cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r3k7m3c
title: Data from: A new family of dissimilarity metrics for discrete character matrices that include inapplicable characters and its importance for disparity studies

description: The use of discrete character data for disparity analyses has become more
 popular, partially due to the recognition that character data describe
 variation at large taxonomic scales, as well as the increasing
 availability of both character matrices co-opted from phylogenetic
 analysis and software tools. As taxonomic scope increases, the need to
 describe variation leads to some characters that may describe traits not
 found across all the taxa. In such situations, it is common practice to
 treat inapplicable characters as missing data when calculating
 dissimilarity matrices for disparity studies. For commonly used
 dissimilarity metrics like Will’s GED and Gower’s coefficient, this can
 lead to the re-ranking of pairwise dissimilarities, resulting in taxa that
 share more primary character states being assigned larger dissimilarity
 values than taxa that share fewer. We introduce a family of metrics that
 proportionally weight primary characters according to the secondary
 characters that describe them, effectively eliminating this problem, and
 compare their performance to common dissimilarity metrics and
 previously-proposed weighting schemes. When applied to empirical datasets,
 we confirm that choice of dissimilarity metric frequently affects the rank
 order of pairwise distances, differentially influencing downstream
 macroevolutionary inferences.
description: ESM_appendicesAppendices 1-4 referenced in main textdissimilarity_functionsR script with functions for calculating dissimilarity matrices using Wills' GED, Gower's coefficient, and the new family of metrics proposed in the associated publicationmyriapods_final_finalNexus file with character matrix for empirical example. Also available from MorphoBank (http://morphobank.org/permalink/?P3189). See Appendix 3 for more information.myriapods_type_205Table with information about hierarchical structure of character matrix used in empirical example. Required for calculating a dissimilarity matrix based on the new family of metrics proposed in the associated paper using the supplied R function.
DOI: 10.15468/dl.pxnncr
title: Occurrence Download

description: A dataset containing 313132 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "IucnRedListCategory is one of (VU, EN, CR)",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 313132 records from 440 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000548-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8r7k5
title: Data from: Prion protein inhibits fast axonal transport through a mechanism involving casein kinase 2

description: Prion diseases include a number of progressive neuropathies involving
 conformational changes in cellular prion protein (PrPc) that may be fatal
 sporadic, familial or infectious. Pathological evidence indicated that
 neurons affected in prion diseases follow a dying-back pattern of
 degeneration. However, specific cellular processes affected by PrPc that
 explain such a pattern have not yet been identified. Results from cell
 biological and pharmacological experiments in isolated squid axoplasm and
 primary cultured neurons reveal inhibition of fast axonal transport (FAT)
 as a novel toxic effect elicited by PrPc. Pharmacological, biochemical and
 cell biological experiments further indicate this toxic effect involves
 casein kinase 2 (CK2) activation, providing a molecular basis for the
 toxic effect of PrPc on FAT. CK2 was found to phosphorylate and inhibit
 light chain subunits of the major motor protein conventional kinesin.
 Collectively, these findings suggest CK2 as a novel therapeutic target to
 prevent the gradual loss of neuronal connectivity that characterizes prion
 diseases.
description: Figure 1. Full length
 PrP (PrP-FL) inhibits vesicular fast axonal transport in isolated squid
 axoplasm.Figure 1
 data.pdfFigure 2. Prion inhibits
 fast axonal transport of mitochondria in primary hippocampal cultured
 neurons.Figure 2
 Data.pdfFigure 3. PrP-induced
 fast axonal transport inhibition is mediated by Casein kinase 2
 activity.Figure 3
 Data.pdfFigure 4. PrP induces
 detachment of conventional kinesin from membrane cargoes through
 CK2-mediated phosphorylation of kinesin light chain
 subunits.Figure 4
 Data.pdfSupplementary Figure 2.
 PrP Full length (PrP-FL) inhibits fast axonal transport.Supplementary Figure 2
 Data.pdfSupplementary Figure. 3
 The CK2 pharmacological inhibitor DMAT does not interfere with
 FAT.Supplementary Figure 3
 Data.pdfSupplementary Figure 5
 Data
DOI: 10.5061/dryad.8797
title: Data from: Wings or winds: inferring bat migration in a stepping-stone archipelago

description: Eocene ocean currents and prevailing winds correlate with over-water
 dispersals of terrestrial mammals from Africa to Madagascar. Since the
 Early Miocene (about 23 Ma), these currents flowed in the reverse
 direction, from the Indian Ocean towards Africa. The Comoro Islands are
 equidistant between Africa and Madagascar and support an endemic land
 vertebrate fauna that shares recent ancestry predominantly with
 Madagascar. We examined whether gene flow in two Miniopterus bat species
 endemic to the Comoros and Madagascar correlates with the direction of
 current winds, using uni- and bi-parentally inherited markers with
 different evolutionary rates. Coalescence-based analyses of mitochondrial
 matrilines support a Pleistocene (approximately 180 000 years ago)
 colonization event from Madagascar west to the Comoros (distance: 300 km)
 in the predicted direction. However, nuclear microsatellites show that
 more recent gene flow is restricted to a few individuals flying against
 the wind, from Grande Comore to Anjouan (distance: 80 km).
description: MapsamplingsitesGeographic location of sampling sites and islandsNucgenotypesaelleni_griveaudi_islandsIndividual genotypes for all 10 microsatellite loci, in Arlequin formatDloop_aell_grivesamplingsitesDescription of haplotype sequences and haplotype composition of each sampled populationDloop_aell_grivesamplingsitesbreak-down of haplotype composition of each population, in arlequin formatD-loop_haplogroupsIndividual haplotypes and their haplogroup assignation
DOI: 10.5061/dryad.gf3qp
title: Data from: Tales of the unexpected: Phylogeography of the arctic-alpine model plant Saxifraga oppositifolia (Saxifragaceae) revisited

description: Arctic-alpine biota occupy enormous areas in the Arctic and the northern
 hemisphere mountain ranges, and have undergone major range shifts during
 their comparatively short history. The origins of individual arctic-alpine
 species remain largely unknown. In the case of the Purple saxifrage,
 Saxifraga oppositifolia, an important model for arctic-alpine plants,
 phylogeographic studies have remained inconclusive about early stages of
 the species’ spatiotemporal diversification, but have provided evidence
 for long-range colonization out of a presumed Beringian origin to cover
 today's circumpolar range. . We re-evaluated the species’ large-scale
 range dynamics based on a geographically extended sampling including
 crucial areas such as Central Asia and the (south-)eastern European
 mountain ranges and employing up-to-date phylogeographic analyses of a
 plastid sequence and a more restricted AFLP data set. In accordance with
 previous studies, we detected two major plastid DNA lineages also
 reflected in AFLP divergence, suggesting a long and independent vicariant
 history. Although we were unable to determine the species’ area of origin,
 our results point to the Alps and probably Central Asia, respectively, as
 the likely ancestral areas of the two main clades. AFLP data suggested
 that contact areas between the two clades in Eastern Europe, Northern
 Siberia and Greenland were secondary. In marked contrast to high levels of
 diversity revealed in previous studies, populations from the major arctic
 refugium Beringia did not exhibit any plastid sequence polymorphism. Our
 study shows that adequate sampling of the southern, refugial populations
 is crucial for understanding the range dynamics of arctic-alpine species.
description: Results Diffusion
 ModelRange connectivity
 (Bayes Factors) and ancestral location probabilities among nine discrete
 geographical regions in Saxifraga oppositifolia inferred using reversible
 and non-reversible models of geographic diffusion of plastid DNA
 sequencesResultsDiffusionModelSaxOpp.txtAFLP MatrixAFLP data matrix (excluding not repeatable, monomorphic and single fragments) with individuals in rows and markers in columns. Regions are given in the second column.SaxOpp_AFLP_Matrix.csvCombined AlignmentCombined alignment of the trnTF and psbA-trnH intergenic spacers in Saxifraga oppositifolia.SaxOpp_Alignment.faspsbA-trnH AlignmentAlignment of psbA-trnH intergenic spacer of Saxifraga oppositifolia including GenBank accession numbers (2nd column).SaxOpp_psbA_trnH.txttrnT-trnF AlignmentAlignment of trnT-trnF intergenic spacers of Saxifraga oppositifolia including GenBank accession numbers (2nd column).SaxOpp_trnT_trnF.txt
DOI: 10.5061/dryad.345v6
title: Data from: R2s for correlated data: phylogenetic models, LMMs, and GLMMs

description: Many researchers want to report an R2 to measure the variance explained by
 a model. When the model includes correlation among data, such as
 phylogenetic models and mixed models, defining an R2 faces two conceptual
 problems. (i) It is unclear how to measure the variance explained by
 predictor (independent) variables when the model contains covariances.
 (ii) Researchers may want the R2 to include the variance explained by the
 covariances by asking questions such as “How much of the data is explained
 by phylogeny?” Here, I investigate three R2s for phylogenetic and mixed
 models. R2resid is an extension of the ordinary least-squares R2 that
 weights residuals by variances and covariances estimated by the model; it
 is closely related to R2glmm presented by Nakagawa and Schielzeth (2013).
 R2pred is based on predicting each residual from the fitted model and
 computing the variance between observed and predicted values. R2lik is
 based on the likelihood of fitted models and therefore reflects the amount
 of information that the models contain. These three R2s are formulated as
 partial R2s, making it possible to compare the contributions of predictor
 variables and variance components (phylogenetic signal and random effects)
 to the fit of models. Because partial R2s compare a full model with a
 reduced model without components of the full model, they are distinct from
 marginal R2s that partition additive components of the variance. The
 properties of the R2s for phylogenetic models were assessed using
 simulations for continuous and binary response data (phylogenetic
 generalized least squares and phylogenetic logistic regression). Because
 the R2s are designed broadly for any model for correlated data, the R2s
 were also compared for LMMs and GLMMs. R2resid, R2pred, and R2lik all have
 similar performance in describing the variance explained by different
 components of models. However, R2pred gives the most direct answer to the
 question of how much variance in the data is explained by a model. R2resid
 is most appropriate for comparing models fit to different datasets,
 because it does not depend on sample sizes. And R2lik is most appropriate
 to assess the importance of different components within the same model
 applied to the same data, because it is most closely associated with
 statistical significance tests.
description: Ives R2 Supplementary
 MaterialSupplementary Section 1:
 More comparisons among the R2s Supplementary Section 2: R code for figures
 A1 and A2
DOI: 10.5061/dryad.t0391
title: Data from: Genes predict long distance migration and large body size in a migratory fish, Pacific lamprey

description: Elucidation of genetic mechanisms underpinning migratory behavior could
 help predict how changes in genetic diversity may affect future
 spatiotemporal distribution of a migratory species. This ability would
 benefit conservation of one such declining species, anadromous Pacific
 lamprey (Entosphenus tridentatus). Nonphilopatric migration of adult
 Pacific lamprey has homogenized population-level neutral variation but has
 maintained adaptive variation that differentiates groups based on
 geography, run-timing and adult body form. To investigate causes for this
 adaptive divergence, we examined 647 adult lamprey sampled at a fixed
 location on the Columbia River and radiotracked during their subsequent
 upstream migration. We tested whether genetic variation [94 neutral and
 adaptive single nucleotide polymorphisms (SNPs) previously identified from
 a genomewide association study] was associated with phenotypes of
 migration distance, migration timing, or morphology. Three adaptive
 markers were strongly associated with morphology, and one marker also
 correlated with upstream migration distance and timing. Genes physically
 linked with these markers plausibly influence differences in body size,
 which is also consistently associated with migration distance in Pacific
 lamprey. Pacific lamprey conservation implications include the potential
 to predict an individual's upstream destination based on its
 genotype. More broadly, the results suggest a genetic basis for
 intrapopulation variation in migration distance in migratory species.
description: DryadData_BonnPacificlampreyThese are the complete metadata of phenotypes and genotypes used in the analyses of this study on Pacific lamprey. The 94 SNP genotypes are formatted into letter codes. The data can be formatted for genepop, TASSEL, and DISTLM with some manipulation of data in this excel spreadsheet. Comments are included on field headings to explain the terms.
DOI: 10.5061/dryad.6qm2n
title: Data from: Lower body mass and higher metabolic rate enhance winter survival in root voles, Microtus oeconomus

description: Although the biological significance of individual variation in
 physiological traits is widely recognized, studies of their association
 with fitness in wild populations are surprisingly scarce. We investigated
 the effect of individual phenotypic variation in body mass, resting (RMR)
 and peak metabolic rates (PMR) on mortality of the root vole Microtus
 oeconomus. Body mass and metabolic rates varied significantly among
 consecutive years and were also age dependent, as individuals born in late
 summer and autumn were characterized by significantly lower body mass and
 metabolic rates than animals born earlier. At the beginning of winter
 voles born in spring and early summer exhibited reduced body mass and
 metabolic rates, whereas animals born later maintained lower body mass and
 RMR, which may be interpreted as phenotypic plasticity enhancing the
 probability of survival. Body mass had no significant effect on vole
 survival during summer. In contrast, smaller individuals were
 characterized by lower mortality during early winter, whereas higher body
 mass was positively associated with survival later in the season. High
 body-mass-corrected RMR positively affected survival in both summer and
 winter. The effect of PMR was apparent only during winter, though its
 direction (and correlation with RMR) varied among years. Deep snow cover
 negatively affected the survival of voles in both early and late winter.
 Ambient temperature was positively associated with winter survival, except
 for late winter, when rising temperature caused flooding of vole habitat.
 We conclude that the lack of consistency in the directionality and
 strength of the effects of body mass and metabolic rates on winter
 survival does not undermine their importance, but rather demonstrates the
 ability of individuals to adjust metabolic rate to changing environmental
 conditions.
description: Phenotypes and mortality
 of volesFile contains data on
 body mass and metabolic rates of individual voles as well as summer and
 winter mortality. There is also data on body temperature and swimming time
 during measuring of peak metabolic rates (PMR).Voles_mortality.xls
DOI: 10.5061/dryad.9kb02
title: Data from: Tracking the progression of speciation: variable patterns of introgression across the genome provide insights on the species delimitation between progenitor-derivative spruces (Picea mariana × P. rubens)

description: The genic species concept implies that while most of the genome can be
 exchanged somewhat freely between species through introgression, some
 genomic regions remain impermeable to interspecific gene flow. Hence,
 interspecific differences can be maintained despite ongoing gene exchange
 within contact zones. This study assessed the heterogeneous patterns of
 introgression at gene loci across the hybrid zone of an incipient
 progenitor–derivative species pair, Picea mariana (black spruce) and Picea
 rubens (red spruce). The spruce taxa likely diverged in geographic
 isolation during the Pleistocene and came into secondary contact during
 late Holocene. A total of 300 SNPs distributed across the 12 linkage
 groups (LG) of black spruce were genotyped for 385 individual trees from
 33 populations distributed across the allopatric zone of each species and
 within the zone of sympatry. An integrative framework combining three
 population genomic approaches was used to scan the genomes, revealing
 heterogeneous patterns of introgression. A total of 23 SNPs scattered over
 10 LG were considered impermeable to introgression and putatively under
 diverging selection. These loci revealed the existence of impermeable
 genomic regions forming the species boundary and are thus indicative of
 ongoing speciation between these two genetic lineages. Another 238 SNPs
 reflected selectively neutral diffusion across the porous species barrier.
 Finally, 39 highly permeable SNPs suggested ancestral polymorphism along
 with balancing selection. The heterogeneous patterns of introgression
 across the genome indicated that the speciation process between black
 spruce and red spruce is young and incomplete, albeit some interspecific
 differences are maintained, allowing ongoing species divergence even in
 sympatry. The approach developed in this study can be used to track the
 progression of ongoing speciation processes.
description: Complete genotype
 data_385individuals_300loci
DOI: 10.5061/dryad.cm02v
title: Data from: A complex mode of aggressive mimicry in a scale-eating cichlid fish

description: Aggressive mimicry is an adaptive tactic of parasitic or predatory species
 that closely resemble inoffensive models in order to increase fitness via
 predatory gains. Although similarity of distantly related species is often
 intuitively implicated with mimicry, the exact mechanisms and evolutionary
 causes remain elusive in many cases. Here, we report a complex aggressive
 mimicry strategy in Plecodus straeleni, a scale-eating cichlid fish from
 Lake Tanganyika, which imitates two other cichlid species. Employing
 targeted sequencing on ingested scales, we show that P. straeleni does not
 preferentially parasitize its models but —contrary to prevailing
 assumptions — targets a variety of co-occurring dissimilar looking fish
 species. Combined with tests for visual resemblance and visual modelling
 from a prey perspective, our results suggest that complex interactions
 among different cichlid species are involved in this mimicry system.
description: ND2 Fragments
 Alignmentfragments of ND2
 sequences of ingested scales
DOI: 10.5061/dryad.6t6k6
title: Data from: Final thermal conditions override the effects of temperature history and dispersal in experimental communities

description: Predicting the effect of climate change on biodiversity is a
 multifactorial problem that is complicated by potentially interactive
 effects with habitat properties and altered species interactions. In a
 microcosm experiment with communities of microalgae, we analysed whether
 the effect of rising temperature on diversity depended on the initial or
 the final temperature of the habitat, on the rate of change, on dispersal
 and on landscape heterogeneity. We also tested whether the response of
 species to temperature measured in monoculture allowed prediction of the
 composition of communities under rising temperature. We found that the
 final temperature of the habitat was the primary driver of diversity in
 our experimental communities. Species richness declined faster at higher
 temperatures. The negative effect of warming was not alleviated by a
 slower rate of warming or by dispersal among habitats and did not depend
 on the initial temperature. The response of evenness, however, did depend
 on the rate of change and on the initial temperature. Community
 composition was not predictable from monoculture assays, but higher
 fitness inequality (as seen by larger variance in growth rate among
 species in monoculture at higher temperatures) explained the faster loss
 of biodiversity with rising temperature.
description: Cell densities,
 biovolume, and measures of diversitydiversity_data.csvAbsorbance data and estimates of r, K, and N0growth_data.csv
DOI: 10.5061/dryad.r60sj21
title: Data from: Electron correlation in Li+, He, H− and the critical nuclear charge system ZC: energies, densities and Coulomb holes

description: This paper presents high accuracy correlation energies, intracule
 densities and Coulomb hole(s) for the lithium cation, helium, hydride ion
 and the system with the critical nuclear charge, Z_C, for binding two
 electrons. The fully-correlated (FC) wavefunction and the Hartree-Fock
 (HF) wavefunction are both determined using a Laguerre-based wavefunction.
 It is found that for the lithium cation and the helium atom a secondary
 Coulomb hole is present, in agreement with a previous literature finding,
 confirming a counter-intuitive conclusion that electron correlation can
 act to bring distant electrons closer together. However, no evidence for a
 tertiary Coulomb hole is found. For the hydride anion and the system just
 prior to electron detachment only a single Coulomb hole is present and
 electron correlation decreases the probability of finding the electrons
 closer together at all radial distances. The emergence of a secondary
 Coulomb hole is investigated and found to occur between Z = Z = 1.15 and Z
 = 1.20. The FC and HF energies and intracule densities (in atomic units)
 used to calculate the correlation energy and Coulomb hole respectively,
 are accurate to at least the nano-scale for helium and the cation and at
 least the micro-scale for the anions.
description: Intracule and Coulomb
 Hole DataThe Hartree-Fock (HF)
 intracule density distribution data and the fully-correlated (FC)
 intracule density distribution data for Li+, He, H- and the critical
 nuclear charge system for two-electron binding. A 1000 data points are
 provided for each distribution. The HF and FC data can be subtracted to
 obtain the Coulomb hole data. Also provided is Coulomb hole data obtained
 by fitting a spline function.Intracule+Coulomb
 hole_data.xlsx