cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15553129
title: Segregated auditory cortico-striatal pathways regulate distinct components of sensory-driven learning

description: This repository expands the main repository accessible at doi: 10.5281/zenodo.15552693, of the study by Palchaudhuri et al. and provides data for Figure 5.

This part of the repository contains only zipped data files. Please find the detailed description and the associated metadata in the main repository.
DOI: 10.15468/dl.62hyrj
title: Occurrence Download

description: A dataset containing 15179 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Carex vaginata Tausch",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 15179 records from 108 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011302-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vcggyb
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Asquamiceps Zugmayer, 1911",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((-16.8057 20.1434,-16.8896 19.8496,-9.0352 19.8496,-9.0352 28.8496,-11.635 28.8496,-11.7824 28.7359,-13.29 28.2942,-13.9623 27.0596,-14.8996 26.4375,-15.2884 25.5014,-15.3356 24.99,-16.4235 23.914,-16.8295 22.8081,-17.1762 22.5133,-17.4325 21.9756,-17.6012 20.7987,-17.3601 20.3805,-16.8057 20.1434))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011303-250525065834625/datasets/export for details.
DOI: 10.15468/dl.ufbjzn
title: Occurrence Download

description: A dataset containing 14976 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Carlina vulgaris L.",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 14976 records from 161 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011305-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5f835z
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Asquamiceps Zugmayer, 1911",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((-16.6672 18.7728,-16.5468 17.7486,-16.9133 16.7746,-17.0265 15.925,-17.4754 15.299,-17.9607 15.0106,-18.0159 14.6088,-17.2825 13.9103,-17.2971 12.4437,-17.1163 12.0176,-16.8424 11.8396,-16.9887 11.3363,-16.91 11.0108,-16.709 10.8496,-9.0352 10.8496,-9.0352 19.8496,-16.8896 19.8496,-17.0371 19.3335,-16.6672 18.7728))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011306-250525065834625/datasets/export for details.
DOI: 10.15468/dl.2z242g
title: Occurrence Download

description: A dataset containing 11389 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Theobroma cacao L."
 ]
}

 The dataset includes 11389 records from 438 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011304-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.z8w9ghxcn
title: Functional diversity of macroinvertebrates as a tool to evaluate wetland restoration

description: Ecological restoration of aquatic ecosystems has become widespread in
 recent decades. Whereas the recovery of biodiversity in restored wetlands
 has been studied from a taxonomic perspective, our knowledge of how
 functional biodiversity recovers remains poorly understood. We studied the
 functional diversity of macroinvertebrate communities in 32 Mediterranean
 temporary ponds six to seven years after their creation during a
 restoration in South-West Spain, and compared them with 10 natural
 reference sites during two consecutive hydroperiods. We compared alpha
 functional diversity indices, and the individual contributions of new
 ponds and reference sites to the regional functional beta diversity, as
 well as to its turnover and nestedness components. We also investigated
 the influence of environmental and spatial variables on the
 dissimilarities of functional beta diversity and its components between
 new ponds and reference sites. Alpha functional diversity in new ponds was
 lower than in reference sites. Although the contribution of new ponds to
 the regional functional beta diversity was similar to that of reference
 sites, the latter contributed more to functional turnover, while new ponds
 contributed more to functional nestedness. Dispersal limitation coupled
 with environmental filtering structured the functional variation in
 communities between new ponds and reference sites, but their relative
 importance differed between beta components. New ponds can hold species
 with unique functional compositions, but their contribution to the
 regional functional beta diversity was mostly due to trait losses with
 respect to reference sites. Synthesis and applications. Considering
 different aspects of functional diversity of invertebrate communities can
 help elucidate the processes and mechanisms through which ecosystems
 recover following restoration. We encourage the use of trait-based
 approaches to identify trends in processes and patterns that can guide
 future wetland restoration projects.
description: See the paper.
description: Data to:<br>Functional diversity of macroinvertebrates as a
 tool to evaluate wetland restoration<br>Coccia et al., Journal of
 Applied Ecology
 ###Coccia_Taxonomic_data.csv###<br># Species-abundance
 table ###Coccia_Traits.csv###<br>#Species-traits
 table ###Trait_group###<br>#Trait variable
 explication
 ###Coccia_Environmental_data.csv###<br>#Environmental and
 spatial data #Pond Type: P=new ponds; R=Reference
 sites #NA indicate missing values
DOI: 10.5061/dryad.gb5mkkwq9
title: Analyzing disparity and rates of morphological evolution with model-based phylogenetic comparative methods

description: Understanding variation in rates of evolution and morphological disparity
 is a goal of macroevolutionary research. In a phylogenetic comparative
 methods framework, we present three explicit models for linking the rate
 of evolution of a trait to the state of another evolving trait. This
 allows testing hypotheses about causal influences on rates of phenotypic
 evolution with phylogenetic comparative data. We develop a statistical
 framework for fitting the models with generalized least-squares
 regression, and use this to discuss issues and limitations in the study of
 rates of evolution more generally. We show that the power to detect
 effects on rates of evolution is low in that even strong causal effects
 are unlikely to explain more than a few percent of observed variance in
 disparity. We illustrate the models and issues by testing if rates of
 beak-shape evolution in birds are influenced by brain size, as may be
 predicted from a Baldwin effect in which presumptively more behaviorally
 flexible large-brained species generate more novel selection on themselves
 leading to higher rates of evolution. From an analysis of morphometric
 data for 645 species we find evidence that both macro- and microevolution
 of the beak are faster in birds with larger brains, but with the caveat
 that there are no consistent effects of relative brain size.
description: The dataset archived here are predominantly taken from published
 sources. References are as follows. Brain mass: Tsuboi
 et al. 2018 <i>Nat Ecol Evol</i> 2: 1492-1500., Fristoe et al. 2017 <i>Nat Ecol Evol</i> 1: 1706-1715. Body mass: Tsuboi et al. 2018 <i>Nat Ecol Evol</i> 2: 1492-1500., Fristoe et al. 2017 <i>Nat Ecol Evol</i> 1: 1706-1715. Standard error of log brain mass: Estimated from within-species variance and a method described in our aerticle.  Standard error of log body mass: Estimated from within-species variance and a method described in our aerticle.  Relative brain size: Estimated from generalized least squares regression of log(brain mass) against log(body mass) including the presented 645 species and phylogeny using SLOUCH as described in our article. Beak shape: Chira et al. 2018. <i>Ecology Letters</i> 21: 1505-1514., Cooney et al. 2017. <i>Nature</i> 542: 344-347. Phylogeny: Jetz et al. 2014. <i>Curr. Biol.</i> 24: 919-930.
description: 1. Brain and body mass data are obtained as individual values, and we archive species mean values and their associated standard errors that were used to perform comparative analyses presented in our article. 2. None of the data analyzed in our article include original data. Our dataset therefore should not be used as primary reference for the data. 3. Sample size for species mean beak shape is one.
DOI: 10.5061/dryad.6wwpzgn01
title: Uncovering the vertebrate scavenger guild composition and functioning in the Cerrado biodiversity hotspot

description: Scavenging is widespread among vertebrates, being very important for
 maintaining certain ecosystem functions. Despite this, the scavenger
 communities remain poorly known in some biomes, especially in the
 Neotropics. Our main objective was to describe for the first time the
 scavenger community and identify the factors affecting scavenging
 efficiency in the Brazilian Cerrado. We analyzed the effects of vegetation
 cover, time of carcass placement and carcass weight, on scavenger species
 richness, individual abundances, carcass detection and consumption times,
 and carcass consumption rate. We monitored 11 large and 45 small carcasses
 using automatic cameras. We documented a total of 19 vertebrate scavenging
 species, four species of vultures and 15 facultative scavengers. We found
 that carcass size was the most important factor affecting the scavenger
 assemblage and consumption patterns. Large carcasses were dominated by
 vultures, whereas small carcasses were consumed mainly by facultative
 scavengers. We also found differences between large and small carcasses in
 all carcass consumption variables except for detection time. However, we
 did not find an effect of vegetation cover or time of carcass placement on
 scavenging patterns. The negligible role of mammals and non-raptor birds
 in large carcasses is also noteworthy, probably due to the consumption and
 foraging efficiency of the vultures, and the more frugivorous habits of
 the mesocarnivores. Our results show a highly diverse and efficient
 scavenging vertebrate community in the Brazilian Cerrado, and the need to
 preserve them in the face of the significant habitat transformations
 suffered by this biodiversity hotspot.
DOI: 10.5061/dryad.pzgmsbcmk
title: Two-photon calcium recordings of cones

description: For colour vision, retinal circuits separate information about intensity
 and wavelength. This requires circuit-level comparison of at least two
 spectrally distinct photoreceptors. However, many vertebrates use all four
 ‘ancestral’ photoreceptors (‘red’, ‘green’, ‘blue’, ‘UV’), and in those
 cases the nature and implementation of this computation remains poorly
 understood. Here, we establish the complete circuit architecture of outer
 retinal circuits underlying colour processing in the tetrachromatic larval
 zebrafish, which involves all four ancestral cone types and three types of
 horizontal cells. Our findings reveal that the synaptic outputs of red-
 and green-cones efficiently rotate the encoding of natural daylight in a
 principal component analysis (PCA)-like manner to yield primary achromatic
 and spectrally-opponent axes, respectively. Together, these two cones
 capture 91.3% of the spectral variance in natural light. Next, blue-cones
 are tuned so as to capture most remaining variance when opposed to
 green-cones. Finally, UV-cones present a UV-achromatic axis for prey
 capture. We note that fruit flies – the only other tetrachromat species
 where comparable circuit-level information is available - use essentially
 the same strategy to extract spectral information from their relatively
 blue-shifted terrestrial visual world. Together, our results suggest that
 rotating colour space into primary achromatic and chromatic axes at the
 eye’s first synapse may be a fundamental principle of colour vision when
 using more than two spectrally well-separated photoreceptor types.
description: The data was collected from zebrafish larvae (7 days
 post-fertilisation) expressing SyGCaMP6f in each cone type. SyGCaMP6f
 fluorescent images during visual stimulation were recorded on a custom
 built two-photon microscope. Detailed information is in the
 manuscript.
DOI: 10.5061/dryad.j0zpc86ff
title: Data from: Skeletal and soft tissue completeness of the acanthodian fossil record

description: Acanthodians are a poorly understood paraphyletic grade of extinct
 Palaeozoic fishes. They play an increasingly prominent role in our
 understanding of vertebrate evolution as part of the chondrichthyan
 stem-group even though their evolutionary history is scarce. The limited
 preservation of their mostly cartilaginous skeleton largely results in a
 bias towards isolated remains such as fin spines and scales. Here, we
 quantify the quality of the acanthodian fossil record by using a variation
 of the Skeletal Completeness Metric (SCM), an approach that calculates how
 complete the skeletons of individuals are compared to their theoretical
 complete skeleton. A novel Soft Tissue Completeness Metric (STCM) is
 introduced to estimate the percentage of soft body tissue preserved as an
 alternate measurement of completeness. Completeness scores for
 &gt;1600 specimens comprising &gt;300 taxa obtained from museum
 collection visits and literature surveys were assembled into a database.
 Acanthodian completeness peaks in the Lochkovian, Givetian,
 Bashkirian-Moscovian, and the Asselian, with lowest scores in the
 Llandovery. There is no correlation between acanthodian taxonomic richness
 and completeness. Acanthodians show a significantly lower completeness
 distribution than many tetrapod groups, but a similarly low distribution
 to bats. Skeletons deposited in freshwater are significantly more complete
 than in marine environments where sea level significantly negatively
 correlates with observed completeness. Our assessment of completeness
 reveals only weak spatial biases influencing the acanthodian fossil record
 while environmental biases are much higher. Variation in completeness will
 have an impact on the utility of characters for assessing the phylogenetic
 relationships and inclusion of the various acanthodian groups.
description: All information on data collection as well as specific details
 can be found in the Material and Methods section of the
 manuscript. 
description: The summary and input sheet section of the excel file has been
 formatted specifically to be load into the R software as easily as
 possible.
DOI: 10.5061/dryad.rxwdbrv8s
title: Measuring the contribution of evolution to community trait structure in freshwater zooplankton

description: There are currently few predictions about when evolutionary processes are
 likely to play an important role in structuring community
 features.Determining predictors that indicate when evolution is expected
 to impact ecological processes in natural landscapes can help researchers
 identify eco-evolutionary 'hotspots', where eco-evolutionary
 interactions are more likely to occur. Using data collected from a survey
 in freshwater cladoceran communities, landscape population genetic data,
 and phenotypic trait data measured in a common garden, we applied a
 Bayesian linear model to assess whether the impact of local trait
 evolution in the keystone species Daphnia magna on cladoceran community
 trait values could be predicted by population genetic properties
 (within-population genetic diversity, genetic distance among populations),
 ecological properties (Simpson’s diversity, phenotypic divergence), or
 environmental divergence. We found that the impact of local trait
 evolution varied among communities. Moreover, community diversity and
 phenotypic divergence were found to be better predictors of the
 contribution of evolution to community trait values than environmental
 features or genetic properties of the evolving species. Our results thus
 indicate the importance of ecological context for the impact of evolution
 on community features. Our study also demonstrates one way to detect
 signatures of eco-evolutionary interactions in communities inhabiting
 heterogeneous landscapes using survey data of contemporary ecological and
 evolutionary structure.
DOI: 10.5061/dryad.gtht76hms
title: Dataset from: Warming effects on grassland productivity depend on plant diversity

description: Aim: Climate warming and biodiversity loss both alter plant productivity,
 yet we lack an understanding of how biodiversity regulates the responses
 of ecosystems to warming. In this study, we examine how plant diversity
 regulates the responses of grassland productivity to experimental warming
 using meta-analytic techniques. Location: Global Major taxa studied:
 Grassland ecosystems Methods: Our meta-analysis is based on warming
 responses of 40 different plant communities obtained from 20 independent
 studies on grasslands across five continents. Results: Our results show
 that plant diversity and its responses to warming were the most important
 factors regulating the warming effects on plant productivity, among all
 the factors considered (plant diversity, climate and experimental
 settings). Specifically, warming increased plant productivity when plant
 diversity (indicated by effective number of species) in grasslands was
 lesser than 10, whereas warming decreased plant productivity when plant
 diversity was greater than 10. Moreover, the structural equation modelling
 showed that the magnitude of warming enhanced plant productivity by
 increasing the performance of dominant plant species in grasslands of
 diversity lesser than 10. The negative effects of warming on productivity
 in grasslands with plant diversity greater than 10 were partly explained
 by diversity-induced decline in plant dominance. Main Conclusions: Our
 findings suggest that the positive or negative effect of warming on
 grassland productivity depends on how biodiverse a grassland is. This
 could mainly owe to differences in how warming may affect plant dominance
 and subsequent shifts in interspecific interactions in grasslands of
 different plant diversity levels.
DOI: 10.5061/dryad.z612jm6cc
title: Data from: Serine ADP-ribosylation marks nucleosomes for ALC1-dependent chromatin remodeling

description: Serine ADP-ribosylation (ADPr) is a DNA damage-induced post-translational
 modification catalyzed by the PARP1/2:HPF1 complex. As the list of
 PARP1/2:HPF1 substrates continues to expand, there is a need for
 technologies to prepare mono- and poly-ADP-ribosylated proteins for
 biochemical interrogation. Here we investigate the unique peptide ADPr
 activities catalyzed by PARP1 in the absence and presence of HPF1. We then
 exploit these activities to develop a method that facilitates installation
 of ADP-ribose polymers onto peptides with precise control over chain
 length and modification site. Importantly, the enzymatically mono- and
 poly-ADP-ribosylated peptides are fully compatible with protein ligation
 technologies. This chemoenzymatic protein synthesis strategy was employed
 to assemble a series of full-length, ADP-ribosylated histones and show
 that ADPr at H2BS6 or H3S10 converts nucleosomes into robust substrates
 for the chromatin remodeler ALC1. We found ALC1 preferentially remodels
 ‘activated’ substrates within heterogeneous mononucleosome populations and
 asymmetrically ADP-ribosylated dinucleosome substrates, and that
 nucleosome serine ADPr is sufficient to stimulate ALC1 activity in nuclear
 extracts. Our study identifies a biochemical function for nucleosome
 serine ADPr and describes a new, highly modular approach to explore the
 impact that site-specific serine mono- and poly-ADPr have on protein
 function.
description: This spreadsheet contains raw data in triplicate for all
 quantitative experiments associated with the manuscript 'Serine
 ADP-ribosylation marks nucleosomes for ALC1-dependent chromatin
 remodeling'. Experiements include HPLC peak integration, fluorescence
 polarization, densitometry, and quantitative PCR.
DOI: 10.5061/dryad.k0p2ngf8h
title: How fern and fern allies respond to heterogeneous habitat

description: The Yuanjiang dry-hot valley features hot and dry climate, low vegetation
 and soil degradation. It had lush vegetation in the past, but has become
 degraded in recent decades. Understanding the interrelationship between
 species and the habitat is necessary to explain this change. In this
 study, a link between fern and fern allies - a group that is
 hypersensitive to environmental factors and their circumstances is
 constructed. Intensive transects and plots were designed to be proxies for
 extant fern and fern allies, and their habitats. Fifty years of
 meteorological records of precipitation and temperature along altitude and
 river running direction (latitudinal) were employed. Alpha and beta
 diversity are used to access diversity. Species_estimated, Singletons,
 Uniques, ACE, ICE, and Chao2, which associate to abundance and rarity, are
 subscribed to the correlation between fern and fern allies, and their
 ecosystem. Eight species, Selaginella pseudopaleifera, Aleuritopteris
 squamosa, Adiantum malesianum, Pteris vittata, Davallia trichomanoides,
 Sinephropteris delavayi, Selaginella jugorum, and Lygodium japonicum are
 used as indicators of a typical xeric and sun-drying habitat. The results
 indicate (1) accompanied by dramatically shrinking habitats, fern and fern
 allies are in very low diversity and abundance, whereas the rarity is
 relatively high; (2) for fern and fern allies, environmental factors are
 positive when altitude goes up; and (3) eight indicator species are
 latitudinally correlated with fern and fern allies along the river running
 direction.