cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1pc19
title: Data from: Evidence for arrested succession in a liana‐infested Amazonian forest

description: 1. Empirical evidence and modelling both suggest that global changes may
 lead to an increased dominance of lianas, and thus to an increased
 prevalence of liana-infested forest formations in tropical forests. The
 implications for tropical forest structure and the carbon cycle remain
 poorly understood. 2. We studied the ecological processes underpinning the
 structure and dynamics of a liana-infested forest in French Guiana, using
 a combination of long-term surveys (tree, liana, seedling and litterfall),
 soil chemical analyses and remote sensing approaches (LiDAR and Landsat).
 3. At stand scale and for adult-trees, the liana-infested forest had
 higher growth, recruitment, and mortality rates than the neighbouring
 high-canopy forest. Both total seedling density and tree seedling
 recruitment were lower in the liana-infested forest. Stand scale
 aboveground biomass of the liana-infested forest was 58% lower than in the
 high-canopy forest. 4. Aboveground net primary productivity (ANPP) was
 comparable in the liana-infested and high-canopy forests. However, due to
 more abundant leaf production, the relative contribution of fast turnover
 carbon pools to ANPP was larger in the liana-infested forest and the
 carbon residence time was half that of the high-canopy forest. 5. Although
 soils of the liana-infested forest were richer in nutrients, soil
 elemental ratios suggest that liana-infested forest and high-canopy forest
 soils both derive from the same geological substrate. The higher nutrient
 concentration in the liana-infested forest may therefore be the result of
 a release of nutrients from vegetation after a forest blow down. 6. Using
 small-footprint LiDAR campaigns, we show that the overall extent of the
 liana-infested forest has remained stable from 2007 to 2012 but about 10%
 of the forest area changed in forest cover type. Landsat optical imagery
 confirms the liana-infested forest presence in the landscape for at least
 25 years. 7. Synthesis: Because persistently high rates of liana
 infestation are maintained by the fast dynamics of the liana-infested
 forest, liana-infested forests here appear to be the result of an arrested
 tropical forest succession. If the prevalence of such arrested succession
 forests were to increase in the future, this would have important
 implications for the carbon sink potential of Amazonian forests.
description: datazip files of the data
 used in the article except for Tree demographical data available at
 www.forestplot.com/.
DOI: 10.5061/dryad.6br16
title: Data from: A case study of extant and extinct Xenarthra cranium covariance structure: implications and applications to paleontology

description: Most of the mammalian diversity is known only from fossils, and only a few
 of these fossils are well preserved or abundant. This under sampling poses
 serious problems for understanding mammalian phenotypic evolution under a
 quantitative genetics framework, since this framework requires estimation
 of a group's additive genetic variance-covariance matrix (G-matrix),
 which is impossible, and estimating a phenotypic variance-covariance
 matrix (P-matrix) requires larger sample sizes then what is often
 available for extinct species. One alternative is to use G- or P-matrices
 from extant taxa as surrogates for the extinct ones. Although there are
 reasons to believe this approach is usually safe, it has not been fully
 explored. By thoroughly determining the extant and some extinct Xenarthra
 (Mammalia) cranium P-matrices, this study aims to explore the feasibility
 of using extant G- or P-matrices as surrogates for the extinct ones, and
 to provide guidelines regarding the reliability of this strategy and the
 necessary sample sizes. Variance-covariance and correlation P-matrices for
 35 cranium traits from 16 xenarthran genera (12 extant and four extinct)
 were estimated and compared between genera. Results show xenarthran
 P-matrix structures are usually very similar if sample sizes are
 reasonable. This study and others developed with extant therian mammals
 suggest, in general, using extant G- or P-matrices as an approximation to
 extinct ones is a valid approach. Nevertheless, the accuracy of this
 approach depends on sample size, selected traits and the type of matrix
 being considered.
description: supplementary
 materialsupplementary text +
 supplementary figures + supplementary tablesall_supplementary_material.pdf
DOI: 10.60507/fk2/iiuh2q/ksbbbw
title: Chous_1380_images.zip
DOI: 10.60507/fk2/iiuh2q/lqghip
title: Chous_1380_model.zip
DOI: 10.60507/fk2/iiuh2q/twdsqf
title: GÜNZEL_Chous_1380_readme.txt
DOI: 10.60507/fk2/iiuh2q
title: Attic Red-Figure Chous in the Museum Alte Kulturen Tübingen (Inv. 1380)

description: Attic Red-Figure Chous in the Museum Alte Kulturen (University of Tübingen, Inv. 1380) showing a youth with a chous pulling a cart with a hare. Date: -430 to -420 BC.
description: Agisoft Metashape/Reality Capture, 2.2.0
description: Blender, 4.0
description: ZBrush, 2023.2
description: SubstanceDesigner, 15.0.3
description: SubstancePainter, 11.1.0
DOI: 10.5061/dryad.1013
title: Data from: Patterns of morphological and plastid DNA variation in the Corallorhiza striata species complex (Orchidaceae)

description: Corallorhiza striata is a wide-ranging, morphologically variable,
 mycoheterotrophic species complex distributed across North America.
 Objectives of this study were to assess relationships and test validity of
 previously delimited varieties of C. striata, including the recently
 described C. bentleyi. Two plastid DNA regions were sequenced for
 individuals from several populations across North America, identifying
 four major clades. The large-flowered C. striata var. striata (northern
 U.S.A., southern Canada) was sister to the smaller-flowered var.
 vreelandii (southwestern U.S.A., Mexico), and these were sister to a
 Californian clade with relatively intermediate-sized flowers. C. striata
 var. involuta (Mexico) and the endangered C. bentleyi (eastern U.S.A.)
 shared a close relationship, sister to the remaining C. striata. Principal
 Components Analysis and Nonparametric Multivariate Analysis of Variance on
 nine quantitative morphological characters, using plastid DNA clades as
 independent variables, demonstrated strong correlations between molecular
 and morphological groupings. Morphological analyses supported
 differentiation of both C. striata var. involuta and C. bentleyi relative
 to all other accessions of C. striata, suggesting their recognition as
 separate species; these findings will have future implications for
 conservation. The biogeographic scenario was more complex than previously
 thought, with members of two major plastid DNA lineages (C. bentleyi/var.
 involuta and the remaining C. striata) existing in Mexico and
 U.S.A./Canada. These findings contribute to a burgeoning body of data on
 poorly studied North American plant distributions extending into southern
 Mexico.
description: Supplementary Figure
 1A.
 Identical Maximum Parsimony (MP) and Maximum Likelihood B. MP and ML
 topologies for rpl32-trnL spacer, and C. ML topology for combined dataset,
 excluding 15 indel charactersSuppl
 Fig1.pdfSupplementary Figure
 2Histograms for nine
 morphological character measurements in millimeters.Suppl
 Fig2.pdf
DOI: 10.5061/dryad.vf345
title: Data from: An assessment of ancient DNA preservation in Holocene-Pleistocene fossil bone excavated from the world heritage Naracoorte Caves, South Australia

description: Although there is a long history of research into the fossil deposits of
 the Naracoorte Caves (South Australia), ancient DNA (aDNA) has not been
 integrated into any palaeontological study from this World Heritage site.
 Here, we provide the first evidence of aDNA preservation in Holocene- and
 Pleistocene-aged fossil bone from a deposit inside Robertson Cave. Using a
 combination of metabarcoding and shotgun next-generation sequencing
 approaches, we demonstrate that aDNA from diverse taxa can be retrieved
 from bulk bone as old as 18 600 cal a BP. However, the DNA is highly
 degraded and contains a lower relative proportion of endogenous sequences
 in bone older than 8400 cal a BP. Furthermore, modelling of DNA
 degradation suggests that the decay rate is rapid, and predicts a very low
 probability of obtaining informative aDNA sequences from extinct
 megafaunal bones from Naracoorte (ca. 50 000 cal a BP). We also provide
 new information regarding the past faunal biodiversity of Robertson Cave,
 including families that have not been formerly described in the fossil
 record from here before. Collectively, these data demonstrate the
 potential for future aDNA studies to be conducted on material from
 Naracoorte, which will aid in the understanding of faunal turnover in
 southern Australia.
description: 12SAO_12SMARSMINI_Amplicon_sequences_all_samplesFiltered NGS sequences of 12SAO and 12SMarsMini amplicons from Layers 1-6 (all subsamples and extracts).Layer1_3_6_Shotgun_sequences
DOI: 10.6084/m9.figshare.31157395
title: NEURAL_MAPPING_ARCHIVE_FINAL: Structural Midbrain Symmetry and Predictive Fluid Dynamics (sub-JED2026)

description: This dataset provides a 1.0_Verified structural and behavioral mapping of an optimized cognitive state, documented over a 31-day acquisition period (December 26, 2025 – January 26, 2026). The project identifies the specific midbrain architecture associated with "Sudden Savant" syndrome and the transition to effortless, zero-friction thinking. Core Research Components: Structural Mapping (The "Stingray" Model): A spatial identification of the mesencephalon where bilateral symmetry of the substantia nigra serves as the primary anchor for cognitive stability. This alignment facilitates a "Basilar Pulse" that synchronizes brainstem activity. Neurological Insulation: Observations of reinforced myelination (Thick Fat Wall) which serves to eliminate "Static Grit"—the neural noise and resistance typical in standard serial processing. Functional Output: The transition to "Predictive Fluid Dynamics," a state where information is synthesized at high speeds without traditional cognitive load or mental effort. Scientific Utility: This archive is formatted according to BIDS 1.8.0 (Brain Imaging Data Structure) standards to allow for seamless integration into clinical databases at the NIH or the Treffert Center. It serves as a longitudinal baseline for researchers studying Acquired Savant Syndrome, Left Hemisphere Inhibition Release, and neural efficiency. Data Integrity: The repository includes a SHA-256 cryptographic hash to ensure the structural mapping remains immutable for future comparative studies. Location of Data Acquisition: Williamsburg, KY.<br>
DOI: 10.6084/m9.figshare.31157395.v1
title: NEURAL_MAPPING_ARCHIVE_FINAL: Structural Midbrain Symmetry and Predictive Fluid Dynamics (sub-JED2026)

description: This dataset provides a 1.0_Verified structural and behavioral mapping of an optimized cognitive state, documented over a 31-day acquisition period (December 26, 2025 – January 26, 2026). The project identifies the specific midbrain architecture associated with "Sudden Savant" syndrome and the transition to effortless, zero-friction thinking. Core Research Components: Structural Mapping (The "Stingray" Model): A spatial identification of the mesencephalon where bilateral symmetry of the substantia nigra serves as the primary anchor for cognitive stability. This alignment facilitates a "Basilar Pulse" that synchronizes brainstem activity. Neurological Insulation: Observations of reinforced myelination (Thick Fat Wall) which serves to eliminate "Static Grit"—the neural noise and resistance typical in standard serial processing. Functional Output: The transition to "Predictive Fluid Dynamics," a state where information is synthesized at high speeds without traditional cognitive load or mental effort. Scientific Utility: This archive is formatted according to BIDS 1.8.0 (Brain Imaging Data Structure) standards to allow for seamless integration into clinical databases at the NIH or the Treffert Center. It serves as a longitudinal baseline for researchers studying Acquired Savant Syndrome, Left Hemisphere Inhibition Release, and neural efficiency. Data Integrity: The repository includes a SHA-256 cryptographic hash to ensure the structural mapping remains immutable for future comparative studies. Location of Data Acquisition: Williamsburg, KY.<br>
DOI: 10.5061/dryad.q2g6h
title: Data from: The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves

description: The process of domestication can exert intense trait-targeted selection on
 genes and regulatory regions. Specifically, rapid shifts in the structure
 and sequence of genomic regulatory elements could provide an explanation
 for the extensive, and sometimes extreme, variation in phenotypic traits
 observed in domesticated species. Here, we explored methylation
 differences from &gt;24 000 cytosines distributed across the genomes
 of the domesticated dog (Canis familiaris) and the grey wolf (Canis
 lupus). PCA and model-based cluster analyses identified two primary
 groups, domestic vs. wild canids. A scan for significantly differentially
 methylated sites (DMSs) revealed species-specific patterns at 68 sites
 after correcting for cell heterogeneity, with weak yet significant
 hypermethylation typical of purebred dogs when compared to wolves (59% and
 58%, P &lt; 0.05, respectively). Additionally, methylation patterns at
 eight genes significantly deviated from neutrality, with similar trends of
 hypermethylation in purebred dogs. The majority (&gt;66%) of
 differentially methylated regions contained or were associated with
 repetitive elements, indicative of a genotype-mediated trend. However,
 DMSs were also often linked to functionally relevant genes (e.g.
 neurotransmitters). Finally, we utilized known genealogical relationships
 among Yellowstone wolves to survey transmission stability of methylation
 marks, from which we found a substantial fraction that demonstrated high
 heritability (both H2 and h2 &gt; 0.99). These analyses provide a
 unique epigenetic insight into the molecular consequences of recent
 selection and radiation of our most ancient domesticated companion, the
 dog. These findings suggest selection has acted on methylation patterns,
 providing a new genomic perspective on phenotypic diversification in
 domesticated species.
description: GO gene
 lists_NeutralityThe gene IDs that were
 used for the GO analyses for the Neutrality results.EWAsher_GOA list of our genes used for GO analyses (from the list of 68 outliers) with the background list that we used in the second tab.Epigenotype_FilesEpigenotype variant files used for ADMIXTURE, dendrograms, and PCAEpigenotype_File.xlsxBS-Seeker_Log_FilesBS-Seeker results log files for dog and wolf samplesShared_Methylation_SitesFile containing the methylation frequency for each individual at all shares sites (24,205)
DOI: 10.5061/dryad.bf486
title: Data from: The conservation value of high elevation habitats to North American migrant birds

description: The basic patterns of faunal community composition and habitat
 associations of high elevation mountainous regions are poorly-known. This
 is true for the avifauna of western North America where our knowledge of
 high elevation use is primarily restricted to breeding assemblages. Here
 we report on systematic avian surveys of high elevation habitats over four
 years in British Columbia conducted during the post-breeding and fall
 migration periods (Aug–Oct). We detected a remarkable diversity of birds
 (95 species in 30 families) using alpine, subalpine, and montane forest,
 many of which used these habitats seasonally. One quarter of the species
 are on lists of conservation concern. Density, species richness, and
 community composition varied considerably between habitats and mountain
 ranges within the study area, especially between the western slope of the
 Coast range and other ranges. Most species exhibited strong temporal
 variation in patterns of abundance that were related to migratory
 behavior. From an extensive literature-based survey, we found that ~ 35%
 of North America's breeding bird species use high elevations, and
 that all primary high elevation habitats are important for full life-cycle
 conservation of this avifauna. Our findings highlight the importance of
 high elevation habitats to migrating birds from wide-ranging breeding
 distributions for at least three months of the year, a period equivalent
 to the length of the breeding season for most species. These results
 emphasize the need for effective conservation of fragile alpine and other
 high elevation habitats that are increasingly threatened by local,
 regional, and global anthropogenic disturbance.
description: British Columbia High
 Elevation Bird DatasetA single flat file in
 .csv format including all raw field-collected observation data included in
 the accompanying articleBritishColumbiaHighElevationBirdDataset.csv
DOI: 10.5061/dryad.d15v3
title: Data from: Congruent deep relationships in the grape family (Vitaceae) based on sequences of chloroplast genomes and mitochondrial genes via genome skimming

description: Vitaceae is well-known for having one of the most economically important
 fruits, i.e., the grape (Vitis vinifera). The deep phylogeny of the grape
 family was not resolved until a recent phylogenomic analysis of 417
 nuclear genes from transcriptome data. However, it has been reported
 extensively that topologies based on nuclear and organellar genes may be
 incongruent due to differences in their evolutionary histories. Therefore,
 it is important to reconstruct a backbone phylogeny of the grape family
 using plastomes and mitochondrial genes. In this study, next-generation
 sequencing data sets of 27 species were obtained using genome skimming
 with total DNAs from silica-gel preserved tissue samples on an Illumina
 HiSeq 2500 instrument. Plastomes were assembled using the combination of
 de novo and reference genome (of V. vinifera) methods. Sixteen
 mitochondrial genes were also obtained via genome skimming using the
 reference genome of V. vinifera. Extensive phylogenetic analyses were
 performed using maximum likelihood and Bayesian methods. The topology
 based on either plastome data or mitochondrial genes is congruent with the
 one using hundreds of nuclear genes, indicating that the grape family did
 not exhibit significant reticulation at the deep level. The results
 showcase the power of genome skimming in capturing extensive phylogenetic
 data: especially from chloroplast and mitochondrial DNAs.
description: 174_coding_noncoding_genes174 regions including 79 coding genes and 95 non-coding regions79genes_concatenated79 coding genes56genes-less-9056 coding genes with the sequence identity less than 90%16mitogenes-modified16 mitochondrial genes26genes-less-8526 coding genes with the sequence identity less than 85%10genes_less_8010 coding genes with sequence identity less than 80%concatenated_non_coding_95genes95 non-coding regions
DOI: 10.5061/dryad.4v131
title: Data from: Optimizing mouse surgery with online rectal temperature monitoring and preoperative heat supply. Effects on post-ischemic acute kidney injury.

description: Body temperature affects outcomes of tissue injury. We hypothesized that
 online body core temperature recording and selective interventions help to
 standardize peri-interventional temperature control and the reliability of
 outcomes in experimental renal ischemia reperfusion injury (IRI). We
 recorded core temperature in up to seven mice in parallel using a Thermes
 USB recorder and ret-3-iso rectal probes with three different protocols.
 Setup A: Heating pad during ischemia time; Setup B: Heating pad from
 incision to wound closure; Setup C: A ventilated heating chamber before
 surgery and during ischemia time with surgeries performed on a heating
 pad. Temperature profile recording displayed significant declines upon
 installing anesthesia. The profile of the baseline experimental setup A
 revealed that &lt;1 % of the temperature readings were within the
 target range of 36.5 to 38.5 °C. Setup B and C increased the target range
 readings to 34.6 ± 28.0 % and 99.3 ± 1.5 %, respectively. Setup C
 significantly increased S3 tubular necrosis, neutrophil influx, and mRNA
 expression of kidney injury markers. In addition, using setup C different
 ischemia times generated a linear correlation with acute tubular necrosis
 parameters at a low variability, which further correlated with the degree
 of kidney atrophy 5 weeks after surgery. Changing temperature control
 setup A to C was equivalent to 10 minutes more ischemia time. We conclude
 that body temperature drops quickly in mice upon initiating anesthesia.
 Immediate heat supply, e.g. in a ventilated heating chamber, and online
 core temperature monitoring can help to standardize and optimize
 experimental outcomes.
description: data_compilation_Marschner_et_alCompilation of ORTR raw data, histopathological and immunopathological scoring, qRT-PCR data for kidney injury markers and kidney weight data. The data refer to the Figures 1, 3, 4 and 7 of the manuscript.
DOI: 10.5061/dryad.11cv0
title: Data from: Coordinated dispersal and pre-Isthmian assembly of the Central American ichthyofauna

description: We document patterns of coordinated dispersal over evolutionary time
 frames in heroine cichlids and poeciliine live-bearers, the two most
 species-rich clades of freshwater fishes in the Caribbean basin. Observed
 dispersal rate (DO) values were estimated from time-calibrated molecular
 phylogenies in Lagrange+, a modified version of the ML-based parametric
 biogeographic program Lagrange. DO is measured in units of ‘wallaces’ (wa)
 as the number of biogeographic range-expansion events per million years.
 DO estimates were generated on a dynamic paleogeographic landscape of five
 areas over three time intervals from Upper Cretaceous to Recent. Expected
 dispersal rate (DE) values were generated from alternative paleogeographic
 models, with dispersal rates proportional to target area and source-river
 discharge volume, and inversely proportional to paleogeographic distance.
 Correlations between DO and DE were used to assess the relative
 contributions of these three biogeographic parameters. DO estimates imply
 a persistent dispersal corridor across the Eastern (Antillean) margin of
 the Caribbean plate, under the influence of prevailing and perennial
 riverine discharge vectors such as the Proto-Orinoco-Amazon (POA) river.
 Ancestral area estimation places the earliest colonizations of the Greater
 Antilles and Central America (GACA) during the Paleocene-Eocene (c. 58-45
 Ma), potentially during the existence of an incomplete Paleogene Arc (~59
 Ma) or Lesser Antilles Arc (~45 Ma), but predating the GAARlandia land
 bridge (~34-33 Ma). Paleogeographic distance is the single best predictor
 of DO. The Western (Central American) plate margin did not serve as a
 dispersal corridor until the Late Neogene (12-0 Ma), and contributed
 relatively little to the formation of modern distributions.
description: Supplementary
 Figures-Caribbean PlateMolecular phylogenies
 and Ancestral area estimates of Poeciliidae and
 CichlidaeSuppl_Figures.docx