cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7pvmcvdv6
title: Seed dormancy and germination traits of 27 species inhabiting the degraded karst mountain from central Yunnan-Guizhou Plateau: Seed mass and moisture content correlates with germination capacity

description: Seed dormancy and germination play an important roles in regulating
 germination timing and plant fitness in harsh environment, especially for
 fragile karst region. Broadening the knowledge regarding seed ecology of
 native plant species can improve local restoration management due to the
 increased biodiversity and success of seedling establishment, yet few
 studies have addressed this. We examined the dormancy types and
 germination responses to temperature regimes as well as light conditions
 of totally 27 that were dominant or common species inhabiting a degraded
 karst mountain from central Yunnan-Guizhou Plateau and assessed the
 relationships between seed traits and germination index using a partial
 least squares regression (PLSR). Approximately 48% of the investigated
 species exhibited physiological dormancy, 37% exhibited nondormancy, 7%
 exhibited morphophysiological dormancy, 4% exhibited morphological
 dormancy and 4% exhibited physical dormancy. Germination behaviors
 occurred in 16 of 27 species. The seed germination of 13 species strongly
 responded to seasonal temperature regimes, whereas 12 species were
 substantially affected by light conditions. About 94% species germinated
 to the maximum percent in warm temperature regimes (20/13 and 25/18 °C),
 while the remaining was in cool temperature regime (10/4 °C). The PLSR
 analysis indicated a significant positive correlation between seed mass
 and T50 m (time to 50% final germination), and a negative correlation
 between seed moisture content and percent germination, showing that small
 seeds, particularly those with a low moisture content, were more likely to
 have a greater germination capacity (including relative less germination
 time and higher germination percent) than large seeds in harsh karst
 environments. In general, these results strengthen the understanding of
 seed dormancy classification of dormant species and germination
 requirements of nondormant ones that representative of pioneer species of
 early stage of positive succession in seriously degraded sites and provide
 suggestion for species selection in local seed-based vegetation
 restoration.
description: To test the main effects (temperature and light conditions) and
 their interactions on the final percent germination, generalized linear
 models (GLMs) with a binomial error distribution and logit function were
 adopted. All models were simplified by using a stepwise backward selection
 of main factors and respective interaction terms until significant
 factors/interaction terms remained. A partial least squares regression
 (PLSR) with full cross-validation was used to relate the variation in a
 single-component response variable to the variation in multicomponent
 explanatory variables.
DOI: 10.6084/m9.figshare.31167793
title: MD_PPI_50ns_ENSP00000352252_ENSP00000256996 molecular docking

description: This dataset provides processed data and computational results related to protein–protein interaction prediction using machine learning methods.<br>It includes model outputs, functional enrichment results, and molecular docking and molecular dynamics simulation data for selected protein pairs.<br>The dataset is intended to support result verification and reuse in related bioinformatics studies.
DOI: 10.6084/m9.figshare.31167793.v1
title: MD_PPI_50ns_ENSP00000352252_ENSP00000256996 molecular docking

description: This dataset provides processed data and computational results related to protein–protein interaction prediction using machine learning methods.<br>It includes model outputs, functional enrichment results, and molecular docking and molecular dynamics simulation data for selected protein pairs.<br>The dataset is intended to support result verification and reuse in related bioinformatics studies.
DOI: 10.6071/m38t0t
title: Data for: Rapid alignment updating with Extensiphy

description: 1. High throughput sequencing has become commonplace in evolutionary
 studies. Large, rapidly collected genomic datasets are used to capture
 biodiversity and for monitoring global and national scale disease
 transmission patterns, among many other applications. Updating homologous
 sequence datasets with new samples is cumbersome, requiring excessive
 program runtimes and data processing. We describe Extensiphy, a
 bioinformatics tool to efficiently update multiple sequence alignments
 with whole-genome short-read data. Extensiphy performs reference based
 sequence assembly and alignment in one process while maintaining the
 alignment length of the original alignment. Input data- types for
 Extensiphy are any multiple sequence alignment in fasta format and
 whole-genome, short-read fastq sequences.  2. To validate
 Extensiphy, we compared its results to those produced by two other methods
 that construct whole-genome scale multiple sequence alignments. We
 measured our comparisons by analyzing program runtimes, base-call
 accuracy, dataset retention in the presence of missing data and
 phylogenetic accuracy.  3. We found that Extensiphy rapidly
 produces high-quality updated sequence alignments while preventing
 alignment shrinkage due to missing data. Phylogenies estimated from
 alignments produced by Extensiphy show similar accuracy to other commonly
 used alignment construction methods.  4. Extensiphy is suitable
 for updating large sequence alignments and is ideal for studies of
 biodiversity, ecology and epidemiological monitoring efforts.
description: All data collection and data processing is described in Rapid
 Alignment Updating with Extensiphy. These are the files of all start and
 end points for both empirical and simulated data.
description: The README.txt file included with these data describes the folder
 structure and what each file or folder contains.
DOI: 10.5061/dryad.bcc2fqzdh
title: Extremely stochastic connectivity of island mangroves

description: Studies of mangrove population connectivity have focused primarily on
 global to regional scales and have suggested potential for long-distance
 connectivity, with archipelagos serving as stepping stones for
 trans-oceanic dispersal. However, the contribution of propagule dispersal
 to connectivity is still largely unknown, especially at local-scale.
 Identifying fine-scale propagule dispersal patterns unique to individual
 island systems is important to understand their contribution to global
 species distributions, and to select appropriate sizes and locations for
 mangrove conservation in archipelagos. Using population genetic methods
 and a release-recapture method employing GPS drifting buoys, we
 investigated the spatiotemporal scale of propagule dispersal of Rhizophora
 stylosa, one of the widely distributed mangrove species in the Indo-West
 Pacific. This study sought to quantify intra- and inter-island
 connectivity and to assess their contributions to oceanic scale dispersal
 of R. stylosa from the Ryukyu Archipelago, which spans over 545 km in
 southwestern Japan. Using 7 microsatellite markers, we tested 354 samples
 collected from 16 fringing populations on 4 islands. We identified 3
 genetic populations, indicating distinct genetic structures comprising 3
 distinguishable bioregions (genetic clusters). The western end of the
 archipelago receives relatively frequent migration (m &gt; 0.1),
 but is genetically isolated from other sites. Based on genetic migration
 rates, we found that the central area of the archipelago serves as a
 stepping stone for southwestward, but not northeastward dispersal. On the
 other hand, with in-situ drifting buoys, we did not confirm prevailing
 dispersal directionality within the archipelago, instead confirming local
 eddies. Some buoys trapped in those eddies demonstrated potential for
 successful beaching from another island. A large portion of buoys were
 carried predominantly northeastward by the Kuroshio Current and drifted
 away from the coastal areas into the Pacific, contrary to local
 migrations. We found that the spatiotemporal scale of propagule dispersal
 is limited by the distance between islands (&lt; 200km), propagule
 viability duration, and fecundity. Over all, recruitment does not occur
 frequently enough to unify the genetic structure in the archipelago, and
 the Ryukyu Archipelago is isolated in the center of the global mangrove
 distribution.
DOI: 10.5061/dryad.xksn02vhk
title: Radiation flux data of BCC-CSM-MR CMIP6 historical experiment

description: The data is about radiation flux of BCC-CSM-MR CMIP6 historical
 experiment. Including SDLR(Surface Downwelling Longwave
 Radiation), SDSR(Surface Downwelling Shortwave Radiation), TISR(TOA
 incident shortwave radiation), and TOLR(TOA outgoing longwave radiation)
 from 1850-2014(using per month averaged data divided into 19
 layers vertically, and a spatial resolution of 1°×1°).The time stability
 and the accuracy of the data are confirmed. Therefore, the BCC-CSM series
 in CMIP6 data has demonstrated climate simulation consistent with the
 actual situation in history.  
description: The data is downloaded from the official website of CMIP6
 program. Because it is the original data, we did not process the data
 except for the standardized processing in our research.
DOI: 10.5061/dryad.wstqjq2nq
title: Data from: Effects of forest degradation on Amazonian ferns in a land-bridge island system as revealed by non-specialist inventories

description: Background: Tropical deforestation and degradation worldwide have rapidly
 outpaced biodiversity field sampling. No study to date has assessed the
 effects of insular habitats induced by hydroelectric dams on Amazonian
 understorey plants. Fern community responses to anthropogenic effects on
 tropical forest islands can be efficiently revealed through simple and
 cheap, yet informative protocols that can be applied by
 non-specialists.  Aims: This study seeks to both understand the
 drivers of fern and lycophyte assemblages on forest islands and
 investigate the relative costs and effectiveness of a simplified sampling
 protocol that can be implemented by non-specialists and has potential to
 be used to crowdsource ecological field data acquisition. Methods: Fern
 and lycophytes species were sampled by a non-specialist in 17
 quarter-hectare plots on 10 forest islands at the lake of Balbina
 Hydroelectric Dam, central Amazonia. Sampling was carried out
 opportunistically during a field expedition planned to conduct tree
 inventory on permanent plots. We used a set of locally measured or
 GIS-derived predictors for each of the surveyed sites. We used Principal
 Coordinates Analysis and Generalized Linear Mixed Models (GLMMs) to
 further assess the influence of predictors on patterns of fern species
 richness and composition. Results: A total of 286 photographed individual
 ferns or lycophytes represented 23 taxa. The average number of taxa per
 plot was 6.1 on islands and 14.3 in the mainland. The insular species pool
 was a subset of the mainland pool of fern species. Richness was positively
 related to island size and negatively related to isolation and fire
 severity. Area, isolation and fire severity significantly explained
 variation in community composition. The relative cost of the
 non-specialist picture-based fern protocol was very modest (in our case,
 only 4% of the total expedition budget), even compared to the typically
 low cost of alternative orthodox field campaigns. Conclusion: Fern
 community structure in this forest archipelago was primarily driven by
 island size, isolation and fire disturbance. We show that a simple
 sampling protocol carried out by a non-specialist can lead to inexpensive
 and highly reliable ecological data. This opens an avenue for
 crowdsourcing ecological fern data collections using a citizen science
 approach.
DOI: 10.6078/d1n13n
title: The impact of metabolic plasticity on winter energy use models

description: Understanding energetic consequences of climate change is critical to
 identifying organismal vulnerabilities, particularly for dormant organisms
 relying on finite energy budgets. Ecophysiological energy use models
 predict long-term energy use from metabolic rates, but we don’t know the
 degree to which plasticity in metabolism impacts estimates. We quantified
 metabolic rate-temperature relationships of dormant willow leaf beetles
 (Chrysomela aeneicollis) monthly from February to May under constant and
 variable acclimation treatments. Metabolic rates increased as diapause
 progressed, and acclimation to variable conditions altered both metabolic
 intensity and the thermal sensitivity. However, incorporating these two
 types of metabolic plasticity into energy use models did not improve
 energy use estimates, validated by empirical measurements of energy
 stores. While metabolic rate temperature relationships are plastic during
 winter, the magnitude of inter-individual variability in energy stores
 overshadows the effects of incorporating plasticity into energy use
 models, highlighting the importance of within-population variation in
 energy reserves.
description: <strong>Respirometry.xlsx</strong>
 This is the data set containing all respirometry data used in
 making the metabolic rate-temperature relationships. The second tab
 includes the metadata for each column.
 <strong>temperature_regime.xlsx</strong>
 This is the data set containing temperature regime data used in
 estimating energy use. For importing into R. Code available at
 https://github.com/kevintroberts/2021_Met_Plast/blob/main/MR-t%20model.
DOI: 10.5061/dryad.2ngf1vhpr
title: Data and supporting information from: Higher metabolic plasticity in temperate compared to tropical lizards suggests increased resilience to climate change

description: We investigate thermal acclimation of three species
 of Takydromus lizards distributed along a broad
 latitudinal gradient in China. The dataset are including
 metabolic rates, organ size, mitochondrial respiration, Cox activities,
 proteomic and metabolomic regulations of
 three Takydromus lizards after warm and cold acclimation
 in the laboratory. See details in related paper.
description: The <i>T. sexlineatus</i> were from Guangdong
 , <i>T. septentrionalis</i> were from Zhejiang and <i>T.
 wolteri</i> were from Anhui. Each species were assigned into warm
 and cold temperature acclimation randomly and evenly for at least 45 days.
 After acclimation, the growth rate, resting metabolic rate, organ size,
 mitochondrial respiration, Cox activities were determined, and proteomic
 and metabolomic analysis were conducted with livers.  
 The growth rates were determined by SVL and BM increase/day. The
 resting metabolic rates were tested with Sable system at 18, 23, 28, 33,
 38℃. The organ sizes were determined by liver, brain, and heart mass
 (±0.001g). The State 3 and State 4 mitochondrial respiration and Cox
 activities were tested at 18, 23, 28, 33, 38℃ with Clark electrode system.
 The proteomic analysis was conducted by Beijing Genomics Institute, and
 the metabolomic analysis was conducted by Shanghai OE Biotech.
 See more details in the related paper.
DOI: 10.5061/dryad.8cz8w9grj
title: Data from: Elevational divergence in pigmentation plasticity is associated with selection and pigment biochemistry

description: Phenotypic plasticity is predicted to evolve in environmentally variable
 habitats, or those experiencing a high frequency of strong selection.
 However, the evolution of plasticity may be constrained by costs or
 physiological constraints. In flowers, UV-absorbing pigmentation
 ameliorates UV damage to pollen, and is linked with elevated UV exposure.
 Whether plasticity contributes to this pattern remains unclear. Petals of
 Argentina anserina have larger UV-absorbing petal areas at high elevations
 where they experience higher and more variable UV exposure compared to low
 elevations. We measured UV-induced pigmentation plasticity in high- and
 low-elevation populations (hereafter, ‘high, ‘low’), and selection on
 pigmentation via male fitness. We dissected UV pigment biochemistry using
 metabolomics to explore biochemical mechanisms underlying plasticity. High
 displayed positive UV-induced pigmentation plasticity but low lacked
 plasticity. Selection favored elevated pigmentation under UV in high,
 supporting adaptive plasticity. In high, UV-absorption was conferred by
 flavonoids produced in one flavonoid pathway branch. However, in low,
 UV-absorption was associated with many compounds spanning many branches.
 Elevated plasticity was thus associated with reduced pigment diversity.
 Results are consistent with adaptive floral pigmentation plasticity in
 more extreme and variable environments. We discuss how biochemical
 underpinnings of pigmentation may permit or constrain the evolution of
 pigmentation plasticity.
description: This dataset contains phenotypic data that was collected in the
 field, and the greenhouse, fitness data (pollen germination rate) that was
 collected on plants in the greenhouse, and petal metabolomic data that was
 collected on plants in the greenhouse. Multiple floral traits have been
 distilled into PC values. 49 flavonoid compounds have been distilled into
 PC values. Pollen germination rate has been standardized for selection
 analyses.
description: Four datasets are provided in a single excel file, each on a
 different tab. Field_Phenotypes was the dataset used to
 assess elevational patterns of floral trait variation among populations
 across two years of field-collected data.
 GreenHouse_Data was the dataset used to assess whether low and
 high elevation populations differed in phenotypic plasticity in response
 to UV treatments. Poll_Germ Data was the dataset used
 to analyze whether selection acted differently on floral pigmentation
 based on UV exposure and elevation-of-origin.
 Flav_andTrait_Data was used to 1) generate Principle Components
 that described extractable flavonoid profiles of petals, 2) analyze
 whether variation in flavonoid PC values was explained by petal traits
 (flower PC1, flower PC2), elevation-of-origin, and UV treatment, and 3)
 correlate flower pigmentation (flower PC1) with each of hte 49 extracted
 flavonoid abundances.
DOI: 10.5061/dryad.xd2547dj2
title: Data For: The developing bird pelvis passes through ancestral Archosaurian and Dinosaurian conditions

description: Living birds (Aves) have bodies dramatically modified from the ancestral
 reptilian condition. The avian pelvis in particular experienced dramatic
 changes during the transition from early archosaurs to living birds. This
 stepwise transformation is well documented by an excellent fossil record;
 however, the ontogenetic alterations that underly it are less
 well-understood. We used embryological imaging techniques to examine the
 morphogenesis of avian pelvic tissues in three dimensions, allowing direct
 comparison with the fossil record. Many ancestral dinosaurian features
 (e.g., forward-facing pubis, short ilium, pubic ‘boot’) are transiently
 present in the early morphogenesis of birds and arrive at their typical
 ‘avian’ form after transitioning through a prenatal developmental sequence
 that mirrors phylogeny. We quantitatively demonstrate that avian pelvic
 ontogeny closely parallels the dinosaur-to-avian transition and provide
 evidence for an evolutionary module within the pelvis that is conserved
 across Archosauria. The presence of ancestral states in avian embryos may
 stem from this conserved modular relationship. These are
 further indications that the avian pelvis evolved via terminal
 addition—a mechanism whereby ancestral states shift to derived
 states during late development, resulting in retention of
 ancestral character states. This phenotypic modularity suggests a
 previously unrecognized mechanism for the promotion of terminal addition,
 hinting that the retention of ancestral states in development may be
 common across evolutionary transitions.
DOI: 10.5061/dryad.djh9w0w1s
title: The functional diversity of marsupial limbs is influenced by both ecology and developmental constraint

description: Extant marsupials are less ecologically diverse than placentals, and this
 is reflected by placentals exhibiting a greater diversity of locomotor
 modes, including powered flight and fully aquatic swimming. One proposed
 explanation for this discrepancy is that the development of more disparate
 marsupial forelimbs is prevented by the neonate’s crawl to the pouch,
 which requires precocious forelimb development for climbing adaptations.
 To test predictions of this Developmental Constraint Hypothesis, we pursue
 a comparative morphometric study on osteological traits of mammalian
 limbs, with an emphasis on functional differentiation of marsupial limbs
 among locomotor modes. We apply multivariate analyses to a large dataset
 of limb metrics and a diverse sample of mammals, with the placental sample
 limited to taxa whose locomotor modes are exhibited in marsupials.
 Overall, we do not find consistent evidence in support of the
 Developmental Constraint Hypothesis. Diprotodontia serves as an exception,
 with comparisons of their forelimbs to hind limbs supporting the
 Developmental Constraint Hypothesis. Our results suggest that
 developmental constraints on marsupial forelimbs may have limited
 marsupial diversity to some degree. Despite this, the marsupial locomotor
 groups show unexpectedly high levels of morphological differentiation
 relative to placentals of the same locomotor modes, indicating that
 ecological functions may overcome developmental constraints on a
 macroevolutionary scale.
description: This dataset was collected by taking photographs of the skulls,
 girdles, and limb elements of mammals. The limb and girdle skeletal
 elements examined included the scapula, humerus, radius, ulna,
 metacarpals, manual phalanges, pelvis, femur, tibia, fibula, calcaneum,
 metatarsals, and pedal phalanges. Linear measurements were collected from
 photographs with scale bars using <i>ImageJ</i>. The data
 included here are these raw measurements, and not the log-shape ratios
 used in downstream analyses. The method by which the log-shape ratios were
 calculated is detailed in the Materials and Methods section of the main
 text of this study.
description: The units for all measurements included in this dataset are in
 millimeters.