cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.80gb5mkpn
title: Data from: Movement and seasonal energetics mediate vulnerability to disturbance in marine mammal populations

description: In marine environments noise from human activities is increasing
 dramatically, causing animals to alter their behavior and forage less
 efficiently. These alterations incur energetic costs that can result in
 reproductive failure, death, and may ultimately influence population
 viability; yet the link between population dynamics and individual
 energetics is poorly understood. We present an energy budget model for
 simulating effects of acoustic disturbance on populations. It accounts for
 environmental variability and individual state, while incorporating
 realistic animal movements. Using harbor porpoises (Phocoena phocoena) as
 a case study, we evaluated population consequences of disturbance from
 seismic surveys and investigated underlying drivers of vulnerability. The
 framework reproduced empirical estimates of population structure and
 seasonal variations in energetics. The largest effects predicted for
 seismic surveys were in late summer and fall, and were unrelated to local
 abundance, but instead to lactation costs, water temperature, and body
 fat. Our results demonstrate that consideration of temporal variation in
 individual energetics and their link to costs associated with disturbances
 is imperative when predicting disturbance impacts. These mechanisms are
 general to animal species, and the framework presented here can be used
 for gaining new insights into the spatiotemporal variability of animal
 movements and energetics that control population dynamics.
description: This repository includes two zip files: 1) agent-based model code
 and associated files (Gallagheretal_Code.zip), and 2) the data and scripts
 used to create the figures presented in the main text
 (Gallagheretal_Figures.zip). Details for each can be found in the
 associated README.md file, in the main text of the manuscript, and in the
 associated supplementary TRACE document.
DOI: 10.5061/dryad.z34tmpgbq
title: Biotic and abiotic drivers of plant-pollinator community assembly across wildfire gradients

description: 1. Understanding how abiotic disturbance and biotic interactions determine
 pollinator and flowering-plant diversity is critically important given
 global climate change and widespread pollinator declines. To predict
 responses of pollinators and flowering-plant communities to changes in
 wildfire disturbance, a mechanistic understanding of how these two trophic
 levels respond to wildfire severity is needed. 2. We compared site-to-site
 variation in community composition (β-diversity), species richness, and
 abundances of pollinators and flowering plants among landscapes with no
 recent wildfire (unburned), mixed-severity wildfire, and high-severity
 wildfire in three sites across the Northern Rockies Ecoregion, USA. We
 used variation partitioning to assess the relative contributions of
 wildfire, other abiotic variables (climate, soils, topography), and biotic
 associations among plant and pollinator composition to community assembly
 of both trophic levels. 3. Wildfire disturbance generally increased
 species richness and total abundance, but decreased β-diversity, of both
 pollinators and flowering plants. However, reductions in β-diversity from
 wildfire appeared to result from increased abundances following fires,
 resulting in higher local species richness of pollinators and flowers in
 burned than unburned landscapes. After accounting for differences in
 abundance, standardized effect sizes of β-diversity were higher in burned
 than unburned landscapes, suggesting that wildfire enhances non-random
 assortment of pollinator and flowering-plant species among local
 communities. 4. Wildfire disturbance mediated the relative importance of
 mutualistic associations to β-diversity of pollinators and flowering
 plants. The influence of pollinator β-diversity on flowering-plant
 β-diversity increased with wildfire severity, whereas the influence of
 flowering-plant β-diversity on pollinator β-diversity was greater in
 mixed-severity than high-severity wildfire or unburned landscapes.
 Moreover, biotic associations among pollinator and plant species explained
 substantial variation in β-diversity of both trophic levels beyond what
 could be explained by wildfire and all other abiotic and spatial factors
 combined. 5. Synthesis: Wildfire disturbance and plant-pollinator
 interactions both strongly influence the assembly of pollinator and
 flowering-plant communities at local and regional scales. However, biotic
 interactions were generally more important drivers of community assembly
 in disturbed than undisturbed landscapes. As wildfire regimes continue to
 change globally, predicting its effects on biodiversity will require a
 deeper understanding of the ecological processes that mediate biotic
 interactions among linked trophic levels.
description: Please find data files (RData files) and R scripts to perform
 analyses. Please read instructions within R script for running
 analyses.
DOI: 10.5061/dryad.34tmpg4hq
title: Gene tree discord, simplex plots, and statistical tests under the coalescent

description: A simple graphical device, the simplex plot of quartet concordance
 factors, is introduced to aid in the exploration of a collection of gene
 trees on a common set of taxa. A single plot summarizes all gene tree
 discord, and allows for visual comparison to the expected discord from the
 multispecies coalescent model (MSC) of incomplete lineage sorting on a
 species tree. A formal statistical procedure is described that can
 quantify the deviation from expectation for each subset of four taxa,
 suggesting when the data is not in accord with the MSC, and thus that
 either gene tree inference error is substantial or a more complex model
 such as that on a network may be required. If the collection of gene trees
 is in accord with the MSC, the plots reveal when substantial incomplete
 lineage sorting is present. Applications to both simulated and empirical
 multilocus data sets illustrate the insights provided.
description: This is a supplement to a research article. No data is
 provided.
description: The supplement contains a complete description of the simulation
 procedure.
DOI: 10.5061/dryad.r4xgxd29x
title: Cooperative excitations within the superionic phase of PbF2

description: Links between dynamical Frenkel defects and collective diffusion of
 fluorides in beta-PbF2 are  explored using Born-Oppenheimer
 molecular dynamics. The calculated self diffusion coefficient and ionic
 conductivity are 3.2 x 10-5 cm2s-1 and 2.4 Omega-1 
 cm-1  at 1000 K in excellent agreement with results from pulsed
 field gradient and conductivity measurements: DPFG = 4 x 10-5 cm2 s-1
 and  sigmad.c. sim 3 Omega-1cm-1. The calculated ratio of tracer
 diffusion to conductivity diffusion is slightly less than unity (about
 0.85), which in previous work has been interpreted as providing little
 evidence for collective diffusion. In contrast, our molecular dynamics
 simulations show that diffusion of fluorides is highly correlated and a
 range of mechanisms play important roles. These include, for example,
 direct collinear ``knock out'' chains - where a fluoride enter
 an occupied tetrahedral hole/cavity and pushes the resident fluorine out
 of its cavity - and `loops'' which  generate no net
 charge transport. Jumps into an occupied cavity leaves behind a vacancy,
 thereby forming dynamic Frenkel defects which trigger a chain of migrating
 fluorides assisted by local relaxations of the leads. The calculated
 lifetime of the Frenkel defects and the collective chains are around
 similar to 1 ps in good agreement with that found from  neutron
 diffraction.
description: The datafile .xml is output file from atomistic ab intio
 molecular dynamics calculations of PbF2 using the VASP software [
 https://www.vasp.at/]. The .xml file contains all input parameters along
 with the  ionic positions dumped along the trajectories (raw outputfiles).
 The trajectories can be analysed and visualised using programs such as
 e.g. VMD and VESTA. See also details of the paper.
DOI: 10.15468/dl.p62564
title: Occurrence Download

description: A dataset containing 17794 records in GBIF matching the query:
SELECT
 '442' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 41.89415215079384
 AND decimalLatitude &lt;= 46.479780028101516
 AND decimalLongitude &gt;= 35.96444851417518
 AND decimalLongitude &lt;= 44.06078664257346
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 17794 records were derived from 178 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002613-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dz08kprw4
title: Appendix for: Light chain neurofilament revealing brain tissue damage in physical contact sport athletes, a systematic review

description: Objective: To evaluate whether participating in physical contact
 sports is associated with a release of neurofilaments and whether this
 release is related to future clinical neurological and/or psychiatric
 impairment. Methods: We have performed a systematic literature
 review of the PubMed, MEDLINE and Cochrane Library databases using a
 combination of the search terms neurofilament(s)/intermediate filament and
 sport(s)/athletes. Only original studies, written in English, that have
 reported on neurofilament measurements in CSF and/or serum/plasma of
 physical contact sport athletes were retained for data extraction. This
 review was conducted following the Preferred Reporting Items for
 Systematic Review and Analyses guidelines. Results: Eighteen
 studies reporting on light chain neurofilament (NfL), in eight different
 contact sports (i.e. boxing, American football, ice hockey, soccer, mixed
 martial arts, lacrosse, rugby and wrestling), matched our inclusion
 criteria. In 13/18 athlete cohorts, significant NfL elevations in CSF or
 serum/plasma were described, as compared to situations of non-exposure.
 Most compelling evidence was present in boxers and American football
 players, where marked and/or immediate exposure-related increases were
 appreciable at the intra-individual level in exclusive cohorts, generally
 paired with control groups who were well-described and matched for age.
 Findings in others sports were less suitable to draw conclusion upon. No
 studies were encountered that have investigated the relationship with the
 targeted clinical endpoints.  Conclusion: Nfl release
 can be seen, as a potential marker of neuronal brain damage, in
 participants of physical contact sports, particularly boxing and American
 football. The exact significance regarding the risk for future clinical
 impairment remains to be elucidated.
DOI: 10.5061/dryad.t1g1jwt10
title: Data from: Characterisation of reproductive gene diversity in the endangered Tasmanian devil

description: Inter-individual variation at genes known to play a role in reproduction
 may impact reproductive fitness. The Tasmanian devil is an endangered
 Australian marsupial with low genetic diversity. Recent work has shown
 concerning declines in productivity in both wild and captive populations
 over time. Understanding whether functional diversity exists at
 reproductive genes in the Tasmanian devil is a key first step in
 identifying genes that may influence productivity. We characterised single
 nucleotide polymorphisms (SNPs) at 214 genes involved in reproduction in
 37 Tasmanian devils. Twenty genes contained non-synonymous substitutions,
 with genes involved in embryogenesis, fertilisation and hormonal
 regulation of reproduction displaying greater numbers of nonsynonymous
 SNPs than synonymous SNPs. Two genes, ADAMTS9 and NANOG, showed putative
 signatures of balancing selection indicating that natural selection is
 maintaining diversity at these genes despite the species exhibiting low
 overall levels of genetic diversity. We will use this information in
 future to examine the interplay between reproductive gene variation and
 reproductive fitness in Tasmanian devil populations.
description: Two existing datasets comprising 37 resequenced genomes (SRA
 Accessions: SRX6096677- SRX6096696, ERS682204-ERS682210, ERS1202857-ERS1202861) were used to explore reproductive gene diversity in the Tasmanian devil. Reads were aligned to the Tasmanian devil reference genome assembly version 7.0 (GenBank Accession: GCA_000189315.1) using Burrows-Wheeler aligner v 0.7.15. SNPs were called within target reproductive genes of interest across the 37 individuals using SAMtools v 1.6 with minimum base and mapping quality of 30 and a coefficient for downgrading mapping quality for reads containing excessive mismatches of 50. Individual sample VCF files were then subset from the multisample VCF file and filtered to exclude variants below a filtered depth threshold using BCFtools v1.3.1. The remaining variants were then merged into a multisample VCF file using VCFtools v0.1.14.
description: Please refer to the published paper for information regarding the
 target genes of interest, sample information, downstream analyses and
 references for associated datasets and software. The readme file contains
 a summary of information relating to this dataset
DOI: 10.5061/dryad.5tb2rbp2x
title: Data from: Effects of maternal genotypic identity and genetic diversity of the red mangrove Rhizophora mangle on associated soil bacterial communities: a field-based experiment

description: Loss of plant biodiversity can result in reduced abundance and diversity
 of associated species with implications for ecosystem functioning. In
 ecosystems low in plant species diversity, such as Neotropical mangrove
 forests, it is thought that genetic diversity within the dominant plant
 species could play an important role in shaping associated communities.
 Here, we used a manipulative field experiment to study the effects of
 maternal genotypic identity and genetic diversity of the red mangrove
 Rhizophora mangle on the composition and richness of associated soil
 bacterial communities. Using terminal restriction fragment length
 polymorphism (T-RFLP) community fingerprinting, we found that bacterial
 community composition differed among R. mangle maternal genotypes but not
 with genetic diversity. Bacterial taxa richness, total soil nitrogen, and
 total soil carbon were not significantly affected by maternal genotypic
 identity or genetic diversity of R. mangle. Our findings show that
 genotype selection in reforestation projects could influence soil
 bacterial community composition. Further research is needed to determine
 what impact these bacterial community differences might have on ecosystem
 processes, such as carbon and nitrogen cycling.
description: Soils were collected from experimental plots planted with
 <em>Rhizophora mangle</em> in different levels of genotpyic
 diversity. DNA was extracted from soils and bacterial community
 composition was assessed using T-RFLPs of the 16S rRNA gene.
description: See ReadMe file for description of column headings in the
 datasets
DOI: 10.5061/dryad.69p8cz90j
title: Characterizing the modern light environment and its influence on circadian rhythms

description: Humans have largely supplanted natural light cycles with a variety of
 electric light sources and schedules misaligned with day-night cycles.
 Circadian disruption has been linked to a number of disease processes, but
 the extent of circadian disruption among the population is unknown. In
 this study, we measured light exposure and wrist temperature among
 residents of an urban area during each of the four seasons, as well as
 light illuminance in nearby outdoor locations. Daily light exposure was
 significantly lower for individuals, compared to outdoor light sensors,
 across all four seasons. There was also little seasonal variation in the
 realized photoperiod experienced by individuals, with the only significant
 difference occurring between winter and summer. We tested the hypothesis
 that differential light exposure impacts circadian phase timing, detected
 via the wrist temperature rhythm. To determine the influence of light
 exposure on circadian rhythms, we modeled the impact of morning and
 nighttime light exposure on the timing of the maximum wrist temperature.
 We found that morning and nighttime light exposure had significant but
 opposing impacts on maximum wrist temperature timing. Our results
 demonstrate that, within the range of exposure seen in everyday life,
 nighttime light can delay the onset of the maximum wrist temperature,
 while morning light can lead to earlier onset. Our results demonstrate
 that humans are minimizing natural seasonal differences in light exposure,
 and that circadian shifts and disruptions may be a more regular occurrence
 in the general population than is currently recognized.
description: Refer to the ReadMe for description of included data files.
DOI: 10.15468/dl.xht6y5
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chesneya yunnanensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 9 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002623-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.gb5mkkwnh
title: Lianas explore the forest canopy more effectively than trees under drier conditions

description: Lianas rely on trees for support and access to high light positions in the
 forest canopy, but the implications for how lianas explore the canopy
 compared to trees remain understudied. We present an in situ forest canopy
 study to test the hypotheses that: (1) lianas favour leaf display over
 stem investment compared to trees and (2) lianas have greater potential to
 colonize non-shaded, high-light areas effectively than trees. We compared
 branches of 16 liana species with those of 16 sympatric tree species in
 two lowland tropical forest canopies in Panama using 40-50 m tall canopy
 cranes. One forest was relatively dry and seasonal in rainfall and in
 associated light availability. The other forest was relatively wet and
 evergreen. We observed that lianas were more efficient in leaf display
 over stem investment than trees, particularly in the forest with lower
 precipitation and stronger seasonality. Specifically, lianas had a lower
 LMA (leaf mass per unit leaf area), stronger apical dominance, higher stem
 slenderness and fewer leaf layers than trees. In the forest with higher
 precipitation and weaker seasonality, lianas also had stronger apical
 control and fewer leaf layers than trees, but both lianas and trees were
 relatively similar in LMA and stem slenderness. Our study shows that
 lianas more effectively explore the canopy than trees under drier
 conditions, but much less so under wetter conditions. We argue that lianas
 display a functional strategy that allow them to better intercept light
 than the tree species in forests with low precipitation and strong
 seasonality, while they are constrained to display such strategy at high
 precipitation – light-limited – sites.
description: This dataset was collected throughout the study presented in the
 article : <em>Lianas explore the forest canopy more effectively than
 trees under drier conditions.</em>
DOI: 10.5061/dryad.sj3tx9637
title: Data from: Putative chromosomal rearrangements are associated primarily with ecotype divergence rather than geographic separation in an intertidal, poorly-dispersing snail

description: Littorina saxatilis is becoming a model system for understanding the
 genomic basis of ecological speciation. The parallel formation of
 crab-adapted ecotypes that exhibit partial reproductive isolation from
 wave-adapted ecotypes has enabled genomic investigation of conspicuous
 shell traits. Recent genomic studies suggest that chromosomal
 rearrangements may enable ecotype divergence by reducing gene flow.
 However, the genomic architecture of traits that are divergent between
 ecotypes remains poorly understood. Here, we use 11,504 single nucleotide
 polymorphism (SNP) markers called using the recently-released L. saxatilis
 genome to genotype 462 crab ecotype, wave ecotype, and
 phenotypically-intermediate L. saxatilis individuals with scored
 phenotypes. We used redundancy analysis to study the genetic architecture
 of loci associated with shell shape, shape corrected for size, shell size,
 and shell ornamentation, and to compare levels of co-association among
 different traits. We discovered 341 SNPs associated with shell traits.
 Loci associated with trait divergence between ecotypes were often located
 inside putative chromosomal rearrangements recently characterized in
 Swedish L. saxatilis. In contrast, we found that shell shape corrected for
 size varied primarily by site rather than by ecotype and showed little
 association with these putative rearrangements. Together, these results
 reveal that genomic regions of elevated divergence with putative
 rearrangements are associated with divergence along steep environmental
 axes in L. saxatilis ecotypes, consistent with models of adaptation with
 gene flow, but these regions are distinct from genomic architecture
 associated with site-specific variation. Our findings here further support
 predictions from models indicating the importance of genomic regions of
 reduced recombination allowing co-association of loci during ecological
 speciation with ongoing gene flow.
description: SNP genotype data in PLINK format output from STACKS 2 SNP
 genotyping using reference genome-aligned double digest RADseq.