Policies and Sovereign Default

description: Data and Code for: Domestic Policies and Sovereign Default<br><br>
DOI: 10.5061/dryad.tht76hf2x
title: Data from: Subtle responses of soil bacterial communities to corn-soybean-wheat rotation

description: Crop rotational diversity can improve crop productivity and soil health
 and boost soil microbial diversity. This research hypothesized that a
 three-year rotation of corn-soybean-wheat (CSW), compared to a two-year
 corn-soybean (CS) rotation, would result in a more diverse and more
 complex soil bacterial community, together with a greater abundance of
 beneficial bacteria. This was evaluated in a replicated experiment
 established in 2013 at two locations in Ohio (USA). The soil bacterial
 communities under soybean were compared between CS and CSW, at both
 studied sites, in 2018 and 2019, through 16S rDNA amplicon
 metabarcoding. 
description: A crop rotation field experiment was established in 2013 at two
 Ohio State University research locations, Northwest Agricultural Research
 Stations (NWARS) and Western Agricultural Research Stations (WARS). The
 experimental treatments were a two-year corn-soybean (CS) rotation
 compared to a three-year corn-soybean-wheat (CSW). The experiment was
 managed as a no-till system, with herbicide and fungicide applications as
 needed. The complete root and associated soil were sampled with a shovel
 at an approximate depth of 10-15 cm. Eight samples were collected within
 each plot and the shovels were cleaned with 70% ethanol between plots.
 Each sample was placed in a plastic bag and kept cool in a cold box while
 it was transferred from the field to the laboratory, and at 8°C until
 processing. Soils were vacuum dried at 60°C for 30 minutes. The total soil
 DNA was extracted from 0.25g of dried soils using the SurePrepTM Soil DNA
 Isolation Kit (Fisher BioReagents, NJ, USA), according to manufacturer
 recommendations, and followed by a ribonuclease A (RNAse A)
 treatment. Bacterial community characterization, through amplicon
 sequencing, was performed using a two-step amplification protocol. In the
 first PCR, the primers 515F and 806R (Apprill et al., 2015; Parada et al.,
 2016) targeting the V3-V4 region of the 16S rDNA were used, followed by a
 double-indexing PCR approach. Samples were pooled into a single sequencing
 library based on equimolar concentrations and sequenced using an Illumina
 MiSeq (Illumina, San Diego, CA, USA) sequencing platform with the 300PE
 chemistry, with two separate runs for samples collected in 2018 and 2019,
 respectively. A total of 256 DNA samples from soybean-associated soils,
 corresponding to two treatments, 4 plots/treatment, and 8 samples/plot for
 two locations in Ohio, and two growing (2018 and 2019) seasons were
 processed. In addition, positive controls, including the commercial
 ZymoBIOMICS Microbial Community DNA Standard (Zymo Research, Irvine, CA,
 USA) and a mixture of DNA of known soil isolates and two types of negative
 controls were included in sequencing runs and analysis for both years of
 analysis.
DOI: 10.15468/dl.kfdrr8
title: Occurrence Download

description: A dataset containing 3619 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lyssa zampa"
 ]
}

 The dataset includes 3619 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003335-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rnxnfj
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "GadmGid is BRA.13_1",
 "TaxonKey is Melanoxylon braunia"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003336-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d51c5b06q
title: MinION reads from CO236 and CO237

description: Xanthomonas translucens, the causal agent responsible for bacterial leaf
 streak disease (BLS) in cereal crops, is re-emerging as a highly
 destructive pathogen on a global scale. Despite historical reports of BLS
 causing yield losses, there is growing anecdotal evidence suggesting that
 newer isolates of X. translucens may have increased virulence. Our
 research demonstrates that two X. translucens isolates, collected from
 different locations in Colorado, exhibit a greater level of aggressiveness
 on wheat and barley varieties when compared to older isolates. We propose
 that genetic variations between recent and older strains contribute
 significantly to the observed differences in isolate aggressiveness. To
 investigate this hypothesis, we conducted phenotypic and genetic analyses
 on two X. translucens isolates collected in Colorado in 2018, designated
 as CO236 (from barley) and CO237 (from wheat). With whole-genomes obtained
 by sequencing using Oxford Nanopore Technology (ONT), we have identified
 both similarities and distinctions between these recently collected
 isolates and previously characterized strains. The dataset provided herein
 contains the raw ONT MinION sequencing reads for isolates Xtt CO236 and
 Xtu CO237.
description: Raw reads were obtained from Oxford Nanopore MinION sequencing.
 gDNA of isolates Xtt CO236 and Xtu CO237 was extracted using Zymo Research
 Quick-DNA<sup>TM</sup> Fungal/Bacterial Miniprep Kit according
 to the manufacturer's instructions. Approximately 300ng of gDNA from
 each strain was barcoded with ONT Rapid Barcoding Kit (SQK-RBK004).
 Barcoded libraries were prepared with the Rapid Sequencing Kit
 (SQK-RAD004). Base calling was done in real-time with Guppy's
 high-accurate algorithm from ONT. Fastq reads obtained
 from basecalling were grouped by each barcode corresponding to isolates
 Xtt CO236 and Xtu CO237, after which they were concatenated and
 compressed. The dataset includes the concatenated and compressed reads of
 Xtt CO236 (CO236.multiple.fastq.gz) and Xtu CO237
 (CO237.multiple.fastq.gz).
description: # MinION reads from CO236 and CO237
 [https://doi.org/10.5061/dryad.d51c5b06q](https://doi.org/10.5061/dryad.d51c5b06q) ## Description of the data and file structure Fastq reads obtained from basecalling were grouped by each barcode corresponding to isolates Xtt CO236 (barcode01) and Xtu CO237 (barcode02), after which they were concatenated and compressed. Dataset includes the concatenated and compressed reads of Xtt CO236 (CO236.multiple.fastq) and Xtu CO237 (CO237.multiple.fastq). The dataset include: * CO236.multiple.fastq: * Reads from barcode01 of the Sequencing run. * CO237.multiple.fastq: * Reads from barcode02 of the Sequencing run. * report\_FAQ44391\_20210811\_1731\_cf511f65.md & final\_summary\_FAQ44391\_42beb99f.txt: * Sequencing file reports and summary from Xtt CO236 and Xtu CO237 MinION sequencing run.
DOI: 10.7291/d17698
title: Social environment influences the temporal dynamics of sneak-spawning in a fish with alternative reproductive tactics

description: Several predictions of sperm competition theory are not well supported
 empirically. One potential reason is that most current theory and
 empirical research ignore how the social environment influences the
 temporal dynamics of mating. We propose that understanding these dynamics
 is key to understanding sexual selection and improving the predictive
 power of theory. To demonstrate the importance of these dynamics, we
 quantify how males’ social roles, interactions among males, and current
 social environment influence the timing of mating in Symphodus ocellatus,
 a species with three alternative male reproductive tactics. Nesting males
 spawn synchronously with females; sneakers and satellites sneak-spawn with
 some time-delay. Satellites also cooperate with nesting males. We found
 that satellites have shorter sneak-spawning delays than sneakers, a
 benefit of their cooperation with nesting males. Sneak-spawning delays
 decreased with increasing nest activity for sneakers but not satellites,
 suggesting sneakers may benefit from increased sperm competition
 intensity. Current sperm competition models ignore this potential benefit
 which may be why the prediction that males should decrease investment when
 sperm competition involves more than two males is not well supported. Our
 study provides insight into mechanisms that drive variation in the timing
 of spawning, which could explain mismatches between theoretical and
 empirical results.
description: Live behavioral observations and video analysis.
description: Analysis is conducted in the R programming language. Data is
 stored as a csv and R data files.