cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pg4f4qrqn
title: Data from: Landscape heterogeneity filters functional traits of rice arthropods in tropical agroecosystems

description: Biological control services of agroecosystems depend on the functional
 diversity of species traits. However, the relationship between arthropod
 traits and landscape heterogeneity is still poorly understood, especially
 in tropical rice agroecosystems which harbour a high diversity of often
 specialized species. We investigated how landscape heterogeneity, measured
 by three metrics of landscape composition and configuration, influenced
 body size, functional group composition, dispersal ability and vertical
 distribution of rice-arthropods in the Philippines.   We found
 that landscape composition and configuration acted to filter arthropod
 traits in tropical rice agroecosystems. Landscape diversity and rice
 habitat fragmentation were the two main gradients influencing
 rice-arthropod traits, indicating that different rice-arthropods have
 distinct habitat requirements. Whereas small parasitoids and species
 mostly present in the rice-canopy were favoured in landscapes with high
 compositional heterogeneity, predators and medium-sized species occupying
 the base of the rice plant, including planthoppers, mostly occurred in
 highly fragmented rice habitats. We demonstrate the importance of
 landscape heterogeneity as an ecological filter for rice-arthropods,
 identifying how the different components of landscape heterogeneity
 selected for or against specific functional traits. However, the
 contrasting effects of landscape parameters on different groups of natural
 enemies indicate that not all beneficial rice-arthropods can be promoted
 at the same time when using a single land management strategy. Increasing
 compositional heterogeneity in rice landscapes can promote parasitoids but
 may also negatively affect predators. Future research should focus on
 identifying trade-offs between fragmented rice habitats and structurally
 diverse landscapes to maximize the presence of multiple groups of
 beneficial arthropods.
description: Data were collected in three regions of the Philippines
 and contain an environmental table (Table R), a species abundance table
 (Table L), and a species traits table (Table Q). Metadata is provided
 within the excel file.  The coordinates and locations
 of the study sites in each region are provided via a .kmz file.
DOI: 10.6084/m9.figshare.31167682
title: A daily catalog of mesoscale eddies over the South China Sea (~0–25°N, 100–125°E) from 1993-01-01 to 2021-12-31.

description: A daily catalog of mesoscale eddies over the South China Sea (~0–25°N, 100–125°E) from 1993-01-01 to 2021-12-31.
DOI: 10.6084/m9.figshare.31167682.v1
title: A daily catalog of mesoscale eddies over the South China Sea (~0–25°N, 100–125°E) from 1993-01-01 to 2021-12-31.

description: A daily catalog of mesoscale eddies over the South China Sea (~0–25°N, 100–125°E) from 1993-01-01 to 2021-12-31.
DOI: 10.5061/dryad.gf1vhhmr0
title: Central and Northern European caterpillar assemblages show strong phylogenetic structure

description: Phylogenetic diversity metrics have been used to tackle an increasing
 number of questions in ecology and evolutionary biology. Here we present a
 novel use of phylogenetic diversity metrics namely the investigation of
 insect herbivore assemblages on select plant species in order to
 investigate possible drivers shaping the phylogenetic structure of those
 assemblages. We investigated the phylogenetic structure of lepidopteran
 herbivore assemblages on 208 species of central European vascular plants.
 A dataset of 2553 species of Lepidoptera from 68 families, comprising 8584
 individual herbivore-host associations, was analyzed for patterns of
 phylogenetic α- and β-diversity in relation to plant growth form, plant
 phylogeny and the accumulation of some characteristic major classes of
 secondary plant metabolites. Distinct patterns of phylogenetic β-diversity
 were detected when plants were partitioned into three growth form
 categories (graminoid, herbaceous, and woody). In contrast, groupings of
 plants according to higher taxa or key secondary metabolites did not yield
 similarly clear patterns. Notable exceptions were assemblages on graminoid
 plants, especially those containing silica, which could be distinguished
 by both plant phylogeny and their phytochemical characteristics.
 Additionally, plants containing highly toxic glucosinolates (all of the
 family Brassicaceae) harbor highly distinct lepidopteran assemblages.
 Phylogenetic α-diversity of associated caterpillars differed greatly
 between graminoid, herbaceous and woody plants. Assemblages on graminoid
 plants were found to be the most phylogenetically clustered, followed by
 herbs and woody plants which showed the least degree of phylogenetic
 clustering. In conclusion, our results indicate that the phylogenetic
 structure of the investigated herbivore assemblages in the nemoral and
 boreal zones of the Western Palaearctic region is most heavily influenced
 by plant growth form while categories derived from higher plant
 systematics or classifications reflecting secondary metabolites leave far
 less signal at this macroecological scale. The approach taken in this
 study proved to be very successful in identifying patterns in the
 phylogenetic structure of herbivore assemblages. Our findings are in line
 with the ‘classical’ plant apparency hypothesis. Plant secondary compounds
 were found to have only limited explanatory power on our scale of
 analysis.
description: See the included readme file and the corresponding paper.
description: See the included readme file and the corresponding paper.
DOI: 10.5281/zenodo.18398778
title: England et al. 2026 Comms Bio
DOI: 10.5281/zenodo.18398777
title: England et al. 2026 Comms Bio
DOI: 10.5061/dryad.mcvdnck27
title: Data from: Harvesting has variable effects on demographic rates and population growth across three dry forest tree species

description: Understanding how anthropogenic activities, such as harvesting, influence
 plant populations is important to quantify sustainable practices that
 conserve species of socioeconomic importance. There is limited knowledge
 on how harvesting of branches and non-timber forest products affect
 populations of trees in the dry tropics. We measure demographic vital
 rates of three dry tropical tree species in the presence and absence of
 harvesting and apply integral projection models to quantify population
 growth rates, which represent the mean fitness across the life cycle. Our
 results show that the three species vary in their demographic rates and
 life history. Harvesting significantly decreases the growth of two
 species. Current levels of harvesting only significantly decreased the
 population growth rate of one species that experienced both branch and
 main stem harvesting. Life table response experiments reveal that the
 negative effect of harvesting on the population growth rate of this
 species is primarily due to individuals being forced to re-sprout from
 their base. Few individuals were observed recruiting from seed, and this
 might be due to the presence of other threats, such as fire, soil erosion,
 and grazing. Our results provide knowledge on the demography and the
 effects of harvesting on endemic tree species of the Eastern Ghats, a
 region for which few demographic studies are available. These results are
 relevant to conserving forest biodiversity for the benefits of people and
 can contribute to quantitative threat assessment for IUCN red listing.
description: Demographic data was collected in two census years 2009 and 2016.
 During both censuses, girth at breast height or collar girth was measured
 for each individual. Girth was converted to diameter for analysis. This
 file contains information of plant sizes (diameter), survival, transition
 of tree to sprout and presence of harvesting for individuals of
 <em>Acacia chundra</em>, <em>Chloroxylon
 swietenia</em> and <em>Gardenia
 gummifera.</em>
DOI: 10.5061/dryad.4mw6m90bk
title: Simulation of the evolution of codon usage in cpDNA

description: The codon usage of the Angiosperm psbA gene is atypical for flowering
 plant chloroplast genes but similar to the codon usage observed in highly
 expressed plastid genes from some other Plantae, particularly
 Chlorobionta, lineages. The pattern of codon bias in these genes is
 suggestive of selection for a set of translationally optimal codons but
 the degree of bias towards these optimal codons is much weaker in the
 flowering plant psbA gene than in high expression plastid genes from
 lineages such as certain green algal groups. Two scenarios have been
 proposed to explain these observations. One is that the flowering plant
 psbA gene is currently under weak selective constraints for translation
 efficiency, the other is that there are no current selective constraints
 and we are observing the remnants of an ancestral codon adaptation that is
 decaying under mutational pressure. We test these two models using
 simulations studies that incorporate the context-dependent mutational
 properties of plant chloroplast DNA. We first reconstruct ancestral
 sequences and then simulate their evolution in the absence of selection on
 codon usage by using mutation dynamics estimated from intergenic regions.
 The results show that psbA has a significantly higher level of codon
 adaptation than expected while other chloroplast genes are within the
 range predicted by the simulations. These results suggest that there have
 been selective constraints on the codon usage of the flowering plant psbA
 gene during Angiosperm evolution.
description: Sequences were downladed from NCBI and aligned using
 Clustal. Code was written by the authors.
description: All information is in the README file.
DOI: 10.15468/dl.rh874g
title: Occurrence Download

description: A dataset containing 363 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Stellaria nipponica"
 ]
}

 The dataset includes 363 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002963-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6078/d1370m
title: Data supporting: Synthesis of higher order feature codes through stimulus-specific supra-linear summation

description: How cortical circuits build representations of complex objects is poorly
 understood. The massive dimensional expansion from the thalamus to the
 primary sensory cortex may enable sparse, comprehensive representations of
 higher order features to facilitate object identification. To generate
 such a code, cortical neurons must integrate broadly over space, yet
 simultaneously obtain sharp tuning to specific stimulus features. The
 logic of cortical integration that may synthesize such a sparse, high
 dimensional code for complex features is not known. To address this
 question, we probed the integration and population coding of higher order
 stimuli in the somatosensory and visual cortices of awake mice using
 two-photon calcium imaging across cortical layers. We found that
 somatosensory and visual cortical neurons sum highly specific combinations
 of sensory inputs supra-linearly, but integrate other inputs sub-linearly,
 leading to selective responses to higher order features. This integrative
 process generates a sparse, but comprehensive code for complex stimuli
 from the earliest stages of cortical processing. These results from
 multiple sensory modalities imply that input-specific supra-linear
 summation may represent a widespread cortical mechanism for the synthesis
 of higher order feature codes. This new mechanism may explain how the
 brain exploits the thalamocortical expansion of dimensionality to encode
 arbitrary complex features of sensory stimuli.
description: Data collected from mice using <em>in
 vivo </em>2-photon calcium imaging. Mice transgenically or virally
 expressed GCaMP6s in pyramidal cells, and recordings were targeted to
 either layer 4 or layer 2/3 of either S1 or V1. Responses to visual or
 vibrissal stimulation were recorded. Putative single cells have been
 segmented, calcium fluorescence traces extracted, and event rates
 deconvolved. Meanwhile, behavioral parameters of the mouse were collected
 (eye movements in the case of V1 data, running speed).
DOI: 10.5281/zenodo.18396814
title: Data to support 'The size of tropical vegetation gross primary production'

description: Satellite-based optical observations have converged to show average estimates of global contemporary gross primary production (GPP), the photosynthetic assimilation of atmospheric CO2 by terrestrial vegetation, at 120-140 Pg C yr–1. This consensus was challenged by a recent modeling study conducted by Lai et al in Nature, which  posits a higher global estimate of 157±8.5 Pg C yr-1, revealing a pronounced discrepancy in the tropics where modeled fluxes of 79 Pg C yr-1 exceed satellite-derived values by a factor of 1.33-1.85. We demonstrate that L24’s extrapolation is methodologically flawed, as it generalizes a site-specific temporal relationship between the ratio of carbonyl sulfide (OCS) to CO2 fluxes (LRU) and photosynthetically active radiation (PAR) from a single boreal station and also neglects the critical influence of vapor pressure deficit (VPD). This finding underscores the need for caution in upscaling site-level physiological constraints to the global scale, warranting the necessity of a global comprehensive validation before conducting for global estimates.
DOI: 10.5061/dryad.cnp5hqc5p
title: Identifying mismatches between conservation area networks and vulnerable populations using spatial randomization

description: Grassland birds are among the most globally threatened bird groups due to
 substantial degradation of native grassland habitats. However, the current
 network of grassland conservation areas may not be adequate for halting
 population declines and biodiversity loss. Here, we evaluate a network of
 grassland conservation areas within Wisconsin, U.S.A. that includes both
 large Focal Landscapes and smaller targeted conservation areas (e.g.,
 Grassland Bird Conservation Areas or GBCAs) established within them. To
 date, this conservation network has lacked baseline information to assess
 whether the current placement of these conservation areas aligns with
 population hotspots of grassland-dependent taxa. To do so, we fitted data
 from thousands of avian point-count surveys collected by citizen
 scientists as part of Wisconsin’s Breeding Bird Atlas II with multinomial
 N-mixture models to estimate habitat-abundance relationships, develop
 spatially-explicit predictions of abundance and establish ecological
 baselines within priority conservation areas for a suite of obligate
 grassland songbirds. Next, we developed spatial randomization tests to
 evaluate the placement of this conservation network relative to randomly
 placed conservation networks. Overall, less than 20% of species statewide
 populations were found within the current grassland conservation network.
 Spatial tests demonstrated high representation of this bird assemblage
 within the entire conservation network, but with a bias towards birds
 associated with moderately tall grasses relative to those associated with
 short or tall grasses. We also found that GBCAs had higher representation
 at Focal Landscape rather than statewide scales. Here, we demonstrated how
 combining citizen science data with hierarchical modeling is a powerful
 tool for estimating ecological baselines and conducting large-scale
 evaluations of an existing conservation network for multiple grassland
 birds. Our flexible spatial randomization approach offers the potential to
 be applied to other protected area networks and serve as a complementary
 tool for conservation planning efforts globally.
description: Spatially-explicit density estimates at 1x1km for obligate
 grassland birds based on Wisconsin's Breeding Bird Atlas II, Wiscland
 2 landcover and PRISM climate data, and multinomial N-mixture
 models.
description: The readme file contains an explanation of each of the variables
 in the dataset. Information on how the data was generated can be found in
 the associated manuscript referenced above.
DOI: 10.5281/zenodo.18396813
title: Data to support 'The size of tropical vegetation gross primary production'

description: Satellite-based optical observations have converged to show average estimates of global contemporary gross primary production (GPP), the photosynthetic assimilation of atmospheric CO2 by terrestrial vegetation, at 120-140 Pg C yr–1. This consensus was challenged by a recent modeling study conducted by Lai et al in Nature, which  posits a higher global estimate of 157±8.5 Pg C yr-1, revealing a pronounced discrepancy in the tropics where modeled fluxes of 79 Pg C yr-1 exceed satellite-derived values by a factor of 1.33-1.85. We demonstrate that L24’s extrapolation is methodologically flawed, as it generalizes a site-specific temporal relationship between the ratio of carbonyl sulfide (OCS) to CO2 fluxes (LRU) and photosynthetically active radiation (PAR) from a single boreal station and also neglects the critical influence of vapor pressure deficit (VPD). This finding underscores the need for caution in upscaling site-level physiological constraints to the global scale, warranting the necessity of a global comprehensive validation before conducting for global estimates.
DOI: 10.7291/d1rh5h
title: Antarctic minke whale acoustic data

description: Acoustic signaling is the predominant form of communication among
 cetaceans. Understanding the behavioral state of calling individuals can
 provide insights into the specific function of sound production; in turn,
 this information can aid the evaluation of passive monitoring data sets to
 estimate species presence, density, and behavior. Antarctic minke whales
 are the most numerous baleen whale species in the Southern Ocean. However,
 our knowledge of their vocal behavior is limited. Utilizing the first
 animal-borne audio-video documentation of underwater behavior in this
 species, we characterize Antarctic minke whale sound production and
 evaluate the association between acoustic behavior, foraging behavior,
 diel patterns, and the presence of conspecifics. In addition to the
 previously described downsweep call, we find evidence of three novel calls
 not previously described in their vocal repertoire. Overall, these signals
 displayed peak frequencies between 200 and 280 Hz and ranged from 0.2 to
 0.9 s on average (90% duration). Additionally, each of the four call types
 were associated with measured behavioral and environmental parameters. Our
 results represent a significant advancement in understanding of the life
 history of this species and improve our capacity to acoustically monitor
 minke whales in a rapidly changing Antarctic region.
DOI: 10.5061/dryad.2bvq83brb
title: Genetic divergence and diversity reflect a predominant freshwater resident life history in Rainbow Trout from southwestern Alaska

description: Rainbow Trout Oncorhynchus mykiss in southwestern Alaska occupy coastal
 watersheds near the northern boundary of the species native range and
 support a world class wild trout sport fishery. Although low
 freshwater temperatures and a short growing season in this region may
 favor anadromy, these populations appear to exhibit a freshwater resident
 life history strategy. In this study we used genetic data to
 evaluate two hypotheses regarding the influence of the presumed migratory
 behavior of these Rainbow Trout on reproductive isolation among and within
 watersheds. The results were largely consistent with the
 predictions but there were exceptions. The data supported the
 hypothesis that the freshwater resident behavior precludes marine-mediated
 gene flow resulting in large genetic divergence and low admixture among
 watersheds. The estimate of FCT (among-watershed differentiation,
 0.350) was large and reflected over 96% of the variation among all sampled
 aggregations (FST = 0.363). However, evidence of admixed
 individuals in two adjacent watersheds and five first generation migrants
 among five watersheds suggests that the potential for coastal migration
 with gene flow exists in these populations. The data also
 supported the hypothesis that aggregations formed within watersheds during
 the spawning period (May-June) represent reproductively isolated
 populations. The pairwise estimates of FST and the G-test results
 revealed population structure in four of the six watersheds
 tested. However, not all aggregation pairs were found genetically
 distinct and there was notable variation in the pairwise FST estimates
 (0.000 – 0.067). In summary, the data reflected the predicted results for
 each hypothesis, but also revealed exceptions that, consistent with
 tagging studies, demonstrate the complexity of migratory behavior in
 southwestern Alaska Rainbow Trout. We discuss the implications of
 these results for fishery management and conservation.
DOI: 10.5061/dryad.qnk98sfht
title: Transcriptional acclimation and spatial differentiation characterize drought response by the ectomycorrhizal fungus Suillus pungens

description: Changing precipitation regimes are a challenge for forest health under
 future climate scenarios. If belowground symbionts can acclimate to
 changing moisture regimes it may buffer forest trees from these changes.
 In this study we exposed the ectomycorrhizal fungus Suillus
 pungens to acute and chronic drought stress and used RNASeq of
 both ectomycorrhizal roots and extraradical mycelium to gauge the
 magnitude of stress, identify key genes involved in drought response, and
 gauge potential ecosystem consequences of drought. We found that there
 were major transcriptional differences for S. pungens in
 ectomycorrhizal roots (28% of genes) and extraradical mycelium (41% of
 genes) under acute drought stress, but only 0.1-2% of genes were
 differentially expressed in chronic drought treatments. Up to 56% of
 differentially expressed genes under acute drought were unique to either
 roots or mycelium. While a number of implicated genes, such as those
 encoding for trehalose, have well-known roles in osmotic stress, others,
 such as fungal hydrophobins and atromentin, have received less study and
 may also impact other ecosystem functions. These results suggest that
 functional compartmentalization is key to ectomycorrhizal fungal
 adaptation to stressful climatic conditions and there is high potential
 for fungal acclimation to ameliorate future climate
 stress.  
description: Approximately ten root tips were removed from one half of a root
 system (which half was determined randomly) for RNA extraction and
 immediately flash frozen. The other half of the root system was used for
 percent colonization where an average of 77 root tips were scored as
 non-mycorrhizal or ectomycorrhizal (min = 27, median = 75, max = 125). To
 assess treatment effects on plant biomass and total moisture content, the
 remaining plant tissue was separated into roots and shoots, weighed fresh
 to assess initial moisture content, dried for 48 hours at 80 °C, and
 weighed again. To determine gravimetric percent soil moisture, 10 g ± 2 g
 soil was weighed out, oven-dried for at least 72 hours at 80 °C, then
 weighed again to determine water mass loss.