cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sn1s14h
title: Data from: Trait convergence in photosynthetic nutrient-use efficiency along a 2-million year dune chronosequence in a global biodiversity hotspot

description: 1. The Jurien Bay dune chronosequence in south-western Australia’s
 biodiversity hotspot comprises sites differing in nutrient availability,
 with phosphorus (P) availability declining strongly with increasing soil
 age. We have explored the exceptionally high photosynthetic P-use
 efficiency (PPUE) of Proteaceae in this region, triggering the question
 what the PPUE of co-occurring species in other families might be along the
 Jurien Bay chronosequence. 2. We explored how traits associated with PPUE,
 photosynthetic nitrogen (N)-use efficiency (PNUE) and leaf respiration
 might converge along the chronosequence, and whether Proteaceae and
 non-Proteaceae species differ in leaf traits associated with nutrient use.
 3. Seven to 10 species were sampled at three sites differing in nutrient
 availability (ranging from N- to P-limited). Measurements of leaf
 light-saturated photosynthesis and dark respiration were integrated with
 measurements of total N and P concentration in both mature and senesced
 leaves, and leaf mass per unit area (LMA). 4. Contrary to what is known
 for other chronosequences, rates of photosynthesis and respiration did not
 decrease with increasing soil age and LMA along the Jurien Bay
 chronosequence. However, they increased when expressed per unit leaf P.
 Both N and P were used much more efficiently for photosynthesis on
 nutrient-poor sites, in both Proteaceae and non-Proteaceae species.
 Proteaceae had the fastest rate of photosynthesis per unit leaf P,
 followed by species that preferentially allocate P to mesophyll cells,
 rather than epidermal cells. 5. Synthesis. Our results show that with
 declining soil P availability, PPUE of all investigated species from
 different families increased. Plants growing on the oldest, most
 nutrient-impoverished soils exhibited similar rates of CO2-exchange as
 plants growing on more nutrient-rich younger soils, and extraordinarily
 high PPUE. This indicates convergence in leaf traits related to
 photosynthetic nutrient use on severely P-impoverished sites.
description: Supporting Information
 (Guilherme Pereira et al. 2019), Journal of EcologyThis file contains the
 individual replicate data reported in Guilherme Pereira et al. (2019).
 Details on site location, sampling procedures and species are provided in
 the paper. The data is provided to others to freely use in their own
 analyses - we ask that users to cite Guilherme Pereira et al. (2019) in
 any output that may emerge.
DOI: 10.5061/dryad.tf806g8
title: Data from: Habitat use and seed removal by invasive rats (Rattus rattus) in disturbed and undisturbed rainforest, Puerto Rico

description: Despite frequent occurrences of invasive rats (Rattus spp.) on islands,
 their known effects on forests are limited. Where invasive rats have been
 studied, they generally have significant negative impacts on native
 plants, birds, and other animals. This study aimed to determine invasive
 rat distribution and effects on native plant populations via short-term
 seed removal trials in tropical rain forest habitats in the Luquillo
 Experimental Forest, Puerto Rico. To address the first objective, we used
 tracking tunnels (inked and baited cards inside tunnels enabling animal
 visitors’ foot prints to be identified) placed on the ground and in the
 lower canopy within disturbed (treefall gaps, hurricane plots, stream
 edges) and undisturbed (continuous forest) habitats. We found that rats
 are present in all habitats tested. Secondly, we compared seed removal of
 four native tree species (Guarea guidonia, Buchenavia capitata,
 Tetragastris balsamifera, and Prestoea acuminata) between
 vertebrate-excluded and free-access treatments in the same disturbed and
 undisturbed habitats. Trail cameras were used to identify animals
 responsible for seed contact and removal. Black rats (R. rattus) were
 responsible for 65.1% of the interactions with seeds, of which 28.6% were
 confirmed seed removals. Two plant species had significantly more seeds
 removed in disturbed (gaps) than undisturbed forest. Prestoea acuminata
 had the lowest seed removal (9% in 10 d), whereas all other species had
 &gt;30% removal. Black rats are likely influencing fates of seeds on
 the forest floor, and possibly forest community composition, through
 dispersal or predation. Further understanding of rat-plant interactions
 may be useful for formulating conservation strategies.
description: Shiels_Seed removal Open
 vs Closed PR Summer REU 20172 tabs of data in Excel:
 "Seeds" tab is the seed removal data, and "Tunnels"
 tab is the tracking tunnel dataShiels_Seed removal and
 Tracking tunnel data Dryad PR Summer REU
 2017.xlsx
DOI: 10.5061/dryad.s86434s
title: Data from: Fifty shades of brown: Macroevolution of plumage brightness in the Furnariida, a large clade of drab Neotropical passerines

description: Both natural and sexual selection are thought to affect the evolution of
 bird color. Most studies of the topic have focused on sexually dichromatic
 taxa and showy plumages, which are expected to be more influenced by
 social selection and usually result in increased conspicuousness. However,
 many bird clades display dull brown or grey plumages that vary greatly in
 brightness (lightness), but little in hue (shade). Here, we examine the
 macroevolution of brightness in one such clade, the Furnariida. We make
 comparisons across light environments, body parts, and across
 monochromatic lineages and each sex of dichromatic lineages. We found that
 support for models including light environments is greater for the dorsum
 than for the venter, and that brightness evolution is more constrained in
 the latter than in the former. Plumages in this clade have evolved to be
 darker in darker habitats, consistent with natural selection for increased
 crypsis. Finally, the features of brightness macroevolution are broadly
 similar across the sexes of the dichromatic clade, challenging the view
 that sexual dichromatism is driven by different evolutionary processes
 acting in each sex. We conclude that, in the Furnariida, light
 environments and dorsal-ventral variation are more important than sex as
 axes of color evolution.
description: Marcondes_Brumfield_2019_color_datafurnarioidea treefurnarioidea.trethamnophiloidea treethamnophiloidea.tre
DOI: 10.5061/dryad.v2j34j1
title: Data from: A field-based analysis of genetic improvement for grain yield in winter wheat cultivars developed in the us central plains from 1992 to 2014

description: [No abstract entered]
description: rpn_wheat_phenotypesThis file includes height, yield, and heading date phenotypic data for the entries evaluated in this study. Everest and TAM 112 were the two check cultivars used in the experimental design. Additional entries are identified in the line_num column by the designation assigned upon entry into the Regional Performance Nursery. Experimental names, when available, are included in the line_name column.
DOI: 10.5281/zenodo.17506939
title: Supplementary Data v1.0 — A two-tier audit of foil–lacquer integration on the Shōsōin Heibun qin

description: Dataset accompanying the study “A two-tier audit of foil–lacquer integration on the Shōsōin Heibun qin”.

 

Release name used in the manuscript: Supplementary Data v1.0.

This Zenodo upload is a revised v1.0 archive intended to ensure internal consistency, auditability, and reviewer-side verification. Please cite the concept DOI (all versions); the Zenodo record documents changes between versions.

 

This revision replaces an earlier Zenodo version and incorporates corrections and consistency updates across the machine-readable corpora (S1–S3), the SI-5 observation register, and the accompanying documentation/validation materials (e.g., README alignment, schema/script synchronization, validation outputs, and archive integrity checks). The purpose of the update is to provide a clean, self-validating package matching the revised manuscript and SI; the Zenodo version history records changes between releases.

 

Contents. Machine-readable TSV corpora in Supplementary_Data/ (S1_WS-Tang_lacquer.tsv; S2_Tang_pingtuo.tsv; S3_Lacquered_qin.tsv) and the SI-5 audit suite in SI-5/ (e.g., SI-5_Observations.tsv, schema files, validation scripts, derived views). SI-5/MANIFEST.tsv provides SHA-256 checksums for files in SI-5/ (paths recorded relative to the SI-5/ directory).

 

Third-party images are not redistributed; figure rights remain with the Imperial Household Agency (Shōsōin).

 

Licensing. Data and accompanying materials: CC BY 4.0.
DOI: 10.5281/zenodo.18389424
title: Supplementary Data v1.0 — A two-tier audit of foil–lacquer integration on the Shōsōin Heibun qin

description: Dataset accompanying the study “A two-tier audit of foil–lacquer integration on the Shōsōin Heibun qin”.

 

Release name used in the manuscript: Supplementary Data v1.0.

This Zenodo upload is a revised v1.0 archive intended to ensure internal consistency, auditability, and reviewer-side verification. Please cite the concept DOI (all versions); the Zenodo record documents changes between versions.

 

This revision replaces an earlier Zenodo version and incorporates corrections and consistency updates across the machine-readable corpora (S1–S3), the SI-5 observation register, and the accompanying documentation/validation materials (e.g., README alignment, schema/script synchronization, validation outputs, and archive integrity checks). The purpose of the update is to provide a clean, self-validating package matching the revised manuscript and SI; the Zenodo version history records changes between releases.

 

Contents. Machine-readable TSV corpora in Supplementary_Data/ (S1_WS-Tang_lacquer.tsv; S2_Tang_pingtuo.tsv; S3_Lacquered_qin.tsv) and the SI-5 audit suite in SI-5/ (e.g., SI-5_Observations.tsv, schema files, validation scripts, derived views). SI-5/MANIFEST.tsv provides SHA-256 checksums for files in SI-5/ (paths recorded relative to the SI-5/ directory).

 

Third-party images are not redistributed; figure rights remain with the Imperial Household Agency (Shōsōin).

 

Licensing. Data and accompanying materials: CC BY 4.0.
DOI: 10.5061/dryad.vv22bs1
title: Data from: Linking dynamical complexities from activation signals to transcription responses

description: The transcription of inducible genes involves signaling pathways that
 induce DNA binding of the downstream transcription factors to form
 functional promoter states. How the transcription dynamics is linked to
 the temporal variations of activation signals is far to be fully
 understood. In this work, we develop a mathematical model with multiple
 promoter states to address this question. Each promoter state has its own
 activation and inactivation rates, and is selected randomly with a
 probability that may change in time. Under the activation of constant
 signals, our analysis shows that if only the activation rates differ among
 the promoter states, then the mean transcription level $m(t)$ displays
 only a monotone or monophasic growth pattern. In a sharp contrast, if the
 inactivation rates change with the promoter states, then $m(t)$ may
 display multiphasic growth patterns. Upon the activation of signals that
 oscillate periodically, $m(t)$ also oscillates later, almost periodically
 in the same frequency, but the magnitude decreases in the frequency and is
 almost completely attenuated at large frequencies. This gives a surprising
 indication that multiple promoter states could filter out the signal
 oscillation and the noise in the random promoter state selection, as
 observed in the transcription of a gene activated by p53 in breast
 carcinoma cells. Our approach may help develop a theoretical framework to
 integrate coherently the genetic circuit with the promoter states to
 elucidate the linkage from the activation signal to the temporal profile
 of transcription outputs.
description: Matlab Code of Figures
 1, 3--7This file is about the
 matlab code of Figures 1, 3--7 used in the paper.
DOI: 10.5061/dryad.n5s8cs5
title: Data from: The roles of morphological traits, resource variation and resource partitioning associated with the dietary niche expansion in the fish-eating bat Myotis pilosus

description: Niche expansion and shifts are involved in the response and adaptation to
 environmental changes. However, it is unclear how niche breadth evolves
 and changes toward higher-quality resources. Myotis pilosus is both an
 insectivore and a piscivore. We examined the dietary composition and
 seasonality in M. pilosus and the closely related Myotis fimbriatus using
 next-generation DNA sequencing. We tested whether resource variation or
 resource partitioning help explain the dietary expansion from insects to
 fish in M. pilosus. While diet composition and diversity varied
 significantly between summer and autumn, the proportion of fish-eating
 individuals did not significantly change between seasons in M. pilosus.
 Dietary overlap between M. pilosus and M. fimbriatus during the same
 seasons was much higher than within individual species across seasons. We
 recorded a larger body size, hind foot length, and body mass in M. pilosus
 than in M. fimbriatus and other insectivorous trawling bats from China.
 Similar morphological differences were found between worldwide fishing
 bats and non-fishing trawling bats. Our results suggest that variation in
 insect availability or interspecific competition may not play important
 roles in the dietary expansion from insects to fish in M. pilosus. M.
 pilosus has morphological advantages that may help it use fish as a diet
 component. The morphological advantage promoting dietary niche evolution
 toward higher-quality resources may be more important than variation in
 the original resource and the effects of interspecific competition.
description: otu_repsRepresentative sequences for each MOTUOTU tableOTU table used for data analysis which had rarefied the data to 12000 sequences per sample and removed those OTUs that represented less than 0.1% of the normalized sequences for each sample.phylogenetic treesPhylogenetic trees generated from metabarcoding sequences using MrBayes 3.2.6 was used for phylogenetic Hill numbers analysis.otu_nwick.tre
DOI: 10.5061/dryad.6d4p06g
title: Data from: Response diversity in Mediterranean coralligenous assemblages facing climate change: Insights from a multispecific thermotolerance experiment

description: Climate change threatens coastal benthic communities on a global scale.
 However, the potential effects of ongoing warming on mesophotic temperate
 reefs at the community level remain poorly understood. Investigating how
 different members of these communities will respond to the future expected
 environmental conditions is, therefore, key to anticipating their future
 trajectories and developing specific management and conservation
 strategies. Here, we examined the responses of some of the main components
 of the highly diverse Mediterranean coralligenous assemblages to thermal
 stress. We performed thermotolerance experiments with different
 temperature treatments (from 26 to 29°C) with 10 species from different
 phyla (three anthozoans, six sponges and one ascidian) and different
 structural roles. Overall, we observed species‐specific contrasting
 responses to warming regardless of phyla or growth form. Moreover, the
 responses ranged from highly resistant species to sensitive species and
 were mostly in agreement with previous field observations from mass
 mortality events (MMEs) linked to Mediterranean marine heat waves. Our
 results unravel the diversity of responses to warming in coralligenous
 outcrops and suggest the presence of potential winners and losers in the
 face of climate change. Finally, this study highlights the importance of
 accounting for species‐specific vulnerabilities and response diversity
 when forecasting the future trajectories of temperate benthic communities
 in a warming ocean.
description: raw_data_thermal_experimentThis data file contains information related to outcomes of the thermal experiments performed with different species of the Mediterranean coralligenous assemblages in 2012 and 2017.
DOI: 10.5061/dryad.g2j4t50
title: Data from: The thermoelectric properties of Au nanoparticle-incorporated Al-doped mesoporous ZnO thin films

description: Mesoporous Al-doped ZnO thin films incorporated with gold nanoparticles
 (Au NPs) were synthesized using a sol-gel and evaporation-induced
 self-assembly process. In this work, the complementary effects of Au NP
 incorporation and Al doping on the mesoporous ZnO thin films’
 thermoelectric properties were analyzed. The incorporated Au NPs induced
 an increase in electrical conductivity but a detriment in the pore
 arrangement of the mesoporous ZnO thin film, which was accompanied by a
 decrease in porosity. However, the addition of the Al dopant minimized the
 pore structural collapse because of the inhibition of the grain growth in
 the ZnO skeletal structure, resulting in an enhancement of the pore
 arrangement and porosity. When the Au NPs and Al dopant were added at the
 same time, the degradation in the pore structure was minimized and the
 electrical conductivity was effectively increased but the absolute value
 of the Seebeck coefficient was decreased. However, as a result, the
 thermoelectric power factor was increased by 2.4 times compared to the
 pristine mesoporous ZnO thin film. It was found that co-introducing the Au
 NPs and Al doping to the mesoporous ZnO structure was effective in
 preserving the pore structure and increasing the electric conductivity,
 thereby enhancing the thermoelectric property of the mesoporous ZnO thin
 film.
description: XRD patterns of the
 pristine mesoporous ZnO, Au NPs-ZnO, and Au NPs-AZO thin
 filmsRaw excel data of Figure
 2.Figure 2
 (raw data).xlsxThe porosity values of
 the pristine mesoporous ZnO, Au NPs-ZnO, and Au NPs-AZO thin
 filmsRaw excel data of Figure
 4.Figure 4
 (raw data).xlsxThe Seebeck coefficient
 values of the pristine mesoporous ZnO, Au NPs-ZnO, and Au NPs-AZO thin
 films according to temperatureRaw excel data of Figure
 5.Figure 5
 (raw data).xlsxThe electrical
 conductivity of the pristine mesoporous ZnO, Au NPs-ZnO, and Au NPs-AZO
 thin films according to temperatureRaw excel data of Figure
 6.Figure 6
 (raw data).xlsx
DOI: 10.5061/dryad.dg03kv8
title: Data from: The distribution of plants and seed dispersers in response to habitat fragmentation in an artificial island archipelago

description: Aim: Small, old-growth forest fragments generally have more small-seeded
 plants than large patches, due to the disappearance of large seed
 dispersing vertebrates. This pattern may differ for secondary forest
 fragments where differential migration ability rather than persistence of
 seed dispersers may be driving plant community assembly. In this paper, we
 investigated the effect of habitat fragmentation on seed dispersers and
 plant community structure in regenerating forests. Location: The Thousand
 Island Lake, China. Taxon: Plants, birds and mammals. Methods: We compiled
 diversity and abundance data for birds and mammals on islands in the
 Thousand Island Lake, China. We also surveyed the secondary plant
 communities and measured seed dispersal traits. Results:
 Community-weighted mean seed size of woody plants decreased with island
 size. This pattern was related to compositional difference of the
 dispersers. We found that mammal diversity and abundance was only weakly
 or not related to island size; whereas bird diversity and abundance
 increased strongly with island size. Density of bird-dispersed plants was
 significantly positively related with island size. Since birds tend to
 disperse smaller seeds than mammals, the trend in seed size may have been
 a consequence of the shift in relative abundance of the two disperser
 guilds. Main Conclusions: Differential responses of seed dispersers to
 habitat fragmentation may lead to pervasive shifts in the plant community
 structure of regenerating forest fragments. Our study highlights the
 importance of keeping large continuous forests in order to retain mammals
 and their dispersal capabilities.
description: JBi-18-0362-suppinfoDatasets used in the paper: The distribution of plants and seed dispersers in response to habitat fragmentation in an artificial island archipelago
DOI: 10.5061/dryad.m55q9p0
title: Data from: Shared extremes by ectotherms and endotherms: body elongation in mustelids is associated with small size and reduced limbs

description: An elongate body with reduced or absent limbs has evolved independently in
 many ectothermic vertebrate lineages. While much effort has been spent
 examining the morphological pathways to elongation in these clades,
 quantitative investigations into the evolution of elongation in
 endothermic clades are lacking. We quantified body shape in 61 musteloid
 mammals (red panda, skunks, raccoons, and weasels) using the head-body
 elongation ratio. We also examined the morphological changes that may
 underlie the evolution towards more extreme body plans. We found that a
 mustelid clade comprised of Helictidinae, Guloninae, Ictonychinae,
 Mustelinae, and Lutrinae exhibited an evolutionary transition towards more
 elongate bodies. Furthermore, we discovered that elongation of the body is
 associated with the evolution of other key traits such as a reduction in
 body size and a reduction in forelimb length but not hindlimb length. This
 relationship between body elongation and forelimb length has not
 previously been quantitatively established for mammals but is consistent
 with trends exhibited by ectothermic vertebrates and suggests a common
 pattern of trait covariance associated with body shape evolution. This
 study provides the framework for documenting body shapes across a wider
 range of mammalian clades to better understand the morphological changes
 influencing shape disparity across all vertebrates.
description: Mean trait
 datamean trait data for
 speciesmeandata.csvR script for OUwie analysis on head-body elongation ratioR script for OUwie analysis on head-body elongation ratio. R scripts for the remaining traits (e.g. AEI_C, AEI_T, AEI_L, etc.) are exactly the same and thus are not uploaded. Just replace "hbER" with "AEI_C" and etc.OUwie_hbER.RR script for PGLS analysesR script for PGLS analysesPGLS.R
DOI: 10.5281/zenodo.18390312
title: Defining Nature: How Age and Culture Shape Human–Nature Representations in France and Colombia [Raw data]
DOI: 10.5281/zenodo.18390313
title: Defining Nature: How Age and Culture Shape Human–Nature Representations in France and Colombia [Raw data]