cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zgmsbcc8x
title: Genetic diversity and structure of wild Vaccinium populations - V. myrtillus, V.vitis-idaea and V. uliginosum in the Baltic States

description: V. myrtillus L., V. vitis-idaea L. and V. uliginosum L. belong to the
 genus Vaccinium. These wild species are widely distributed and
 ecologically important within the Baltic countries but they have not been
 extensively studied using molecular markers. EST-SSR and cpSSR markers
 were used to investigate the population structure and genetic diversity of
 these species to obtain information useful for the development of in situ
 conservation strategies for these species. Wild Vaccinium species
 populations are moderately genetically differentiated, with some
 populations more highly differentiated, but without higher order
 clustering of groups of populations, indicating that there are no
 dispersal barriers for these species within the Baltic countries. Genetic
 diversity of populations growing in protected areas, managed forests and
 intensively utilised public recreational areas is similar.
description: Vaccinium myrtillus samples were collected at 22 locations in
 Latvia, 9 locations in Lithuania and 7 locations in Estonia. Vaccinium
 vitis-idaea samples were collected at 20 locations in Latvia, 9 locations
 in Lithuania and 7 locations in Estonia. Vaccinium uliginosum samples were
 collected at 22 locations in Latvia, 8 locations in Lithuania and 5
 locations in Estonia. For each species, eight accessions from different
 populations were tested with 25 EST-SSR markers (Boches et al. 2005), and
 8 markers were determined to be suitable for bilberry analyses, 10 markers
 for lingonberries, and 8 markers for bog bilberries.
 Six universal angiosperm primer pairs for chloroplast
 microsatellites – ccmp2, ccmp3, ccmp4, ccmp6, ccmp7, ccmp10 (Weising and
 Gardner 1999) were tested. In addition, six chloroplast microsatellite
 markers developed from V. macrocarpon (CP6, CP9, CP12, CP13, CP14 CP16),
 which were also reported to be transferable to other Vaccinium taxa and
 non-Vaccinium Ericaceae species (Schlautman et al. 2016), were tested in
 16 accessions from different populations for each species. 192 bilberry
 accessions from 15 populations (four from Latvia, five from Estonia and
 six from Lithuania), 186 lingonberry accessions from 12 populations (six
 from Latvia, three from Estonia and three from Lithuania) were tested with
 marker CP6. 233 lingonberry accessions from 35 populations (19 from
 Latvia, seven from Estonia and nine from Lithuania) and 237 bog bilberry
 accessions from 21 populations (eight from Latvia, five from Estonia and
 eight from Lithuania) were tested with marker ccmp7.
description: All genotype files are uploaded in GenAlEx format with geographic
 coordinates for each population. V. mytillus and V. vitis-idaea samples
 are scored as diploid codominant markers. V. uliginosum samples include
 tetraploids, and are scored as binary data. Chloroplast
 data files contain allele sizes in base pairs.
DOI: 10.5061/dryad.3bk3j9khk
title: Stability analysis of roadside backfill body at gob-side entry retaining under combined static and dynamic loading

description: The applications of gob-side entry retaining (GER) techniques tends to
 increase over time as it can increase the minerals recovery rate and
 reduce the output of the waste. In the literature, only the performance of
 the roadside backfill body (RBB) at gob-side entry retaining under static
 loading has been investigated. However, failure mechanisms of the RBB
 under dynamic loading with various roof cutting angles have not been
 addressed. This study presented a numerical simulation of the fracture
 propagation and distribution in the roadside backfill body along the
 gob-side under combined static and dynamic loadings using the Trigon model
 built in UDEC (Discrete element methods) software. The influence of the
 roof cutting angles on the behavior of the RBB was also discussed. The
 input parameters were determined by back analysis with the field data.
 Results of the model show that static loading is a bigger contributor to
 the failure of the RBB compared to the dynamic loading. Several clear
 fractures were observed at top left and bottom right of the RBB and the
 fracture was more intensive at top left. In addition, it was found that if
 the roof cutting angle is 70°, the influence of the dynamic loading on the
 RBB is minimum, and the area and severity of the shearing failure in the
 RBB is minimum as well. As a result, it was determined the optimal roof
 cutting angle was 70° and a combined support measure of “roof cutting +
 roof support above RBBs + RBB reinforcement” is proposed. The application
 of roof cutting in gob-side entry retaining (RCGER) techniques in the
 Lingzhida coal mine indicates that deformation of the surrounding rocks
 can be effectively controlled.
description: Distance to 15214 panel Roof to floor RBB rib Coal rib -120 559 68 225 -112 559 68 225 -106 559 67.5 225 -99 555 67.1 221 -90 547 65.8 215 -81 521.8 64 208 -70 519.2 62 203 -60 496.4 57.5 192 -50 468.6 48.4 185 -40 442.5 41 167.6 -30 398.9 32.9 151.2 -22 353.5 25.5 128.6 -16 310.4 19 109 -13 275.5 15.6 95.5 -10 244.8 11.1 81.5 -6 200.4 7.7 71.6 -3 158 3.5 51.2 0 128 1.8 40.1 2 83.8 -- 32.5 6 50 -- 19.1 8 36.6 -- 11.4 12 23 -- 8 19 12 -- 4
DOI: 10.5061/dryad.wm37pvmm0
title: Conservation planning across realms: enhancing connectivity for multi-realm species

description: Connectivity plays a key role in biodiversity conservation as it sustains
 ecological processes important for the maintenance of populations such as
 migrations. Connectivity is especially relevant for species that rely on
 different realms during their life cycle or use different realms daily or
 seasonally (multi-realm species). However, effort to address conservation
 across multiple realms have focused on identifying priority areas for
 conservation in a single realm (mostly marine) accounting for threats
 propagating from other realms or single species needs. Here, we
 demonstrate how to identify priority areas for conservation across three
 different realms (freshwater-terrestrial, estuary and marine) for multiple
 species, including some multi-realm species, that inhabit or move across
 the three realms. We use the whole Tagus River Basin, its estuary and
 nearby marine area as a case study. We compared the allocation of priority
 areas and spatial connectivity achieved under three scenarios:
 no-connectivity, within-realm and cross-realm connectivity scenarios.
 There were some differences in the spatial allocation of priority areas
 across scenarios. The most remarkable difference laid on the connectivity
 achieved under each scenario, which experienced a 3-fold increase when
 considering connectivity across realms, compared to solutions that
 considered only connectivity within each realm independently. This
 improvement in connectivity was especially marked for some of the species
 that occur across the three realms. There were, however, trade-offs
 between this improvement in connectivity: i) an increase in the number of
 planning units selected, especially in the estuary, the realm that links
 the other two; and ii) a decline in connectivity achieved within the
 freshwater—terrestrial and marine realms. Synthesis and applications:
 Addressing connectivity across realms deserves especial attention when
 planning for conservation of multi-realm species to ensure adequacy of
 conservation recommendations to respond to the needs of these species.
 Given the potential trade-offs between enhanced cross-realm connectivity
 and total area needed or internal within-realm connectivity, consideration
 of cross-realm connectivity must be cautiously evaluated and integrated in
 multi-realm conservation plans.
DOI: 10.5061/dryad.8gtht76nd
title: Investigations on Fire-Gilding

description: Fire-gilding is a historic technique for the application of golden layers
 on a number of different base materials, identifiable by the Hg content of
 these layers. Considering recent findings, the previously accepted lower
 limit for Hg content comes into scrutiny, motivating the development of a
 new, destruction-free identification method independent of the absolute Hg
 content. During the course of development, we identified a characteristic
 Hg profile in fire-gildings on Ag substrates and gathered evidence to
 further corroborate the accept lower limit.
description: The dataset was gathered at the BAMline of BESSY II at the
 Helmholtz-Zentrum Berlin and processed with the AXIL code to give the
 intensities of the relevant elements in the spectra. [B. Vekemans et al.
 Analysis of X-ray spectra by iterative least squares (AXIL): New
 developments. X-Ray Spectrometry 23.6 (1994), pp. 278285.]
DOI: 10.5061/dryad.9kd51c5fn
title: Locating large insects using automated VHF radio telemetry with a multi-antennae array

description: 1. We describe an automated radio telemetry system (ARTS) designed for
 estimating the location of 0.50g butterflies that was constructed with
 commercially available materials. Previously described systems were not
 designed to estimate fine-scale locations of large insects within
 approximately 200m$^2$ study areas. 2. The ARTS consists of four receiving
 stations. Each receiving station has four 3-element, directional Yagi
 antennae (separated by 60\si{\degree}) connected to an automated receiver
 that records detected power sequentially from each antenna. To develop and
 evaluate the ARTS performance, four receiving stations were installed in
 the corners of 4-ha and 6.25-ha square fields with varying heights of
 vegetative cover. The location of a 0.22g transmitter was estimated with a
 statistical method implementing both distance- and angle-power
 relationships. Calibrated model parameters were based on power detected
 from transmitters at known locations. Using independently collected data,
 model performance was evaluated based on estimated locations of a
 georeferenced stationary transmitter, a moving transmitter with a known
 georeferenced path, and a transmitter attached to a monarch butterfly
 (\textit{Danaus plexippus}). Estimated locations were calculated as
 frequently as every 5 seconds, which is at least 12 times greater than the
 sampling frequency previously reported for tracking insects. 3. When
 sufficient power data was received, the median estimated locations of a
 transmitter attached to an investigator's hat were $&lt;$16m from
 the true location. The median effective radius of the 95\% confidence
 ellipse was 18.3m for stationary targets and 15.9m for a moving
 transmitter. Greater error in location estimation was expected when the
 transmitter was attached to a monarch butterfly due to interference from
 vegetation and variability in antenna orientation and transmitter height.
 As such, the median distance between the estimated and true locations was
 72m. After applying a correction for the effect of vegetation, median
 location error was reduced by 12m. 4. While our ARTS has likely reached
 the limit of current technology, the system is still a substantial
 methodological advancement for locating butterflies. Our efforts should
 provide a benchmark as technology improves.
DOI: 10.5061/dryad.1ns1rn8s6
title: Behavioral variation in natural contests: integrating plasticity and personality

description: Animals often interact aggressively when competing over limited resources.
 Aggressive decisions can be complex, and may result from multiple sources
 of behavioral variation. The outcome of contests may be explained through
 contest theory and personality, by considering conjointly plasticity and
 individual consistency. This integrative approach also allows
 investigating individual differences in responsiveness to environmental
 changes. Here we observed multiple agonistic interactions occurring among
 eastern chipmunks (Tamias striatus) competing for food resources supplied
 at different distances from their burrows. Using an individual reaction
 norm approach, we found that the probability of winning a contest depended
 on an individual’s own intrinsic characteristics (mass, age, but not sex)
 but was also adjusted to characteristics of its opponents. Winning a
 contest also depended on extrinsic environmental characteristics such as
 distance to the contestants’ burrows, but not the order of arrival at the
 feeding patch. We found consistent individual differences in the
 probability of winning, potentially related to differences in
 aggressiveness and territoriality. We also found that individuals differed
 in their plasticity level in response to changes in different
 characteristics of their social and physical environments. Plasticity,
 personality and individual differences in responsiveness may thus all play
 a role in predicting contest outcome and in the evolution of animal
 contests.
description: For details on the methods see the Material and Methods section
 in the article.
description: For details on the variables included in the dataset presented in
 the Excel file see the README file.
DOI: 10.15468/dl.sx8jjv
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cochliasanthus caracalla",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002642-260126135527185/datasets/export for details.
DOI: 10.5061/dryad.6t1g1jwxf
title: Datasets for phylogenetic analysis on Angelica

description: There are four datasets used for constructing the phylogenetic trees in
 "A systematic study of North American Angelica species (Apiaceae)
 based on nrDNA ITS and cpDNA sequences and fruit morphology" Dataset
 I included the entire ITS region from 231 representatives of Apiaceae
 subfamily Apioideae. Datasets II-IV each included the same 176 accessions
 and comprised all 26 NA species of Angelica (represented by 132
 accessions) and other related species. Dataset II included the entire ITS
 region; Dataset III included the cpDNA ndhF-rpl32, rpl32-trnL, and
 psbM-psbD regions; and Dataset IV included combined ITS and cpDNA data.
description: DNA sequences were
 initially aligned using Muscle (www.ebi.ac.uk/Tools/msa/muscle) and its
 default pairwise and multiple alignment parameters, then rechecked and
 adjusted manually as necessary using MEGA7. Gaps were positioned to
 minimize nucleotide mismatches. Uncorrected pairwise nucleotide
 differences were determined using PAUP* vers. 4.0b10
description: See abstract and methods for usage
DOI: 10.5061/dryad.rxwdbrv6s
title: Petal size in rapeseed: novel QTL and candidate genes detected through genome-wide association study and transcriptome comparison

description: Petal size determines the value of ornamental plants, and thus their
 economic worth. However, the molecular mechanisms controlling petal size
 remain unclear in most non-model species. To identify quantitative trait
 loci and candidate genes regulating petal size in rapeseed (Brassica
 napus), we performed a genome-wide association study (GWAS) using data
 from 588 accessions over three consecutive years. We detected 17
 signiﬁcant single nucleotide polymorphisms (SNPs) associated with petal
 size, with the most significant SNPs located on chromosomes A05 and C06. A
 combination of GWAS and transcriptomic sequencing based on two accessions
 with extreme differences in petal size identified 11 differentially
 expressed genes (DEGs) that may control petal size variation in rapeseed.
 In particular, BnaA05.RAP2.2 homologous to RAP2.2 in rapeseed may be a
 critical gene negatively influencing petal size through the ethylene
 signaling pathway. In addition, a comparison of petal epidermal cells
 indicated that petal size differences between the two extreme accessions
 were determined mainly by cell number differences. Finally, we propose a
 preliminary model for the control of petal size in rapeseed. Our results
 provide insights into the genetic mechanisms regulating petal size, and
 also lay the foundation for a better understanding of petal development in
 plants.
DOI: 10.5061/dryad.fn2z34tsc
title: Fluid-preserved fishes are one solution for assessing historical change in fish trophic level

description: There are few resources available for assessing historical change in fish
 trophic dynamics, but specimens held in natural history collections could
 serve as this resource. In contemporary trophic ecology studies, trophic
 and source information can be obtained from compound-specific stable
 nitrogen isotope analysis (CSIA-AA-N). Can this method yield reliable
 trophic information from chemically-altered fish specimens held in natural
 history collections? We tested whether CSIA-AA-N can be used on
 fluid-preserved specimens by experimentally subjecting specimens to the
 most common natural history collections preservation protocol, and
 determining the effects of preservation on trophic level estimates and
 whether these effects stabilize over time. We subjected whole Sebastes
 ruberrimus and Clupea pallasii to formalin fixation and 70% ethanol
 preservation. We extracted tissue samples from each fish pre-fixation,
 after each chemical change, and then in doubling time for 32–64 days once
 placed in the final preservative. All samples were subjected to CSIA-AA-N,
 and their glutamic acid and phenylalanine profiles and associated trophic
 position were examined for differences over time by species. Glutamic acid
 and phenylalanine values were inconsistent in direction and magnitude,
 particularly during formalin fixation, but stabilized similarly (in 70%
 ethanol) among conspecifics. In some cases, the amino acid values of our
 final samples were significantly different than our initial
 pre-preservation samples. Nonetheless, significant differences in glutamic
 acid, phenylalanine, and estimated trophic position were not detected
 among samples that were in 70% ethanol for &gt;24h. Our results
 suggest that the relative trophic position of fluid-preserved specimens
 can be estimated using CSIA-AA-N, and CSIA-AA-N estimates for
 fluid-preserved specimens should only be reported as relative differences.
 Timelines of trophic position change can be developed by comparing
 specimens collected at different points in time, revealing trophic
 information of the past and cryptic ecosystem responses.
description: Please see main publication and appendices for detailed
 methods.
DOI: 10.5061/dryad.p8cz8w9nw
title: Data from: Constrained optimization of landscape indices in conservation planning to support ecological restoration in New Caledonia

description: 1. Curbing habitat loss, reducing fragmentation, and restoring
 connectivity are frequent concerns of conservation planning. In this
 respect, the incorporation of spatial constraints, fragmentation, and
 connectivity indices into optimization procedures is an important
 challenge for improving decision support. 2. Here we present a novel
 optimization approach developed to accurately represent a broad range of
 conservation planning questions with spatial constraints and landscape
 indices. Relying on constraint programming, a technique from artificial
 intelligence based on automatic reasoning, this approach provides both
 constraint satisfaction and optimality guarantees. 3. We applied this
 approach in a real case study to support managers of the ``Côte Oubliée --
 `Woen Vùù -- Pwa Pereeù'' provincial park project, in the
 biodiversity hotspot of New Caledonia. Under budget, accessibility, and
 equitable allocation constraints, we identified restorable areas optimal
 for reducing forest fragmentation and improving inter-patch structural
 connectivity, respectively measured with the effective mesh size and the
 integral index of connectivity. 4. Synthesis and applications. Our work
 contributes to more effective and policy-relevant conservation planning by
 providing a spatially-explicit and problem-focused optimization approach.
 By allowing an exact representation of spatial constraints and landscape
 indices, it can address new questions and ensure whether the solutions
 will be socio-economically feasible, through optimality and satisfiability
 guarantees. Our approach is generic and flexible, thus applicable to a
 wide range of conservation planning problems such as ecological
 restoration planning, reserve or corridor design.
DOI: 10.6076/d1f593
title: Dimensional analysis of spring-wing systems reveals performance metrics for resonant flapping-wing flight

description: Flapping-wing insects, birds, and robots are thought to offset the high
 power cost of oscillatory wing motion by using elastic elements for energy
 storage and return. Insects possess highly resilient elastic regions in
 their flight anatomy that may enable high dynamic efficiency. However,
 recent experiments highlight losses due to damping in the insect thorax
 that could reduce the benefit of those elastic elements. We performed
 experiments on, and simulations of a dynamically-scaled robophysical
 flapping model with an elastic element and biologically-relevant
 structural damping to elucidate the roles of body mechanics, aerodynamics,
 and actuation in spring-wing energetics. We measured oscillatory flapping
 wing dynamics and energetics subject to a range of actuation parameters,
 system inertia, and spring elasticity. To generalize these results, we
 derive the non-dimensional spring-wing equation of motion and present
 variables that describe the resonance properties of flapping systems: the
 Weis-Fogh number, a measure of the relative influence of inertia and
 aerodynamics, and the reduced stiffness. We show that internal damping
 scales with Weis-Fogh number, revealing that dynamic efficiency
 monotonically decreases with increasing Weis-Fogh number. Based on these
 results, we introduce a general framework for understanding the roles of
 internal damping, aerodynamic and inertial forces, and elastic structures
 within all spring-wing systems.
description: This dataset consists of two elements: 1) A
 set of 9 experimental data folders from combined stiffness and inertia
 tests with dynamically scaled flapping robotic wing. 2)
 Simulation code to reproduce dynamic efficiency plots for series
 spring-wing systems.  The data was processed in matlab,
 and simulation results were generated in matlab with all code provided to
 generate the datasets and plot.
description: The data set includes a readme file process the data which we
 reproduce below. --------------------------
 In this directory we provide code to reproduce the experimental
 and simulation results for the manuscript:  "Dimensional analysis of
 spring-wing systems reveals performance metrics for resonant flapping-wing
 flight". James Lynch, Jeff Gau, Simon Sponberg, Nick
 Gravish Contact: <br> James Lynch
 (jelynch@eng.ucsd.edu)<br> Nick Gravish
 (ngravish@eng.ucsd.edu) Folder
 subdirectories:<br> Functions -- This directory contains the
 functions used for analysis. Please add it to the Matlab path
 Experiment_Data_analysis -- This directory contains the
 experimental data organized by spring stiffness K1 - K3, and inertia I1 -
 I3 totaling 9 datasets. The script Experiment_data_analysis.m will perform
 the experimental analysis. Simulation_functions --
 Contains the functions to perform simulations of spring-wing systems.
 Figure 10 simulation data is generated from series_parallel_comparison.m
 and then the plots are generated from sim_analysis_hysteretic.m