cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6086/d1xt3v
title: Pinyon Flats rainfall manipulation experiments: species composition and biomass

description: While altered precipitation regimes can greatly impact biodiversity and
 ecosystem functioning, we lack a comprehensive view of how these impacts
 are mediated by changes to the seasonality of precipitation (i.e., whether
 it rains more/less in one season relative to another). Over two years we
 examined how altered seasonal precipitation influenced annual plant
 biomass and species richness, Simpson’s diversity, and community
 composition of annual plant communities in a dryland ecosystem that
 receives both winter and summer rainfall and has distinct annual plant
 communities in each season. Using a rainfall exclusion, collection, and
 distribution system we excluded precipitation and added water during each
 season individually and compared responses to control plots which received
 ambient summer and winter precipitation. In control plots, we found five
 times greater annual plant biomass, twice as many species, and higher
 diversity in winter relative to summer. Adding water increased annual
 plant biomass in summer only, did not change richness or diversity in
 either summer or winter, and modestly shifted community composition.
 Excluding precipitation in either season reduced annual plant biomass,
 richness and Simpson’s diversity. However, in the second winter season,
 biomass was higher in the plots where precipitation was excluded in the
 previous summer seasons suggesting that reduced productivity in the summer
 may facilitate biomass in the winter. Our results suggest that increased
 precipitation in summer may have stronger short-term impacts on annual
 plant biodiversity and ecosystem function relative to increased winter
 precipitation. In contrast, decreasing precipitation may have ubiquitous
 negative effects on annual plants across both summer and winter but may
 lead to increased biomass in the following off-seasons. These patterns
 suggest that annual plant communities exhibit asymmetries in their
 community and ecosystem responses to altered seasonal precipitation and
 that considering the seasonality of precipitation is important for
 predicting the effects of altered precipitation regimes.
description: To sample species composition and biomass of the annual plant
 community in each treatment, we established six
 1-m<sup>2</sup> subplots in each plot. Within the central 0.5
 m<sup>2</sup> of each subplot we measured community
 composition, in the same location every year, using a point-intercept
 approach with 50 points recording all hits at each point. In the area
 between where species composition was sampled and the outer edge of the
 sub-plot, we sampled aboveground biomass in an additional 0.25
 m<sup>2</sup> area. We rotated the location of biomass
 sampling to a different side each season to not re-sample the same
 location, and for each harvest we clipped all aboveground biomass, dried
 it for 4-days at 60°C, and weighed it to the nearest 0.01 g. All subplots
 were placed at least 1m from the edge of the plot to reduce the potential
 for edge effects from the rainfall manipulation shelters.
DOI: 10.5061/dryad.vdncjsxwx
title: Data and source code from: Contingency and selection in mitochondrial genome dynamics

description: Eukaryotic cells contain numerous copies of mitochondrial DNA (mtDNA),
 allowing for the coexistence of mutant and wild-type mtDNA in individual
 cells. The fate of mutant mtDNA depends on their relative replicative
 fitness within cells and the resulting cellular fitness within populations
 of cells. Yet the dynamics of the generation of mutant mtDNA and features
 that inform their fitness remain unaddressed. Here we utilize long read
 single-molecule sequencing to track mtDNA mutational trajectories in
 Saccharomyces cerevisiae. We show a previously unseen pattern that
 constrains subsequent excision events in mtDNA fragmentation. We also
 provide evidence for the generation of rare and contentious non-periodic
 mtDNA structures that lead to persistent diversity within individual
 cells. Finally, we show that measurements of relative fitness of mtDNA fit
 a phenomenological model that highlights important biophysical parameters
 governing mtDNA fitness. Altogether, our study provides techniques and
 insights into the dynamics of large structural changes in genomes that may
 be applicable in more complex organisms.
description: Dataset was collected with an Oxford Nanopore MinION Mk1B
 following the experimental description in methods. Raw Nanopore reads were
 basecalled and demultiplexed with the ONT Guppy package 3.1.5-1.
description: See README file
DOI: 10.5061/dryad.c59zw3r8x
title: Specimen list and landmark coordinates for the palate of early salamanders

description: Ecological preferences and life history strategies have enormous impacts
 on the evolution and phenotypic diversity of salamanders, but the yet
 established reliable ecological indicators hinder investigations on the
 paleobiology of early salamanders. Here we statistically demonstrate using
 geometric morphometric analysis that both the shape of the palate and many
 non-shape variables particularly associated with vomerine teeth are
 ecologically informative in early stem- and basal crown-group salamanders.
 The morphology of the palate is heavily impacted by convergence
 constrained by feeding mechanisms and also exhibits clear stepwise
 evolutionary patterns with alternative phenotypic designs to cope with
 similar functional demand. Paleoecological disparities in early
 salamanders had took place before the Middle Jurassic and have achieved
 all ecological preferences in the Early Cretaceous. Metamorphosis is
 significant in the expansion of ecomorphospace of the palate in early
 salamanders. The common ancestor of salamanders is metamorphosed and
 terrestrial, and share unified lifestyles with other modern amphibians.
description: Data S1 contains the details on the taxonomy, ecological
 preference, life history strategy of the salamander specimens
 investigated, and the parameters of CT scan Data S2
 contains the raw and procrusted coordinates of 24 2-D landmark points and
 centroid size of the palate for 70 specimens Data
 S3 contains the raw and procrusted coordinates of 7 2-D landmark points
 and centroid size of the right vomer for 71 specimens
DOI: 10.6078/d1m420
title: Dietary ethanol ingestion by free-ranging spider monkeys (Ateles geoffroyi)

description: Ethanol within ripe and over-ripe fruit is produced naturally through the
 metabolic activity of fermentative yeasts.  As a consequence,
 frugivorous animals may chronically consume ethanol as part of their
 routine diet, although direct measurements of such exposure are lacking.
  Here, we present data on ethanol concentrations within fruits of
 the Neotropical tree Spondias mombin (Anacardiaceae) that are eaten by
 Geoffroy's spider monkeys (Ateles geoffroyi) on Barro Colorado
 Island, Panama.  Of collected fruits that were partially consumed
 and then dropped by foraging monkeys, pulp-ethanol content was typically
 in the range of 1–2%; the percentage of pulp for consumed fruits was not
 significantly correlated with ethanol concentration of the pulp remaining
 within each fruit.  Urine samples from foraging spider monkeys
 were also evaluated for the ethanol metabolites ethyl glucuronide (EtG)
 and ethyl sulfate (EtS); five of six samples tested positive for both
 compounds.  In aggregate, these data indicate natural exposure to
 fruit-associated ethanol in a wild primate species.
description: See the published literature associated with this data.
description: The data provided here is for analysis of the <em>Spondias
 mombin</em> fruit ethanol data collected on the infrared
 spectrometer. See the README.txt file for further instructions.
DOI: 10.5061/dryad.vq83bk3tx
title: Data to accompany 'New evidence suggests no sex bias in herbivory or plant defence'

description: Dioecious plants can exhibit sexual dimorphism across a
 suite of plant traits, including susceptibility to herbivory and secondary
 chemistry. One hypothesis is that, due to greater costs of
 reproduction in females, males should grow faster and invest less in
 defense, resulting in male-biased herbivory. Indeed, a series of papers
 and a prominent meta-analysis have established male-biased herbivory as a
 robust result. However, more recent reviews have raised questions about
 how general the pattern is, citing the low breadth of taxon
 sampling. The literature on this topic has not been formally quantified by
 meta-analysis in over 15 years. Here we report the results of a
 meta-analysis of studies that measured sex bias in either herbivory and/or
 secondary defense in 71 dioecious plant species. We
 added 58 observations of herbivory and 41 of secondary
 chemistry to the original. We control for non-independence of effects from
 the same study and taxonomic group to address critiques of earlier
 studies. For secondary chemistry, we found no support for any consistent
 difference between male and female plants. For herbivory, results
 are directionally similar to earlier reports, although not statistically
 significant once we accounted for taxonomic group and study. We also
 found that the magnitude and direction of the effect of plant
 sex on herbivory declines, with earlier studies reporting a
 stronger male-bias. We discuss our results in light of the ‘decline
 effect’ and consider whether the datasets exhibit signs of evidence of the
 type(s) of biases that can result in declining effect sizes over time.
DOI: 10.5061/dryad.1c59zw3wr
title: Adverse effects of remdesivir, hydroxychloroquine, and lopinavir/ritonavir when used for COVID-19: systematic review and meta-analysis of randomized trials

description: Background: To summarize specific adverse effects of remdesivir,
 hydroxychloroquine, and lopinavir/ritonavir in patients with COVID-19.
 Methods: We searched 32 databases through 27 October 2020. We included
 randomized trials comparing any of the drugs of interest to placebo or
 standard care, or against each other. We conducted fixed-effects pairwise
 meta-analysis and assessed the certainty of evidence using the GRADE
 approach. Results: We included 16 randomized trials which enrolled 8226
 patients. For most interventions and outcomes the certainty of the
 evidence was very low to low except for gastrointestinal adverse effects
 from hydroxychloroquine, which was moderate certainty. Compared to
 standard care or placebo, low certainty evidence suggests that remdesivir
 may not have an important effect on acute kidney injury or cognitive
 dysfunction/delirium. Low certainty evidence suggests that
 hydroxychloroquine may increase the risk of cardiac toxicity (and
 cognitive dysfunction/delirium, whereas moderate certainty evidence
 suggests hydroxychloroquine probably increases the risk of diarrhoea (RD
 106 more per 1000, 95% CI: 48 more to 175 more) and nausea and/or vomiting
 (RD 62 more per 1000, 95% CI: 23 more to 110 more) compared to standard
 care or placebo. Low certainty evidence suggests lopinavir/ritonavir may
 increase the risk of diarrhoea and nausea and/or vomiting compared to
 standard care or placebo. Discussion: Hydroxychloroquine probably
 increases the risk of diarrhoea and nausea and/or vomiting and may
 increase the risk of cardiac toxicity and cognitive dysfunction/delirium.
 Lopinavir/ritonavir may increase the risk of diarrhoea and nausea and/or
 vomiting. Remdesivir may have no important effect on risk of acute kidney
 injury or cognitive dysfunction/delirium. These findings provide important
 information to support the development of evidence-based management
 strategies for patients with COVID-19. Funding: This study was supported
 by the Canadian Institutes of Health Research (grant: VR4-172738)
 Registration: Not registered in PROSPERO, protocol available in the
 supplementary material of BMJ 2020;370:m2980;
 http://dx.doi.org/10.1136/bmj.m2980.
description: See README.txt.
DOI: 10.5061/dryad.dfn2z353m
title: A new marrellomorph arthropod from southern Ontario: A rare case of soft tissue preservation on a late Ordovician open marine shelf

description: Ordovician open marine lagerstätten are relatively rare and widely
 dispersed, producing a patchy picture of the diversity and biogeography of
 non-mineralized marine organisms, and challenging our understanding of the
 fate of Cambrian groups. Here, for the first time, we report soft-bodied
 fossils, including a well-preserved marrellomorph arthropod, fragmentary
 carapaces, and macroalgae, from the late Ordovician (Katian) Upper Member
 of the Kirkfield Formation near Brechin, Ontario. The unmineralized
 elements and associated exceptionally preserved shelly biota were entombed
 rapidly in storm deposits that smothered the shallow, carbonate-dominated
 shelf. The marrellomorph, Tomlinsonus dimitrii gen. et sp. nov., is
 remarkable for its ornate, curving cephalic spines and pair of
 hypertrophied appendages, suggesting a slow-moving, benthic lifestyle.
 Re-evaluation of marrellomorph phylogeny using new data favours an
 arachnomorph affinity, though internal relationships are robust to
 differing outgroup selection. Clades Marrellida and Acercostraca are
 recovered, but the monophyly of Marrellomorpha is uncertain. The new taxon
 is recovered as sister to the Devonian Mimetaster, and, as the second
 youngest known marrellid, bridges an important gap in the evolution of
 this clade. More generally, the Brechin biota represents a rare window
 into Ordovician open marine shelf environments in Laurentia, representing
 an important point of comparison with contemporaneous lagerstätten from
 other paleocontinents, with great potential for further discoveries.
DOI: 10.5061/dryad.9ghx3ffk0
title: Data from: Computed tomographic analysis of dental system of three Jurassic ceratopsians: implications for the evolution of the tooth replacement pattern and diet in early-diverging ceratopsians

description: The dental system of ceratopsids is among the most specialized structure
 in Dinosauria, and includes high angled wear surfaces, split tooth roots,
 and multiple teeth in each tooth family. However, the early evolution of
 this unique dental system is generally poorly understood due to a lack of
 knowledge of the dental morphology and development in early-diverging
 ceratopsians. Here we study the dental system of three of the
 earliest-diverging Chinese ceratopsians: Yinlong and Hualianceratops from
 the early Late Jurassic of Xinjiang, and Chaoyangsaurus from the Late
 Jurassic of Liaoning. By using micro-computed tomographic analyses, our
 study has revealed significant new information regarding the dental system
 of these early ceratopsians, including no more than five replacement teeth
 in each jaw quadrant; at most one generation of replacement teeth in each
 alveolus; nearly full resorption of the functional tooth root during tooth
 replacement; and occlusion with low-angled, concave wear facets that
 differs significantly from the shearing occlusal system seen in
 ceratopsids. Yinlong displays an increase in the number of maxillary tooth
 alveoli and a decrease in the number of replacement teeth during ontogeny
 as well as the retention of remnants of functional teeth in the largest
 individual. Early-diverging ceratopsians thus display a relatively slow
 tooth replacement rate compared to late-diverging ceratopsians. Combined
 with paleobotany and palaeoenvironment data, Yinlong likely uses
 gastroliths to triturate foodstuffs, and the difference in diet strategy
 might have influenced the pattern of tooth replacement in later-diverging
 ceratopsians.
DOI: 10.5061/dryad.34tmpg4mt
title: Shrirangia: a new genus of Apiaceae from lateritic plateaus of Konkan region of Maharashtra, India

description: Shrirangia, a new monotypic genus of the family Apiaceae from low elevated
 lateritic plateaus of south Konkan region of Maharashtra, India, is
 described and illustrated with a new species, Shrirangia concanensis. The
 new genus is related to Himalayan genus Chamaesium Wolff by the characters
 of: many (ca 10) ribbed fruit, primary and secondary types of ribs present
 but very distinct from it by having tuberous habit, ternate to bi-ternate
 leaves, commissure plain undulate with 6–7 secondary ribs and vallecular
 and second types of vittae at dorsal face.
description: The specimens of new genus
 <i>Shrirangia</i> were studies from 4 years and collected from
 lateritic plateaus of Ratnagiri district (i.e. Konkan region), Maharashtra
 state. The morphological characters were studied under Leica EZ4 Stereo
 Zoom microscope. Diagnostic characters of the unknown species were
 compared with protologue and type specimens of its related genera
 <i>Chamaesium.</i> Photographs in the field and different parts of the plants were taken by using M50 Canon camera. The type specimens have been deposited at BSI, CAL and SUK herbaria.
DOI: 10.5061/dryad.1c59zw3ws
title: Data for Diniz et al. (2022) Changing the main course: strong bat visitation to the ornithophilous mistletoe Psittacanthus robustus (Loranthaceae) in a Neotropical savanna (Biotropica)

description: The Neotropical genus Psittacanthus comprises mostly specialized
 ornithophilous mistletoes, with rare exceptions. Psittacanthus robustus is
 a common ornithophilous species from the South American savannas whose
 bright-yellow flowers secrete copious diluted nectar. Due to a
 three-day-long anthesis and a short, non-restrictive floral tube, we
 suggest that the species also serves as a resource for flower-visiting
 bats. In a Cerrado area in central Brazil, we investigated the usage of
 the species by bats through systematic bat captures for pollen sampling,
 its nocturnal nectar secretion dynamics, mating system, and the relative
 dependence on diurnal and nocturnal pollinators for reproduction. Nine
 phyllostomid bat species visited P. robustus. Up to 50% of pollen samples
 from bats contained the species during peak flowering, equating or
 surpassing the prevalence of chiropterophilous species and representing
 roughly a third of the floral resources consumed by specialized
 nectarivores Glossophaga soricina and Anoura caudifer. Flowers actively
 produced nectar at night with volume and concentration values in the ideal
 ranges for bat consumption. Nectar is continuously secreted after sunset
 and accumulates in the absence of visitors. Psittacanthus robustus is
 self-compatible but seeds are set mostly by diurnal visitors. Nocturnal
 animals had a low and secondary contribution to plant fitness. This is the
 second report of bat pollination for the genus Psittacanthus, and the
 largest assemblage of bat visitors for the family Loranthaceae. Although
 ornithophilous, P. robustus is an important resource for bats in the
 Brazilian savanna, potentially representing a mixed or early transitional
 state towards bat pollination.
DOI: 10.5061/dryad.80gb5mksc
title: Genetic diversity, differentiation and historical origin of the isolated population of rooksCorvus frugilegusin Iberia

description: Current bird populations in southern temperate latitudes often represent
 relicts of glacial refugia from which northern populations expanded as the
 climate became suitable following the last glacial maximum, 18 000 years
 before present. Alternatively, these southern populations could be the
 result of the fragmentation of large distributions and other processes not
 related to glaciations, like recent recolonization from northern
 populations and human impact in historical times. Here, we investigate the
 origin of a small, isolated population of rooks Corvus frugilegus in
 north-western Iberia. We use genetic data from mitochondrial sequence
 markers and seven microsatellite loci to assess levels of genetic
 diversity, structure and gene flow among extant populations in Iberia and
 its broad distribution across western Europe. Microsatellite markers
 revealed the existence of two genetic clusters corresponding to Iberia and
 the remaining European populations, respectively. Haplotype networks based
 on mtDNA markers revealed a marked star-like phylogenetic pattern and
 evidence of a recent population expansion in northern Europe, but not in
 the Iberian population. Our results suggest that contemporary gene flow
 between Iberia and western Europe is restricted, and that breeding
 recruitment over recent generations in the Iberian population is local.
 The results are consistent with a relatively recent post-glacial
 colonization of Europe and western Siberia by rooks surviving the last
 glacial maximum in an Iberian refugium, and likely from refugia in other
 southern peninsulas. The unique ecological features and genetic
 differentiation of the Iberian rooks underscore the importance of ensuring
 the long-term conservation of this declining population.
DOI: 10.5061/dryad.p2ngf1vs7
title: Secondary production increases with species richness but decreases with species evenness of benthic invertebrates

description: Biodiversity is known to regulate ecosystem functioning under controlled
 experimental conditions. However, the ‘real-world’ consequences of
 biodiversity change remain uncertain, as biodiversity–ecosystem function
 (BEF) relationships observed in nature may be influenced by other drivers.
 Attempts to disentangle BEF relationships from the effects of confounding
 factors have so far focused mainly on primary producers, leaving
 relatively little known about the impact of changes in consumer diversity
 despite ecosystems experiencing species extirpations and introductions
 across trophic levels. Using data from 176 benthic invertebrate
 assemblages distributed throughout the North Sea, we studied how a
 fundamental ecological function – secondary production – varies in
 relation to two components of biodiversity – consumer species richness and
 evenness – while statistically controlling the effects of abiotic and
 biotic covariates. Production was enhanced as richness increased or
 evenness decreased. The relationship with evenness was attributable to its
 negative covariance with the abundance of small organisms; however, the
 relationship with richness could not be fully explained by other drivers.
 Our study reaffirms experimental findings about the functional importance
 of species richness and suggests that losing or gaining consumer species
 will affect secondary production over a broad range of biodiversity (20 to
 118 species) in natural ecosystems.
description: This is the dataset analysed in the paper by Clare et al.
 'Secondary production increases with species richness but decreases
 with species evenness of benthic invertebrates'. The data include the
 biodiversity (species richness and evenness) and secondary production of
 benthic invertebrate assemblages sampled throughout the North Sea during
 the summers of 2003 and 2004. Data on relevant abiotic and biotic
 covariates used in the analyses of Clare et al. are also included. A full
 description of the methods used to produce this dataset are provided in
 the paper.
description: The R code used by Clare et al. to analyse this dataset is
 provided for inspection and re-use.