cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h140qq7
title: Data from: Evolution alters post-invasion temporal dynamics in experimental communities.

description: 1. The causes and consequences of temporal variation in the abundance of
 organisms constitute central themes in ecological inquiry. Rapid evolution
 can occur over ecological time scales, potentially resulting in altered
 temporal variation in abundance and complicating inferences about the
 consequences of temporal variation. 2. We assessed whether evolution
 altered the temporal variability in species’ abundances in simple
 assemblages of species. We then compared experimental results to
 predictions from two-species models to better understand our results in
 the context of competitive and predator-prey interactions. 3. We compared
 founder populations and their evolved descendants in experimental
 communities of ciliates and rotifers. Using a series of orthogonal
 contrasts, we then evaluated whether: 1) evolutionary history of invaders
 or 2) residents, 3) coevolution among invaders and residents, and 4)
 invasion itself altered temporal variability in species abundances
 following invasion by a novel species. Using two-species competition and
 predator-prey models, we also generated predictions to better understand
 the effects of evolution on temporal variation in the abundances of
 interacting species. Finally, we compared experimental and modeling
 results to aid in the interpretation of which interspecific interactions
 might be affected by ongoing evolution in our communities. 4. In
 experimental populations, differing evolutionary histories resulted in
 significant differences among treatments in abundances and temporal
 variation in abundances of both resident and invading species. For the
 contrasts, we found evidence that evolutionary history of the invader and
 residents, coevolution among invaders and residents, and invasion itself
 affected temporal variability in abundance, but the importance of each
 differed for the two communities and the species within those communities.
 When comparing experimental results to model predictions, the increased
 abundance and decreased temporal variation of one invader, Euplotes
 daidaleos, are potentially consistent with evolution resulting in reduced
 attack rates in the novel community. 5. Evolutionary history alone can
 affect temporal variation in the abundances of species, generating
 important consequences for interspecific interactions among species and
 complicating inferences about the consequences of temporal variability in
 biological communities. 
description: Temporal variability
 data from "Evolution alters post-invasion temporal dynamics in
 experimental communities"Standard deviation over
 time of log10-transformed abundance data for species in two experimental
 communities of ciliates and rotifers.Dryad
 dataset.xlsx
DOI: 10.5061/dryad.198q4p4
title: Data from: Fecundity compensation is dependent on the generalised stress response in a nematode host

description: Background: Fecundity compensation, increased offspring output following
 parasite exposure, is widely reported, but the underlying mechanisms
 remain unclear. General stress responses are linked to other indirect
 defences against parasites, and therefore may be responsible. We
 challenged strains of Caenorhabditis elegans (wild-type and mutants with
 compromised or strengthened stress responses) with Staphylococcus aureus.
 Results: In all strains except the compromised stress response mutant, we
 saw elevated offspring production if hosts survived initial parasite
 exposure. Conclusion: We infer that general stress responses are linked
 with fecundity compensation. These results may explain why trade-offs are
 not observed among parasite defence mechanisms.
description: Data from Fecundity
 compensation is dependent on the generalised stress response in a nematode
 hostData used in Fecundity
 compensation is dependent on the generalised response in a nematode
 host
DOI: 10.5061/dryad.8gs9388
title: Data from: Sex is determined by XY chromosomes across the radiation of dioecious Nepenthes pitcher plants

description: Species with separate sexes (dioecy) are a minority among flowering
 plants, but dioecy has evolved multiple times independently in their
 history. The sex determination system and sex-linked genomic regions are
 currently identified in a limited number of dioecious plants only. Here,
 we study the sex-determination system in a genus of dioecious plants that
 lack heteromorphic sex chromosomes and are not amenable to controlled
 breeding: Nepenthes pitcher plants. We genotyped wild populations of
 flowering males and females of three Nepenthes taxa using ddRAD-seq, and
 sequenced a male inflorescence transcriptome. We developed a statistical
 tool (privacy rarefaction) to distinguish true sex-specificity from
 stochastic noise in read coverage of sequencing data from wild populations
 and identified male-specific loci and XY-patterned SNPs in all three
 Nepenthes taxa, suggesting the presence of homomorphic XY sex chromosomes.
 The male-specific region of the Y chromosome showed little conservation
 among the three taxa, except for the essential pollen development gene
 DYT1 which was confirmed as male-specific by PCR in additional Nepenthes
 taxa. Hence, dioecy and part of the male-specific region of the Nepenthes
 Y-chromosomes likely have a single evolutionary origin.
description: dryad_data_Scharmann_et_al_Evol_Lett_2019
DOI: 10.5061/dryad.j74b646
title: Data from: Contributions of bats to the local economy through durian pollination in Sulawesi, Indonesia

description: Durian is economically important for local livelihoods in Indonesia. Our
 study investigated the identity of pollinators of semi-wild durian, and
 subsequently estimated the economic contribution of these pollination
 services. We conducted pollination exclusion experiments and deployed
 camera traps at durian trees from October 2017 to January 2018 in an area
 where the local economy depends on durian production in West Sulawesi,
 Indonesia. Durian flowers in the experiment that were accessible to bats
 had significantly higher fruit set compared to flowers that were
 completely closed to animal visitors or those that could only be visited
 by insects, suggesting that bats were the primary durian pollinator. The
 small, highly nectarivorous cave nectar bat (Eonycteris spelaea) visited
 more inflorescences (n = 25) and had visits of much longer duration (X ̅ =
 116.87 sec/visit) than the two species of flying foxes: Pteropus alecto (n
 = 7 inflorescences visited,X ̅ = 11.07 sec/visit) and Acerodon celebensis
 (n = 6 inflorescences visited,X ̅ = 11.60 sec/visit). Visits by large and
 small bats were influential in differentiating successful durian fruit
 production from unsuccessful. Using a bioeconomic approach, we
 conservatively estimate that bat pollination services are valued at
 ~$117/ha/fruiting season. By demonstrating an ecological link between bats
 and the local economy, this research provides an urgent message for
 Southeast Asian governments regarding the need to promote bat conservation
 in order to increase the production of durian grown under semi-wild
 conditions.
description: fruit_set_durianfruit set durian from different treatment under pollination exclusion experimentdataset_durian_productiondataset to model durian production
DOI: 10.5061/dryad.tm8038t
title: Data from: Dynamic phenotypic correlates of social status and mating effort in male and female red junglefowl, Gallus gallus

description: Despite widespread evidence that mating and intra-sexual competition are
 costly, relatively little is known about how these costs dynamically
 change male and female phenotypes. Here, we test multiple hypotheses
 addressing this question in replicate flocks of red junglefowl (Gallus
 gallus). First, we test the inter-relationships between social status,
 comb size (a fleshy ornament) and body mass at the onset of a mating
 trial. While comb size covaried positively with body mass across
 individuals of both sexes, comb size was positively related to social
 status in females but not in males. Second, we test for changes within
 individuals in body mass and comb size throughout the mating trial. Both
 body mass and comb size declined at the end of a trial in both sexes,
 suggesting that mating effort and exposure to the opposite sex are
 generally costly. Males lost more body mass if they: i) were socially
 subordinate, ii) were chased by other males, or iii) mated frequently,
 indicating that subordinate status and mating are independently costly.
 Conversely, females lost more body mass if they were exposed to a higher
 frequency of coerced matings, suggesting costs associated with male sexual
 harassment and female resistance, although costs of mating per se could
 not be completely ruled out. Neither competitive nor mating interactions
 predicted comb size change in either sex. Collectively, these results
 support the notion that sex-specific costs associated with social status
 and mating effort result in differential, sex-specific dynamics of
 phenotypic change.
description: Data on individual
 malesThis .csv file contains
 all relevant information on individual males across the 20 replicate
 groups of red junglefowl. It was used for all the main analyses described
 in this study.Male_data.csvData on individual femalesThis .csv file contains all relevant information on individual females across the 20 replicate groups of red junglefowl. It was used for all the main analyses described in this study.Female_data.csvComb area measurements for repeatability analysisTwo independent comb area measurements of a random subset of 44 individuals (24 females and 20 males), used to run the repeatability analysis described in the study methods (section 2.2, Phenotypic measurements)Repeatability_comb_area.csv
DOI: 10.5061/dryad.87vt6hm
title: Data from: Re-assessing the diversity of negative strand RNA viruses in insects

description: The spectrum of viruses in insects is important for subjects as diverse as
 public health, veterinary medicine, food production, and biodiversity
 conservation. The traditional interest in vector-borne diseases of humans
 and livestock has drawn the attention of virus studies to hematophagous
 insect species. However, these represent only a tiny fraction of the broad
 diversity of Hexapoda, the most speciose group of animals. Here, we
 systematically probed the diversity of negative strand RNA viruses in the
 largest and most representative collection of insect transcriptomes from
 samples representing all 34 extant orders of Hexapoda and 3 orders of
 Entognatha, as well as outgroups, altogether representing 1243 species.
 Based on profile hidden Markov models we detected 488 viral RNA-directed
 RNA polymerase (RdRp) sequences with similarity to negative strand RNA
 viruses. These were identified in members of 324
 arthropod species. Selection for length, quality, and uniqueness
 left 234 sequences for analyses, showing similarity to genomes of viruses
 classified in Bunyavirales (n=86), Articulavirales (n=54), and several
 orders within Haploviricotina (n=94). Coding-complete genomes or
 nearly-complete subgenomic assemblies were obtained in 61 cases. Based on
 phylogenetic topology and the availability of coding complete genomes we
 estimate that at least 20 novel viral genera in seven families need to be
 defined, only two of them monospecific. Seven additional viral clades
 emerge when adding sequences from the present study to formerly
 monospecific lineages, potentially requiring up to seven additional
 genera. One long sequence may indicate a novel family. For segmented
 viruses, cophylogenies between genome segments were generally improved by
 the inclusion of viruses from the present study, suggesting that in silico
 misassembly of segmented genomes is rare or absent. Contrary to previous
 assessments, significant virus-host codivergence was identified in major
 phylogenetic lineages based on two different approaches of codivergence
 analysis in a hypotheses testing framework. In spite of these additions to
 the known spectrum of viruses in insects, we caution that basing taxonomic
 decisions on genome information alone is challenging due to technical
 uncertainties, such as the inability to prove integrity of complete genome
 assemblies of segmented viruses.
description: Data from: Re-assessing
 the diversity of negative strand RNA viruses in insects Table-host-annotations.csv contains information of the negative strand RNA viruses described in this study. Data such as host taxonomy, insect sample locations, open reading frame coordinates, and predicted protein annotations are shown. The file negativeStrand_OKIAVs_NT.fasta contains the nucleotide sequences (genomes, partial genomes, and genomic segments) of the negative strand RNA viruses described in this study.
DOI: 10.5061/dryad.3j6d0g3
title: Data from: Biodiversity, systematics, and new taxa of cladid crinoids from the Ordovician Brechin Lagerstätte

description: Upper Ordovician (Katian) strata of the Lake Simcoe region of Ontario
 record a spectacularly diverse and abundant echinoderm fauna known as the
 Brechin Lagerstätte. Despite recognition as the most taxonomically diverse
 Katian crinoid paleocommunity, the Brechin Lagerstätte has received
 relatively little taxonomic study since Frank Springer published his
 classic monograph on the “Kirkfield fauna” in 1911. Using a new collection
 of exceptionally preserved material, we evaluate all dicyclic inadunate
 crinoids occurring in the Brechin Lagerstätte, which is predominately
 comprised of cladids (Eucladida and Flexibilia). We document 15 species
 across 11 genera, including descriptions of two new genera and four new
 species. New taxa include Konieckicrinus brechinensis n. gen. n. sp., K.
 josephi n. gen. n. sp., Simcoecrinus mahalaki n. gen. n. sp., and
 Dendrocrinus simcoensis n. sp. Although cladids are not commonly
 considered major components of the Early Paleozoic Crinoid
 Macroevolutionary Fauna, which is traditionally conceived as dominated by
 disparids and diplobathrid camerates, they are the most diverse major
 lineage of crinoids occurring in the Brechin Lagerstätte. This unexpected
 result highlights the important roles of specimen-based taxonomy and
 systematic revisions in the study of large-scale diversity patterns.
description: Wright_et_al._Supplemental_dataTable with taxonomic names, specimen numbers, locality data, and stratigraphic information for UMMP specimens.
DOI: 10.5061/dryad.qf36q53
title: Data from: Telemedicine in neurology: telemedicine work group of the American Academy of Neurology update

description: ABSTRACT Purpose: While there is strong evidence supporting the importance
 of telemedicine in stroke, its role in other areas of neurology is not as
 clear. The goal of this review is to provide an overview of evidence-based
 data regarding the role of teleneurology in the care of patients with
 neurologic disorders other than stroke. Recent findings: Studies across
 multiple specialties report noninferiority of evaluations by telemedicine
 compared with traditional, in-person evaluations in terms of patient and
 caregiver satisfaction. Evidence reports benefits in expediting care,
 increasing access, reducing cost, and improving diagnostic accuracy and
 health outcomes. However, many studies are limited and gaps in knowledge
 remain. Summary: Telemedicine use is expanding across the vast array of
 neurologic disorders. More studies are needed to validate and support its
 use.
description: 2019-08-27-E-references-Telemedicine Practice PaperReferences for citations beyond 60 (e-references)
DOI: 10.5061/dryad.27s8k0p
title: Data from: Current ecology, not ancestral dispersal patterns, influences menopause symptom severity

description: All human females who reach midlife experience menopause, however, it is
 currently unclear why women experience this period of infertility, and why
 it is accompanied by many unpleasant symptoms. Using primary data from
 four ethnic groups in China, we test an existing theory that age of
 menopause and its symptoms are the result of intragenomic conflict between
 maternally and paternally inherited genes, with the outcome of such
 conflict predicted to be contingent on the ancestral post-marital
 residence pattern of the female (Úbeda et al., 2014). The model predicts
 that being ancestrally patrilocal results in less intragenomic conflict,
 causing a shorter, less symptomatic peri-menopause that terminates in a
 later menopause. Our findings show no support for this hypothesis, and
 suggest current, rather than ancestral, residence patterns better predict
 aspects of the menopausal transition. Furthermore, current patrilocality
 when compared to duolocality is associated with more severe menopause
 symptoms, which may be due to sexual, rather than intragenomic, conflict.
description: h1_symptomsData on peri-menopause symptom severity used to test hypothesis 1 in manuscript.h2_durationData on peri-menopause symptom duration used to test hypothesis 2 in manuscript.h3_agemenoData on age of menopause used to test hypothesis 3 in manuscript.
DOI: 10.5061/dryad.rb4b420
title: Data from: A phenotype-genotype codon model for detecting adaptive evolution

description: A central objective in biology is to link adaptive evolution in a gene to
 structural and/or functional phenotypic novelties. Yet most analytic
 methods make inferences mainly from either phenotypic data or genetic data
 alone. A small number of models have been developed to infer correlations
 between the rate of molecular evolution and changes in a discrete or
 continuous life history trait. But such correlations are not necessarily
 evidence of adaptation. Here we present a novel approach called the
 phenotype-genotype branch-site model (PG-BSM) designed to detect evidence
 of adaptive codon evolution associated with discrete-state phenotype
 evolution. An episode of adaptation is inferred under standard codon
 substitution models when there is evidence of positive selection in the
 form of an elevation in the nonsynonymous-to-synonymous rate ratio ω to a
 value ω &gt; 1. As it is becoming increasingly clear that ω &gt; 1
 can occur without adaptation, the PG-BSM was formulated to infer an
 instance of adaptive evolution without appealing to evidence of positive
 selection. The null model makes use of a covarion-like component to
 account for general heterotachy (i.e., random changes in the evolutionary
 rate at a site over time). The alternative model employs samples of the
 phenotypic evolutionary history to test for phenomenological patterns of
 heterotachy consistent with specific mechanisms of molecular adaptation.
 These include (i) a persistent increase/decrease in ω at a site following
 a change in phenotype (the pattern) consistent with an increase/decrease
 in the functional importance of the site (the mechanism); and (ii) a
 transient increase in ω at a site along a branch over which the phenotype
 changed (the pattern) consistent with a change in the site's optimal
 amino acid (the mechanism). Rejection of the null is followed by post hoc
 analyses to identify sites with strongest evidence for adaptation in
 association with changes in the phenotype as well as the most likely
 evolutionary history of the phenotype. Simulation studies based on a novel
 method for generating mechanistically realistic signatures of molecular
 adaptation show that the PG-BSM has good statistical properties. Analyses
 of three real alignments show that site patterns identified post hoc are
 consistent with the specific mechanisms of adaptation included in the
 alternate model. Further simulation studies show that the covarion-like
 component of the PG-BSM plays a crucial role in mitigating recently
 discovered statistical pathologies associated with confounding by
 accounting for heterotachy-by-any-means.
description: <strong>systbio_paper_simulations</strong>
 Contains all of the simulated alignments used in the
 study
 <strong>sysbio_paper_real_alignments</strong> Contains the three real alignments used in the study. <strong>Supplementary material</strong> A detailed description of the PG-BSM
DOI: 10.5061/dryad.td2p55f
title: Data from: Controlled release of basic fibroblast growth factor from a peptide biomaterial for bone regeneration

description: Self-assembled peptide scaffolds based on D-RADA16 (D16) are an important
 matrix for controlled drug release and 3D cell culture. In this work, D16
 peptide hydrogels were coated on artificial bone composed of
 nano-hydroxyapatite/polyamide 66 (NHA/PA66) to obtain a porous
 drug-releasing structure for treating bone defects. The developed
 materials were characterized via transmission electron microscopy (TEM),
 scanning electron microscopy (SEM). The proliferation and adhesion of bone
 mesenchymal stem cells (BMSCs) were examined by Confocal laser microscopy
 (CLS) and CCK-8 experiments. The osteogenic ability of the porous
 materials towards bone BMSCs was examined in vitro by staining with
 Alizarin Red S and alkaline phosphatase (ALP) and bioactivity were
 evaluated in vivo. The results revealed that NHA/PA66/D-RADA16/bFGF reduce
 the degradation rate of D16 hydrogels and prolong sustained release of
 bFGF, which would promote BMSCs proliferation, adhesion and osteogenesis
 in vitro and bone repair in vivo. Thus, it deserves more attention and is
 worthy of further research.
description: Osteogenic observation of various materials 8 weeks and 12 weeks
 after implantation Osteogenic observation of various
 materials 8 weeks and 12 weeks after implantation
 CCK-8 kite Cell proliferation
 CCK.pzf cell roundness
 cell roundness test by ImageJ OD
 ALP Plate reader results for osteogenesis (ARS
 ALP) Edu Edu staining for cell
 proliferation degradation
 materials degradation