cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0t407
title: Data from: Convergent local adaptation to climate in distantly related conifers

description: When confronted with an adaptive challenge, such as extreme temperature,
 closely related species frequently evolve similar phenotypes using the
 same genes. Although such repeated evolution is thought to be less likely
 in highly polygenic traits and distantly related species, this has not
 been tested at the genome scale. We performed a population genomic study
 of convergent local adaptation among two distantly related species,
 lodgepole pine and interior spruce. We identified a suite of 47 genes,
 enriched for duplicated genes, with variants associated with spatial
 variation in temperature or cold hardiness in both species, providing
 evidence of convergent local adaptation despite 140 million years of
 separate evolution. These results show that adaptation to climate can be
 genetically constrained, with certain key genes playing nonredundant
 roles.
description: Data_archive_part1This archive contains all of the intermediate data files and R-scripts needed to generate the main figures and most of the supplementary materials. The original sequence data are stored on the Short Read Archive.yeaman_pine_spruce_convergence_archive.tbzData_archive_part2This contains the second part of the data (too large for a single file upload)yeaman_pine_spruce_convergence_archive2.tbz
DOI: 10.4121/bb78b529-73e0-4efe-a026-fd9ac71c6b48
title: Data on “Matured gullies act primarily as sediment pathways rather than sources in catchment-scale sediment budgets”

description: This dataset contains rainfall, monitored flow and sediment rates, gully morphology, and erosion model simulation data collected between August 2023 and August 2024. The data were collected to support analyses of rainfall-runoff processes, sediment transport, gully erosion, and the calibration of the SIMWE erosion model.<br>Rainfall data include daily rainfall intensity, duration, and total rainfall amount from August 2023 to August 2024. Rainfall was measured with a rain gauge or an automated weather station and aggregated to daily values, following standard quality control procedures.<br>Hydrological and sediment data were collected using both manual field measurements and automated sensors. Manual measurements of water depth, flow, and sediment rate were taken twice daily in the morning and evening using standardised field methods. Automated measurements were collected using TD Diver sensors installed at fixed locations at the catchment outlet locations. These sensors recorded water depth and derived flow and sediment rates at ten-minute intervals. Sensor data were corrected and processed using site-specific calibration relationships.<br>Gully morphology data were collected during a field-based gully inventory conducted in Summer 2024. Measurements include gully dimensions and geometric characteristics obtained through direct field observation using measuring tools and GPS. The inventory followed a consistent protocol to ensure repeatability.The dataset also includes model outputs from the SIMWE erosion model. Flow simulations were generated for spring, summer, and autumn seasons and calibrated using Manning roughness coefficients. Sediment simulations were generated for the same seasons using transport coefficient, detachment coefficient, and critical shear parameters. Model calibration and evaluation were performed by comparing simulated results with observed field and sensor data.<br>All data collection was conducted in accordance with applicable legal and ethical requirements, with permission from relevant landowners and authorities. No personal or sensitive human data are included. The dataset is intended to support reproducible research in hydrology, erosion modelling, and sediment transport analysis.
DOI: 10.5061/dryad.62t17
title: Data from: Predictive modeling of ecological patterns along linear-feature networks

description: Ecological patterns and processes often take place within linear-feature
 networks, and this has implications when analysing the spatial
 configuration of such patterns or processes across a landscape. One such
 pattern is the use of landscapes by human recreationists: an important
 variable in animal habitat selection and behaviour. Due to the difficulty
 in obtaining data, ecologists tend to use coarse metrics such as
 linear-feature density, while the extent and timing of human activity are
 often ignored. Remote detector equipment and its increasing use in
 ecological studies allow for large volumes of data on human activity to be
 collected. However, the analysis of these data still can be challenging.
 Using a combination of generalised linear mixed-effects models and
 network-based ordinary kriging, we developed a method for estimating
 spatial and temporal variations in motorised and non-motorised activities
 across a complex linear-feature network. Trail cameras were set up between
 2012 and 2014 and monitored motorised and non-motorised activities at 238
 different trail sites across a 2824 km2 region of the eastern slopes and
 foothills of central Alberta's Rocky Mountains. We evaluate the
 predictive capacity of this approach, demonstrate its application and
 discuss its merits and limitations. This method offers a straightforward
 analysis that can be applied to remotely acquired data to give a useful
 metric for assessing wildlife responses to human activity, and has
 potential application beyond the highlighted example.
description: Data and
 codeRaw data and R
 coderandom_to_sample_200m_1Random points for interpolation, part 1random_to_sample_200m_2Random points for interpolation part 2
DOI: 10.4121/bb78b529-73e0-4efe-a026-fd9ac71c6b48.v1
title: Data on “Matured gullies act primarily as sediment pathways rather than sources in catchment-scale sediment budgets”

description: This dataset contains rainfall, monitored flow and sediment rates, gully morphology, and erosion model simulation data collected between August 2023 and August 2024. The data were collected to support analyses of rainfall-runoff processes, sediment transport, gully erosion, and the calibration of the SIMWE erosion model.<br>Rainfall data include daily rainfall intensity, duration, and total rainfall amount from August 2023 to August 2024. Rainfall was measured with a rain gauge or an automated weather station and aggregated to daily values, following standard quality control procedures.<br>Hydrological and sediment data were collected using both manual field measurements and automated sensors. Manual measurements of water depth, flow, and sediment rate were taken twice daily in the morning and evening using standardised field methods. Automated measurements were collected using TD Diver sensors installed at fixed locations at the catchment outlet locations. These sensors recorded water depth and derived flow and sediment rates at ten-minute intervals. Sensor data were corrected and processed using site-specific calibration relationships.<br>Gully morphology data were collected during a field-based gully inventory conducted in Summer 2024. Measurements include gully dimensions and geometric characteristics obtained through direct field observation using measuring tools and GPS. The inventory followed a consistent protocol to ensure repeatability.The dataset also includes model outputs from the SIMWE erosion model. Flow simulations were generated for spring, summer, and autumn seasons and calibrated using Manning roughness coefficients. Sediment simulations were generated for the same seasons using transport coefficient, detachment coefficient, and critical shear parameters. Model calibration and evaluation were performed by comparing simulated results with observed field and sensor data.<br>All data collection was conducted in accordance with applicable legal and ethical requirements, with permission from relevant landowners and authorities. No personal or sensitive human data are included. The dataset is intended to support reproducible research in hydrology, erosion modelling, and sediment transport analysis.
DOI: 10.5061/dryad.70t85k2
title: Data from: Multi-proxy evidence highlights a complex evolutionary legacy of maize in South America

description: Domesticated maize evolved from wild teosinte under human influences in
 Mexico beginning around 9,000 BP, traversed Central America by ~7,500 BP,
 and spread into South America by ~6,500 BP. Landrace and archaeological
 maize genomes from South America suggest that the ancestral population to
 South American maize was brought out of the domestication center in Mexico
 and became isolated from the wild teosinte gene pool before traits of
 domesticated maize were fixed. Deeply structured lineages then evolved
 within South America out of this partially domesticated progenitor
 population. Genomic, linguistic, archaeological, and paleoecological data
 suggest that the southwestern Amazon was a secondary improvement center
 for partially domesticated maize. Multiple waves of human-mediated
 dispersal are responsible for the diversity and biogeography of modern
 South American maize.
description: GERP scores and neutral
 model- GERP; mutation load
 analysis. - chr10.4degen.tre; newick-format neutral model tree generated
 from fourfold-degenerate sites of plant genomes aligned to chromosome 10
 of maize. - Zea_mays.allChr.rates.gz; gerpcol output (expected
 substitutions and RS scores) used for analysis across the maize
 genome.GERP.tar.gzMaize SNP callsBinary plink-formatted files containing the complete set of SNP calls before processing for linkage.snpCalls.tar.gzmapDamage resultsComplete mapDamage output files for nine newly sequenced ancient maize genomes.mapDamage.tar.gzCustom scriptsContains custom scripts with functions described in the supplemental methods. Refer the commented header lines of each for details of usage.scripts.tar.gzMappable regionsContains 'ZeaV4.map35.plus20.bed', a conservative mappability bed file described in the supplemental methods.mappability.tar.gzREADMEREADME for repository contents
DOI: 10.5061/dryad.cq2rb
title: Data from: Compositional and functional shifts in arctic fungal communities in response to experimentally increased snow depth

description: Climate warming leads to more intensive evaporation from the Arctic sea
 resulting in increased precipitation in the low Arctic, e.g., higher
 snowfall during winter. Deeper snow keeps the arctic soils warmer and
 alters soil attributes and vegetation, e.g., increase in nitrogen
 availability, expansion of shrubs and decline in shade-intolerant lichens
 and bryophytes. Changes in soil properties and vegetation are expected to
 influence on saprotrophic and plant-symbiotic fungi, but how increased
 snow depth affects their community composition remain unknown. In the
 present work, we used DNA metabarcoding to study the effects of long-term
 experimental manipulations of snow depth on soil fungal communities in dry
 heath and moist tussock tundra in Arctic Alaska. We report strong changes
 in fungal community compositions in the two tundra types, with pronounced
 declines observed in the majority of fungal functional guilds, including
 ectomycorrhizal, lichenized, plant pathogenic, saprotrophic and
 bryophyte-associated species. The observed changes in lichenized and
 bryophyte-associated fungi are in agreement with previously published
 above-ground changes, i.e. decrease of lichen and bryophyte cover and
 diversity. However, the majority of observed trends, including the decline
 of ectomycorrhizal fungi (that were anticipated to benefit from the
 expansion of their host plants), suggest that changes in fungal
 communities do not entirely correspond to and are not primarily driven by
 shifts in vegetation. Instead, arctic fungal communities appear to exhibit
 faster turnover that may be influenced by dynamic interactions with
 numerous biotic and abiotic factors, e.g., soil nutrient cycling and
 community dynamics in other groups of soil microorganisms. We highlight
 the importance of “below-ground studies” in assessing ecosystem responses
 to climatic changes, because faster turnover of microbial communities may
 be applicable for monitoring early-stage alterations caused by climatic
 changes.
description: DC1DC2DC3DC4DC5DS1DS2DS3DS4DS5MC1MC2MC3MC4MC5MS1MS2MS3MS4MS5
DOI: 10.5061/dryad.dp8b07r
title: Data from: Differential processing of nociceptive input within upper limb muscles

description: The cutaneous silent period is an inhibitory evoked response that
 demonstrates a wide variety of responses in muscles of the human upper
 limb. Classically, the cutaneous silent period results in a characteristic
 muscle pattern of extensor inhibition and flexor facilitation within the
 upper limb, in the presence of nociceptive input. The aims of the current
 study were: 1) to primarily investigate the presence and characteristics
 of the cutaneous silent period response across multiple extensor and
 flexor muscles of the upper limb, and 2) to secondarily investigate the
 influence of stimulation site on this nociceptive reflex response. It was
 hypothesized that the cutaneous silent period would be present in all
 muscles, regardless of role (flexion/extension) or the stimulation site.
 Twenty-two healthy, university-age adults (14 males; 8 females; 23 5 yrs)
 participated in the study. Testing consisted of three different
 stimulation sites (Digit II, V, and II+III nociceptive stimulation) during
 a low intensity, sustained muscle contraction, in which, 7 upper limb
 muscles were monitored via surface EMG recording electrodes. Distal
 muscles of the upper limb presented with the earliest reflex onset times,
 longest reflex duration, and lowest level of EMG suppression when compared
 to the more proximal muscles, regardless of extensor/flexor role.
 Additionally, the greatest overall inhibitory influence was expressed
 within the distal muscles. In conclusion, the present study provides a new
 level of refinement within the current understanding of the spinal
 organization associated with nociceptive input processing and the
 associated motor control of the upper limb. Subsequently, these results
 have further implications on the impact of nociception on supraspinal
 processing.
description: Raw data (.S2R/.smr
 format) with associated individual matlab filesRaw data files of the
 entire electrically stimulated data collection process for each digit.
 Exported individual subject matlab files of separate digit stimulations
 and responses.Sub01.zipSub02Sub03Sub04Sub05Sub06Sub07Sub08Sub09Sub10Sub11Sub12Sub13Sub14Sub15Sub16Sub17Sub18Sub19Sub20Sub21
DOI: 10.5061/dryad.fn82qp6
title: Data from: The evolutionary road from wild moth to domestic silkworm

description: The Silk Road, which derives its name from the trade of silk produced by
 the domestic silkworm Bombyx mori, was an important episode in the
 development and interaction of human civilizations. However, the detailed
 history behind silkworm domestication remains ambiguous, and little is
 known about the underlying genetics with respect to important aspects of
 its domestication. Here, we reconstruct the domestication processes and
 identify selective sweeps by sequencing 137 representative silkworm
 strains. The results present an evolutionary scenario in which silkworms
 may have been initially domesticated in China as trimoulting lines, then
 subjected to independent spreads along the Silk Road that gave rise to the
 development of most local strains, and further improved for modern silk
 production in Japan and China, having descended from diverse ancestral
 sources. We find that genes with key roles in nitrogen and amino acid
 metabolism may have contributed to the promotion of silk production, and
 that circadian-related genes are generally selected for their adaptation.
 We additionally identify associations between several candidate genes and
 important breeding traits, thereby advancing the applicable value of our
 resources.
description: select sweeps
 scriptsselect_sweeps_scripts.zipgenome referencegenome_reference.zipvariations.vcf
DOI: 10.5061/dryad.1bd3931
title: Data from: The telomere bouquet is a hub where meiotic double-strand breaks, synapsis, and stable homolog juxtaposition are coordinated in the zebrafish, Danio rerio

description: Meiosis is a cellular program that generates haploid gametes for sexual
 reproduction. While chromosome events that contribute to reducing ploidy
 (homologous chromosome pairing, synapsis, and recombination) are well
 conserved, their execution varies across species and even between sexes of
 the same species. The telomere bouquet is a conserved feature of meiosis
 that was first described nearly a century ago, yet its role is still
 debated. Here we took advantage of the prominent telomere bouquet in
 zebrafish, Danio rerio, and super-resolution microscopy to show that axis
 morphogenesis, synapsis, and the formation of double-strand breaks (DSBs)
 all take place within the immediate vicinity of telomeres. We established
 a coherent timeline of events and tested the dependence of each event on
 the formation of Spo11-induced DSBs. First, we found that the axis protein
 Sycp3 loads adjacent to telomeres and extends inward, suggesting a
 specific feature common to all telomeres seeds the development of the
 axis. Second, we found that newly formed axes near telomeres engage in
 presynaptic co-alignment by a mechanism that depends on DSBs, even when
 stable juxtaposition of homologous chromosomes at interstitial regions is
 not yet evident. Third, we were surprised to discover that ~30% of
 telomeres in early prophase I engage in associations between two or more
 chromosome ends and these interactions decrease in later stages. Finally,
 while pairing and synapsis were disrupted in both spo11 males and females,
 their reproductive phenotypes were starkly different; spo11 mutant males
 failed to produce sperm while females produced offspring with severe
 developmental defects. Our results support zebrafish as an important
 vertebrate model for meiosis with implications for differences in
 fertility and genetically derived birth defects in males and females.
description: Image
 files.nd2 Nikon image files
 and .oib Olympus FV 10000-image filesBlokhina_et_al_Figure_image_files.zip
DOI: 10.5061/dryad.7309b
title: Data from: Symmetry-breaking phase transitions in highly concentrated semen

description: New experimental evidence of self-motion of a confined active suspension
 is presented. Depositing fresh semen sample in an annular shaped
 microfluidic chip leads to a spontaneous vortex state of the fluid at
 sufficiently large sperm concentration. The rotation occurs unpredictably
 clockwise or counterclockwise and is robust and stable. Furthermore, for
 highly active and concentrated semen, richer dynamics can occur such as
 self-sustained or damped rotation oscillations. Experimental results
 obtained with systematic dilution provide a clear evidence of a phase
 transition towards collective motion associated with local alignment of
 spermatozoa akin to the Vicsek model. A macroscopic theory based on
 previously derived self-organized hydrodynamics models is adapted to this
 context and provides predictions consistent with the observed stationary
 motion.
description: Sample E889,
 concentration=0.63 Billon/mlE889_c0.63_o.tar.bz2Sample E889, concentration=0.84 Billon/mlE889_c0.84_o.tar.bz2Sample E889, concentration=1.27 Billon/mlE889_c1.27_o.tar.bz2Sample E889, concentration=1.45 Billon/mlE889_c1.45_o.tar.bz2Sample E889, concentration=1.69 Billon/mlE889_c1.69_o.tar.bz2Sample E889, concentration=2.54 Billon/mlE889_c2.54_o.tar.bz2Sample E889, concentration=2.03 Billon/mlE889_c2.03_o.tar.bz2Sample E890, concentration=0.65 Billon/mlE890_c0.65_o.tar.bz2Sample E890, concentration=0.49 Billon/mlE890_c0.49_o.tar.bz2Sample E890, concentration=1.11 Billon/mlE890_c1.11_o.tar.bz2Sample E890, concentration=0.97 Billon/mlE890_c0.97_o.tar.bz2Sample E890, concentration=1.30 Billion/mlE890_c1.30_o.tar.bz2Sample E890, concentration=1.56 Billion/mlE890_c1.56_o.tar.bz2Sample E890, concentration=1.95 Billion/mlE890_c1.95_o.tar.bz2Sample E769, concentration=0.51 Billion/mlE769_c0.51_o.tar.bz2Sample E769, concentration=0.85 Billion/mlE769_c0.85_o.tar.bz2Sample E769, concentration=1.27 Billion/mlE769_c1.27_o.tar.bz2Sample E769, concentration=1.46 Billion/mlE769_c1.46_o.tar.bz2Sample E769, concentration=1.70 Billion/mlE769_c1.70_o.tar.bz2Sample E769, concentration=2.04 Billion/mlE769_c2.04_o.tar.bz2Sample E828, concentration=0.30 Billion/mlE828_c0.30_o.tar.bz2Sample E828, concentration=0.41 Billion/mlE828_c0.41_o.tar.bz2Sample E828, concentration=0.61 Billion/mlE828_c0.61_o.tar.bz2Sample E828, concentration=0.70 Billion/mlE828_c0.70_o.tar.bz2Sample E828, concentration=0.81 Billion/mlE828_c0.81_o.tar.bz2Sample E828, concentration=0.98 Billion/mlE828_c0.98_o.tar.bz2Sample E828, concentration=1.22 Billion/mlE828_c1.22_o.tar.bz2Sample E7264, concentration=2.96 Billion/mlE7264_c2.96_o.tar.bz2Sample E509, concentration=0.85 Billion/mlE509_c0.85_o.tar.bz2Sample E510, concentration=0.43 Billion/mlE510_c0.43_o.tar.bz2Read meRead_me.pdf
DOI: 10.5061/dryad.3d7kq
title: Data from: Prediction error and repetition suppression have distinct effects on neural representations of visual information

description: Predictive coding theories argue that recent experience establishes
 expectations in the brain that generate prediction errors when violated.
 Prediction errors provide a possible explanation for repetition
 suppression, where evoked neural activity is attenuated across repeated
 presentations of the same stimulus. The predictive coding account argues
 repetition suppression arises because repeated stimuli are expected,
 whereas non-repeated stimuli are unexpected and thus elicit larger neural
 responses. Here we employed electroencephalography in humans to test the
 predictive coding account of repetition suppression by presenting
 sequences of visual gratings with orientations that were expected either
 to repeat or change in separate blocks of trials. We applied multivariate
 forward modelling to determine how orientation selectivity was affected by
 repetition and prediction. Unexpected stimuli were associated with
 significantly enhanced orientation selectivity, whereas selectivity was
 unaffected for repeated stimuli. Our results suggest that repetition
 suppression and expectation have separable effects on neural
 representations of visual feature information.
description: Participant 1 EEG
 dataParticipant 1 EEG
 dataP-1(Combinedcleaned).setParticipant 2 EEG dataP-2(Combinedcleaned).setParticipant 3 EEG dataP-3(Combinedcleaned).setParticipant 4 EEG dataP-4(Combinedcleaned).setParticipant 5 EEG dataP-5(Combinedcleaned).setParticipant 6 EEG dataP-6(Combinedcleaned).setParticipant 7 EEG dataP-7(Combinedcleaned).setParticipant 8 EEG dataP-8(Combinedcleaned).setParticipant 10 EEG dataP-10(Combinedcleaned).setParticipant 11 EEG dataP-11(Combinedcleaned).setParticipant 13 EEG dataP-13(Combinedcleaned).setParticipant 14 EEG dataP-14(Combinedcleaned).setParticipant 15 EEG dataP-15(Combinedcleaned).setParticipant 16 EEG dataP-16(Combinedcleaned).setParticipant 17 EEG dataP-17(Combinedcleaned).set