cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s1rn8pk8v
title: How early does the selfing syndrome arise? Associations between selfing ability and flower size within populations of the mixed mater Collinsia verna

description: Widespread associations between selfing rate and floral size within and
 among taxa suggest that these traits may evolve in concert. Does this
 association develop immediately, because of shared genetic/developmental
 control, or stepwise with selection shaping the evolution of one trait
 following the other? If the former, then association ought to appear
 within and across populations. We explore this fundamental question in
 three populations of the mixed-mater Collinsia verna where autonomous
 selfing (AS) ability has been shown to be under selection by the
 pollination environment. We grew clonal replicates of C. verna in
 a controlled environment to characterize broad-sense genetic correlations
 among traits within populations and to assess whether divergence in mating
 system and floral traits among these populations is consistent with their
 previously observed selection pressures. As predicted by their respective
 pollination environments, we demonstrate significant genetic divergence
 among populations in AS ability. However, patterns of divergence in floral
 traits (petal, stamen, and style size, stigmatic receptivity, and
 stigma-anther distance) were not as expected. Within populations,
 genetic variation in AS appeared largely independent from floral traits,
 except for a single weak negative association in one population between
 flower size and AS rate. Together, these results suggest that associations
 between selfing rate and floral traits across Collinsia species are not
 reflected at microevolutionary scales. If C. verna were to continue
 evolving toward the selfing syndrome, floral trait evolution would likely
 follow stepwise from mating system evolution.
description: <strong>Experimental Design</strong>
 Genotypes from 3 populations: Enlow Fork (EF), Braddock Trail
 (BT), and Ten Mile Creek (TMC),all in Western Pennsylvania, were cloned in
 1999, and clones were designated to either the morphology study or the
 autogamy study. Genotypes 100-199 are from EF, 200-299 are from BT, and
 300-399 are from TMC. Multiple floral traits were
 measured together on single flowers, and several flowers were measured for
 each clone. Stigmatic receptivity was measured on several flowers per
 clone, but not the same flowers that were measured for floral traits.
 Autonomous selfing ability was measured on different clones of the same
 parent plant (genotype) from which clones originated that were measured
 for floral traits and receptivity. To account for this sampling scheme,
 Floral traits and stigmatic receptivity were aggregated to clonal means
 before merging them together. To merge with selfing ability, clonal mean
 trait values were aggregated to genotypic means to match the level of
 selfing measurement.
description: There are three comma separated files comprising this dataset,
 which does contain some missing values. Metadata are described in the
 README file and in the annotated R script
 "McElderry_etal_GenVarSelfing.html".
DOI: 10.5061/dryad.sn02v6x53
title: Local thermal environment and warming influence supercooling and drive widespread shifts in the metabolome of diapausing Pieris rapae butterflies

description: Global climate change has the potential to negatively impact biological
 systems as organisms are exposed to novel temperature regimes. Increases
 in annual mean temperature have been accompanied by disproportionate rates
 of change in temperature across seasons, and winter is the season warming
 most rapidly. Yet, we know relatively little about how warming will alter
 the physiology of overwintering organisms. Here, we simulated future
 warming conditions by comparing diapausing Pieris rapae butterfly pupae
 collected from disparate thermal environments and by exposing P. rapae
 pupae to acute and chronic increases in temperature. First, we compared
 internal freezing temperatures (supercooling points) of diapausing pupae
 that were developed in common-garden conditions but whose parents were
 collected from northern Vermont, USA, or North Carolina, USA. Matching the
 warmer winter climate of North Carolina, North Carolina pupae had
 significantly higher supercooling points than Vermont pupae. Next, we
 measured the effects of acute and chronic warming exposure in Vermont
 pupae and found that warming induced higher supercooling points. We
 further characterized the effects of chronic warming by profiling the
 metabolomes of Vermont pupae via untargeted LC-MS metabolomics. Warming
 caused significant changes in abundance of hundreds of metabolites across
 the metabolome. Notably, there were warming-induced shifts in key
 biochemical pathways, such as pyruvate metabolism, fructose and mannose
 metabolism, and β-alanine metabolism, suggesting shifts in energy
 metabolism and cryoprotection. These results suggest that warming affects
 various aspects of overwintering physiology in P. rapae and may be
 detrimental depending on the frequency and variation of winter warming
 events. Further research is needed to ascertain the extent to which the
 effects of warming are felt among a broader set of populations of P.
 rapae, and among other species, in order to better predict how insects may
 respond to changes in winter thermal environments.
description: We measured supercooling points (internal freezing
 temperatures) under control conditions in diapausing <em>Pieris
 rapae</em> pupae from Vermont and North Carolina, USA to determine
 the ecological relevancy of the supercooling point. We then exposed
 diapausing Vermont pupae to acute and chronic warming scenarios
 representative of future conditions under global climate change, and
 compared differences in supercooling points due to warming. We further
 determined the effects of warming on overwintering by profiling the
 metabolomes of Vermont pupae from the control and chornic warming
 treatments via untargeted LC-MS metabolomics.
description: Provided are the metadata for each individual, the supercooling
 point data for the Vermont and North Carolina pupae and the Vermont
 warming treatments, and the negative and positive mode raw metabolomics
 data for the control and chronic warming Vermont pupae.
DOI: 10.5061/dryad.7m0cfxpvx
title: Non-human primate white matter development during the first year of life as assessed by diffusion tensor imaging and quantitative relaxometry

description: In this project, we use diffusion tensor imaging (DTI) and quantitative
 relaxometry (QR) metrics to assess longitudinal changes in white matter
 (WM) throughout the postnatal rhesus macaque brain across the first year
 of life. DTI and QR metrics are measured at 3, 7, 13, 25, and 53 weeks of
 age in each of 35 non-human primates (NHPs) in this sample, for a total
 175 datapoints (i.e., scans). Leveraging a previously published NHP WM
 atlas (Adluru et al., 2012; Zakszewski et al., 2014), we assess WM
 microstructure in 76 WM regions across the brain. DTI metrics include
 fractional anisotropy (FA), mean diffusivity (MD), radial diffusivity
 (RD), and axial diffusivity (AD); the QR metric assessed is the
 longitudinal relaxation rate (qR1). These longitudinal data enable the
 direct comparison of DTI and QR metrics in very early life on a
 within-subject level, as well as robust, multimodal modeling of WM growth
 in infancy, providing insights into early postnatal neurodevelopment that
 may have important implications neuropsychiatric and neurodevelopmental
 disorders in childhood.
DOI: 10.5061/dryad.cnp5hqc5v
title: Anthropogenic land‐use change shapes bird diversity along the eastern Himalayan altitudinal gradient

description: Globally, the conversion of natural forest into agricultural land and
 human settlement has altered avian diversity and structure often leading
 to functional and/or phylogenetic homogenisation. While the effects of
 land-use change on avian functional and phylogenetic diversity is well
 studied in the tropics, it is poorly understood and scarcely studied in
 the Himalayas, let alone in the eastern Himalayan bird communities. This
 dataset comprises observations of 336 bird species from a replicated
 point-count transect survey conducted between 2019 and 2020 in Bhutan. We
 used a multispecies occupancy model to estimate occupancy probability
 while accounting for detection probability. The detection-corrected
 z-matrix was used to calculate functional and phylogenetic
 diversity.  Our study shows that bird community occupancy along
 the elevational gradient is negatively associated with human land use
 (agriculture and settlement). Bird assemblages were functionally and
 phylogenetically clustered at higher elevations. Agriculture and
 settlement harboured higher functional and phylogenetic diversity whereas
 forests had phylogenetically diverse communities within functionally
 convergent traits. The higher functional and phylogenetic diversity in
 agriculture and settlement suggests that bird diversity offers an
 opportunity for a broad range of ecosystem services. Protection of forests
 abutting human settlements and agriculture will help preserve higher
 phylogenetic diversity. We recommend that agricultural practices that
 safeguard and improve bird-friendly habitats should be promulgated.
 Educational programmes on the importance of the roles of birds should be
 implemented and integrating bird conservation with farm
 production will help conserve bird diversity in human-dominated
 landscapes. To enhance the conservation value of working landscapes in the
 Himalayas, avitourism can be explored further. 
description: We direct the readers to README.txt for the details.
DOI: 10.11583/dtu.31157830
title: Metagenome-assembled genomes (MAGs) sequences

description: This archive contained 196 dereplicated metagenome-assembled genomes (MAGs) derived from anaerobic enriched consortia. There were estimated to be complete at least at 70% and with less than 10% of contamination.152 MAGs are coming from the study of Ginevra <i>et al</i>. 2025 (see bellow). Five of these MAGs were manually refined (named "-refined") using the Anvi'o v8 platform (Eren <i>et al</i>. 2020). With the add of new metagenomes coming from the enrichment of the same cultures, 44 new MAGs were recovered and are named "New2025.bin.".The related study is currently under revision.References:Giangeri, G., Tsapekos, P., Pitsikoglou, D., Ghiotto, G., Tracy Hong Lin, M. K., Treu, L., et al. (2025b). Deciphering direct interspecies electron transfer activity in microbial interactions: The influence of conductive materials in anoxic ecosystems. <i>Chemical Engineering Journal</i> 503, 158716. doi: 10.1016/J.CEJ.2024.158716Eren, A. M., Kiefl, E., Shaiber, A., Veseli, I., Miller, S. E., Schechter, M. S., et al. (2020). Community-led, integrated, reproducible multi-omics with anvi’o. <i>Nature Microbiology 2020 6:1</i> 6, 3–6. doi: 10.1038/s41564-020-00834-3
DOI: 10.11583/dtu.31157830.v1
title: Metagenome-assembled genomes (MAGs) sequences

description: This archive contained 196 dereplicated metagenome-assembled genomes (MAGs) derived from anaerobic enriched consortia. There were estimated to be complete at least at 70% and with less than 10% of contamination.152 MAGs are coming from the study of Ginevra <i>et al</i>. 2025 (see bellow). Five of these MAGs were manually refined (named "-refined") using the Anvi'o v8 platform (Eren <i>et al</i>. 2020). With the add of new metagenomes coming from the enrichment of the same cultures, 44 new MAGs were recovered and are named "New2025.bin.".The related study is currently under revision.References:Giangeri, G., Tsapekos, P., Pitsikoglou, D., Ghiotto, G., Tracy Hong Lin, M. K., Treu, L., et al. (2025b). Deciphering direct interspecies electron transfer activity in microbial interactions: The influence of conductive materials in anoxic ecosystems. <i>Chemical Engineering Journal</i> 503, 158716. doi: 10.1016/J.CEJ.2024.158716Eren, A. M., Kiefl, E., Shaiber, A., Veseli, I., Miller, S. E., Schechter, M. S., et al. (2020). Community-led, integrated, reproducible multi-omics with anvi’o. <i>Nature Microbiology 2020 6:1</i> 6, 3–6. doi: 10.1038/s41564-020-00834-3
DOI: 10.5061/dryad.qbzkh18j9
title: Economies of scale shape energetics of solitary and group living spiders and their webs

description: Metabolic scaling, whereby larger individuals use less energy per unit
 mass than smaller ones, may apply to the combined metabolic rate of
 group-living organisms as group size increases. Spiders that form groups
 in high disturbance environments can serve to test the hypothesis that
 economies of scale benefit social groups. Using solitary and group-living
 spiders, we tested the hypothesis that spiders exhibit negative allometry
 between body or colony mass and the standing mass of their webs and
 whether, and how, such a relationship may contribute to group-living
 benefits in a cooperative spider. Given the diverse architecture of spider
 webs—orb, tangle, and sheet-and-tangle, and associated differences in silk
 content, we first assessed how standing web mass scales with spider mass
 as a function of web architecture and whether investment in silk differs
 among web types. As group-living spiders are predominantly found in clades
 that build the presumably costlier sheet-and-tangle webs, we then asked
 whether cost-sharing through cooperative web maintenance contributes to a
 positive energy budget in a social species. We found that larger spiders
 had a relatively smaller investment in silk per unit mass than smaller
 ones, but more complex sheet-and-tangle webs contained orders of magnitude
 more silk than simpler orb or tangle ones. In the group-living species,
 standing web mass per unit spider mass continued to decline as colony size
 increased with a similar slope as for unitary spiders. When web
 maintenance activities were considered, colonies also experienced reduced
 mass-specific energy expenditure with increasing colony size. Activity
 savings contributed to a net positive energy balance for medium and large
 colonies after inputs from the cooperative capture of large prey were
 accounted for. Economies of scale have been previously demonstrated in
 animal societies characterized by reproductive and worker castes, but not
 in relatively egalitarian societies as those of social spiders. Our
 findings illustrate the universality of scaling laws and how economies of
 scale may contribute to setting limits on social behaviour and hunting
 strategies.
description: Data are split into two folders. Folder entitled
 "raw_data" includes all raw field and laboratory data (.csv
 files), plus an accompanying metadata file. The folder entitled
 "downstream_data" includes .csv files created during the
 cleaning and analysis process, and includes an accompanying metadata file.
 The folder entitled "code" includes all of the R scripts used
 for analysis. SpiderCommunity_WebScaling.R runs the analyses of economies
 of scale in the web-building spider community at Jatun Sacha.
 Anelosimus_total_outputs.R processes energetic outputs from web-building,
 Anelosimus_total_inputs.R processes energetic inputs from prey capture,
 and "Anelosimus_BudgetAnalysis_Figures.R runs the linear, quadratic
 and cubic spline analyses and generates figures used in the
 paper.
DOI: 10.5061/dryad.2547d7wrq
title: Kinematics of sea star legged locomotion

description: Sea stars have slower crawling and faster bouncing gaits. Both speed and
 oscillation amplitude increase during the transition from crawling to
 oscillating. In the bouncy gait, vertical velocities precede horizontal
 velocities by 98&[deg], as reflected by clockwise circular
 hodographs. Potential energy precedes horizontal energy by
 16&[deg] and so are nearly in phase. These phase relationships
 resemble terrestrial running gaits, except that podia are always on the
 ground. Kinetic and potential energy scale as mass1.1, with the change in
 kinetic energy consistently two orders of magnitude less, indicating that
 efficient exchange is not feasible. Frequency of the bouncy gait scales
 with mass-0.14, which is similar to continuously running vertebrates and
 indicates that gravitational forces are important. This scaling differs
 from the Hill model, in which scaling of muscle forces determine
 frequency. We propose a simple torque stabilized inverted pendulum (TS-IP)
 model to conceptualize the dynamics of this gait. The TS-IP model
 incorporates mathematics equivalent to an angular spring, but implemented
 by a nearly constant upward force generated by the podia in each step.
 That upward force is just larger than the force required to sustain the
 underwater weight of the sea star. Even though the bouncy gait is the
 rapid gait for these sea stars, the pace of movement is still very slow.
 In fact, the observed Froude numbers (10-2 to 10-3) are much lower than
 those typical of vertebrate locomotion and are as low or lower than those
 reported for slow walking fruit flies, which are the lowest values for
 pedestrian Froude numbers of which we are aware. --
description: We took video of ambulating seastars, <em>Asterias
 forbesi</em>, in a plexiglass raceway. There were two cameras
 simultaneously recording from the side and from underneath at a nominal
 frame rate of 30 Hz. There are 128 pairs of  side and bottom films and 54
 unique seastars each filmed one to several times. Open Source Physics
 software called Tracker 5.1.3 by Douglas Brown was used to track the
 apical point from the side and the mouth from the bottom. The data files
 give 5 columns: time, x position from the bottom view, y position from the
 bottom view, x position from the side view and z position from the side
 view. The name of each file indicates which seastar that file pertains to
 and also gives the DSC number that indexes the pair of side and bottom
 film data in each file. There is also one file that
 gives the mass of each sea star filmed and the underwater weight of each
 sea star.
description: The files are csv files with the first row being a header giving
 the column content and the units. Note that the zero value in each of the
 axis directions is arbitrary.
DOI: 10.5061/dryad.bvq83bk9r
title: The role of aerosol-radiation interaction in the meteorology prediction at the weather scale

description: The current capabilities of the numerical weather prediction (NWP) model
 to simulate aerosol-radiation interaction (ARI) impacts on weather
 prediction are still rarely considered compared with climate models. Here,
 the NWP model GRAPES_CUACE is used to evaluate the role of the ARI in
 meteorology prediction at the weather scale in China. The results show
 that the online calculation of ARI in the model can extensively improve
 the meteorology prediction accuracy involving temperature, wind, and
 pressure at most vertical levels in relatively clean, light, and heavy
 pollution stages. This improvement significantly occurs in the meteorology
 factors below 950 hPa prediction such as temperature at 2 m, 1000, and 950
 hPa, and mean sea level pressure, particularly in heavy pollution areas
 and stages. Unlike temperature, the improvement of ARI in the predicted
 wind at the height of the boundary layer is more significant than
 near-surface. However, this improvement declines when the low-cloud
 exists.
DOI: 10.6078/d1j99r
title: The effects of drought and nutrients on stream communities

description: Drought and nutrient pollution can affect the dynamics of stream
 ecosystems in diverse ways. While the individual effects of both stressors
 are broadly examined in the literature, we still know relatively little
 about if and how these stressors interact. Here, we performed a mesocosm
 experiment that explores the compounded effects of seasonal drought via
 water withdrawals and nutrient pollution (1.0 mg/L of N and 0.1 mg/L of P)
 on a subset of Ozark stream community fauna and ecosystem processes. We
 observed biological responses to individual stressors as well as both
 additive and antagonistic stressor interactions. We found that drying
 negatively affected periphyton assemblages, macroinvertebrate
 colonization, and leaf litter decomposition in shallow habitats. However,
 in deep habitats, drought-based concentration effects caused trophic
 cascades that released algal communities from grazing pressures; while
 nutrient enrichment caused bottom-up cascades that influenced periphyton
 variables and crayfish growth rates. Finally, the combined effects of
 drought and nutrient enrichment interacted antagonistically to increase
 survival in longear sunfish; and stressors acted synergistically on
 grazers causing a trophic cascade that increased periphyton variables.
 Because stressors can differentially impact biota—and that the same
 stressor pairing can act both additively and antagonistically on different
 portions of the community simultaneously—our broad understanding of
 individual stressors might not adequately inform our knowledge of
 multi-stressor systems.
DOI: 10.5061/dryad.pc866t1q2
title: Data from: Ponerorchis wolongensis (Orchidaceae, Orchidinae), a new species with variable labellum from Hengduan Mountains, western Sichuan, China

description: Ponerorchis wolongensis, a new orchid species from the Hengduan Mountains,
 western Sichuan, China, is described and illustrated here based
 on morphological and phylogenetic evidence. Morphologically, the new
 species is similar to P. capitata, but they can easily be
 differentiated by the number of leaves and flowers, the shape of leaves,
 and the mid-lobe of the labellum. Phylogenetically, based on
 seven DNA sequences, the new species is more close to P .
 sichuanica, but these two species are very different in
 both growth habit and morphological characteristics.
DOI: 10.5061/dryad.qv9s4mwg0
title: Soluble T-cadherin promotes pancreatic β-cell proliferation by upregulating Notch signaling

description: Endogenous humoral factors that link systemic and/or local insulin demand
 to pancreatic β-cells have not been identified. Here, we demonstrated that
 T-cadherin, a unique glycosylphosphatidylinositol-anchored cadherin
 primarily expressed in vascular endothelial cells and cardiac and skeletal
 muscle cells, but not in pancreatic β-cells, was secreted as soluble forms
 and was important for β-cell proliferation. Cdh13 (T-cadherin) knockout
 mice exhibited impaired glucose handling due to attenuated β-cell
 proliferation under high-fat diet conditions. The gene expression analyses
 indicated the impairment in cell cycle and Notch signaling in the islets
 of T-cadherin knockout mice under high-fat diet conditions. In
 streptozotocin-induced diabetes, the replacement of soluble T-cadherin
 improved β-cell mass and blood glucose levels in T-cadherin knockout mice.
 Recombinant soluble T-cadherin upregulated Notch signaling in cultured
 murine islets. We concluded that soluble T-cadherin could work as an
 endogenous humoral factor whose signaling pathways including Notch
 signaling regulate β-cell proliferation under diabetic conditions in mice.
description: See STAR methods in the Journal website with figure
 legends. The methods how we evaluate pancreatic insulin
 contents, beta-cell mass, and beta-cell proliferation will be seen in the
 STAR methods in the Journal website with this Dryad data deposition. The
 dataset in each figure is summarized in an excel sheet, occasionally with
 raw data and its processed data in one folder. Please see the readme file
 in each folder. Our methods also cover the making of total knockout mice
 from flox mice, measurement of soluble T-cadherin, production of
 recombinant soluble T-cadherin, and stable plasmid-based in vivo
 expression of recombinant soluble T-cadherin from the liver. These methods
 may be helpful for a wide-range of readers.
description: Image files can be opened with Fiji.;
 https://imagej.net/software/fiji/