cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f1vhhmgzt
title: Data from: The megaherbivore gap after the non-avian dinosaur extinctions modified trait evolution and diversification of tropical palms

description: The Cretaceous–Paleogene (K-Pg) extinction of the non-avian dinosaurs (66
 Ma) led to a 25 million year gap of megaherbivores (&gt;1000 kg)
 before the evolution of megaherbivorous mammals in the Late Eocene (40
 Ma). The botanical consequences of this ‘Paleocene megaherbivore gap’
 (PMHG) remain poorly explored. We hypothesize that the absence of
 megaherbivores should result in changes in the diversification and trait
 evolution of associated plant lineages. We used phylogenetic time- and
 trait-dependent diversification models with palms (Arecaceae) and show
 that the PMHG was characterized by speciation slowdowns, decreased
 evolution of armature, and increased evolution of megafaunal (≥4cm)
 fruits. This suggests that the absence of browsing by megaherbivores
 during the PMHG may have led to a loss of defence traits, but absence of
 megaherbivorous seed dispersers did not lead to a loss of megafaunal
 fruits. Instead, increases in PMHG fruit sizes may be explained by Late
 Paleocene rising temperatures, rainforest expansion, and the subsequent
 radiation of seed dispersing birds and mammals. We show that the profound
 impact of the PMHG on plant diversification can be detected even with the
 overwriting of adaptations by the subsequent Late Eocene opening-up of
 megaherbivore-associated ecological opportunities. Our study provides a
 quantitative, comparative framework to assess diversification and
 adaptation during one of the most enigmatic periods in angiosperm history.
description: See manuscript text: 10.1098/rspb.2021.2633.
 Fossil data: We searched the literature for palm fossil fruits
 and seeds following a review of the palm fossil record. This resulted in
 90 observations for which we assembled the taxonomy of the fossil and its
 nearest living relatives (tribe, genus, species), fossil site location,
 fossil age, and length and/or width of the fossil fruit or
 seed.  Trait data: on fruit lengths and armature type
 in palms (Arecaceae) Analytical pipeline: All R script
 and markdown files, and underlying trait and phylogenetic data, to conduct
 the analyses as presented in Onstein et al. 2022, including ancestral
 state reconstructions and diversification rate analyses.
DOI: 10.5061/dryad.zcrjdfnf7
title: Male adaptive plasticity can explain the evolution of sexual perception costs

description: Sensory perception of environmental cues has been shown to trigger plastic
 responses that can induce important fitness costs, including the dramatic
 modulation of ageing across distant taxa. For example, male Drosophila
 melanogaster suffer a marked decrease in fitness, including faster
 reproductive and actuarial ageing, if they perceive female cues but fail
 to mate shortly after (ageing via sexual perception). While this has been
 a breakthrough for our understanding of the mechanisms of ageing, it poses
 the question as to why such plastic responses evolved. Here, we used D.
 melanogaster to ask whether sexual perception costs may be a by-product of
 plastic adaptive responses to female cues. We found that: a) short-term (1
 day) perception of female cues prior to mating opportunities increases
 male relative lifetime reproductive success in a competitive environment,
 b) medium-term (3-7 days) perception is neutral, and c) long-term (15
 days) perception leads to reproductive costs. We then ran mathematical
 simulations under a wide range of socio-sexual and demographic scenarios
 to show that such plastic male responses can be adaptive whenever mating
 rates fluctuate within the range experienced by D. melanogaster and other
 insects in the wild, suggesting this may be a widespread strategy in
 nature. Finally, we show that, because the short-term benefits of plastic
 responses will be mostly acquired by high-quality males while long-term
 costs will be mostly paid by low-quality males, sexual perception can
 significantly magnify sexual selection (15-27% average increase in the
 opportunity for selection).
DOI: 10.5061/dryad.1ns1rn8wd
title: Social environment influences termination of nomadic migration

description: The final stage of migration, when animals terminate migratory movements
 and transition to a more sedentary state, remains the least understood
 phase of migration. Whereas migrants that return to the same locations
 each year may use mechanisms associated with locating a specific
 destination, migrants with low site fidelity, such as nomadic migrants,
 may rely on local environmental cues to determine when to cease migratory
 movements. Using an experiment with captive birds, we tested whether the
 presence of a conspecific influences the termination of migration,
 indicated by changes in behaviour and physiology, in a nomadic migrant
 (the pine siskin, Spinus pinus). We paired migratory birds with a
 non-migratory individual or left migratory and non-migratory individuals
 unpaired. Migratory paired birds had a significant decline in nocturnal
 activity immediately after pairing and activity levels remained lower two
 weeks later, with significant declines in energetic reserves and flight
 muscle size also observed. In contrast, migratory unpaired birds
 maintained high levels of activity and energetic reserves. These results
 provide evidence for a role of the social environment in migratory
 termination decisions. Social cues may be particularly useful in nomadic
 migrants, such as pine siskins, to facilitate settling in high quality,
 but unfamiliar, habitats.
description: Data were collected from captive pine siskins (<em>Spinus
 pinus</em>). Behavioral data were collected from video recordings of
 birds between 23:00 – 3:00 using instantaneous scan sampling at 5-min
 intervals. The frequency of jumping, flight, fast wing beating, and beak
 up hopping behaviors were summed to calculate the proportion of time that
 each bird engaged in locomotor behavior. For each individual and phase of
 the experiment (Pre, Initial, and Final), behavioral data were averaged
 across two nights of recording. Birds were weighed on an electronic
 balance to the nearest 0.01 g to measure body mass. Furcular and abdominal
 fat deposits were visually scored on a scale from 0 to 5 and summed to
 estimate fat deposits. Flight muscle size was scored visually on a scale
 from 0 to 3. Principal components analysis implemented in JMP Pro 14.0 was
 used to distill mass and summed fat score into a single variable - the
 first principal component. 
description: All metadata are provided in
 Robart_et_al_PineSiskin_SettlementSocialEnv_Readme.txt
DOI: 10.5061/dryad.1g1jwstzm
title: Phylogenomic testing of root hypotheses - demonstrative datasets - Opisthokonta and Proteobacteria

description: The determination of the last common ancestor (LCA) of a group of species
 plays a vital role in evolutionary theory. Traditionally, an LCA is
 inferred by the rooting of a fully resolved species tree. From a
 theoretical perspective, however, inference of the LCA amounts to the
 reconstruction of just one branch - the root branch - of the true species
 tree, and should therefore be a much easier task than the full resolution
 of the species tree. Discarding the reliance on a hypothesised species
 tree and its rooting leads us to re-evaluate what phylogenetic signal is
 directly relevant to LCA inference, and to recast the task as that of
 sampling the total evidence from all gene families at the genomic scope.
 Here we reformulate LCA and root inference in the framework of statistical
 hypothesis testing and outline an analytical procedure to formally test
 competing a-priori LCA hypotheses and to infer confidence sets for the
 earliest speciation events in the history of a group of species. Applying
 our methods to two demonstrative datasets we show that our inference of
 the opisthokonta LCA is well in agreement with the common knowledge.
 Inference of the proteobacteria LCA shows that it is most closely related
 to modern Epsilonproteobacteria, raising the possibility that it may have
 been characterized by a chemolithoautotrophic and anaerobic life-style.
 Our inference is based on data comprising between 43% (opisthokonta) and
 86% (proteobacteria) of all gene families. Approaching LCA inference
 within a statistical framework renders the phylogenomic inference powerful
 and robust.
description: Please see https://www.biorxiv.org/content/10.1101/758581v2
description: Two gzipped nexus files with alignments and trees.
 For file format see
 https://en.wikipedia.org/wiki/Nexus_file For dataset
 definition and methods used see
 https://www.biorxiv.org/content/10.1101/758581v2
DOI: 10.5061/dryad.rv15dv496
title: A meta-analysis of the effects of habitat aridity, evolutionary history of grazing, and grazing intensity on bee and butterfly communities worldwide

description: A variety of habitat-associated factors moderate effects of grazing on
 insect biodiversity. Here, we examine how aridity, evolutionary history of
 grazing, and grazing intensity individually and interactively mediate the
 effect of livestock grazing on pollinator diversity (native bees and
 butterflies). Using a meta-analysis of 59 studies published in the primary
 literature we characterized the response of pollinator communities to
 grazing across several continents. In very humid habitats high grazing
 intensities generally had negative impacts on pollinator abundance and
 richness, but these effects were not found in semi-arid habitats, where
 livestock grazing intensity did not interact with aridity to impact
 pollinator abundance or richness. However, within semi-arid habitats
 livestock grazing was associated with reduced pollinator richness in areas
 with short evolutionary histories grazing. Pollinator life history
 mediated effects of livestock grazing on pollinator communities: livestock
 grazing had negative impacts on richness of social bees and butterflies
 but not solitary bees, though abundances of all three pollinator
 categories were consistently reduced under livestock grazing. Our
 synthesis suggests that effects of cattle on pollinators may be driven by
 impacts on nesting habitats (e.g., soil compaction), rather than
 consumption or alteration of forb cover. Our collective findings have
 importance for coordinating grazing management and pollinator conservation
 efforts and help to distinguish how grazing practices could impact
 pollinator biodiversity across ecoclimatic regions.
DOI: 10.5061/dryad.4qrfj6qcc
title: Data and script files: Gene expression in response to estrone sulfate in Trachemys scripta

description: Variation in developmental conditions can affect a variety of embryonic
 processes and shape a number of phenotypic characteristics that can affect
 offspring throughout their lives. This is particularly true of oviparous
 species where development typically occurs outside of the female, and
 studies have shown that traits such as survival and behavior can be
 altered by both temperature and exposure to steroid hormones during
 development. In species with temperature-dependent sex determination
 (TSD), the fate of gonadal development can be affected by temperature and
 by maternal estrogens present in the egg at oviposition and there is
 evidence that these factors can affect gene expression patterns. Here, we
 explore how thermal fluctuations and exposure to an estrogen metabolite,
 estrone sulfate, affect the expression of several genes known to be
 involved in sexual differentiation; Kdm6b, Dmrt1, Sox9, FoxL2, and
 Cyp19A1. We found that most of the genes responded to both temperature and
 estrone sulfate exposure, but that the responses to these factors was not
 identical in that estrone sulfate effects occur downstream of temperature
 effects. Our findings demonstrate that conjugated hormones such as estrone
 sulfate are capable of influencing temperature dependent pathways to
 potentially alter how embryos respond to temperature and highlight the
 importance of studying the interaction of maternal hormone and temperature
 effects.
description: Methods have been described in the body of the manuscript.
description: Dryad 2022_Study1_Dmrt1 R code has two data files:
 Dryad 2022_Study1_Dmrt1.xlsx and Dryad
 2022_Study1_Dmrt1_Baseline.xlsx Dryad
 2022_Study1_Hatchling R code has two data files: Dryad
 2022_Study1_Hatchling_Dmrt1.xlsx and Dryad
 2022_Study1_Hatchling_FoxL2.xlsx All other R code has a
 single xlsx file with a corresponding name.
DOI: 10.15468/dl.kgnnqb
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "Geometry POLYGON((115 29,119 29,119 34,115 34,115 29))",
 "TaxonKey is Ginkgo biloba"
 ]
}

 The dataset includes 46 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003070-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.tx95x6b0k
title: Chipmunk body mass variations and life-histories in a pulsed resource ecosystem

description: Phenotypic plasticity is the most immediate mechanism of adaptative
 response to environmental change. Studying plastic changes in response to
 fluctuating environments provides insights into how such adjustments may
 impact life-history traits. Here, we used a 14-year dataset of repeated
 body mass measurements in male eastern chipmunks (Tamias striatus) to
 assess the extent of plastic changes for this trait in a resource pulse
 ecosystem. We first determined the magnitude of variation in body mass at
 the population level in response to the drastic change in food resource
 availability from American beech tree seeds (Fagus grandifolia). Males
 that emerged in the spring from winter torpor following a non-mast year
 had a lower body mass than males emerging after a mast year, but they
 tended to recover this loss by mid-June. We found significant
 among-individual variation in spring body mass plasticity (i.e.,
 individual by environment interaction, I x E). We then investigated the
 relationships between individual spring body mass plasticity, longevity
 and lifetime reproductive success. Interestingly, heavier males lived
 longer than lighter males, but more plastic males had a lower longevity
 and lower lifetime reproductive success than less plastic males. The
 report of such plastic response in a stochastic resource system provides
 valuable insights into the interplay between the costs and benefits of
 phenotypic plasticity as an adaptation to environmental fluctuations.
DOI: 10.5061/dryad.0cfxpnw4k
title: Mutualism has its limits: consequences of asymmetric interactions between a well-defended plant and its herbivorous pollinator

description: Concern for pollinator health has focused on social bees and their
 agricultural services, but not all pollinators are bees, and their
 ecosystem services also promote biodiversity and conservation. Pollinating
 herbivores generate ecological conflicts when they utilize the same plant
 as a nectar source and larval host. We tracked individual-level metrics of
 pollinator health – growth, survivorship, fecundity – across the life
 cycle of a pollinating herbivore, the hawkmoth Hyles lineata, through its
 interactions with Oenothera harringtonii, a rare plant polymorphic for the
 floral volatile (R)-(-)-linalool. Linalool had no impact on moth
 attraction to O. harringtonii flowers but suppressed oviposition on
 experimentally supplemented plants. Leaves of O. harringtonii showed
 robust resistance against herbivory by H. lineata from leaf-disc to
 wholeplant scales, through poor larval growth and survivorship. Higher
 larval performance on other Oenothera species indicates that constitutive
 herbivore resistance by O. harringtonii is not generic. Leaf volatiles
 differed among populations of O. harringtonii but were not induced by
 larval herbivory. Elagitannins and other phenolics varied among leaf, bud
 and seed tissues but showed no evidence of herbivore induction. Our
 findings highlight asymmetric plant-pollinator interactions and the
 importance of third parties, such as alternative host plants, in
 maintaining pollinator health.
description: Please see "read me" file.
DOI: 10.5061/dryad.0vt4b8h1s
title: Polymorphisms of cytochromes P450 and glutathione S-transferases synergistically modulate risk for Parkinson’s disease

description: Background: Environmental substances such as pesticides are well-known in
 link with PD risk. Enzymes including cytochromes P450 (CYPs), esterases
 and glutathione S-transferases (GSTs) are responsible for the xenobiotic
 metabolism and may functionally compensate each other for subtypes in the
 same class. We hypothesize that the genetic effects of each class modulate
 PD risk stronger in a synergistic way than individually. Methods: We
 selected 14 polymorphic loci out of 13 enzymes in the classes of CYP,
 esterase, and GST, and recruited a cohort of 1026 PD and control subjects
 from eastern China. The genotypes were identified using improved multiplex
 ligation detection reaction, and analyzed using multiple models. Results:
 A total of 13 polymorphisms remained after Hardy-Weinberg equilibrium
 analysis. None of the polymorphisms were independently associated with PD
 risk after Bonferroni correction either by logistic regression or genetic
 models. In contrast, interaction analyses detected increased resistance to
 PD risk in individuals carrying the rs12441817/CC (CYP1A1) and rs2070676/G
 (CYP2E1) genotypes (P = 0.002, OR = 0.393, 95% CI = 0.216-0.715), or
 carrying the GSTM1-present, GSTT1-null, rs156697/G (GSTO2) and rs1695/AA
 (GSTP1) genotypes (P = 0.003, OR = 0.348, 95% CI = 0.171-0.706), but not
 with genotypes of esterases. Conclusions: We demonstrate a presence of
 synergistic but not individual impact on PD susceptibility in
 polymorphisms of CYPs and GSTs. The results indicate that the genetic
 interplay leads the way to PD development for xenobiotic metabolizing
 enzymes.
DOI: 10.5281/zenodo.18399826
title: Dataset for paper "Integrating Newton's equations of motion in the reciprocal space" (https://doi.org/10.1063/5.0224108)
DOI: 10.5281/zenodo.18399827
title: Dataset for paper "Integrating Newton's equations of motion in the reciprocal space" (https://doi.org/10.1063/5.0224108)
DOI: 10.57707/fmi-b2share.jnk0k-96726
title: Data for manuscript:"Atmospheric and cryospheric observations at the high-altitude Zarafshon River Basin and the hydrographic party glacier (GGP), Tajikistan"

description: These data are atmospheric and cryospheric observations made at the GGP glacier in Tajikistan between 2018 and 2025. The data consists of autumn expedition observations (2018, 2019, 2021, 2023, 2024 and 2025), as well as continuous meteorological observations at the site. Observations include 
- Glacier surface area and evolution with in situ, UAV-based and remote sensing observations
- Meteorological measurements
- Glacier snow and - ice properties including impurities
- Atmospheric aerosol observations
The observations tell about the state of the GGP glacier, its evolution and environmental drivers of that evolution.
The data are available as 1) "GGP_in_situ_data.zip" containing sub-folders for in situ measurements of:
- surface reflectance
- snow impurities
- ablation stakes
- atmospheric aerosol measurements
- terminus coordinates
- weather;
2) "Trail Camera", containing a .7z package of daily photos taken of the GGP glacier surroundings,
3) "UAV", containing .zip packages annual expedition, UAV aerial photography: digital surface model (DSM) and orthomosaic overlays,
4) "Pix4D- projects", containing .7z packages of annual expedition, full UAV- 3D imaging project processed in the Pix4D software version 4.9.0.
DOI: 10.57707/fmi-b2share.weahp-0ja81
title: Data for manuscript:"Atmospheric and cryospheric observations at the high-altitude Zarafshon River Basin and the hydrographic party glacier (GGP), Tajikistan"

description: These data are atmospheric and cryospheric observations made at the GGP glacier in Tajikistan between 2018 and 2025. The data consists of autumn expedition observations (2018, 2019, 2021, 2023, 2024 and 2025), as well as continuous meteorological observations at the site. Observations include 
- Glacier surface area and evolution with in situ, UAV-based and remote sensing observations
- Meteorological measurements
- Glacier snow and - ice properties including impurities
- Atmospheric aerosol observations
The observations tell about the state of the GGP glacier, its evolution and environmental drivers of that evolution.
The data are available as 1) "GGP_in_situ_data.zip" containing sub-folders for in situ measurements of:
- surface reflectance
- snow impurities
- ablation stakes
- atmospheric aerosol measurements
- terminus coordinates
- weather;
2) "Trail Camera", containing a .7z package of daily photos taken of the GGP glacier surroundings,
3) "UAV", containing .zip packages annual expedition, UAV aerial photography: digital surface model (DSM) and orthomosaic overlays,
4) "Pix4D- projects", containing .7z packages of annual expedition, full UAV- 3D imaging project processed in the Pix4D software version 4.9.0.
DOI: 10.15468/dl.b73p6g
title: Occurrence Download

description: A dataset containing 7008855 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "Year 1970-2025"
 ]
}

 The dataset includes 7008855 records from 4213 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049518-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc2k8p9v
title: CCDC 2361837: Experimental Crystal Structure Determination

description: Related Article: Yu Liu, Wen Yang, Jian Luan, Xiao-Sa Zhang, Jun-Hong Jian, Hong-Xiao Liu, Zheng-Kai Li, Wen-Ze Li|2024|Inorg.Chem.Commun.|170|113354|doi:10.1016/j.inoche.2024.113354
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2l6g1b
title: CCDC 2389481: Experimental Crystal Structure Determination

description: Related Article: Sourav Nath, Sourav Roy, Nabajyoti Baildya, Saddam Hussain, Swastika Dhar, Ghodrat Mahmoudi, Akalesh Kumar Verma, Subhadip Roy, Suman Adhikari|2025|J.Heterocycl.Chem.|62|1378|doi:10.1002/jhet.70087
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2pc65g
title: CCDC 2483415: Experimental Crystal Structure Determination

description: Related Article: Jan Rosenboom, Leon Teichmeier, Karsten Paul Lüdtke, Jonas Bresien, Axel Schulz|2025|Z.Anorg.Allg.Chem.|651|e202500183|doi:10.1002/zaac.202500183
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.