cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tqjq2bvvd
title: Estimating occupancy of Chinese pangolin (Manis pentadactyla) in a protected and non-protected area of Nepal

description: Chinese pangolin is the world’s most heavily trafficked small mammal for
 luxury food and traditional medicine. Although their populations are
 declining worldwide, it is difficult to monitor their population status
 because of its rarity and nocturnal behavior. We used site occupancy
 (presence/absence) sampling of pangolin sign (i.e. active burrows) in a
 protected (Gaurishankar Conservation Area) and non-protected area
 (Ramechhap district) of central Nepal with multiple environmental
 covariates to understand factors that may influence occupancy of Chinese
 pangolin. The average Chinese pangolin occupancy and detection
 probabilities was Ψ ± SE = 0.77 ±0.08; p  ± SE =0.27 ± 0.05
 respectively. The detection probabilities of Chinese pangolin was higher
 in PA ( p  ± SE =0.33 ± 0.03) than compared to non-PA ( p
  ± SE =0.25 ± 0.04). The most important covariates for Chinese
 pangolin detectability were red soil (97%), food source (97.6%), distance
 to road (97.9%), Protected Area (97%) and with respect to occupancy was
 elevation (97.9%). We recommended use of remote cameras and potentially
 GPS collar surveys to further investigate habitat use and site occupancy
 at regular intervals to provide more reliable conservation assessments.
DOI: 10.5061/dryad.j0zpc869r
title: Dysbiosis individualizes fitness effect of antibiotic resistance in the mammalian gut

description: The fitness cost of antibiotic resistance in the absence of antibiotics is
 crucial to the success of suspending antibiotics as a strategy to lower
 resistance. Here we show that after antibiotic treatment the cost of
 resistance within the complex ecosystem of the mammalian gut is
 personalized. Using mice as an in vivo model, we find
 that the fitness effect of the same resistant mutation can be deleterious
 in a host, but neutral or even beneficial in other hosts. Such
 antagonistic pleiotropy is shaped by the microbiota, as in germ-free
 mice resistance is consistently costly across all hosts and in
 hosts with similar microbiotas the host specific effect of resistance is
 reduced. An eco-evolutionary model of competition for resources identifies
 a general mechanism underlying between host variation and predicts that
 the dynamics of compensatory evolution of resistant bacteria should be
 host specific, a prediction that was supported by experimental
 evolution in vivo. The microbiome of each human is close to
 unique and our results suggest that the short-term costs of resistance and
 its long-term within-host evolution will also be highly personalized, a
 finding that may contribute to the observed variable outcome of
 withdrawing antibiotics to reduce resistance levels.
DOI: 10.15468/dl.dycxa8
title: Occurrence Download

description: A dataset containing 192 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Adenopodia patens",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 192 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002217-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k0p2ngf4x
title: Phylogeny and biogeography of the hollies (Ilex L., Aquifoliaceae)

description: The holly genus, Ilex L., in the monogeneric Aquifoliaceae, is the largest
 woody dioecious genus (&gt;664 spp.), with a near‐cosmopolitan
 distribution in mesic environments. We constructed a phylogeny based on
 two nuclear genes, representing 177 species spread across the geographical
 range, and dated using macrofossil records. The ﬁve main clades had a
 common ancestor in the early Eocene, much earlier than previously
 suggested. Ilex originated in subtropical Asia and extant clades colonized
 South America by 30 Ma, North America by 23 Ma, Australia by 8 Ma, Europe
 by 6 Ma, and Africa by 4 Ma. South and North America were colonized
 multiple times. Ilex also reached Hawaii (10 Ma) and other oceanic
 islands. Macrofossil and pollen records show the genus has tracked mesic
 climates through time and space, and had a wider distribution before late
 Miocene global cooling. Our phylogeny provides a framework for studies in
 comparative ecology and evolution.
description: The chronogram we reconstructed in the paper, which based on two
 nuclear markers (ITS and <em>nepGS</em>) of 177 identified
 <em>Ilex</em> species and Bayesain Inference
 method.
DOI: 10.5061/dryad.j0zpc869s
title: Data from: Mycorrhizal symbiosis pathway and edaphic fertility frame root economics space among tree species

description: The root economics space (RES) is multidimensional and largely shaped by
 belowground biotic and abiotic influences. However, how root-fungal
 symbioses and edaphic fertility drive this complexity remains unclear.
 Here, we measured absorptive root traits of 112 tree species in temperate
 and subtropical forests of China, including traits linked to functional
 differences between arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM)
 hosts. Our data, from known mycorrhizal tree species, revealed a
 ‘fungal-symbiosis’ dimension distinguishing AM from ECM species. This
 divergence likely resulted from the contrasting mycorrhizal evolutionary
 development of AM versus ECM associations. Increased root tissue cortical
 space facilitates AM symbiosis, whereas increased root branching favors
 ECM symbiosis. Irrespective of mycorrhizal type, a ‘root-lifespan’
 dimension reflecting aspects of root construction cost and defense was
 controlled by variation in specific root length and root tissue density,
 which was fully independent of root nitrogen content. Within this
 function-based RES, we observed a substantial covariation of axes with
 soil phosphorus and nitrate levels, highlighting the role played by these
 two axes in nutrient acquisition and conservation. Overall, our findings
 demonstrate the importance of evolved mycorrhizal symbiosis pathway and
 edaphic fertility in framing the RES, and provide theoretical and
 mechanistic insights into the complexity of root economics.
DOI: 10.5061/dryad.nk98sf7qc
title: Data from: Diversity-decomposition relationships in forests worldwide

description: Plant species diversity affects carbon and nutrient cycling during litter
 decomposition, yet the generality of the direction of this effect and its
 magnitude remain uncertain. With a meta-analysis including 65 field
 studies across the Earth’s major forest ecosystems, we showed here that on
 average decomposition was faster when litter was composed of more than one
 species. These positive biodiversity effects were mostly driven by
 temperate forests, but more variable in other forests. Litter mixture
 effects emerged most strongly in early decomposition stages and were
 related to divergence in litter quality. Litter diversity also accelerated
 nitrogen, but not phosphorus release, potentially indicating a decoupling
 of nitrogen and phosphorus cycling and perhaps a shift in ecosystem
 nutrient limitation with changing biodiversity. Our findings demonstrate
 the importance of litter diversity effects for carbon and nutrient
 dynamics during decomposition, and show how these effects vary with litter
 traits, decomposer complexity and forest characteristics.
description: All the data were extracted from the corresponding references
 using GetData Graph Digitizer. The effect sizes for mass loss, N release
 and P release were calculated in MetaWin.
DOI: 10.5061/dryad.hqbzkh1cb
title: End-user involvement to improve predictions and management of populations with complex dynamics and multiple drivers

description: Sustainable management of wildlife populations can be aided by building
 models that both identify current drivers of natural dynamics and provide
 near-term predictions of future states. We employed a Strategic Foresight
 Protocol (SFP) involving stakeholders to decide the purpose and structure
 of a dynamic state-space model for the population dynamics of the willow
 ptarmigan - a popular game species in Norway. Based on local knowledge of
 stakeholders, it was decided that the model should include food web
 interactions and climatic drivers to provide explanatory predictions.
 Modelling confirmed observations from stakeholders that climate change
 impacts ptarmigan populations negatively through intensified outbreaks of
 insect defoliators and later onset of winter. Stakeholders also decided
 that the model should provide anticipatory predictions. The ability to
 forecast population density ahead of the harvest season was valued by the
 stakeholders as it provides the management extra time to consider
 appropriate harvest regulations and communicate with hunters, prior to the
 hunting season. Overall, exploring potential drivers and predicting
 short-term future states, facilitate collaborative learning and refined
 data collection, monitoring designs and management priorities. Our
 experience from adapting a SFP to a management target with inherently
 complex dynamics and drivers of environmental change, is that an open,
 flexible, and iterative process, rather than a rigid step-wise protocol,
 facilitates rapid learning, trust, and legitimacy.
description: Data on willow ptarmigan are collected through annaual transect
 surveys with pointing dogs using distance sampling. See
 appurtenant article in Ecological Applications and metadata file for
 further information. 
description: It is important to read the appurtenant article in Ecological
 Applications for important information about the ptarmigan data and the
 different predictors.
DOI: 10.5061/dryad.ghx3ffbk2
title: Data from: Herbivory and climate as drivers of woody plant growth: Do deer decrease the impacts of warming?

description: Vegetation at ecotone transitions between open and forested areas is often
 heavily affected by two key processes: climate change and management of
 large herbivore densities. These both drive woody plant state-shifts,
 determining the location and the nature of the limit between open and tree
 or shrub-dominated landscapes. In order to adapt management to prevailing
 and future climate, we need to understand how browsing and climatic
 factors together affect the growth of plants at biome borders. To
 disentangle herbivory and climate effects, we combined long-term tree
 growth monitoring and dendroecology to investigate woody plant growth
 under different temperatures and red deer (Cervus elaphus) herbivory
 pressures at forest-moorland ecotones in the Scottish highlands.
 Reforestation and deer densities are core and conflicting management
 concerns in the area, and there is an urgent need for additional
 knowledge. We found that deer herbivory and climate had significant and
 interactive effects on tree growth: in the presence of red deer, pine
 (Pinus sylvestris) growth responded more strongly to annual temperature
 than in the absence of deer, possibly reflecting differing plant-plant
 competition and facilitation conditions. As expected, pine growth was
 negatively related to deer density and positively to temperature. However,
 at the tree population level, warming decreased growth when more than 60%
 of shoots were browsed. Heather (Calluna vulgaris) growth was negatively
 related to temperature and the direction of the response to deer switched
 from negative to positive when mean annual temperatures fell below 6.0°C.
 In addition, our models allow estimates to be made of how woody plant
 growth responds under specific combinations of temperature and herbivory,
 and show how deer management can be adapted to predicted climatic changes
 in order to more effectively achieve reforestation goals. Our results
 support the hypothesis that temperature and herbivory have interactive
 effects on woody plant growth, and thus accounting for just one of these
 two factors is insufficient for understanding plant growth mechanics at
 biome transitions. Furthermore, we show that climate-driven woody plant
 growth increases can be negated by herbivory.
description: See Methods in Vuorinen et al. 2020
DOI: 10.15468/dl.3vjax5
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Vanilla penicillata"
 ]
}

 The dataset's 1 records were derived from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002194-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.905qfttgs
title: Seasonal dietary niche contraction in coexisting Neotropical frugivorous bats (Stenodermatinae)

description: Tropical dry forests are characterized by punctuated seasonal
 precipitation patterns that drive primary production and the availability
 of fruits, seeds, flowers, and insects throughout the year. In
 environments in which the quantity and quality of food resources varies
 seasonally, consumers should adjust their foraging behavior to maximize
 energy intake while minimizing overlap with competitors during periods of
 low food availability. Here, we investigated how the diets of frugivorous
 bats in tropical dry forests of NW Mexico varied in response to seasonal
 availability and how this affected dietary overlap of morphologically
 similar species. We performed stable isotope analyses to understand
 temporal and interspecific patterns of overall isotopic niche breadth,
 trophic position, and niche overlap in the diet of six frugivorous species
 of closely related New World Leaf-nosed Bats (family Phyllostomidae,
 subfamily Stenodermatinae). We estimated seasonal changes in resource
 abundance in two complementary ways: 1) vegetative phenology based on
 long-term remote-sensing data, and 2) observational data on food
 availability from previously published insect and plant fruiting surveys.
 In all species, there was a consistent pattern of reduced isotopic niche
 breadth during periods of low food availability. However, patterns of
 niche overlap varied between morphologically similar species. Overall,
 results from our study and others suggest that seasonal food availability
 likely determines overall dietary niche breadth in Phyllostomidae and that
 despite morphological specialization, it is likely that other mechanisms,
 such as opportunistic foraging and spatiotemporal niche segregation may
 play a role in maintaining coexistence rather than simply dietary
 displacement.
description: Collected from museum specimens during 1972 and 1973 Colima
 Expeditions, curated at Sam Noble Museum of Natural History, see
 manuscript for more details on location. These are the first toenail cross
 sections.
DOI: 10.5061/dryad.nzs7h44nh
title: Dynamics of a host-parasitoid interaction clarified by modelling and DNA sequencing

description: It has been hypothesized that the 2-year oscillations in abundance of
 Xestia moths are mediated by interactions with 1-year Ophion parasitoid
 wasps. We tested this hypothesis by modelling a 35-year time series of
 Xestia and Ophion from northern Finland. Additionally, we used DNA
 barcoding to ascertain the species diversity of Ophion and targeted
 amplicon sequencing of their gut contents to confirm their larval hosts.
 Modelling of the time-series data strongly supported the hypothesized
 host–parasitoid dynamics and that periodic occurrence of Xestia moths is
 mediated by Ophion. DNA barcodes revealed that Ophion included five
 species rather than just one while targeted amplicon sequencing verified
 that Ophion does parasitize Xestia. At least one Ophion species employs
 1-year Syngrapha interrogationis as an alternate host, but it did not
 detectably affect Xestia–Ophion dynamics. We also demonstrate the
 previously unrecognized complexity of this system due to cryptic
 parasitoid diversity.
DOI: 10.5061/dryad.kprr4xh1v
title: Micro-stepping Extended Focus reduces photobleaching and preserves structured illumination super-resolution features

description: Despite progress made in confocal microscopy, even fast systems still have
 insufficient temporal resolution for detailed live cell volume imaging,
 such as tracking rapid movement of membrane vesicles in three-dimensional
 space. Depending on the shortfall, this may result in undersampling and/or
 motion artifacts that ultimately limit the quality of the imaging data. By
 sacrificing the detailed information in the Z-direction, we propose a new
 imaging modality that involves capturing fast “projections” from the field
 of depth which shortens imaging time by approximately an order of
 magnitude as compared to standard volumetric confocal imaging. With faster
 imaging, radiation exposure to the sample is reduced, resulting in less
 fluorophore photobleaching and potential photodamage.  The
 implementation minimally requires two synchronized control signals that
 drive a piezo stage and trigger the camera exposure. The device generating
 the signals has been tested on spinning disk confocals and instant
 structured-illumination-microscopy (iSIM) microscopes. Our calibration
 images show that the approach provides highly repeatable and stable
 imaging conditions that enable photometric measurements of the acquired
 data, in both standard live imaging and super-resolution
 modes.  
description: Discribed in the manuscript
DOI: 10.6078/d1th7j
title: Nucleation and heterochromatin establishment in Drosophila miranda

description: Heterochromatin is a key architectural
 feature of eukaryotic genomes, crucial for silencing of
 repetitive elements and maintaining genome
 stability. Heterochromatin shows stereotypical
 enrichment patterns around centromeres and repetitive sequences,
 but the molecular details of how heterochromatin is
 established in vivo are poorly understood. Here, we map
 the genome-wide distribution of H3K9me3-dependent heterochromatin
 in individual Drosophila early embryos at
 precisely staged developmental time points.
DOI: 10.82294/dvn39t34b
title: Observaciones semiestructuradas. Territorio: Cali. Eje medular: Corporalidad. Sector: Educación. Año: 2025

description: La corporalidad se concibe como una dimensión dinámica y multidimensional que trasciende lo biológico para integrar aspectos históricos, sociales y políticos. En el campo de la educación artística, constituye el medio esencial para percibir, actuar y pensar, pues a través del cuerpo se expresan discursos creativos, se experimenta el mundo desde la sensibilidad y se construyen vínculos afectivos y colectivos. Al mismo tiempo, la corporalidad funciona como un espacio de reflexión y conciencia, favoreciendo el autoconocimiento, el cuidado de sí y la transformación personal.
DOI: 10.5061/dryad.tht76hdw5
title: Wolbachia-infected ant colonies have increased reproductive investment and an accelerated life cycle

description: Wolbachia is a widespread group of maternally-transmitted endosymbiotic
 bacteria that often manipulates the reproductive strategy and life history
 of its hosts to favor its own transmission. Wolbachia mediated
 phenotypic effects are well characterized in solitary hosts, although
 evidence of similar effects are rare in eusocial insects, such as ants.
 The invasive pharaoh ant, Monomorium pharaonis, shows natural variation in
 Wolbachia infection between colonies and can be readily bred
 under laboratory conditions. We previously showed that Wolbachia-infected
 pharaoh ant colonies had a queen-biased sex ratio, which is expected to
 favor the spread of maternally-transmitted Wolbachia. Here, we further
 characterize the effects of Wolbachia on the short- and
 longer-term reproductive and life history traits of pharaoh ant colonies.
 First we characterized reproductive differences between naturally infected
 and uninfected colonies at three discrete time points and found that
 infected colonies had higher reproductive investment (i.e. infected
 colonies produce more new queens), in particular when colony queens were
 three months old. Next, we compared the long-term growth and reproduction
 dynamics of infected and uninfected colonies across their whole life
 cycle. Infected colonies had increased colony-level growth and early
 colony reproduction, resulting in a shorter colony life cycle, when
 compared to uninfected colonies.
description: We have provided 3 datasets, all of which include the raw values
 collected over the course of the experiment and have been used in the
 article to support our conclusions. Please refer to the article for
 details about experimental design and data collection. These raw valued
 were analyzed to assess fitness differences
 between <em>Wolbachia</em>-infected and uinfected pharaoh ant
 colonies in two different experimental regimes. 
 SuppFile-S1-assay 1: contains the raw census values collected
 for Assay 1 SuppFile-S2-assay 2: contains the raw
 census and dry mass of worker pupae collected for Assay 2
 SuppFile-S3-colony-relatedness: raw values of relatedness among
 heterogenous lab stock colonies used to create experimental colonies in
 the current article.
description: We have provided details of our statistical analysis in R in the
 following documents -  
 SuppFile-s4-script-assay1: R script used for statistical
 analysis for Assay 1 SuppFile-s5-script-assay2: R
 script used for statistical analysis for Assay 2
 SuppFile-s6-script-relatedness-comparisons: R script used for
 comparing colony relatedness
 SuppFile-s7-script-assay1-output: output from the statistical
 analysis done in R for Assay 1. These values have been quoted in the
 article to support our claim.
 SuppFile-s8-script-assay2-output: output from the statistical
 analysis done in R for Assay 2. These values have been quoted in the
 article to support our claim.
DOI: 10.5061/dryad.rxwdbrv4x
title: Data from: Tracing the patterns of non-marine turtle richness from Triassic–Palaeogene: from origin through global spread

description: Turtles are key components of modern vertebrate faunas and it is predicted
 that their diversity and distributions will be affected by anthropogenic
 climate change. Despite this, few studies have attempted to provide
 baseline data on turtle taxonomic richness through time or assess their
 past responses to global environmental change. We used the extensive
 Triassic–Palaeogene (252–23 Ma) fossil record of terrestrial and
 freshwater turtles to investigate diversity patterns, finding substantial
 variation in richness through time and between continents. Subsampled
 turtle richness was low globally from their Triassic origin until the Late
 Jurassic. There is strong evidence for high richness in the earliest
 Cretaceous of Europe. Richness was especially high following the
 Cretaceous Thermal Maximum and declined in all continents by the
 end-Cretaceous. At the K-Pg boundary, South American richness levels
 changed little while North American richness increased. Subsampled North
 American turtle richness was very high during the earliest Palaeogene
 (Danian) while South American richness was low; informative data on
 earliest Palaeogene turtle richness are lacking elsewhere. However, the
 Selandian–Thanetian interval, approximately 5 million years after the K-Pg
 mass extinction, shows low turtle richness in Asia, Europe and South
 America. This suggests the occurrence of exceptional turtle richness in
 the post-extinction Paleocene fauna of North America is not globally
 representative. Richness decreased over the Eocene–Oligocene boundary in
 North America but increased to its greatest known level for Europe,
 implying very different responses to dramatic Eocene–Oligocene climatic
 shifts. Time series regressions suggest number of formations sampled and
 palaeotemperature are the primary influencers of face-value richness
 counts, but additional factors not tested here may also be involved.