cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m8q30
title: Data from: Isolation-by-distance in landscapes: considerations for landscape genetics

description: In landscape genetics, isolation-by-distance (IBD) is regarded as a
 baseline pattern that is obtained without additional effects of landscape
 elements on gene flow. However, the configuration of suitable habitat
 patches determines deme topology, which in turn should affect rates of
 gene flow. IBD patterns can be characterized either by monotonically
 increasing pairwise genetic differentiation (for example, FST) with
 increasing interdeme geographic distance (case-I pattern) or by
 monotonically increasing pairwise genetic differentiation up to a certain
 geographical distance beyond which no correlation is detectable anymore
 (case-IV pattern). We investigated if landscape configuration influenced
 the rate at which a case-IV pattern changed to a case-I pattern. We also
 determined at what interdeme distance the highest correlation was measured
 between genetic differentiation and geographic distance and whether this
 distance corresponded to the maximum migration distance. We set up a
 population genetic simulation study and assessed the development of IBD
 patterns for several habitat configurations and maximum migration
 distances. We show that the rate and likelihood of the transition of
 case-IV to case-I FST–distance relationships was strongly influenced by
 habitat configuration and maximum migration distance. We also found that
 the maximum correlation between genetic differentiation and geographic
 distance was not related to the maximum migration distance and was
 measured across all deme pairs in a case-I pattern and, for a case-IV
 pattern, at the distance where the FST–distance curve flattens out. We
 argue that in landscape genetics, separate analyses should be performed to
 either assess IBD or the landscape effects on gene flow.
description: Concordia; code for
 simulating gene flow between demesThe
 "Concordia140519.zip" file contains the Matlab code. The main
 script is "Concordia.m" and all settings for a simulation run
 can be specified in this script. A description of the settings can be
 found in the user guide (+Text\+UserGuide\UserGuide.pdf). The user guide
 also contains more details about the functioning of Concorida as well as
 some comparisons of simulation results with those expected from analytical
 solutions.Concordia140519.zip
DOI: 10.5067/tsis/sim/data320
title: TSIS SIM Level 3 Solar Spectral Irradiance 24-Hour Means V10
DOI: 10.5067/tsis/sim/data322
title: TSIS SIM Level 3 Solar Spectral Irradiance 24-Hour Means V11
DOI: 10.5061/dryad.3523q
title: Data from: Meteorological conditions influence short-term survival and dispersal in a reinforced bird population.

description: A high immediate mortality rate of released animals is an important cause
 of translocation failure (“release cost”). Post-release dispersal (i.e.
 the movements from the release site to the first breeding site) has
 recently been identified as another source of local translocation failure.
 In spite of their potential effects on conservation program outcomes,
 little is known about the quantitative effects of these two sources of
 translocation failure and their interactions with environmental factors
 and management designs. Based on long-term monitoring data of captive-bred
 North African houbara bustards Chlamydotis undulata undulata (hereafter,
 houbara) over large spatial scales, we investigated the relative effects
 of release (e.g. release group size, period of release), individual (e.g.
 sex and body condition) and meteorological (e.g. temperature and rainfall)
 conditions on post-release survival (N = 957 individuals) and dispersal (N
 = 436 individuals). We found that (i) rainfall and ambient air temperature
 had, respectively, a negative and a positive effect on houbara
 post-release dispersal distance, (ii) in interaction with the release
 period, harsh meteorological conditions had negative impact on the
 survival of houbara, (iii) density-dependent processes influenced the
 pattern of departure from the release site and (iv) post-release dispersal
 distance was male-biased, as natal dispersal of wild birds (although the
 dispersal patterns and movements may be influenced by different processes
 in captive-bred and in wild birds). Synthesis and applications. Our
 results demonstrate that post-release dispersal and mortality costs in
 translocated species may be mediated by meteorological factors, which in
 turn can be buffered by the release method. As the consequences of
 translocation programs on population dynamics depend primarily upon
 release costs and colonisation process, we suggest that their potential
 interactions with meteorological conditions must be carefully addressed in
 future programs (i) through monitoring of short-term post-release
 mortality to understand its link with environmental conditions; (ii) by
 carefully choosing the season of release to minimize exposition of
 inexperienced individuals to harsh conditions and (iii) generalising the
 use of long-term weather forecast to adapt release effort and staggering
 releases over several years to buffer meteorological effects.
description: Dispersal and survival
 data filesThis zip file contains
 all the data necessary to perform the analyses from the paper. The column
 heads are easily identifiable and follow the same terminology than the one
 used in the paper.datafiles_Hardouinetal.zip
DOI: 10.5067/tsis/sim/data324
title: TSIS SIM Level 3 Solar Spectral Irradiance 24-Hour Means V12
DOI: 10.5067/tsis/sim/data326
title: TSIS SIM Level 3 Solar Spectral Irradiance 24-Hour Means V13
DOI: 10.5061/dryad.n56t9
title: Data from: ITS1: a DNA barcode better than ITS2 in eukaryotes?

description: A DNA barcode is a short piece of DNA sequence used for species
 determination and discovery. The internal transcribed spacer (ITS/ITS2)
 region has been proposed as the standard DNA barcode for fungi and seed
 plants, and has been widely used in DNA barcoding analyses for other
 biological groups, e.g. algae, protists, and animals. The ITS region
 consists of both ITS1 and ITS2 regions. Here, a large scale meta-analysis
 was carried out to compare ITS1 and ITS2 from three aspects: PCR
 amplification, DNA sequencing and species discrimination, in terms of the
 presence of DNA barcoding gaps, species discrimination efficiency,
 sequence length distribution, GC content distribution and primer
 universality. In total, 85,345 sequence pairs in ten major groups of
 eukaryotes, including ascomycetes, basidiomycetes, liverworts, mosses,
 ferns, gymnosperms, monocotyledons, eudicotyledons, insects, and fishes,
 covering 611 families, 3,694 genera, and 19,060 species, were analyzed.
 Using similarity-based methods, we calculated species discrimination
 efficiencies for ITS1 and ITS2 in all major groups, families, and genera.
 Using Fisher's exact test, we found that ITS1 has significantly
 higher efficiencies than ITS2 in 17 of the 47 families and 20 of the 49
 genera, which are sample-rich. By in silico PCR amplification evaluation,
 primer universality of the extensively applied ITS1 primers was found
 superior to that of ITS2 primers. Additionally, shorter length of
 amplification product and lower GC content were discovered to be two other
 advantages of ITS1 for sequencing. In summary, ITS1 represents a better
 DNA barcode than ITS2 for eukaryotic species.
description: Code for DNA barcoding
 GapsA
 custom Python script ‘getSixValue.py’ for calculating intra- and
 interspecific Kimura 2-parameter (K2P) distances of the congeneric species
 of the ITS1 and ITS2 regions in different taxonomic
 groupsCodes for Species
 Identification EfficienciesA custom Perl package
 called PESDET (version 0.1) for calculating species identification success
 rates, using the BLAST and BLAST+P distance (BLAST+PD)
 methodsDataset
 IDataset I used for the
 analyses of DNA barcoding gaps, species identification efficiency,
 sequence length and GC contentDataset_I.xlsxDataset IIDataset II used for the analysis of primer universalityDataset_II.xlsx
DOI: 10.5067/tsis/sim/data328
title: TSIS SIM Level 3 Solar Spectral Irradiance 24-Hour Means V14
DOI: 10.5061/dryad.kt24p
title: Data from: Systematic and historical biogeography of the Bryconidae (Ostariophysi: Characiformes) suggesting a new rearrangement of its genera and an old origin of Mesoamerican ichthyofauna

description: Recent molecular hypotheses suggest that some traditional suprageneric
 taxa of Characiformes require revision, as they may not constitute
 monophyletic groups. This is the case for the Bryconidae. Various studies
 have proposed that this family (considered a subfamily by some authors)
 may be composed of different genera. However, until now, no phylogenetic
 study of all putative genera has been conducted. In the present study, we
 analyzed 27 species (46 specimens) of all currently recognized genera of
 the Bryconidae (ingroup) and 208 species representing all other families
 and most genera of the Characiformes (outgroup). Five genes were
 sequenced: 16SrRNA, Cytochrome b, recombination activating gene 1 and 2
 and myosin heavy chain 6 cardiac muscle. The final matrix contained 4699
 bp and was analyzed by maximum likelihood, maximum parsimony and Bayesian
 analyses. The results show that the Bryconidae, composed of Brycon,
 Chilobrycon, Henochilus and Salminus, is monophyletic and is the sister
 group of Gasteropelecidae + Triportheidae. However, the genus Brycon is
 polyphyletic. Fossil studies suggest that the family originated
 approximately 33 million years ago (Ma) and that one of the two main
 lineages persisted only in trans-Andean rivers, including Central American
 rivers, suggesting a much older origin of Mesoamerican ichthyofauna than
 previously accepted. Bryconidae is composed by five main clades, including
 the genera Brycon, Chilobrycon, Henochilus and Salminus, but a taxonomic
 review of these groups is needed. Our results points to a possible ancient
 invasion of Central America, dating about 17.4+/-8 Ma (late Oligocene/late
 Miocene), to explain the occurrence of Brycon in Central America.
description: BryconidaeNexusSequences of all Characiformes analyzedBryconidaePaupContain data of Bryconidae, Gasteropelecidae and Triportheidae
DOI: 10.5061/dryad.4m94c
title: Data from: Are statin trials in diabetes representative of real-world diabetes care: a population-based study on statin initiators in Finland

description: Objective: To assess the representativeness of the Heart Protection Study
 (HPS) and the Collaborative Atorvastatin Diabetes Study (CARDS) for
 incident statin users. Design: A population based analysis with linked
 register data. Setting: Finland. Population: 56 963 diabetic patients
 initiating statin use in 2005 to 2008. Main outcome measures: We
 determined the proportions of real-world patients who fulfilled the
 eligibility criteria for HPS and CARDS trials and assessed the
 cardiovascular disease (CVD) event rates, assumed to reflect the
 background CVD risk, for those eligible and ineligible. We used
 descriptive statistics to identify the patient characteristics,
 lipid-lowering interventions, and adherence to statin therapy. Results: Of
 the real-world patients 57% (N=32 582) fulfilled the eligibility criteria
 for HPS(DM) and 49% (N=20 499) of those without CVD for CARDS. The
 patients ineligible for HPS(DM) had a higher cumulative risk for CVD
 events than those eligible, whereas regarding CARDS the cumulative risks
 were of similar magnitude. The overall CVD event rates seemed comparable
 to those in the reviewed trials. Both trials were under-representative for
 women, users of antihypertensive agents and metformin. 27% and 29% of real
 world patients had an initial statin dose corresponding to &lt;20mg of
 simvastatin. The proportions of patients deemed adherent were 57% in the
 real world and 85% in both trials. Conclusions: Only half of the
 real-world patients would have qualified for the HPS(DM) and CARDS,
 limiting their representativeness for clinical practice. Women and users
 of antihypertensive agents and of metformin were under-represented in both
 trials. These deviations reflect the changes in diabetes treatment over
 the years and are not expected to modify the average treatment effects of
 statins on CVD. Prescribing of lower statin doses in clinical practice
 than used in the trials and lower adherence may, however, attenuate the
 benefits in the real-world.
description: Cumulative Hazard data
 (HPS DM)Cumulative hazard data
 from the date of the first statin purchase until the date of major
 cardiovascular event or censoring and stratified according to eligibility
 for the HPS(DM) trial.Graph2a_nelson_data_Ruokoniemi.xlsxCumulative Hazard data (CARDS)Cumulative hazard data from the date of the first statin purchase until the date of major cardiovascular event or censoring and stratified according to eligibility for the CARDS trial.Graph2b_nelson_data_Ruokoniemi.xlsx
DOI: 10.5061/dryad.s71t4
title: Data from: Analysis of transposable elements in the genome of Asparagus officinalis from high coverage sequence data

description: Asparagus officinalis is an economically and nutritionally important
 vegetable crop that is widely cultivated and is used as a model dioecious
 species to study plant sex determination and sex chromosome evolution. To
 improve our understanding of its genome composition, especially with
 respect to transposable elements (TEs), which make up the majority of the
 genome, we performed Illumina HiSeq2000 sequencing of both male and female
 asparagus genomes followed by bioinformatics analysis. We generated 17 Gb
 of sequence (12×coverage) and assembled them into 163,406 scaffolds with a
 total cumulated length of 400 Mbp, which represent about 30% of asparagus
 genome. Overall, TEs masked about 53% of the A. officinalis assembly.
 Majority of the identified TEs belonged to LTR retrotransposons, which
 constitute about 28% of genomic DNA, with Ty1/copia elements being more
 diverse and accumulated to higher copy numbers than Ty3/gypsy. Compared
 with LTR retrotransposons, non-LTR retrotransposons and DNA transposons
 were relatively rare. In addition, comparison of the abundance of the TE
 groups between male and female genomes showed that the overall TE
 composition was highly similar, with only slight differences in the
 abundance of several TE groups, which is consistent with the relatively
 recent origin of asparagus sex chromosomes. This study greatly improves
 our knowledge of the repetitive sequence construction of asparagus, which
 facilitates the identification of TEs responsible for the early evolution
 of plant sex chromosomes and is helpful for further studies on this
 dioecious plant.
description: scafSeq_TE_annotation.fastaEach sequence in the file represents a saffold produced via de novo assembly methods that RepeatMasker identified as a tranposable element. The header for each sequence includes a saffold number (e.g., scaffold20) followed by the annotation for that particular element (e.g., Retrotransposons/Ty3-gypsy ).
DOI: 10.5061/dryad.9p670
title: Data from: Demographic responses of rare forest plants to multiple stressors: the role of deer, invasive species and nutrients

description: Forest ecosystems in eastern North America face multiple threats or
 stressors including plant and animal invasions and increased white-tailed
 deer (Odocoileus virginianus) herbivory. While each stressor may have
 independent detrimental effects on native biota, stressors often co-occur
 and are likely to have interactive effects. Despite recognition that
 concurrent processes drive plant demographic responses, few studies
 evaluate independent and combined effect of stressors. Using a network of
 12 sites that varied in non-native plant cover and introduced earthworm
 density and biomass we experimentally assessed effects of deer exclusion
 (30 x 30 m paired plots), slug exclusion and nutrient addition on
 survival, growth and fecundity of four rare forest understorey plant
 species (Aristolochia serpentaria L., Agrimonia rostellata Wallr., Carex
 retroflexa Muhl. ex Willd, and Trillium erectum L). We found that single
 and combined effects of stressors were species-specific and varied
 according to plant stage and demographic parameter. Interactions were
 prevalent among all studied stressors and, for most cases, did not follow
 predicted responses. We found detrimental deer herbivory effects on
 reproductive A. rostellata and non-consumptive effects on A. serpentaria
 and T. erectum. Negative deer effects follow underlying predictions, and
 override effects of other stressors, even when other concurrent processes
 are at play. Contrary to expectations, we did not find negative effects of
 non-native plants. Earthworms had positive effects on A. rostellata and C.
 retroflexa (especially when deer were excluded), but negative effects on
 T. erectum. Slug effects were dependent on other stressors, especially on
 interactions with non-native plants and earthworms. Nutrient addition had
 a negative effect on survival of A. serpentaria and T. erectum, but
 positive effects on C. retroflexa and T. erectum growth. Synthesis: We
 found prevalent but unpredictable interactions among all study factors and
 plant species. Negative direct and indirect deer effects overrode impacts
 of all other stressors we investigated. A multi-factor approach is
 critical to predict plant responses to concurrent environmental forces.
 Assessment of combined effects should form an essential component of
 subsequent research on plant demography and management of declining
 species.
description: Transplant experiment
 data 2011-2013Transplant experiment
 data 2011-2013
DOI: 10.24435/materialscloud:ym-my
title: Enhanced Climbing Image Nudged Elastic Band method with Hessian Eigenmode Alignment

description: Accurate determination of transition states is central to an understanding of reaction kinetics. Double-endpoint methods where both initial and final states are specified, such as the climbing image nudged elastic band (CI-NEB), identify the minimum energy path between the two and thereby the saddle point on the energy surface that is relevant for the given transition, thus providing an estimate of the transition state within the harmonic approximation of transition state theory. Such calculations can, however, incur high computational costs and may suffer stagnation on exceptionally flat or rough energy surfaces. Conversely, methods that only require specification of an initial set of atomic coordinates, such as the minimum mode following (MMF) method, offer efficiency but can converge on saddle points that are not relevant for transition of interest. Here, we present an adaptive hybrid algorithm that dynamically switches between the CI-NEB with the MMF method ("off-path" CI-NEB) so as to get faster convergence to the relevant saddle point. The method is benchmarked for the Baker-Chan (BC) saddle point test set using the PET-MAD machine-learned potential as well as 59 transitions of a heptamer island on Pt(111) from the OptBench benchmark set. A Bayesian analysis of the performance shows a median change in energy and force calculations of -46% [95% CrI: -55%, -37%] relative to CI-NEB for the BC set, while a 28% reduction is found for the transitions of the heptamer island. A fixed cutoff static switch mechanism for the BC leads to a median increase of 31% calculations compared to the OCI-NEB algorithm.  These results establish the OCI-NEB method as a highly effective tool for high-throughput automated chemical discovery of atomic rearrangements.

 

This record provides the reproduction data, transition state search logs, and statistical models for the Off-path Climbing Image Nudged Elastic Band (OCI-NEB) algorithm. It includes the complete outputs to accompany the Github repository of scripts which support the manuscript.
DOI: 10.24435/materialscloud:6q-ev
title: Enhanced Climbing Image Nudged Elastic Band method with Hessian Eigenmode Alignment

description: Accurate determination of transition states is central to an understanding of reaction kinetics. Double-endpoint methods where both initial and final states are specified, such as the climbing image nudged elastic band (CI-NEB), identify the minimum energy path between the two and thereby the saddle point on the energy surface that is relevant for the given transition, thus providing an estimate of the transition state within the harmonic approximation of transition state theory. Such calculations can, however, incur high computational costs and may suffer stagnation on exceptionally flat or rough energy surfaces. Conversely, methods that only require specification of an initial set of atomic coordinates, such as the minimum mode following (MMF) method, offer efficiency but can converge on saddle points that are not relevant for transition of interest. Here, we present an adaptive hybrid algorithm that dynamically switches between the CI-NEB with the MMF method ("off-path" CI-NEB) so as to get faster convergence to the relevant saddle point. The method is benchmarked for the Baker-Chan (BC) saddle point test set using the PET-MAD machine-learned potential as well as 59 transitions of a heptamer island on Pt(111) from the OptBench benchmark set. A Bayesian analysis of the performance shows a median change in energy and force calculations of -46% [95% CrI: -55%, -37%] relative to CI-NEB for the BC set, while a 28% reduction is found for the transitions of the heptamer island. A fixed cutoff static switch mechanism for the BC leads to a median increase of 31% calculations compared to the OCI-NEB algorithm.  These results establish the OCI-NEB method as a highly effective tool for high-throughput automated chemical discovery of atomic rearrangements.

 

This record provides the reproduction data, transition state search logs, and statistical models for the Off-path Climbing Image Nudged Elastic Band (OCI-NEB) algorithm. It includes the complete outputs to accompany the Github repository of scripts which support the manuscript.
DOI: 10.5061/dryad.18v85
title: Data from: Introgression study reveals two quantitative trait loci involved in interspecific variation in memory retention among Nasonia wasp species

description: Genes involved in the process of memory formation have been studied
 intensively in model organisms; however, little is known about the
 mechanisms that are responsible for natural variation in memory dynamics.
 There is substantial variation in memory retention among closely related
 species in the parasitic wasp genus Nasonia. After a single olfactory
 conditioning trial, N. vitripennis consolidates long-term memory that
 lasts at least 6 days. Memory of the closely related species N. giraulti
 is present at 24 h but is lost within 2 days after a single trial. The
 genetic basis of this interspecific difference in memory retention was
 studied in a backcrossing experiment in which the phenotype of N. giraulti
 was selected for in the background of N. vitripennis for up to five
 generations. A genotyping microarray revealed five regions that were
 retained in wasps with decreased memory retention. Independent
 introgressions of individual candidate regions were created using linked
 molecular markers and tested for memory retention. One region on
 chromosome 1 (spanning ~5.8 cM) and another on chromosome 5 (spanning
 ~25.6 cM) resulted in decreased memory after 72 h, without affecting
 24-h-memory retention. This phenotype was observed in both heterozygous
 and homozygous individuals. Transcription factor CCAAT/enhancer-binding
 protein and a dopamine receptor, both with a known function in memory
 formation, are within these genomic regions and are candidates for the
 regulation of memory retention. Concluding, this study demonstrates a
 powerful approach to study variation in memory retention and provides a
 basis for future research on its genetic basis.
description: Hoedjes et al
 2014_Heredity_MemoryIntrogressionData from all memory
 retention test as described in the manuscript and results from the
 genotyping microarray.Hoedjes_MemoryIntrogression_alldata.xlsx