cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sn02v6x26
title: Data from: Heterochronic origin of spherical fusulinid foraminifera in the Late Paleozoic

description: Heterochrony describes acceleration, displacement and/or retardation of
 descendants’ development events compared to ancestral states and has often
 been cited as an important process to bring about morphological novelty.
 It was coined one and half centuries ago and has been discussed by both
 paleobiologists and biologists frequently ever since. Many types of fossil
 organisms preserve aspects of their development histories in their bones
 or shells that have been used for heterochrony analyses, with body size
 being used as a developmental age indicator, despite raised questions
 regarding this practice. For organisms whose hard structures consist of
 multiple chambers, or that contain growth lines, age information suggested
 by these structures independently can facilitate ontogenetic modeling. In
 this way, relations among size, shape and age can be established in order
 to document patterns of morphological development. Morphological analysis
 of pseudoschwagerine fusulinids, a fossil foraminifera group that
 developed a morphologically novel spherical shell, along with their
 presumptive triticitid ancestors illustrates this approach to heterochrony
 analysis. Ontogenetic trajectory comparisons of four major
 pseudoschwagerine genera, as well as those of triticitid foraminifera,
 document relations between their shape, size and developmental ages. A
 complex of heterochronic patterns including peramorphic pre-displacement,
 hypermorphosis and acceleration characterize pseudoschwagerine development
 and appear to be responsible for the novel appearance of large, inflated
 fusiform and spherical tests in these Late Paleozoic benthic foraminifera.
 The morphometric approach employed in this investigation could be applied
 widely in the quantitative morphological studies of development histories
 in a variety of other fossil groups.
description: To analyze
 the heterochronic pattern embedded in the development of pseudoschwagerine
 fusulinids development, a set of 106 specimens belonging to four
 pseudoschwagerine genera and their presumptive ancestor,
 <i>Triticites</i>, have been included in this study. Their
 test morphology at each whorl-growing stage could be recognized in the
 axial thin sections and the test outlines were then digitized. In total
 1396 test outlines representing ontogenetic form changes in the 106
 specimens were acquired and each outline is represented by four Type 2
 landmarks and 36 semi-landmarks. The data file is
 present as .dat file, and contains X, Y coordinates of landmarks and
 semi-landmarks for all the 1396 test outline. The data were arranged in
 the file as 1396 matrixes with each composed of a title line presenting
 outline name and the following 40 lines of two numbers as X, Y
 coordinates. Abbreviated name of each specimen is used as part of the
 outline name and presented here in Table 1. The number in outline name
 represents the whorl-growing stage.
DOI: 10.5061/dryad.t76hdr7zh
title: Data from: Genome size influences adaptive plasticity of water loss, but not metabolic rates in lungless salamanders

description: Many expressions of phenotype, such as physiological performance,
 integrate multiple underlying traits to function. Linking component traits
 to adaptive physiology thus gives insight into mechanisms of selection
 acting on performance. Genome size (C-value) is a trait that influences
 physiology in multiple taxa by exerting a nucleotypic effect, constraining
 cell size and cellular physiology such that whole-organism mass-specific
 metabolism is reduced with increasing C-value. We tested for this
 mechanism of C-value function acting in lungless salamanders, plus an
 unexplored potential mechanism of C-value effects constraining water
 transport across the body surface to influence cutaneous water loss rates.
 We found no evidence for a nucleotypic effect on metabolic rates, but we
 demonstrate a relationship between C-value and water loss physiology.
 Under warmer experimental conditions, C-value was inversely correlated
 with water loss and positively correlated with resistance to water loss,
 which demonstrated adaptive plasticity at higher temperatures. We
 hypothesize this pattern results from differences in cell size
 constraining diffusion and evaporation of water from the skin under warm
 conditions when cutaneous perfusion is reduced. Testing this hypothesis
 may confirm a previously unappreciated adaptive role for C-value variation
 in this group, and reveals the possibility that genome size influences
 physiological exchange across transport barriers more broadly.
description: README_Johnson_JEB.txt : readme file with detailed information on
 all data files Johnson_JEB_physiol.csv : Raw,
 untransformed data for all morphological and physiological measurements
 from each individual experiment trial.
 Johnson_JEB_phydat.csv : Species mean values for morphological
 predictors, physiological responses, and species climate profiles under
 different experimental treatments. All morphological and physiological
 values are natural-log transformed. Johnson_JEB_r10.csv
 : R10 values calculated for each species under different experimental
 treatments. Johnson_JEB_supplement2.xlsx : Additional
 supplementary summary tables. Includes model comparisons, allometry
 variance analysis, path model coefficients, and GenBank accession numbers
 used in phylogeny construction. Table descriptions within the
 file.  Johnson_JEB_Pleth60.con.tre : Nexus format
 60-species consensus phylogeny of North American plethodontidae, direct
 output from MrBayes v3.2.7. Used to accurately construct broad
 phylogenetic relationships among focal species under analysis. 
 Johnson_JEB_Pleth09_trimmed.con.tre : Tree format 8-species
 phylogeny used in all comparative analyses, trimmed from the 60-species
 MrBayes consensus phylogeny.
DOI: 10.5061/dryad.mkkwh70x7
title: Enhancing the usefulness of artificial seeds in seed beetle model systems research

description: Seed beetles are among textbook examples of experimental model systems
 used to better understand nature’s complexities. A potential seed beetle
 model systems strength is the use of artificial seeds to remove
 experimental confounds. This is particularly relevant for scaling life
 histories to population dynamics but requires many artificial seeds.
 Current methods of producing seeds are laborious, limiting their
 application. Building on previous work, we developed efficient methods to
 produce artificial seeds and expand their use. We outline steps to produce
 artificial seeds and describe a new technique for transferring beetle eggs
 laid on natural seeds to artificial seeds.  Our methods yielded a
 100-fold increase in artificial seed production that is 80% more efficient
 than current methods. Burrowing success of beetle larvae from eggs laid on
 natural seeds and transferred to artificial seeds (85.4%) was comparable
 to rates on natural seeds.   Streamlining artificial seed
 production enables highly replicated life-history and time-series assays
 with large sample sizes. The ability to transfer eggs from natural to
 artificial seeds allows research on many phenomena including oviposition
 strategies, maternal provisioning, and competitive strategies, broadening
 the usefulness of seed beetle model systems in ecological and evolutionary
 research.
DOI: 10.5061/dryad.wm37pvmkf
title: Adequate vitamin A liver stores estimated by the Modified-Relative Dose Response test are positively associated with breastfeeding but not vitamin A supplementation in Senegalese urban children 9-23 months old: a comparative cross-sectional study

description: Vitamin A supplementation (VAS) in 6-59 month old children is recommended
 but its sustainability is currently
 questioned. In Senegal, data suggest that VAS should be
 maintained, but geographic and age-related specificities need to be
 addressed by gathering more evidence on the impact of this
 program. The objective of this comparative
 cross-sectional study, conducted in urban settings of
 Dakar, was to evaluate the effectiveness of VAS on vitamin A
 liver stores (VALS) among 9-23 month old children. The
 supplemented group (n = 119) received VAS (either 100 000 UI or 200 000
 UI) 2 to 6 months before evaluation while the non-supplemented group (n =
 110) had not received VAS during the past 6 months. VALS were
 assessed using the modified-relative dose response (MRDR) test. Serum
 retinol concentrations (SR) and biomarkers of subclinical inflammation
 were measured. Children’s health-related data and feeding patterns were
 collected. Mean MRDR values (VAS: 0.030 ± 0.017, non-VAS: 0.028 ±
 0.016, P = 0.39) and inflammation-adjusted SR (VAS: 1.34 ± 0.37, non-VAS:
 1.3 ± 0.35, P = 0.51) of children were adequate. Low prevalence of VALS
 (VAS: 5.2%, non-VAS: 5.4%) and inflammation-adjusted VAD (VAS: 2.6%,
 non-VAS: 0.9%) were detected despite high presence of infections and
 inflammation. Children were mostly still being breastfed (VAS: 85.7%,
 non-VAS: 77.3%) and complementary feeding indicators were similar in both
 groups. Only breastfeeding was associated with VALS (adjusted OR = 0.24,
 95% CI: 0.07-0.8, P = 0.02). Based on MRDR values, VAS was not
 related to improved VALS and SR as well as VAD reduction among these
 children with adequate VALS. Reinforcing breastfeeding advocacy and
 morbidity prevention/control are essential in this setting. Scaling-back
 VAS in this subpopulation should be examined regarding the risk of
 hypervitaminosis A. However, an evaluation of dietary VA intake
 sufficiency and a more quantitative assessment of VALS should be prior
 considered.
description: The ReadMe file is entitled
 "Glossary_of_variables_MRDR_Dakar_11082020"
 This database consists of a sample of 229 Senegalese children in
 whom antropometry, health, socioeconomic information were collected. This
 also contains biological measurements (serum retinol, C-reactive protein,
 Alpha-1 acid glycoprotein) as well as ratio of 3,4 didehydroretinol:
 retinol of children
DOI: 10.5061/dryad.7d7wm37sm
title: Fatal outcome of chikungunya virus infection in Brazil

description: Abstract Background Chikungunya virus (CHIKV) emerged in the Americas in
 2013 and has caused ~2.1 million cases and over 600 deaths. A
 retrospective investigation was undertaken to describe clinical,
 epidemiological and virus genomic features associated with deaths caused
 by CHIKV in Ceará state, northeast Brazil. Methods Sera, cerebrospinal
 fluid (CSF) and tissue samples from 100 fatal cases with suspected
 arbovirus infection were tested for CHIKV, dengue (DENV) and Zika virus
 (ZIKV). Clinical, epidemiological and death reports were obtained for
 patients with confirmed CHIKV infection. Logistic regression analysis was
 undertaken to identify independent factors associated with risk of death
 during CHIKV infection. Phylogenetic analysis was conducted using whole
 genomes from a subset of cases. Results 68 fatal cases had CHIKV infection
 confirmed by RT-qPCR (52.9%), viral antigen (41.1%), and/or specific-IgM
 (63.2%). Co-detection of CHIKV with DENV were found in 22% of fatal cases,
 ZIKV in 2.9%, and DENV and ZIKV in 1.5%. A total of 39 CHIKV-deaths
 presented with neurological signs and symptoms, and CHIKV-RNA was found in
 the CSF of 92.3% of these patients. Fatal outcomes were associated with
 irreversible multiple organ dysfunction syndrome. Patients with diabetes
 appear to die at a higher frequency during the sub-acute phase. Genetic
 analysis showed circulation of two CHIKV-East Central South African (ECSA)
 lineages in Ceará and revealed no unique virus genomic mutation associated
 with fatal outcome. Conclusion The investigation of the largest
 cross-sectional cohort of CHIKV-deaths to date reveals that CHIKV-ECSA
 strains can cause death in individuals from both risk and non-risk groups,
 including young adults.
description: Epidemiological data, phylogenetic trees, XMLs, and Ceará CHIKV
 genome sequences.
DOI: 10.5061/dryad.v15dv41tp
title: Ecosystem services enhanced through soundscape management link people and wildlife

description: Burgeoning urbanization, development and human activities have led to
 reduced opportunities for nature experience in quiet acoustic
 environments. Increasing noise affects both humans and wildlife alike. We
 experimentally altered human-caused sound levels in a paired study using
 informational signs that encouraged quiet behaviours in week-on, week-off
 blocks on the trail system of Muir Woods National Monument, California,
 USA to test if the soundscape influences both wildlife and human
 experiences. Using continuous measurements from acoustic recording units
 (n = 13) spatially distributed within the park, we found signs
 significantly lowered sound levels by approximately 1.2 decibels
 (A-weighted), thereby increasing listening area by 24% and bird
 availability by approximately 5.8% for every 1 decibel decrease.
 Visitor-intercept surveys (n = 537) revealed that our mitigation increased
 the number of birds perceived by visitors, rankings of soundscape
 pleasantness, and importantly, preferences for soundscape management. By
 lowering human-caused sound levels we created an acoustic environment
 equivalent to a ~21% reduction in visitors. The positive feedback cycle we
 describe may lead to increased conservation support in a time when the
 extinction of nature experience looms.
description: See paper for more details on methodology.
DOI: 10.5061/dryad.fj6q573s0
title: Combining molecular data sets with strongly heterogeneous taxon coverage enlightens the peculiar biogeographic history of stoneflies (Insecta: Plecoptera)

description: Extant members of the ancient insect order of stoneflies exhibit a
 disjunct, antitropical distribution, with one major lineage exclusively
 occurring in the Southern Hemisphere and the other, with few exceptions,
 on the Northern continents. Here, we address the biogeographic
 distribution and phylogenetic relationships of stoneflies using a
 phylogenetic workflow that combines both transcriptomic and Sanger
 sequence datasets with heterogeneous taxon coverage. We used a dataset
 comprising 2997 genes derived from the transcriptomes of 30 species and
 Sanger sequences of seven genes for 498 species. The backbone phylogeny
 was mainly inferred from the transcriptomic data, whereas the Sanger
 nucleotide sequence data provided high species density for divergence time
 estimation and diversification analyses. Our results show that the
 biogeographic pattern we observe today is primarily more likely shaped by
 long-distance over-land dispersal than by vicariance. We inferred that the
 ancestors of extant stoneflies originated in the Northern Hemisphere
 approximately 265 Ma and were presumably restricted to this area due to
 climatic and geographic boundaries. Our analyses suggest that with the
 break-up of Pangaea around 200 Ma and the associated climatic and
 geographical changes, two groups of stoneflies, the Anarctoperlaria and
 the Notonemouridae, dispersed to Gondwana and subsequently went extinct on
 the northern continents. Both groups likely dispersed across Gondwana
 before its break-up into the modern continents. At least one member of
 another group of ‘northern’ stoneflies, the Acroneuriinae, seems to have
 migrated from North America to South America around 67 Ma. We found four
 major net diversification rate shifts, indicating rapid radiation patterns
 that hampered a robust phylogenetic placement of these stonefly groups.
 Our study provides the first conclusive evolutionary explanation for the
 unique distribution pattern of stoneflies.
DOI: 10.15468/dl.9hh6ah
title: Occurrence Download

description: A dataset containing 1103 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Anolis vittigerus"
 ]
}

 The dataset includes 1103 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002512-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1g1jwstt2
title: Evidence for an extreme founding effect in a highly successful invasive species: data and R code

description: The adaptive potential of invasive species is  thought to
 decrease during founding events due to reduced genetic diversity, limiting
 the new population’s ability to colonize novel habitats. Barbary ground
 squirrels (Atlantoxerus getulus) were purportedly introduced as a single
 breeding pair to the island of Fuerteventura but have expanded to over a
 million individuals spread across the island in just over 50 years. We
 estimated the number of founders and measured the level of genetic
 diversity in this population using the mitochondrial displacement loop and
 microsatellite markers. Island samples (n = 19) showed no variation in the
 d-loop, suggesting a single founding female, while Moroccan samples (n =
 6) each had unique mitochondrial haplotypes. The microsatellite data of
 the island population (n = 256 individuals) revealed a small effective
 population size, low levels of heterozygosity, and high levels of
 inbreeding, supporting a founding population size of two to three
 individuals. Our results suggest that A. getulus has undergone an intense
 genetic bottleneck during their colonization of the island. They are one
 of the few species where introduction effort does not explain invasion
 success, although further investigation may explain how they have avoided
 the worst expected effects following an extreme genetic bottleneck.
description: <b>(b) Genetic analysis – mitochondrial
 DNA</b> We extracted DNA from 85 samples using
 the E.Z.N.A.® Tissue DNA Kit (Omega Bio-tek, Norcross, GA), from which 45
 were successfully amplified and sequenced (34 island, 11 mainland). We
 included 25 (19 island, six mainland) complete displacement loop sequences
 in our mtDNA analysis. We used four primers to target the d-loop (S. I.
 Table 3). We aligned d-loop sequences using the automatic ClustalW
 parameters in MEGA7 [53]. Samples with missing or ambiguous nucleotide
 data were removed from the analysis, and d-loop sequences were trimmed to
 a uniform length using the most closely related reference sequence
 available (<i>Spermophilus dauricus</i>, GenBank
 NC_027283.1). <b>(c) Genetic analysis – nuclear
 DNA</b> We isolated the genomic DNA of 256
 individuals using Chelex beads (Bio-Rad) [54].Two microsatellite primers
 were previously designed for Cape ground squirrels (<i>Xerus
 inauris</i>; Xin09 and Xin10) [55] and we newly developed nine
 primers, which we labelled with fluorescent dyes and pooled according to
 annealing temperatures [51]. We examined nuclear DNA using GeneMarker
 (SoftGenetics, State College, PA, USA), which scored the loci
 semi-automatically. At least two observers scored the alleles in an
 objective scoring procedure [56]. We conducted tests for null alleles
 using Micro-Checker [36].
DOI: 10.5061/dryad.47d7wm3b9
title: Protected by dragons: density surface modeling confirms large population of the critically endangered Yellow-crested Cockatoo on Komodo island

description: Intense trapping of the critically endangered Yellow-crested
 Cockatoo Cacatua sulphurea  for the International pet
 trade has devastated its populations across Indonesia such that
 populations &gt;100 individuals remain at only a handful of sites. We
 combined distance sampling with density surface modeling (DSM) to predict
 local densities and estimate total population size for one of these areas,
 Komodo Island, part of Komodo National Park (KNP) in Indonesia. We modeled
 local density based on topography (topographic wetness index) and habitat
 types (percentage of palm savanna and deciduous monsoon forest). Our
 population estimate of 1,113 (95% CI: 587–2,109) individuals on Komodo
 Island was considerably larger than previous conservative estimates. Our
 density surface maps showed cockatoos to be absent over much of the
 island, but present at high densities in wooded valleys. Coincidence
 between our DSM and a set of independent cockatoo observations was high
 (93%). Standardized annual counts by KNP staff in selected areas of the
 island showed increases in cockatoo records from &lt;400 in 2011 to
 ~650 in 2017. Taken together, our results indicate that KNP, alongside and
 indeed because of preserving its iconic Komodo Dragons Varanus
 komodoensis, is succeeding in protecting a significant population of
 Indonesia’s rarest cockatoo species. To our knowledge this is the first
 time DSM has been applied to a Critically Endangered species. Our findings
 highlight the potential of DSM for locating abundance hotspots,
 identifying habitat associations, and estimating global population size in
 a range of threatened taxa, especially if independent datasets can be used
 to validate model predictions.
description: The dataset was collected by point count distance sampling and
 analysed with density surface modeling in R.  
description: To avoid informing illegal trapping of the critically endangered
 target species, all location information has been deleted from the version
 published here. This was requested by the journal but makes it impossible
 to re-produce our results with the dataset provided.
DOI: 10.5061/dryad.k98sf7m4f
title: The STARS phase 2 study: a randomized controlled trial of gaboxadol in Angelman syndrome

description: Objective: To evaluate safety and tolerability and exploratory efficacy
 endpoints for gaboxadol (OV101) compared with placebo in individuals with
 Angelman syndrome (AS). Methods: Gaboxadol is a highly selective
 orthosteric agonist that activates γ-subunit–containing extrasynaptic
 γ-aminobutyric acid type A (GABAA) receptors. In a multicenter,
 double-blind, placebo-controlled, parallel-group trial, adolescent and
 adult individuals with a molecular diagnosis of AS were randomized (1:1:1)
 to 1 of 3 dosing regimens for a duration of 12 weeks: placebo morning dose
 and gaboxadol 15 mg evening dose (qd); gaboxadol 10 mg morning dose and 15
 mg evening dose (bid); or placebo morning and evening dose. Safety and
 tolerability were monitored throughout the study. Prespecified exploratory
 efficacy endpoints included adapted Clinical Global Impression–Severity
 (CGI-S) and Clinical Global Impression–Improvement (CGI-I) scales which
 documented the clinical severity at baseline and change after treatment,
 respectively. Results: Eighty-eight individuals were randomized. Of 87
 individuals (aged 13–45 years) who received at least 1 dose of study drug,
 78 (90%) completed the study. Most adverse events (AEs) were mild to
 moderate, and no life-threatening AEs were reported. Efficacy of
 gaboxadol, as measured by CGI-I improvement in an exploratory analysis,
 was observed in gaboxadol qd vs placebo (p = 0.0006). Conclusion: After 12
 weeks of treatment, gaboxadol was found to be generally well tolerated
 with a favorable safety profile. The efficacy as measured by the
 AS-adapted CGI-I scale warrants further studies.