cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b258r
title: Data from: Mountain metacommunities: climate and spatial connectivity shape ant diversity in a complex landscape

description: Understanding what drives biodiversity patterns across scales is the
 central goal of ecology. Both environmental gradients and spatial
 landscape structure have been found to be important factors influencing
 species distributions and community composition, and partly reflect the
 balance of underlying deterministic and stochastic community processes. In
 some systems, environmental gradients and spatial connectivity are
 intertwined in that steep environmental gradients serve as boundaries on
 species movements and impose environment-derived complex spatial structure
 to metacommunities. Mountainous landscapes are prime examples of this, and
 recent theory has linked principles of geomorphology, environmental
 gradients, and spatial structure to make predictions for resulting
 community patterns. In this context, we examine variation in taxonomic and
 phylogenetic ant diversity patterns along a geographic transect spanning
 &gt;5000 m in elevational range in the Hengduan mountains of southern
 China. We found that environmental gradients dominate variation in both
 alpha and beta diversity in this landscape, with alpha diversity strongly
 declining with elevation and beta diversity driven by elevational
 differences. However, within an elevational band spatial connectivity
 predicts beta diversity better than geographic distance. Our findings
 deviate from theoretical predictions in several ways, notably alpha
 diversity is monotonically declining and within-band beta diversity is
 invariant with increasing elevation. The discrepancies between theory and
 observation may be explained by differences in the Hengduan landscape from
 idealized fluvial landscapes, such as a lack of a mid-elevation peak in
 connectivity, as well as evolutionary limits on the source pool of species
 available to populate metacommunities at different elevations. The latter
 is supported by variation in phylogenetic community structure with
 elevation. Our results demonstrate the power of conceptual, statistical,
 and theoretical frameworks that integrate the roles of environment and
 spatial structure in metacommunities, but that additional work is needed
 to bridge the gap between abstract theory and real systems.
description: Liu et al.
 2017_dataThe uploaded data
 include 1. Environmental data for all the sites; 2. Ant community data; 3.
 The pairwise geographic distance of all sites; 4-6. The pairwise cost
 distance of all sites with different elevational buffer (300, 400, 500m);
 7. The pairwise cost distance of all 3000 randomly selected sites; 8. Site
 and species information.Liu et
 al.2017_DATA.zip
DOI: 10.5061/dryad.p8n59
title: Data from: Wide but not impermeable: Testing the riverine barrier hypothesis for an Amazonian plant species

description: Wallace's riverine barrier hypothesis postulates that large rivers,
 such as the Amazon and its tributaries, reduce or prevent gene flow
 between populations on opposite banks, leading to allopatry and areas of
 species endemism occupying interfluvial regions. Several studies have
 shown that two major tributaries, Rio Branco and Rio Negro, are important
 barriers to gene flow for birds, amphibians and primates. No botanical
 studies have considered the potential role of the Rio Branco as a barrier,
 while a single botanical study has evaluated the Rio Negro as a barrier.
 We studied an Amazon shrub, Amphirrhox longifolia (A. St.-Hil.) Spreng
 (Violaceae), as a model to test the riverine barrier hypothesis.
 Twenty-six populations of A. longifolia were sampled on both banks of the
 Rio Branco and Rio Negro in the core Amazon basin. Double digest RADseq
 was used to identify 8,010 unlinked SNP markers from the nuclear genome of
 156 individuals. Data relating to population structure support the
 hypothesis that the Rio Negro acted as a significant genetic barrier for
 A. longifolia. On the other hand, no genetic differentiation was detected
 among populations spanning the narrower Rio Branco, which is a tributary
 of the Rio Negro. This study shows that the strength of riverine barriers
 for Amazon plants is dependent on the width of the river separating
 populations and species-specific dispersal traits. Future studies of
 plants with contrasting life history traits will further improve our
 understanding of the landscape genetics and allopatric speciation history
 of Amazon plant diversity.
description: 8100SNPsData set for all Amphirrhox longifolia populations.Input file for TREEMIXInput file for TREEMIX analysesinputTREEMIXallpopsinputSPAGEDIInput file for SPAGeDiInput file for BayescanInput file for Bayescan analysisinputallpopsBayescan(pops separadas)
DOI: 10.5061/dryad.pq622
title: Data from: From animal tracks to fine-scale movement modes: a straightforward approach for identifying multiple, spatial movement patterns

description: 1. Thanks to developments in animal tracking technology, detailed data on
 the movement tracks of individual animals are now attainable for many
 species. However, straightforward methods to decompose individual tracks
 into high-resolution, spatial modes are lacking but are essential to
 understand what an animal is doing. 2. We developed an analytical approach
 that combines separately-validated methods into a straightforward tool for
 converting animal GPS tracks to short-range movement modes. Our three-step
 analytical process comprises: (1) decomposing data into separate movement
 segments using behavioural change point analysis; (2) defining candidate
 movement modes and translating them into non-linear or linear equations
 between net squared displacement (NSD) and time; and (3) fitting each
 candidate equation to NSD segments and determining the best-fitting modes
 using Concordance Criteria, Akaike’s Information Criteria and other
 fine-scale segment characteristics. We illustrate our approach for three
 sub-adults, male wild boar Sus scrofa tracked at 15 min intervals over 4
 months using GPS collars. We defined five candidate movement modes based
 on previously published studies of short-term movements: encamped,
 ranging, round trips (complete and partial), and wandering. 3. Our
 approach successfully classified over 80% of the tracks into these
 movement modes lasting between 5 and 54 hours and covering between 300 m
 to 20 km. Repeated analyses of GPS data resampled at different rates
 indicated that one positional fix every 3-4 h was sufficient for
 &gt;70% classification success. Classified modes were consistent with
 published observations of wild boar movement, further validating our
 method. 4. The proposed approach advances the status quo by permitting
 classification into multiple movement modes (where these are adequately
 discernable from spatial fixes) facilitating analyses at high temporal and
 spatial resolutions, and is straightforward, largely objective, and
 without restrictive assumptions, necessary parameterizations or visual
 interpretation. Thus, it should capture the complexity and variability of
 tracked animal movement mode for a variety of taxa across a wide range of
 spatial and temporal scales.
description: SubAdults_BoarsThe csv file contains the GPS tracks of three ("gilbert", "leopold" and "lactose") sub-adult males wild boar (Sus scrofa). The three individuals were tracked in agroecosystems of Southern Belgium in the framework of the PhD Thesis of Kevin Morelle.
DOI: 10.5061/dryad.rb86d
title: Data from: On formation-based sampling proxies and why they should not be used to correct the fossil record

description: The fossil record is a unique resource on the history of life, but it is
 well known to be incomplete. In a series of high-profile papers, a
 residual modelling technique has been applied to correct the raw
 palaeodiversity signal for this bias and incompleteness, and the claim is
 made that the processed time series are more accurate than the raw data.
 We apply empirical and simulation approaches to test for correlation and
 directionality of any relationships between rock and fossil data. The
 empirical data comprise samples of the global fossil record through the
 Phanerozoic, and we use simulations to assess whether randomly sampled
 subsets of modelled data can be improved by application of the residual
 modelling technique. Our results show that using formation counts as a
 sampling proxy to correct the fossil record via residual modelling is ill
 founded. The supposedly independent model of sampling is
 information-redundant with respect to the raw palaeodiversity data it
 seeks to correct, and so the outputs are generally likely to be further
 from the truth than the raw data. We recommend that students of
 palaeodiversity cease to use residual modelling estimates based on
 formation counts, and suggest that results from a substantial number of
 papers published in the past ten years require re-evaluation.
description: expanded_Supplementary
 dataSupplementary file of
 empirical data and simulation resultsresidual_simulation_expandedSimulations R script
DOI: 10.5061/dryad.p8n72
title: Data from: A temporal banding approach for consistent taxonomic ranking above the species level

description: Comparable taxonomic ranks within clades can facilitate more consistent
 classifications and objective comparisons among taxa. Here we use a
 temporal approach to identify taxonomic ranks. This is an extension of the
 temporal banding approach including a Temporal Error Score that finds an
 objective cut-off for each taxonomic rank using information for the
 current classification. We illustrate this method using a data set of the
 lichenized fungal family Parmeliaceae. To assess its performance, we
 simulated the effect of taxon sampling and compared our method with the
 other temporal banding method. For our sampled phylogeny, 11 of the 12
 included families remained intact and 55 genera were confirmed, whereas 32
 genera were lumped and 15 genera were split. Taxon sampling impacted the
 method at the genus level, whereas yielded only insignificant changes at
 the family level. The other available temporal approach also gives a
 similar cutoff point to our method. Our approach to identify taxonomic
 ranks enables taxonomists to revise and propose classifications on an
 objective basis, changing ranks of clades only when inconsistent with most
 taxa in a phylogenetic tree. An R script to find the time point with the
 minimal temporal error is provided.
description: Example taxonomy for R
 Codetaxonomy.csvExample chronogram for R codechronogram.nexMain R code for Temporal banding methodtemporal_banding.RAssociated functions for the main R codebanding_functions.R
DOI: 10.5061/dryad.60210
title: Data from: Teosinte in Europe – searching for the origin of a novel weed

description: A novel weed has recently emerged, causing serious agronomic damage in one
 of the most important maize-growing regions of Western Europe, the
 Northern Provinces of Spain. The weed has morphological similarities to a
 wild relative of maize and has generally been referred to as teosinte.
 However, the identity, origin or genetic composition of ‘Spanish teosinte’
 was unknown. Here, we present a genome-wide analysis of single-nucleotide
 polymorphism (SNP) data for Spanish teosinte, sympatric populations of
 cultivated maize and samples of reference teosinte taxa. Our data are
 complemented with previously published SNP datasets of cultivated maize
 and two Mexican teosinte subspecies. Our analyses reveal that Spanish
 teosinte does not group with any of the currently recognized teosinte
 taxa. Based on Bayesian clustering analysis and hybridization simulations,
 we infer that Spanish teosinte is of admixed origin, most likely involving
 Zea mays ssp. mexicana as one parental taxon, and an unidentified
 cultivated maize variety as the other. Analyses of plants grown from seeds
 collected in Spanish maize fields and experimental crosses under
 controlled conditions reveal that hybridization does occur between Spanish
 teosinte and cultivated maize in Spain, and that current hybridization is
 asymmetric, favouring the introgression of Spanish teosinte into
 cultivated maize, rather than vice versa.
description: SNP
 dataHere we provide the SNP
 table generated with MaizeSNP50 BeadChip and Infinium HD Assay (Illumina,
 San Diego, CA, USA). Only SNPs with a GenTrain score of larger than 0.7
 were retained (GenomeStudio V2009.1). The table lists the genotypes of 142
 plant individuals (maize, teosinte and maize-teosinte hybrids) for each
 SNP Id (ID). The table contains 41,784 SNPs. Missing data is indicated by
 NA.raw_data.txt
DOI: 10.5061/dryad.61kr4
title: Data from: Frequency dependence limits divergent evolution by favouring rare immigrants over residents

description: Two distinct forms of natural selection promote adaptive biological
 diversity. Divergent selection occurs when different environments favour
 different phenotypes, leading to increased differences between
 populations. Negative frequency-dependent selection occurs when rare
 variants within a population are favoured over common ones, increasing
 diversity within populations. These two diversifying forces promote
 genetic variation at different spatial scales, and may act in opposition,
 but their relative effects remain unclear because they are rarely measured
 concurrently. Here we show that negative frequency-dependent selection
 within populations can favor rare immigrants over locally adapted
 residents. We reciprocally transplanted lake and stream ecotypes of
 threespine stickleback into lake and stream habitats, while manipulating
 the relative abundance of residents versus immigrants. We found negative
 frequency-dependence: survival was highest for the locally rare ecotype,
 rather than natives. Also, individuals with locally rare major
 histocompatibility complex (MHC) class IIb genotypes were infected by
 fewer parasites. This negative frequency-dependent selection will tend to
 favour rare immigrants over common residents, amplifying the effect of
 migration and undermining the efficacy of divergent natural selection to
 drive population differences. The only signal of divergent selection was a
 tendency for foreign fish to have higher parasite loads than residents,
 after controlling for MHC genotype rarity. Frequency-dependent ecological
 interactions have long been thought to promote speciation. Our results
 suggest a more nuanced view in which negative frequency dependence alters
 the fate of migrants to promote or constrain evolutionary divergence
 between populations.
description: Bolnick
 traitsData on stickleback
 origin, destination, treatment, phenotype, sex, growth, and
 survivalBolnick_traits.txtBolnick_parasitesParasite load data on control and recaptured caged stickleback.Bolnick_mhcMHC class IIb exon 2 genotype data from released and recaptured stickleback.dna2protConverts MHC DNA sequence haplotype identifiers into amino acid sequence identifiersMHC_masterFASTA file of MHC sequence readsTAs_alnAligned sequences of inferred alleles of MHC IIb exon 2.
DOI: 10.5061/dryad.3353b
title: Data from: The Victoria West: earliest prepared core technology in the Acheulean at Canteen Kopje and implications for the cognitive evolution of early hominids

description: Prepared core technology illustrates in-depth planning and the presence of
 a mental template during the core reduction process. This technology is,
 therefore, a significant indicator in studying the evolution of abstract
 thought and the cognitive abilities of hominids. Here, we report on
 Victoria West cores excavated from the Canteen Kopje site in central South
 Africa, with a preliminary age estimate of approximately 1 Ma (million
 years ago) for these cores. Technological analysis shows that the Victoria
 West cores bear similarities to the ‘Volumetric Concept’ as defined for
 the Levallois, a popular and widely distributed prepared core technology
 from at least 200 ka (thousand years ago). Although these similarities are
 present, several notable differences also occur that make the Victoria
 West a unique and distinctive prepared core technology; these are:
 elongated and convergent core shapes, consistent blow directions for flake
 removal, a predominance of large side-struck flakes, and the use of these
 flakes to make Acheulean large cutting tools. This innovative core
 reduction strategy at Canteen Kopje extends the roots of prepared core
 technology to the latter part of the Early Acheulean and clearly
 demonstrates an increase in the cognitive abilities and complexities of
 hominids in this time period.
description: Figure S1: Victoria West
 cores with overshot preferential removals (a, b, c) and small sized
 removal (d). Note that although the size of specimen a is also small, the
 preferential removal is still large when compared with the overall size of
 the core. The yellow arrows show the preparation of the two surfaces, the
 red arrows show the preferential flake removal directions, and the blue
 arrows show scars overlapping the preferential removal. a, b , c and d
 correspond to the specimens CK2919, CK8091, CK4916 and CK4597 respectively
 (see Table S1 for raw data).figure
 S1.jpgFigure S2: Victoria West
 cores with small removals (a, b, c) and non-ideal blow direction (d). The
 yellow arrows show the preparation of the two surfaces, and the red arrows
 show the preferential flake removal directions. a, b , c and d correspond
 to the specimens CK3708, CK8702, CK5837 and CK3936 respectively (see Table
 S1 for raw data).figure
 S2.jpgFigure S3: Victoria West
 cores from the top of the layer containing the Victoria West core
 assemblage. The yellow arrows show the preparation of the two surfaces,
 the red arrows show the preferential flake removal directions, and the
 blue arrows show scars overlapping the preferential removal. a, b , c and
 d correspond to the specimens CK3142, CK3004, CK2225 and CK2208
 respectively (see Table S1 for raw data).Figure
 S3.jpgTable S1.Raw data for
 the Victoria West cores excavated from the Canteen Kopje
 site.Table
 S1.xls
DOI: 10.5061/dryad.vb724
title: Data from: The plastoquinone pool of Nannochloropsis oceanica is not completely reduced during bright light pulses

description: The lipid-producing model alga Nannochloropsis oceanica has a distinct
 photosynthetic machinery. This organism possesses chlorophyll a as its
 only chlorophyll species, and has a high ratio of PSI to PSII. This high
 ratio of PSI to PSII may affect the redox state of the plastoquinone pool
 during exposure to light, and consequently may play a role in activating
 photoprotection mechanisms. We utilized pulse-amplitude modulated
 fluorometry to investigate the redox state of the plastoquinone pool
 during and after bright light pulses. Our data indicate that even very
 intense (5910 μmol photons s-1m-2 of blue light having a wavelength of 440
 nm) light pulses of 0.8 second duration are not sufficient to completely
 reduce the plastoquinone pool in Nannochloropsis. In order to achieve
 extensive reduction of the plastoquinone pool by bright light pulses,
 anaerobic conditions or an inhibitor of the photosynthetic electron
 transport chain has to be utilized. The implication of this finding for
 the application of the widely used saturating pulse method in algae is
 discussed.
description: High light data, figure
 1, 2, 3aData from high light
 experiment performed without DBMIB, used to generate figure 1, 2 and
 3aAnaerobic data, figure
 1, 2, 3aData from anaerobic
 experiment, used in figure 1, 2, and 3aHigh light + DBMIB data,
 figure 1, 2, 3aData from high light
 experiment performed with DBMIB, used in figure 1, 2, and
 3aLight_pulse_intensity_experiment_figure_3bData from experiment investigating the effect of light pulse intensity, used to generate figure 3b
DOI: 10.5281/zenodo.18388409
title: Conceptual Framework for Onco-Physics: Innovative Modulation of Tumor Physical Properties through Osmotic Pressure and Surface Tension Engineering

description: This conceptual manuscript delineates a pioneering paradigm in onco-physics, conceptualizing solid tumors as physical materials endowed with quantifiable osmotic pressure, surface tension, and fluid-mechanical attributes. We posit unprecedented innovations for tumor remediation by precisely modulating these physical properties, eschewing conventional chemical interventions. Leveraging rigorous mathematical derivations, reproducible Python simulations grounded in empirical data from published literature, advanced sensitivity analyses including Sobol indices, Bayesian inference, uncertainty quantification, and falsifiability criteria, we substantiate the conceptual feasibility and prospective impact. A multi-phased roadmap from experimental validation to industrial manufacturing is articulated, augmented by high-fidelity TikZ visualizations and comparative tabular analyses. Applications in nuclear and radiation medicine are expounded, alongside ethical deliberations and a comprehensive literature review. This manuscript is self-contained, with all requisite data embedded therein. The framework is positioned as a hypothesis-generating theoretical study, with detailed methodological descriptions to facilitate reproducibility and future empirical testing.
DOI: 10.5061/dryad.tc28h
title: Data from: Non-traditional isotope perspectives in vertebrate palaeobiology

description: The recent development of multi-collector inductively coupled plasma mass
 spectrometry (MC-ICP-MS) notably in the disciplines of earth sciences, now
 allows the precise measurement of isotope ratios, even at low
 concentration. Non-traditional isotope systems, such as alkaline earth
 (Ca, Mg) and transition (Cu, Fe, Zn) metals are now being measured in a
 variety of biological tissues, including bone and teeth. Although our
 understanding of the environmental and biological mechanisms behind the
 fractionation of such elements is still in its infancy, some of these
 isotopes are suspected to fractionate along the food chain, as has been
 reported in the literature for calcium, magnesium and zinc. Other
 geochemical methods, such as concentration analyses, permit a prior
 assessment of diagenesis in the fossils and such an approach indicates
 that in some circumstances, not only enamel but also dentine or bone can
 preserve its original biogenic composition. The aims here are to: review
 the current knowledge surrounding these various isotopic tools; address
 their potential preservation in biological apatite; and provide the
 palaeobiologist with a guide to the different toolkits available,
 including a discussion of their potential applications in vertebrate
 palaeobiology with a case study involving two mammal assemblages from the
 Pleistocene of Europe.
description: SuppFig1-mass frac line
 suppFig. S1. Triple isotope
 plot (δ44/42Ca versus δ43/42Ca in ‰) of all data analysed in this study.
 Regression line is Y = 0.487 (± 0.022) X – 0.024 (± 0.030) with R2 =
 0.974. This is in agreement with mass dependent fractionation slope of
 0.507 according to exponential law.SuppFig2-Ca vs
 MnFig. S2. Manganese
 plotted against δ44/42Ca values for bone and enamel samples measured in
 this study.TableS2R1Table S2. Calcium isotope values (expressed as δ44/42Ca and δ43/42Ca (in ‰) relative to standard ICP Ca-Lyon) measured on two Pleistocene assemblages as well as elemental concentrations for some major and trace elements. (1) δ13C and δ15N values from Bochoerens et al. 1997. Tooth type: capital letters refer to the upper tooth row.SuppFig3-Jaurens sampling 1-2Photographs of samples analysed for this study; Canis lupus, Crocuta crocuta, Panthera spelaea, P. pardus, Ursos arctos; Jaurens, Corrèze, France.SuppFig4-Jaurens sampling 2-2Figure S4. Photographs of samples analysed for this study; Ursos arctos, Coelondonta antiquitatis, Rangifer tarandus, Bison priscus; Jaurens, Corrèze, France.TableS1Table S1. Data from the literature used in the model of the water/rock ratio presented in Fig. 2.