cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4236t
title: Data from: The impact of even-aged and uneven-aged forest management on regional biodiversity of multiple taxa in European beech forests

description: For managed temperate forests, conservationists and policymakers favour
 fine-grained uneven-aged management over more traditional coarse-grained
 even-aged management, based on the assumption that within-stand habitat
 heterogeneity enhances biodiversity. There is, however, little empirical
 evidence to support this assumption. We investigated for the first time
 how differently grained forest management systems affect the biodiversity
 of multiple above- and below-ground taxa across spatial scales. We sampled
 15 taxa of animals, plants, fungi and bacteria within the largest
 contiguous beech forest landscape of Germany and classified them into
 functional groups. Selected forest stands have been managed for more than
 a century at different spatial grains. The even-aged (coarse-grained
 management) and uneven-aged (fine-grained) forests are comparable in
 spatial arrangement, climate and soil conditions. These were compared to
 forests of a nearby national park that have been unmanaged for at least 20
 years. We used diversity accumulation curves to compare γ-diversity for
 Hill-numbers 0D (species richness), 1D (Shannon diversity) and 2D (Simpson
 diversity) between the management systems. Beta diversity was quantified
 as multiple-site dissimilarity. Gamma diversity was higher in even-aged
 than in uneven-aged forests for at least one of the three Hill-numbers for
 six taxa (up to 77%), while eight showed no difference. Only bacteria
 showed the opposite pattern. Higher γ-diversity in even-aged forests was
 also found for forest specialists and saproxylic beetles. Between-stand
 β-diversity was higher in even-aged than in uneven-aged forests for one
 third (all species) and half (forest specialists) of all taxa, driven by
 environmental heterogeneity between age-classes, while α-diversity showed
 no directional response across taxa or for forest specialists. Synthesis
 and applications. Comparing even-aged and uneven-aged forest management in
 Central European beech forests, our results show that a mosaic of
 different age-classes is more important for regional biodiversity than
 high within-stand heterogeneity. We suggest reconsidering the current
 trend of replacing even-aged management in temperate forests. Instead, the
 variability of stages and stand structures should be increased to promote
 landscape scale biodiversity.
description: Species in even-aged,
 uneven-aged and unmanaged beech forestsThe data file comprises
 abundance, cover or presence of species from 15 taxonomic groups for
 even-aged, uneven-aged and unmanaged beech forest plots of the Hainich-Dün
 Biodiversity Exploratory (http://www.biodiversity-exploratories.de). The
 work has been funded by the DFG Priority Program 1374
 "Infrastructure-Biodiversity-Exploratories".Site_Species_Abu_Dryad.xlsx
DOI: 10.5061/dryad.t5pv8
title: Data from: The lncRNA H19 mediates breast cancer cell plasticity during EMT and MET plasticity by differentially sponging miR-200b/c and let-7b

description: Metastasis is a multistep process by which tumor cells disseminate from
 their primary site and form secondary tumors at a distant site. The
 pathophysiological course of metastasis is mediated by the dynamic
 plasticity of cancer cells, which enables them to shift between epithelial
 and mesenchymal phenotypes through a transcriptionally regulated program
 termed epithelial-to-mesenchymal transition (EMT) and its reverse process,
 mesenchymal-to-epithelial transition (MET). Using a mouse model of
 spontaneous metastatic breast cancer, we investigated the molecular
 mediators of metastatic competence within a heterogeneous primary tumor
 and how these cells then manipulated their epithelial-mesenchymal
 plasticity during the metastatic process. We isolated cells from the
 primary mammary tumor, the circulation, and metastatic lesions in the lung
 in TA2 mice and found that the long noncoding RNA (lncRNA) H19 mediated
 EMT and MET by differentially acting as a sponge for the microRNAs
 miR-200b/c and let-7b. We found that this ability enabled H19 to modulate
 the expression of the microRNA targets Git2 and Cyth3, respectively, which
 encode regulators of the RAS superfamily member adenosine 5′-diphosphate
 (ADP) ribosylation factor (ARF), a guanosine triphosphatase (GTPase) that
 promotes cell migration associated with EMT and disseminating tumor cells.
 Decreasing the abundance of H19 or manipulating that of members in its
 axis prevented metastasis from grafts in syngeneic mice. Abundance of H19,
 GIT2, and CYTH3 in patient samples further suggests that H19 might be
 exploited as a biomarker for metastatic cells within breast tumors and
 perhaps as a therapeutic target to prevent metastasis.
description: submit Dryad
 data
DOI: 10.5061/dryad.b7040
title: Data from: Effectiveness of government anti-smoking policy on nonsmoking youth in Korea: a four-year trend analysis of national survey data

description: Objectives: Since the Health Promotion Act was introduced in Korea in
 1995, anti-smoking policies and regulations have undergone numerous
 revisions, and non-smoking areas have gradually been expanded. The purpose
 of this study was to examine the impact of a partial legislative ban on
 adolescent exposure to secondhand smoke using objective urinary cotinine
 levels in a nationwide representative sample. Methods: Urine cotinine
 levels were measured in the Korea National Health and Nutrition
 Examination Survey from 2008 to 2011. This study was a trend analysis of
 4 years of national survey data from 2197 Korean youth aged 10–18 years.
 Among non-smokers, the 75th percentile urinary cotinine level was
 estimated. We also considered the number of household smokers. Results:
 The 75th percentile urine cotinine level of non-smokers showed a
 significant decreasing trend from 2008 to 2011, from 15.47 to 5.37 ng/mL,
 respectively. Urine cotinine did not decline significantly in non-smokers
 living with smokers during the study period. The results did not show a
 statistically significant reduction in smoking rate in adolescents from
 2008 to 2011, although there was a trend towards a decrease (p=0.081).
 Conclusions: Based on urine cotinine levels, government-initiated
 anti-smoking policies have only been effective among highly exposed
 non-smoking adolescents during the study period. Further study needs to
 evaluate whether or not the legislative ban affects domestic smoking
 exposure.
description: KNHANES_iv&v170519
DOI: 10.5061/dryad.bk203
title: Data from: Generalized bootstrap supports for phylogenetic analyses of protein sequences incorporating alignment uncertainty

description: Phylogenetic reconstructions are essential in genomics data analyses and
 depend on accurate multiple sequence alignment (MSA) models. We show that
 all currently available large-scale progressive multiple alignment methods
 are numerically unstable when dealing with amino-acid sequences. They
 produce significantly different output when changing sequence input order.
 We used the HOMFAM protein sequences dataset to show that on datasets
 larger than 100 sequences, this instability affects on average 21.5% of
 the aligned residues. The resulting Maximum Likelihood trees estimated
 from these multiple sequence alignments are equally unstable with over 38%
 of the branches being sensitive to the sequence input order. We
 established that about two-thirds of this uncertainty stems from the
 unordered nature of children nodes within the guide trees used to estimate
 MSAs. To quantify this uncertainty we developed unistrap, a novel approach
 that estimates the combined effect of alignment uncertainty and site
 sampling on phylogenetic tree branch supports. Compared to the regular
 bootstrap procedure, unistrap provides branch support estimates that take
 into account a larger fraction of the parameters impacting tree
 instability when processing datasets containing a large number of
 sequences.
description: SUP_FIGS_TABLES_v2This folder includes the supplementary material, along with the figures and the tables.
DOI: 10.5061/dryad.63474
title: Data from: Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau

description: Permafrost represents an important understudied genetic resource. Soil
 microorganisms play important roles in regulating biogeochemical cycles
 and maintaining ecosystem function. However, our knowledge of patterns and
 drivers of permafrost microbial communities is limited over broad
 geographic scales. Using high-throughput Illumina sequencing, this study
 compared soil bacterial, archaeal and fungal communities between the
 active and permafrost layers on the Tibetan Plateau. Our results indicated
 that microbial alpha diversity was significantly higher in the active
 layer than in the permafrost layer with the exception of fungal
 Shannon-Wiener index and Simpson’s diversity index, and microbial
 community structures were significantly different between the two layers.
 Our results also revealed that environmental factors such as soil
 fertility (soil organic carbon and nitrogen contents) were the primary
 drivers of the beta diversity of bacterial, archaeal and fungal
 communities in the active layer. In contrast, environmental variables such
 as the mean annual precipitation and total phosphorus played dominant
 roles in driving the microbial beta diversity in the permafrost layer.
 Spatial distance was important for predicting the bacterial and archaeal
 beta diversity in both the active and permafrost layers, but not for
 fungal communities. Collectively, these results demonstrated different
 driving factors of microbial beta diversity between the active layer and
 permafrost layer, implying that the drivers of the microbial beta
 diversity observed in the active layer cannot be used to predict the
 biogeographic patterns of the microbial beta diversity in the permafrost
 layer.
description: 16S-[UPARSE_otu_table.txt]the OTU table of prokaryotes generated by UPARSEITS-[UPARSE_otu_table.txt]the OTU table of fungi generated by PUARSE
DOI: 10.5061/dryad.24tm0
title: Data from: Subtle but ubiquitous selection on body size in a natural population of collared flycatchers over 33 years

description: Understanding the magnitude and long-term patterns of selection in natural
 populations is of importance, for example, when analyzing the evolutionary
 impact of climate change. We estimated univariate and multivariate
 directional, quadratic and correlational selection on four morphological
 traits (adult wing, tarsus and tail length, body mass) over a time period
 of 33 years (≈ 19 000 observations) in a nest-box breeding population of
 collared flycatchers (Ficedula albicollis). In general, selection was weak
 in both males and females over the years regardless of fitness measure
 (fledged young, recruits and survival) with only few cases with
 statistically significant selection. When data were analyzed in a
 multivariate context and as time series a number of patterns emerged;
 there was a consistent, but weak, selection for longer wings in both
 sexes, selection was stronger on females when the number of fledged young
 was used as a fitness measure, there were no indications of sexually
 antagonistic selection and we found a negative correlation between
 selection on tarsus and wing length in both sexes but using different
 fitness measures. Uni- and multivariate selection gradients were
 correlated only for wing length and mass. Multivariate selection gradient
 vectors were longer than corresponding vector of univariate gradients and
 had more constrained direction. Correlational selection had little
 importance. Overall, the fitness surface was more or less flat with few
 cases of significant curvature indicating that the adaptive peak with
 regard to body size in this species is broader than the phenotypic
 distribution, which has resulted in weak estimates of selection.
description: Comments to data
 setsBackground information
 to the data setsFemaleFledge_Dryad_TotFemales FledgedFemaleRecruit_Dryad_TotFemales RecruitsFemaleSurvival_Dryad_TotFemales SurvivalMaleFledge_DryadTotMales FledgedMaleRecruit_DryadTotMales RecruitsMaleSurv_DryadTotMales Survival
DOI: 10.5061/dryad.1j05f
title: Data from: Acoustic monitoring of coastal dolphins and their response to naval mine neutralization exercises

description: To investigate the potential impacts of naval mine neutralization
 exercises (MINEX) on odontocete cetaceans, a long-term passive acoustic
 monitoring study was conducted at a US Navy training range near Virginia
 Beach, USA. Bottom-moored acoustic recorders were deployed in 2012–2016
 near the epicentre of MINEX training activity and were refurbished every
 2–4 months. Recordings were analysed for the daily presence/absence of
 dolphins, and dolphin acoustic activity was quantified in detail for the
 hours and days before and after 31 MINEX training events. Dolphins
 occurred in the area year-round, but there was clear seasonal variability,
 with lower presence during winter months. Dolphins exhibited a behavioural
 response to underwater detonations. Dolphin acoustic activity near the
 training location was lower during the hours and days following
 detonations, suggesting that animals left the area and/or reduced their
 signalling. Concurrent acoustic monitoring farther away from the training
 area suggested that the radius of response was between 3 and 6 km. A
 generalized additive model indicated that the predictors that explained
 the greatest amount of deviance in the data were the day relative to the
 training event, the hour of the day and circumstances specific to each
 training event.
description: Lammers et al MINEX
 Acoustic Monitoring dataSpreadsheet containing
 the data used for statistical calculationsMINEX GAM
 OutputExplanation of
 generalized additive modelMINEX_linear_array_dep_01-14_rawExplosions detected to date_EJZData file used for creating GAM
DOI: 10.5061/dryad.dh0dv
title: Data from: Bayesian and likelihood phylogenetic reconstructions of morphological traits are not discordant when taking uncertainty into consideration: a comment on Puttick et al

description: Puttick et al. (2017 Proc. R. Soc. B 284, 20162290
 (doi:10.1098/rspb.2016.2290)) performed a simulation study to compare
 accuracy among methods of inferring phylogeny from discrete morphological
 characters. They report that a Bayesian implementation of the Mk model
 (Lewis 2001 Syst. Biol. 50, 913–925 (doi:10.1080/106351501753462876)) was
 most accurate (but with low resolution), while a maximum-likelihood (ML)
 implementation of the same model was least accurate. They conclude by
 strongly advocating that Bayesian implementations of the Mk model should
 be the default method of analysis for such data. While we appreciate the
 authors' attempt to investigate the accuracy of alternative methods
 of analysis, their conclusion is based on an inappropriate comparison of
 the ML point estimate, which does not consider confidence, with the
 Bayesian consensus, which incorporates estimation credibility into the
 summary tree. Using simulation, we demonstrate that ML and Bayesian
 estimates are concordant when confidence and credibility are comparably
 reflected in summary trees, a result expected from statistical theory. We
 therefore disagree with the conclusions of Puttick et al. and consider
 their prescription of any default method to be poorly founded. Instead, we
 recommend caution and thoughtful consideration of the model or method
 being applied to a morphological dataset.
description: READMEDescription of
 supporting filesTrue_trees1000 simulated 32-tip pectinate trees.BMR_treesInferred Bayesian majority-rule consensus trees.ML_BS_treesInferred MLE trees annotated with support from 200 non-parametric bootstrap replicates.ML_50col_treesInferred MLE trees where edges with &lt; 50% bootstrap support have been collapsed.tree_distsCSV file listing the various tree distances. See README for description.phylip_alignmentsSimulated character alignments (phylip format) .
DOI: 10.5061/dryad.c57t1
title: Data from: The microbiota of diapause: how host-microbe associations are formed after dormancy in an aquatic crustacean

description: 1. A critical question in symbiosis research is where and how organisms
 obtain beneficial microbial symbionts in different ecological contexts.
 Microbiota of juveniles are often derived directly from their mother or
 from the immediate environment. The origin of beneficial symbionts,
 however, is less obvious in organisms with diapause and dispersal stages,
 such as plants with dormant seeds and animals in ephemeral or strongly
 seasonal habitats. In these cases, parents and offspring are separated in
 time and space, which may affect opportunities for both vertical and
 horizontal transmission of symbionts. 2. The planktonic crustacean Daphnia
 produces long-lasting resting eggs to endure winter freezing and summer
 droughts and requires microbiota for growth and reproduction. It is
 unknown how hatchlings from resting stages form associations with
 microbial consorts after diapause. 3. Using natural samples of D. magna
 resting eggs after several years of storage, we show that the total
 bacterial community derived from both the exterior and interior of the
 eggs’ ephippial cases is sufficiently beneficial to ensure normal Daphnia
 functioning in otherwise bacteria-free conditions. We do not find direct
 evidence that the required bacteria are of maternal origin, though
 sequencing reveals that the resting stage is accompanied by bacterial taxa
 previously found in association with adult animals. 4. These findings
 suggest that while Daphnia are strongly dependent on environmental
 bacteria for normal functioning, host-bacteria associations are somewhat
 general and availability of specific bacteria is not a strong constraint
 on host ecology. Nevertheless, animals and microbes may be ecologically
 linked through co-dispersal.
description: Majority_present_taxa_ss16S sequences of bacterial OTUs present in a majority of surface-sterilized ephippia.Outside_surface_taxa16S sequences of bacterial OTUs overrepresented on the outside surfaces of natural ephippiaOTU tableOTU table of bacterial OTUs from Illumina sequencing of ephippia.p303_eph_map97_ab5_utax_GGtax_parsable.txtMap fileDescriptions of sequenced samplesephippiaexpt_mapfile.txtp303_eph_OTU_ab5_id97FASTA file of consensus 16S sequencesTree fileTree file associated with consensus 16S sequencesp303_eph_OTU_ab5_id97.tre
DOI: 10.5061/dryad.js5k0
title: Data from: Mating timing, dispersal and local adaptation in patchy environments

description: Dispersal is a life-history trait that can evolve under various known
 selective pressures as identified by a multitude of theoretical and
 empirical studies. Yet only few of them are considering the succession of
 mating and dispersal. The sequence of these events influences gene flow
 and consequently affects the dynamics and evolution of populations. We use
 individual-based simulations to investigate the evolution of the timing of
 dispersal and mating, i.e. mating before or after dispersal. We assume a
 discrete insect meta-population in a heterogeneous environment, where
 populations may adapt to local conditions and only females are allowed to
 disperse. We run the model assuming different levels of species habitat
 tolerance, carrying capacity, and temporal environmental variability. Our
 results show that in species with narrow habitat tolerance low to moderate
 dispersal evolves in combination with mating after dispersal
 (post-dispersal mating). With such a strategy dispersing females benefit
 from mating with a resident male, as their offspring will be better
 adapted to the local habitat conditions. On the contrary, in species with
 wide habitat tolerance higher dispersal rates in combination with
 pre-dispersal mating evolves. In this case individuals are adapted to the
 'average' habitat where pre-dispersal mating conveys the benefit
 of carrying relatives' genes into a new population. With high
 dispersal rates and large population size, local adaptation and
 kin-structure both vanish and the temporal sequence of dispersal and
 mating may become a (nearly) neutral trait.
description: MatingTiming_LazarusCode_ReplaceWe are submitting the code for individual based model simulations, written in Lazarus 1.6.MatingTiming_LazarusCode.zip
DOI: 10.5061/dryad.8b69r
title: Data from: Speciation history of a species complex of Primulina eburnea (Gesneriaceae) from limestone karsts of south China, a biodiversity hotspot

description: Limestone karsts in southern China are characterized by high edaphic and
 topographic heterogeneity and host high levels of species richness and
 endemism. However, the evolutionary mechanisms for generating such
 biodiversity remain poorly understood. Here, we performed species
 delimitation, population genetic analyses, simulations of gene flow, and
 analyses of floral morphological traits to infer the geographic history of
 speciation in a species complex of Primulina eburnea from limestone karsts
 of south China. Using Bayesian species delimitation, we determined that
 there are seven distinct species that correspond well to the putative
 morphological species. Species-tree reconstruction, Structure and
 Neighbour-Net analyses all recovered four lineages in agreement with
 currently species geographic boundaries. High levels of genetic
 differentiation were observed both within and among species.
 Isolation–migration coalescent analysis provides evidence for significant
 but low gene flow among species. Approximate Bayesian computation (ABC)
 analysis supports a scenario of historical gene flow rather than recent
 contemporary gene flow for most species divergences. Finally, we found no
 evidence of divergent selection contributing to population differentiation
 of a suite of flower traits. These results support the prevalence of
 allopatric speciation and highlight the role of geographic isolation in
 the diversification process. At small geographic scales, limited
 hybridization occurred in the past between proximate populations but did
 not eliminate species boundaries. We conclude that limited gene flow might
 have been the predominant evolutionary force in promoting population
 differentiation and speciation.
description: The SNP data for
 population genetic analysisSNP-data-results.xlsxThe sequence data for phylogenetic reconstruction and genetic analysisMatrix.zipFlower trait dataset for Qst analysisFlower trait dataset.xlsx