cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.00000002m
title: Population structure of giant clams (sub-family: Tridacninae) across Palau: implications for conservation

description: Giant clams (Sub-family: Tridacninae) are an important food and economic
 resource for the Republic of Palau. Previous surveys of giant clams
 conducted over 20 years ago found diverse, localized populations across
 Helen Reef and the Rock Islands Southern Lagoon. This study updates
 population structure data for Palauan giant clams and investigates the
 impacts of conservation on these important bivalves. We surveyed eleven
 sites within fringing, barrier, atoll, and oceanic reefs across the
 Palauan archipelago (total area = 1650m2). A total of 831 clams were
 measured across seven species (Tridacna crocea, T. maxima, T. noae, T.
 squamosa, T. derasa, T. gigas, and Hippopus hippopus). In addition, this
 is the first documented case of T. noae in Palau. Our measurements show
 that giant clams in Palau are among the most abundant and densely
 distributed compared to other Indo-Pacific reefs. T. crocea exhibited the
 highest abundance (521 individuals) and density (20.0 ± 2.9 per 50m2) of
 all species in this survey. However, high demand from local and
 international markets may have resulted in low average shell lengths and
 reduced abundances of adult clams within the most abundant species: T.
 crocea, T. maxima, and T. squamosa. Despite these harvesting pressures,
 Palau’s incorporation of bottom-up traditional and modern conservation
 initiatives has positively impacted T. crocea, the most targeted species
 by local fishers. Within the Ngermedellim Marine Sanctuary, T. crocea
 exhibit high abundances of recruits and adults, suggesting that protection
 from fishing has increased replenishment rates and reduced mortality
 within this conservation area. As these bivalves continue to be exploited,
 we suggest that continued protection of and the implementation of
 size-limits will enable giant clams to remain abundant and diverse in
 Palau.
description: Details for each dataset and code file are in the readme.txt
 file.
DOI: 10.5061/dryad.dv41ns1wr
title: Sun compass neurons are tuned to migratory orientation in monarch butterflies

description: Every autumn, monarch butterflies migrate from North America to their
 overwintering sites in Central Mexico. To maintain their southward
 direction, these butterflies rely on celestial cues as orientation
 references. The position of the sun combined with additional skylight cues
 are integrated in the central complex, a region in the butterfly’s brain
 that acts as an internal compass. However, the central complex does not
 solely guide the butterflies on their migration but helps monarchs in
 their non-migratory form manoeuvre on foraging trips through their
 habitat. By comparing the activity of input neurons of the central complex
 between migratory and non-migratory butterflies, we investigated how a
 different lifestyle affects the coding of orientation information in the
 brain. During recording, we presented the animals with different simulated
 celestial cues and found that the encoding of the sun was narrower in
 migratory compared to non-migratory butterflies. This feature might
 reflect the need of the migratory monarchs to rely on a precise sun
 compass to keep their direction during their journey. Taken together, our
 study sheds light on the neural coding of celestial cues and provides
 insights into how a compass is adapted in migratory animals to
 successfully steer them to their destination.
description: Intracellular recordings from the monarch butterfly central
 complex. The data were analysed in Matlab (version 2019.b) through
 custom-written scripts. We provide the scripts as Matlab file as well as
 txt.file and the raw data (as mat. and csv. files).
DOI: 10.5061/dryad.612jm642f
title: Supplementary information for: Using networks to identify structure in phylogenetic tree sets

description: Modern phylogenomic studies produce large sets of trees that can represent
 variation in inferred phylogenies across genes, uncertainty in estimated
 phylogenies for a given gene, or both. Standard practice is to condense
 this variation down to a small set of point estimates or consensus trees
 in order to facilitate display and interpretation. However, doing so
 results in the loss of enormous amounts of information about the structure
 of the underlying tree set. Here, we propose new approaches to explore and
 detect structure in the tree set itself. These approaches rely on the
 well-developed mathematical foundations of community detection in networks
 and leverage two different network types. The first type uses nodes to
 represent trees and connects these nodes with edges whose weights are
 determined by the similarity (affinity) of the trees. The second type uses
 nodes to represent bipartitions and connects nodes with edges whose
 weights represent the covariance in bipartition presence/absence across
 trees in the set. These two network types carry information that is
 complementary, but not identical. A variety of methods may be applied to
 both networks in order to identify interesting community structure. These
 community detection approaches provide a rich view of the information
 contained in phylogenomic data sets and facilitate investigation into the
 forces driving inferred phylogenetic variation across genomes.
DOI: 10.6084/m9.figshare.31152148
title: Dataset for PAG Reconstruction

description: dataset for pag reconstruction
DOI: 10.6084/m9.figshare.31152148.v1
title: Dataset for PAG Reconstruction

description: dataset for pag reconstruction
DOI: 10.5061/dryad.v41ns1rtv
title: Multiscale legacy responses of soil gas concentrations to soil moisture and temperature fluctuations

description: The sensitivity of soil carbon dynamics to climate change is a major
 uncertainty in carbon cycle models. Of particular interest is the response
 of soil biogeochemical cycles to variability in hydroclimatic states and
 the related quantification of soil memory. Toward this goal, the power
 spectra of soil hydrologic and biogeochemical states were analyzed using
 measurements of soil temperature, moisture, oxygen, and carbon dioxide at
 two sites. Power spectra indicated multiscale power law scaling across
 sub-hourly to annual timescales. Precipitation fluctuations were most
 strongly expressed in the soil biogeochemical signals at monthly to annual
 timescales. Soil moisture and temperature fluctuations were comparable in
 strength at one site, while temperature was dominant at the other. The
 effect of soil hydrologic, thermal, and biogeochemical processes on gas
 concentration variability was evidenced by low spectral entropy relative
 to the white noise character of precipitation. A full mass balance model
 was unable to capture high-frequency soil temperature influence,
 indicating a gap in commonly used model assumptions. A linearized model
 was shown to capture the main features of the observed and modeled gas
 concentration spectra and demonstrated how the means and variances of soil
 moisture and temperature interact to produce the gas concentration
 spectra. Breakpoints in the spectra corresponded to the mean rate of gas
 efflux, providing a first-order estimate of the soil biogeochemical
 integral timescale ($\sim 1$ minute). These methods can be used to
 identify biogeochemical system dynamics to develop robust, process-based
 soil biogeochemistry models that capture variability in addition to
 long-term mean values.
DOI: 10.5061/dryad.fttdz08rd
title: How does prescribed fire shape bird and plant communities in a temperate dry forest ecosystem?

description: To mitigate the impact of severe wildfire on human society and the
 environment, prescribed fire is widely used in forest ecosystems to reduce
 fuel loads and limit fire spread. To avoid detrimental effects on
 conservation values, it is imperative to understand how prescribed fire
 affects taxa having a range of different adaptations to disturbance. Such
 studies will have greatest benefit if they extend beyond short-term
 impacts of burning. We used a field study to examine the effects of
 prescribed fire on birds and plants across a 36-year post-fire
 chronosequence in a temperate dry forest ecosystem in south-eastern
 Australia, and by making comparison with long-unburnt reference sites (79
 years since wildfire). We modelled changes in the relative abundance of 22
 bird species and the cover of 39 plant species, and examined how
 individual species, functional groups, species richness and community
 composition differed between sites with different fire history. For most
 individual bird and plant species modelled, relative abundance or cover at
 sites subject to prescribed fire did not change significantly with time
 since fire or differ from that of long-unburnt vegetation. When bird
 species were pooled into functional groups, time since prescribed fire had
 strong effects on birds that forage in the lower-midstorey,
 facultative-resprouting shrubs and obligate-seeding shrubs. Species
 richness for both taxa did not differ between sites subject to prescribed
 fire and those in long-unburnt vegetation. Bird communities varied
 significantly between the youngest (0-3 years) and oldest (79 years)
 post-fire age-classes, driven by species associated with understorey
 vegetation. Plant community composition showed little evidence of a
 post-fire successional trajectory. The prevalence of bird species with
 broad habitat and dietary niches and plant regeneration through
 resprouting, make bird and plant communities in these forests relatively
 resilient to small and patchy prescribed fires they have experienced to
 date. Application of prescribed fire will be most compatible with
 maintaining biodiversity by taking a landscape approach that: 1) plans for
 a geographic spread of stands with a range of between-prescribed-fire
 intervals to ensure provision of suitable habitat for all taxa, and 2)
 avoids burning in moist gullies to maintain their value as fire refuges.
DOI: 10.15468/dl.r8zp4c
title: Occurrence Download

description: A dataset containing 96 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Diplacrum caricinum"
 ]
}

 The dataset includes 96 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002684-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.59zw3r25z
title: Data from: Invasive Impatiens glandulifera: a driver of changes in native vegetation?

description: Biological invasions are one of the major threats to biodiversity
 worldwide and contribute to changing community patterns and ecosystem
 processes. However, it is often not obvious whether an invader is the
 “driver” causing ecosystem changes or a “passenger” which is facilitated
 by previous ecosystem changes. Causality of the impact can be demonstrated
 by experimental removal of the invader or introduction into a native
 community. Using such an experimental approach, we tested whether the
 impact of the invasive plant Impatiens glandulifera on native vegetation
 is causal, and whether the impact is habitat-dependent. We conducted a
 field study comparing invaded and uninvaded plots with plots from which
 I. glandulifera was removed and plots where
 I. glandulifera was planted within two riparian habitats, alder
 forests and meadows. A negative impact of planting
 I. glandulifera and a concurrent positive effect of removal on
 the native vegetation indicated a causal effect of
 I. glandulifera on total native biomass and growth of Urtica
 dioica. Species α-diversity and composition were not affected by
 I. glandulifera manipulations. Thus, I. glandulifera had
 a causal but low effect on the native vegetation. The impact depended
 slightly on habitat as only the effect of I. glandulifera
 planting on total biomass was slightly stronger in alder forests than
 meadows. We suggest that I. glandulifera is a “back-seat driver”
 of changes, which is facilitated by previous ecosystem changes but is also
 a driver of further changes. Small restrictions of growth of the planted
 I. glandulifera and general association of
 I. glandulifera with disturbances indicate characteristics of a
 back-seat driver. For management of I. glandulifera populations
 this requires habitat restoration along with removal of the invader.
DOI: 10.5061/dryad.rjdfn2z8w
title: Anatomical partitioning has little influence in topologies from Bayesian phylogenetic analyses of morphological data

description: Morphological data is a fundamental source of evidence to reconstruct the
 Tree of Life, and Bayesian phylogenetic methods are increasingly being
 used for this task, along with, or instead of, traditional parsimony
 approaches. Bayesian phylogenetic analyses require the use of proper
 evolutionary models and their performance have been intensively studied in
 the past few years, with significant improvements to our knowledge
 regarding their performance. Notwithstanding, it was only recently that
 partitioned models for morphology received attention in studies of
 empirical data, but a systematic evaluation of its performances using
 simulations was never performed. Here we evaluate the influence of
 partitioned models defined by anatomical criterion in the precision and
 accuracy of consensus tree topologies, evaluating the possible negative
 effects of under and overpartitioning. For that, we analysed datasets
 simulated using parameters and properties of two empirical datasets, using
 Bayesian phylogenetic analyses in MrBayes. Additionally, we reanalysed 32
 empirical datasets for diverse groups of vertebrates, applying
 unpartitioned and partitioned models. We found that in general,
 partitioning by anatomy has little to no influences in the performance of
 Bayesian phylogenetic methods in respect to the metrics studied here, with
 analyses under alternative partitioning schemes presenting very similar
 tree precision and accuracy. We discuss the possible reasons for the
 disagreement between the results obtained here and previous studies for
 empirical morphological data, and with empirical and simulation studies of
 molecular data, discussing the adequacy of anatomical partitioning
 relative to alternative methods to partition morphological datasets and
 how morphological and molecular partitioning are related.
DOI: 10.5061/dryad.zcrjdfn9c
title: The ontogenetic pattern of neurocentral suture closure in the axial skeleton of Hyperodapedontinae (Archosauromorpha: Rhynchosauria) and its evolutionary implication

description: Understanding ontogeny of a taxon is a crucial step to properly elucidate
 its taxonomy and evolution. However, aside from histological data,
 osteological criteria for assessing maturity are considered lineage
 specific or controversial. The sequence of neurocentral suture closure of
 the axial skeleton of extant crocodilians, which occurs in a
 postero-anterior sequence, has being used as a non-destructive method to
 determine maturity in extinct reptiles. However, the use of this criterion
 in extinct archosaurs not closely related to crocodilians is debatable, as
 the ancestral condition of Archosauria is unknown and variation occurs in
 timing and sequence orientation within the clade. We have assessed the
 pattern of neurocentral suture closure of the Hyperodapedontinae
 rhynchosaurs, an early archosauromorph clade distantly related to
 archosaurs. Different from extant crocodilians, they exhibit an
 antero-posterior sequence neurocentral suture closure. Relative size and
 other ontogenetic markers suggest the neurocentral closure in the
 Hyperodapedontinae is correlated to aging, although closed sutures were
 rare in the sample. A high number of open or partially open sutures in
 mature individuals indicate that they remained open during most of their
 life. Our study indicates that (i) the delayed neurocentral closure can be
 a paedomorphic heterochronic process in Hyperodapedontinae, as it
 contrasts with the fully closed neurocentral sutures of early diverging
 non-hyperodapedontine rhynchosaurs; (ii) the assumption opened
 neurocentral sutures indicates immaturity in extinct reptiles is not
 always correct; and (iii) the delayed closure may have originated
 independently in several archosauromorph lineages, but the ancestral
 condition of Archosauria likely follows the crocodilian closure pattern.
DOI: 10.5061/dryad.wh70rxwmb
title: Topography strongly affects drought stress and xylem embolism resistance in woody plants from a karst forest in Southwest China

description: 1. Xylem resistance to drought-induced embolism is an important trait
 determining plant distribution. In the karst hills of Southwest China,
 with a relatively small variation in altitude, soil depth and water
 availability strongly decrease from the foot towards the top, and woody
 plant species display distinct spatial distribution. 2. For testing the
 hypothesis that embolism resistance of leaf and stem xylem reflects the
 spatial distribution across species along a topographical gradient of the
 karst hills, we measured the xylem water potential in the dry season,
 vulnerability to drought-induced embolism in stems and leaves, and
 relevant anatomical traits in 17 evergreen species with a different
 topographical distribution. 3. We found that from the foot towards the
 hill top, plant water potential sharply decreased, and both stem and leaf
 xylem showed increasing resistance to hydraulic dysfunction and
 drought-resistant anatomical characteristics, but non-significant
 variation in specific hydraulic conductivity. Also, hydraulic safety
 margins increased with relative altitude and thus increasing water
 deficit, which underlies the local distribution of the species, but does
 not come at the cost of hydraulic efficiency. 4. Our results demonstrate
 that plant hydraulic safety largely shape the niche differentiation and
 hence community assembly in highly heterogeneous and water-limited
 landscapes.
DOI: 10.5061/dryad.jh9w0vt9h
title: Data from: Testing hypotheses of marsupial brain size variation using phylogenetic multiple imputations and a Bayesian comparative framework

description: Considerable controversy exists about which hypotheses and variables best
 explain mammalian brain size variation. We use a new, high-coverage
 dataset of marsupial brain and body sizes, and the first phylogenetically
 imputed full datasets of 16 predictor variables, to model the prevalent
 hypotheses explaining brain size evolution using phylogenetically
 corrected Bayesian generalised linear mixed-effects modelling. Despite
 this comprehensive analysis, litter size emerges as the only significant
 predictor. Marsupials differ from the more frequently studied placentals
 in displaying much lower diversity of reproductive traits, which are known
 to interact extensively with many behavioural and ecological predictors of
 brain size. Our results therefore suggest that studies of relative brain
 size evolution in placental mammals may require targeted co-analysis or
 adjustment of reproductive parameters like litter size, weaning age, or
 gestation length. This supports suggestions that significant associations
 between behavioural or ecological variables with relative brain size may
 be due to a confounding influence of the extensive reproductive diversity
 of placental mammals.
DOI: 10.5061/dryad.w0vt4b8pw
title: Data from: Multi-omics analyses on rheumatoid arthritis in CD4+ T cells

description: Objective: CD4+ T cells have been suggested as the most disease-relevant
 cell type in rheumatoid arthritis (RA) in which RA-risk non-coding
 variants exhibit allele-specific effects on regulation of RA-driving
 genes. This study aimed to understand RA-specific signatures in CD4+ T
 cells using multi-omics data, interpreting inter-omics relationships in
 shaping the RA transcriptomic landscape. Methods: We profiled genome-wide
 variants, gene expression, and DNA methylation in CD4+ T cells from 82 RA
 patients and 40 healthy controls using high-throughput technologies. We
 investigated differentially expressed genes (DEGs) and differentially
 methylated regions (DMRs) in RA and localized quantitative trait loci
 (QTLs) for expression and methylation. We then integrated these based on
 individual-level correlations to inspect DEG-regulating sources and
 investigated the potential regulatory roles of RA-risk variants by a
 partitioned-heritability enrichment analysis with RA genome-wide
 association summary statistics. Results: A large number of RA-specific
 DEGs were identified (n=2,575), highlighting T-cell differentiation and
 activation pathways. RA-specific DMRs, preferentially located in T-cell
 regulatory regions, were correlated with the expression levels of 548 DEGs
 mostly in the same topologically associating domains. In addition,
 expressional variances in 771 and 83 DEGs were partially explained by
 expression QTLs for DEGs and methylation QTLs for DEG-correlated DMRs,
 respectively. A large number of RA variants were moderately to strongly
 correlated with meQTLs. DEG-correlated DMRs, enriched with meQTLs, had
 strongly enriched heritability of RA. Conclusion: Our findings revealed
 that the methylomic changes, driven by RA heritability-explaining
 variants, shape the differential expression of a substantial fraction of
 DEGs in CD4+ T cells in RA patients, reinforcing the importance of a
 multi-dimensional approach in disease-relevant tissues.
description: The different genetic patterns (differentially expressed genes
 and methylated regions) between RA patients and healthy controls were
 identified from microarray and NGS data analyses in a Korean cohort
 (n=122). In addition, eQTLs and meQTLs were detected by linear
 regression.
description: Please find detailed information from our research
 article: Eunji Ha and So-Young Bang et al.;
 "Genetic
 variants shape rheumatoid arthritis-specific transcriptomic features in
 CD4<sup>+</sup> T cells through differential DNA methylation,
 explaining a substantial proportion of
 heritability."; <em>Annals of the Rheumatic Disease</em>; in press<em>.</em>
DOI: 10.5061/dryad.pnvx0k6kq
title: Non-alcoholic fatty liver disease animal models database

description: Selecting and designing an optimal animal model is a key component of
 translational science, though there is often no consensus on which model
 is optimal for a particular disease. Here, we generated a database of 3920
 rodent models of non-alcoholic fatty liver disease (NAFLD). Due to high
 heterogeneity in design, few models had been cited more than once.
 Analysis of genetic models provided evidence for the role of adipose
 dysfunction and perturbation of the innate immune system in the
 progression of NAFLD. We identified that high fat, high fructose diet
 models most closely recapitulate the human phenotype of NAFLD. There was
 substantial variability in the nomenclature of animal models; a consensus
 on terminology of specialist diets is needed. More broadly, this analysis
 demonstrates the variation in preclinical study design and how this may
 limit the reproducibility of animal studies.
description: See ReadMe File.