cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.158m0
title: Data from: Statistical evidence for common ancestry: application to primates

description: Since Darwin, biologists have come to recognize that the theory of descent
 from common ancestry is very well supported by diverse lines of evidence.
 However, while the qualitative evidence is overwhelming, we also need
 formal methods for quantifying the evidential support for common ancestry
 (CA) over the alternative hypothesis of separate ancestry (SA). In this
 paper we explore a diversity of statistical methods, using data from the
 primates. We focus on two alternatives to CA, species SA (the separate
 origin of each named species) and family SA (the separate origin of each
 family). We implemented statistical tests based on morphological,
 molecular, and biogeographic data and developed two new methods: one that
 tests for phylogenetic autocorrelation while correcting for variation due
 to confounding ecological traits and a method for examining whether fossil
 taxa have fewer derived differences than living taxa. We overwhelmingly
 rejected both species and family SA, with infinitesimal p-values. We
 compare these results with those from two companion papers, which also
 found tremendously strong support for the CA of all primates, and discuss
 future directions and general philosophical issues that pertain to
 statistical testing of historical hypotheses such as CA.
description: molecular sequences from
 54 primate genesMolecular sequence data,
 used for the PTP tests, the tree-to-tree agreement test, and for the tests
 in companion papers (Bontrager et al. and Larget et al.). The archive
 contains aligned sequences for 54 primate genes, for a total of 178
 species, originally from Perelman et al. 2011
 (http://dx.doi.org/10.1371/journal.pgen.1001342).molecular.zipmorphology dataArchive with all morphology data used in the publication, along with R script for analysismorphology.zipevidence from silent sitesdata and scripts from companion paper Bontrager et al. http://dx.doi.org/10.1101/035915
DOI: 10.5061/dryad.p4r84
title: Data from: COI is better than 16S rRNA for DNA barcoding Asiatic salamanders (Amphibia: Caudata: Hynobiidae)

description: The 5’ region of the mitochondrial DNA (mtDNA) gene cytochrome c oxidase I
 (COI) is the standard marker for DNA barcoding. However, because COI tends
 to be highly variable in amphibians, sequencing is often challenging.
 Consequently, another mtDNA gene, 16S rRNA gene, is often advocated for
 amphibian barcoding. Herein, we directly compare the usefulness of COI and
 16S in discriminating species of hynobiid salamanders using 130
 individuals. Species identification and classification of these animals,
 which are endemic to Asia, is often based on morphology only. Analysis of
 Kimura 2-parameter genetic distances (K2P) documents the mean
 intraspecific variation for COI and 16S rRNA genes to be 1.4% and 0.3%,
 respectively. Whereas COI can always identify species, sometimes 16S
 cannot. Intra- and interspecific genetic divergences occasionally overlap
 in both markers thus reducing the value of a barcoding gap to identify
 genera. Regardless, COI is the better DNA barcoding marker for hynobiids.
 In addition to the comparison of two potential markers, high levels of
 intraspecific divergence in COI (&gt;5%) suggest that both
 Onychodactylus fischeri and Salamandrella keyserlingii might be composites
 of cryptic species.
description: Table
 S1Data for the hynobiids
 used in this study on DNA barcoding. DNA vouchers are deposited at Chengdu
 Institute of Biology (CIB), Chinese Academy of
 Sciences.Table
 S2Homologous DNA sequences
 downloaded from GenBank.Table
 S3Intraspecific and
 interspecific genetic divergence (K2P model) for 31 species in the
 Hynobiidae.
DOI: 10.5061/dryad.3s4d3
title: Data from: Characterization of Pythium spp. associated with asymptomatic soybeans in southeastern Pennsylvania

description: Soybean production in Pennsylvania has increased substantially over the
 past twenty years and is a highly valued field crop together with corn.
 Soilborne pathogens such as Pythium spp. can contribute to soybean stand
 establishment issues, particularly under the conservation tillage
 practices that are common in the state. In this study, we collected soil
 samples from eight asymptomatic soybean-corn rotation fields across six
 counties in southeastern Pennsylvania between May and June, 2012. Pythium
 species were isolated via baiting, and tested for aggressiveness on both
 soybean and corn using laboratory pathogenicity assays. In addition to our
 culture-based survey, we also assessed the use of cytochrome oxidase
 subunit 1 (COI) pyrosequencing as a culture-independent method for
 measuring Pythium species diversity from environmental samples. Diversity
 estimates were consistent between the culture-based and pyrosequencing
 datasets; however, important methodological biases inherent to
 culture-independent methods may have led to some differences. Our results
 show that several Pythium species previously characterized as soybean
 and/or corn pathogens are present in southeastern Pennsylvania, including
 P. irregulare, P. sylvaticum, and P. ultimum var. sporangiiferum, with
 isolates showing aggressive phenotypes in lab assays.
description: COI
 alignmentCOI alignment file in
 Nexus format. NCBI block included after data block, which gives organism
 and isolation information for each sequence (as submitted to
 GenBank).C12Cox1_Data.nexusCOI alignment MEGA formatCOI alignment formatted for analysis in MEGA. Missing data coded as '?'C12Cox1_Data.megCOI Neighbor-joining TreeNewick format tree file from neighbor-joining analysis in MEGA (Kimura 2-Parameter model, pairwise deletion of gaps/missing data).C12_NJ_K2P_pairwisedeletion.nwkCOI Neighbor-joining Tree with Species LabelsPDF file of tree from neighbor-joining analysis with species (or aff) designations labeled.SpeciesLabeled.pdfCOI alignment with Reference Sequences in MEGA formatPythium (and select other oomycetes) included with COI sequences generated here. Sequences were obtained from NCBI.Cox1_C12plusRefs.megCOI Neighbor-joining Tree with Reference SequencesPDF of neighbor-joining tree from alignment with Pythium and other oomycete reference sequences included.Cox1NJtree_C12plusRefs.pdf
DOI: 10.5061/dryad.5s3v5
title: Data from: Root heterogeneity along an arctic elevational gradient: the importance of resolution

description: Spatial heterogeneity affects plant performance and is influenced by
 plants, but the scale at which fine roots react to or generate spatial
 heterogeneity has received little attention. Fine roots might be expected
 to respond to heterogeneity at a scale comparable to their diameter (mm),
 but studies to date have been conducted at much coarser resolutions (cm –
 m). Here we quantify root heterogeneity in contrasting habitats with
 special attention to the influence of resolution. We measured fine root
 length heterogeneity at resolutions ranging from 1 to 300 mm2, at four
 elevations along an arctic alpine gradient from 500 m a.s.l. (forest) to
 1100 m (tundra). We calculated the magnitude of heterogeneity as the
 coefficient of variation of root length, and the scale of heterogeneity
 using semivariance analysis. The magnitude of heterogeneity was about
 twofold greater at fine than coarse resolution. Further, the magnitude of
 heterogeneity was generally greatest at the highest elevation, suggesting
 that soil at 1100 m was less evenly occupied by plant roots than soils at
 lower elevations. The exception to this was at the 1 mm2 resolution, for
 which the magnitude of heterogeneity did not vary with elevation, possibly
 because heterogeneity at this scale is related to ecophysiological
 processes common to all vegetation types. The scale of root length
 heterogeneity increased significantly with resolution coarseness,
 suggesting that roots respond to or generate patchiness at small scales
 that have not previously been examined. In contrast, the scale of
 heterogeneity did not vary significantly with elevation and the
 accompanying turnover in growth form. Our results suggest that roots in
 four vegetation types respond to or generate very fine scales of spatial
 heterogeneity, including scales much smaller than those that have
 previously been examined. Both the magnitude and scale of heterogeneity
 varied with sampling resolution, suggesting resolutions as small as a few
 millimetres are relevant to studies of spatial root interactions and
 below-ground processes.
description: Root_length_HeterogeneityPresented are data of root length (in mm) for each single root per minirhizotron image within a specific minirhizotron tube, sampled on a specific sampling date (June, August, September). The file is a modified output of Rootfly, the program with which root length was determined.
DOI: 10.5061/dryad.0r9p1
title: Data from: Catecholaminergic regulation of learning rate in a dynamic environment

description: Adaptive behavior in a changing world requires flexibly adapting one’s
 rate of learning to the rate of environmental change. Recent studies have
 examined the computational mechanisms by which various environmental
 factors determine the impact of new outcomes on existing beliefs (i.e.,
 the ‘learning rate’). However, the brain mechanisms, and in particular the
 neuromodulators, involved in this process are still largely unknown. The
 brain-wide neurophysiological effects of the catecholamines norepinephrine
 and dopamine on stimulus-evoked cortical responses suggest that the
 catecholamine systems are well positioned to regulate learning about
 environmental change, but more direct evidence for a role of this system
 is scant. Here, we report evidence from a study employing pharmacology,
 scalp electrophysiology and computational modeling (N = 32) that suggests
 an important role for catecholamines in learning rate regulation. We found
 that the P3 component of the EEG—an electrophysiological index of
 outcome-evoked phasic catecholamine release in the cortex—predicted
 learning rate, and formally mediated the effect of prediction-error
 magnitude on learning rate. P3 amplitude also mediated the effects of two
 computational variables—capturing the unexpectedness of an outcome and the
 uncertainty of a preexisting belief—on learning rate. Furthermore, a
 pharmacological manipulation of catecholamine activity affected learning
 rate following unanticipated task changes, in a way that depended on
 participants’ baseline learning rate. Our findings provide converging
 evidence for a causal role of the human catecholamine systems in
 learning-rate regulation as a function of environmental change.
description: Single-trial behavioral
 and P3 dataMATLAB file with
 single-trial behavioral/task data and P3 amplitudes. See the README file
 for more information.RepositedData.mat
DOI: 10.5061/dryad.72193
title: Data from: A new non-parametric method for analyzing replicated point patterns in ecology

description: Most ecological studies that involve point pattern analyses are based on a
 single plot, which prevent the separation of the effects of various
 processes that could act simultaneously, as well as limiting the
 conclusions that can be extracted from these studies. However, considering
 the spatial distribution of individuals in several plots as replicates of
 the same process could help to differentiate its specific effects from
 those of other confounding processes. Thus, we introduce a new method for
 analyzing spatial point patterns that are replicated according to a
 two–factorial design. By summarizing the spatial patterns as K–functions,
 the proposed method computes the average K–functions for each level of the
 two factors (i.e., predictors) and for each combination of levels, before
 estimating the sum of squared deviations from the overall mean K–function.
 Inferences of the strength of the relationship between the predictors,
 their interaction, and the spatial structure are made based on a
 non–parametric bootstrap procedure, which considers the dependency among
 spatial scales. We illustrate the proposed approach based on an analysis
 of the effects of altitude (with two levels: low and high) and slope (with
 two levels: flat and steep slopes) on the spatial pattern of Croton
 wagneri, a dominant shrub in an Andean dry scrubland. Our method detected
 a significant effect of the interaction between slope and altitude, which
 could not have been detected using current point pattern analysis
 methodology. The prevalence of single–plot analysis in ecological studies
 may be due to a lack of familiarity with appropriate methods for
 replicated point patterns, as well as the greater complexity of these
 methods and the absence of appropriate software. Our approach can be
 applied to a significant number of ecological questions while maintaining
 a simple, understandable, and easily reportable methodological framework.
description: Coordinates of Croton
 wagneriCoordinates
 corresponding to 10850 individual croton shrubs, separated into 16 plots
 of 30x30m. Plots were established along an altitudinal gradient in dry
 scrubland of southern Ecuador. Plot-1 to Plot-8 located between 1400 and
 1500 m.a.s.l. and plot-9 to plot-16 located between 1750 and 1900
 m.a.s.l.coord_croton_replicated_16plots.xls
DOI: 10.5061/dryad.ft1d5
title: Data from: Multilevel and quasi-Monte Carlo methods for uncertainty quantification in particle travel times through random heterogeneous porous media

description: In this study, we apply four Monte Carlo simulation methods, namely, Monte
 Carlo, quasi-Monte Carlo, multilevel Monte Carlo and multilevel
 quasi-Monte Carlo to the problem of uncertainty quantification in the
 estimation of the average travel time during the transport of particles
 through random heterogeneous porous media. We apply the four methodologies
 to a model problem where the only input parameter, the hydraulic
 conductivity, is modelled as a log-Gaussian random field by using direct
 Karhunen–Loéve decompositions. The random terms in such expansions
 represent the coefficients in the equations. Numerical calculations
 demonstrating the effectiveness of each of the methods are presented. A
 comparison of the computational cost incurred by each of the methods for
 three different tolerances is provided. The accuracy of the approaches is
 quantified via the mean square error.
description: Data_RSOS-170203
DOI: 10.15468/dl.vckhbz
title: Occurrence Download

description: A dataset containing 45347 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "DatasetKey is one of (Bee, wasp and ant (Hymenoptera: Aculeata) records verified via iRecord, NBIS Records to December 2016, Rotherham Biological Records Centre - Non-sensitive Records from all taxonomic groups, Invertebrate Site Register - England 1738-2005, iNaturalist Research-grade Observations, SEWBReC Bees, Wasps and Ants (South East Wales), Welsh Invertebrate Database (WID), HBRG Insects Dataset Vol 1, Suffolk Biodiversity Information Service (SBIS) Dataset, National Trust Species Records)",
 "OccurrenceStatus is Present",
 "TaxonKey is Formicidae"
 ]
}

 The dataset includes 45347 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000526-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.c119t
title: Data from: Contrasting the roles of section length and instream habitat enhancement for river restoration success: a field study on 20 European restoration projects

description: 1. Restoration of river hydromorphology often has limited detected effects
 on river biota. One frequently discussed reason is that the restored river
 length is insufficient to allow populations to develop and give the room
 for geomorphologic processes to occur. 2. We investigated ten pairs of
 restored river sections of which one was a large project involving a long,
 intensively restored river section and one represented a smaller
 restoration effort. The restoration effect was quantified by comparing
 each restored river section to an upstream non-restored section. We
 sampled the following response variables: habitat composition in the river
 and its floodplain, three aquatic organism groups (aquatic macrophytes,
 benthic invertebrates and fish), two floodplain-inhabiting organism groups
 (floodplain vegetation, ground beetles), as well as food web composition
 and land–water interactions reflected by stable isotopes. 3. For each
 response variable, we compared the difference in dissimilarity of the
 restored and nearby non-restored section between the larger and the
 smaller restoration projects. In a second step, we regrouped the pairs and
 compared restored sections with large changes in substrate composition to
 those with small changes. 4. When comparing all restored to all
 non-restored sections, ground beetles were most strongly responding to
 restoration, followed by fish, floodplain vegetation, benthic
 invertebrates and aquatic macrophytes. Aquatic habitats and stable isotope
 signatures responded less strongly. 5. When grouping the restored sections
 by project size, there was no difference in the response to restoration
 between the projects targeting long and short river sections with regard
 to any of the measured response variables except nitrogen isotopic
 composition. In contrast, when grouping the restored sections by substrate
 composition, the responses of fish, benthic invertebrates, aquatic
 macrophytes, floodplain vegetation and nitrogen isotopic composition were
 greater in sections with larger changes in substrate composition as
 compared to those with smaller changes. 6. Synthesis and applications. The
 effects of hydromorphological restoration measures on aquatic and
 floodplain biota strongly depend on the creation of habitat for aquatic
 organisms, which were limited or not present prior to restoration. These
 positive effects on habitats are not necessarily related to the restored
 river length. Therefore, we recommend a focus on habitat enhancement in
 river restoration projects.
description: Hering_etal_JAPPL_2015_DataAbundance data of the organism groups and raw values of abiotic response variables investigated (e.g. habitat diversity). These values were used to calculate Bray-Curtis dissimilarity indices for the restored and respective degraded sites.
DOI: 10.5061/dryad.pr4d0
title: Data from: Pleistocene sea level fluctuation and host plant habitat requirement influenced the historical phylogeography of the invasive species Amphiareus obscuriceps (Hemiptera: Anthocoridae) in its native range

description: Background: On account of repeated exposure and submergence of the East
 China Sea (ECS) land bridge, sea level fluctuation played an important
 role in shaping the population structure of many temperate species across
 the ECS during the glacial period. The flower bug Amphiareus obscuriceps
 (Poppius, 1909) (Hemiptera: Anthocoridae) is an invasive species native to
 the Sino-Japanese Region (SJR) of East Asia. We tested the hypothesis of
 the ECS land bridge acting as a dispersal corridor or filter for A.
 obscuriceps during the glacial period. Specifically, we tested whether and
 the extent to which dispersal ability and host plant habitat requirement
 influenced the genetic structure of A. obscuriceps during the exposure of
 the ECS land bridge. Results: Phylogenetic and network analyses indicated
 that A. obscuriceps is composed of two major lineages, i.e., China and
 Japan. Divergence time on both sides of the ECS was estimated to be
 approximately 1.07 (0.79-1.32) Ma, which was about the same period that
 the sea level increased. No significant Isolation by Distance (IBD)
 relationship was found between Фst and Euclidean distances in the Mantel
 tests, which is consistent with the hypothesis that this species has a
 good dispersal ability. Our Last Glacial Maximum (LGM) niche modeling of
 plants that constitute preferred habitats for A. obscuriceps exhibited a
 similar habitat gap on the exposed ECS continental shelf between China and
 Japan, but showed a continuous distribution across the Taiwan Strait.
 Conclusion: Our results suggest that ecological properties (habitat
 requirement and dispersal ability), together with sea level fluctuation
 during the Pleistocene across the ECS, have shaped the genetic structure
 and demographic history of A. obscuriceps in its native area. The host
 plant habitat requirement could also be a key to the colonization of the
 A. obscuriceps species during the exposure of the ECS land bridge. Our
 findings will shed light on the potential role of habitat requirement in
 the process of biological invasion in future studies.
description: All
 ITSnuclear DNA (nuclear
 marker internal transcribed spacer 1)All MTmitochondrial DNA (COI,
 COII and CytB)BI TREE
 exportmitochondrial
 haplotypes182.nexITS
 haplotypes10
DOI: 10.5061/dryad.32ht688
title: Data from: Fitness costs of key point mutations that underlie acaricide target-site resistance in the two-spotted spider mite Tetranychus urticae

description: The frequency of insecticide/acaricide target-site resistance is
 increasing in arthropod pest populations and is typically underpinned by
 single point mutations that affect the binding strength between the
 insecticide/acaricide and its target-site. Theory predicts that although
 resistance mutations clearly have advantageous effects under the selection
 pressure of the insecticide/acaricide, they might convey negative
 pleiotropic effects on other aspects of fitness. If such fitness costs are
 in place, target-site resistance is thus likely to disappear in the
 absence of insecticide/acaricide treatment, a process that would
 counteract the spread of resistance in agricultural crops. Hence, there is
 a great need to reliably quantify the various potential pleiotropic
 effects of target-site resistance point mutations on arthropod fitness.
 Here, we used near-isogenic lines of the spider mite pest Tetranychus
 urticae that carry well-characterized acaricide target-site resistance
 mutations to quantify potential fitness costs. Specifically, we analyzed
 P262T in the mitochondrial cytochrome b, the combined G314D and G326E
 substitutions in the glutamate-gated chloride channels, L1024V in the
 voltage gated sodium channel and I1017F in chitin synthase 1. Five
 fertility lifetable parameters and nine single-generation life history
 traits were quantified and compared across a total of 15 mite lines. In
 addition, we monitored the temporal resistance level dynamics of
 populations with different starting frequency levels of the chitin
 synthase resistant allele to further support our findings. Three
 target-site resistance mutations, I1017F and the co-occurring G314D and
 G326E mutations, were shown to significantly and consistently alter
 certain fitness parameters in T. urticae. The other two mutations (P262T
 and L1024V) did not result in any consistent change in a fitness parameter
 analyzed in our study. Our findings are discussed in the context of the
 global spread of T. urticae pesticide resistance within an integrated pest
 management context.
description: Raw_DataExcel files containing raw data, used to calculate nine single-generation life history traits; developmental time, immature stage survivorship, sex ratio, daily and total fecundity, longevity, lengths of pre-, post-, oviposition periods, as well as 5 fertility life table parameters; the net reproductive rate (R0), intrinsic rate of increase (rm), mean generation time (T), the finite rate of increase (LM) and the doubling time (DT) for 15 isogenic lines of Tetranychus urticae as well as data obtained from the monitoring of the temporal resistance level dynamics, of the T. urticae populations with different starting frequencies of the CHS1 resistant allele