cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0gb5mkkz6
title: Data from: Infection dynamics, dispersal, and adaptation: understanding the lack of recovery in a remnant frog population following a disease outbreak

description: Emerging infectious diseases can cause dramatic declines in wildlife
 populations. Sometimes these declines are followed by recovery, but many
 populations do not recover. Studying differential recovery patterns may
 yield important information for managing disease-afflicted populations and
 facilitating population recoveries. In the late1980s, a chytridiomycosis
 outbreak caused multiple frog species in Australia's Wet Tropics to
 decline. Populations of some species (e.g., Litoria nannotis) subsequently
 recovered, while others (e.g., Litoria dayi) did not. We examined the
 population genetics and current infection status of L. dayi, to test
 several hypotheses regarding the failure of its populations to recover: 1)
 a lack of individual dispersal abilities has prevented recolonization of
 previously occupied locations, 2) a loss of genetic variation has resulted
 in limited adaptive potential, and 3) L. dayi is currently adapting to
 chytridiomycosis. We found moderate to hig h levels of gene flow and
 diversity (Fst range: &lt;0.01–0.15; minor allele frequency:
 0.192–0.245), which were similar to previously published levels for
 recovered L. nannotis populations. This suggests that dispersal ability
 and genetic diversity do not limit the ability of L dayi to recolonize
 upland sites. Further, infection intensity and prevalence increased with
 elevation, suggesting that chytridiomycosis is still limiting the
 elevational range of L. dayi. Outlier tests comparing infected and
 uninfected individuals consistently identified 18 markers as putatively
 under selection, and several of those markers matched genes that were
 previously implicated in infection. This suggests that L. dayi has genetic
 variation for genes that affect infection dynamics and may be undergoing
 adaptation.
description: Metadata are contained within the file
DOI: 10.5061/dryad.qjq2bvqcw
title: Catering to the Patient

description: Introduction: It has been shown that communication skills acquired during
 undergraduate medical education are of great importance. Hence, many
 countries require teaching communication as part of their medical
 curricula. To assess students’ learning progress, “Catering to the
 Patient”, as an aspect of showing empathy, should be evaluated. Since
 there was no description of a validated instrument fitting for this
 purpose, one had to be developed. To describe its process of development
 and its psychometric properties were the aims of this study. Methods:
 Based on the Calgary-Cambridge Observation Guide (CCOG), items describing
 catering to the patient were selected and modified. Cognitive pretest
 interviews were conducted to check understandability. Therefore, 7 raters
 assessed 1 video (R=7, V=1). In the following pilot study (R=3, V=10)
 first psychometric properties were evaluated and necessary corrections in
 the preliminary evaluation form were carried out before the final
 evaluation form was used to assess students’ ability to cater to the
 patient and psychometric properties were described in detail (R=2, V=35).
 Results: The final assessment instrument, “Catering to the Patient”,
 contains 11 checklist items and two global ratings (items 12 and 13). In
 the final evaluation, the inter-rater reliability (IRR) ranged from 0 to
 0.562, the median was r=0.305. Concerning item 13 (a global rating), 88.6%
 of the videos were scored with the maximum difference of one point. The
 internal consistency was very high (Cronbach’s α: α=0.937 and α=0.962),
 and the correlation between the checklist items and the global rating was
 high (Pearson’s r: r=0.856 and r=0.898). Discussion: The assessment
 instrument “Catering to the Patient” is suitable for giving feedback and
 for using it in formative examinations. Its use for summative examinations
 can be considered. Further examinations should evaluate if a three-point
 Likert scale could reach higher values and if item 13 can be used as a
 stand-alone item.
description: <strong>For
 Pilotstudy_Data_1.1</strong>: Data was collected
 during the pilot study. Preexisting videos were evaluated.
 <strong>For EaP_Data_1.1</strong>:
 Part 1 (colums A-D): Data collected by the conductor of the
 study. Part 2 (colums E-S): Data collected by a
 questionnaire that the students answered after the Mini-CEX.
 Part 3 (colums T-BG): Data collected by the evaluation of the
 videos of the Mini-CEX.
description: See README file.
DOI: 10.5061/dryad.w9ghx3fm5
title: Data from: Intra-specific variation in tree growth responses to neighborhood composition and seasonal drought in a tropical forest

description: 1. Functional traits are expected to provide insights into the abiotic and
 biotic drivers of plant demography. However, successfully linking traits
 to plant demographic performance likely requires the consideration of
 important contextual and individual-level information that is often
 ignored in trait-based ecology. 2. Here, we modeled 8 years of growth from
 1,138 individual trees from 36 tropical rain forest species. We compared
 models of tree growth parameterized using individual-level versus species
 mean trait data. We also compared models that considered regional
 climatic, local biotic and whole-plant allocation contexts to those that
 do not. 3. Our analyses show that growth models parameterized using
 individual-level trait information outperformed those that used species
 mean trait information and that these models often contradicted one
 another indicating that the common practice of using species mean trait
 data requires more scrutiny. Additionally, we found that models including
 climatic, biotic and allocation contexts outperformed those that did not
 and provide nuanced insights into the drivers of tree growth in a tropical
 forest. 4. Synthesis. Here, we have shown that the development of models
 of tree demographic performance upon the basis of traits can be improved
 through a consideration of individual-level trait variation as well as
 phenotypic and climatic contexts. We highlight that our ability to
 understand the drivers of tree population and community structure and
 dynamics in current and in future climates will be limited if contextual
 and individual-level data remains understudied.
description: This study uses a subset of trees in the forest plot that have
 growth monitored on a fine temporal scale using dendrometer bands.For each
 focal tree, tree circumference increments were transformed into diameter
 first, we then calculated its annual absolute diameter growth (AGR) during
 the dry season and wet season per year from November 2009 to May 2018. All
 AGR values that exceed four standard deviations from the mean were
 discarded (c. 5%), we finally obtained a dataset containing 65,506 growth
 records for 1,138 individual trees belonging to 36 species. We measured
 four functional traits for each tree with a dendrometer band using the
 standard protocols described in Cornelissen et al. (2003).
DOI: 10.5061/dryad.4qrfj6q7g
title: Data from: Changes in soil microbial communities in post mine ecological restoration: implications for monitoring using high throughput DNA sequencing

description: The ecological restoration of ecosystem services and biodiversity is a key
 intervention used to reverse the impacts of anthropogenic activities such
 as mining. Assessment of the performance of restoration against completion
 criteria relies on biodiversity monitoring. However, monitoring usually
 overlooks soil microbial communities (SMC), despite increased awareness of
 their pivotal role in many ecological functions. Recent advances in cost,
 scalability and technology has led to DNA sequencing being considered as a
 cost-effective biological monitoring tool, particularly for otherwise
 difficult to survey groups such as microbes. However, such approaches for
 monitoring complex restoration sites such as post-mined landscapes have
 not yet been tested. Here we examine bacterial and fungal communities
 across chronosequences of mine site restoration at three locations in
 Western Australia to determine if there are consistent changes in SMC
 diversity, community composition and functional capacity. Although we
 detected directional changes in community composition indicative of
 microbial recovery, these were inconsistent between locations and
 microbial taxa (bacteria or fungi). Assessing functional diversity
 provided greater understanding of changes in site conditions and microbial
 recovery than could be determined through assessment of community
 composition alone. These results demonstrate that high-throughput amplicon
 sequencing of environmental DNA (eDNA) is an effective approach for
 monitoring the complex changes in SMC following restoration. Future
 monitoring of mine site restoration using eDNA should consider archiving
 samples to provide improved understanding of changes in communities over
 time. Expansion to include other biological groups (e.g. soil fauna) and
 substrates would also provide a more holistic understanding of
 biodiversity recovery.
DOI: 10.5061/dryad.6wwpzgmvs
title: Data from: RADseq resolves the Hawaiian Island radiation of Myrsine L. (Primulaceae) and provides evidence for hybridization

description: The Hawaiian radiation of Myrsine (primrose family, Primulaceae) is the
 only one of the ten most species Hawaiian plant lineages that has never
 been included in a phylogenetic analysis. Our study is based on a RADseq
 dataset of nearly all Hawaiian Myrsine species and a Sanger sequencing
 dataset based on a worldwide sampling of Myrsine and related genera.
 Myrsine as a whole might be paraphyletic with respect to the monotypic
 Macaronesian genera Heberdenia and Pleiomeris, while Hawaiian Myrsine is
 resolved as monophyletic. Hawaiian Myrsine consists of three main lineages
 of which one contains the majority of species and is mainly confined to
 Kauaʻi, while the other two lineages primarily consist of few widespread
 species. While phylogenetic reconstructions delivered fully resolved and
 supported tree topologies, Quartet Sampling and HyDe analyses reveal
 phylogenetic incongruence throughout the phylogeny and provide the first
 molecular evidence of extensive hybridization in the lineage.
description: The dataset consists of Sanger (ITS, ETS) sequences and RADseq
 data. For the Sanger datasets, alignments are provided. The RADseq data
 has been processed with ipyrad 0.7.28 and de-multiplexed raw reads have
 been deposited at SRA (https://www.ncbi.nlm.nih.gov/sra; BioProject number
 PRJNA614459). For the RADseq dataset, phylogenetic
 trees are provided, which have been calculated using ExaBayes 1.5
 and RAxML 8.2.4. We also tested for phylogenetic incongruence and signs of
 hybridization in our datasets using Quartet Sampling v.1.2.1 and
 HyDe v.0.4.3. Phylogenetic trees with Quartet Sampling results and tables
 with the HyDe results are included here.
DOI: 10.5061/dryad.cvdncjt1q
title: Data from: Longevity, body dimension and reproductive mode drive differences in aquatic versus terrestrial life history strategies

description: 1. Aquatic and terrestrial environments display stark differences in key
 environmental factors and phylogenetic composition but their consequences
 for the evolution of species’ life history strategies remain poorly
 understood. 2. Here, we examine whether and how life history strategies
 vary between terrestrial and aquatic species. We use demographic
 information for 685 terrestrial and 122 aquatic animal and plant species
 to estimate key life history traits. We then use phylogenetically
 corrected least squares regression to explore potential differences in
 trade-offs between life history traits between both environments. We
 contrast life history strategies of aquatic vs. terrestrial species in a
 principal component analysis while accounting for body dimensions and
 phylogenetic relationships. 3. Our results show that the same trade-offs
 structure terrestrial and aquatic life histories, resulting in two
 dominant axes of variation that describe species’ pace-of-life and
 reproductive strategies. Terrestrial plants display a large diversity of
 strategies, including the longest-lived species in this study. Aquatic
 animals exhibit higher reproductive frequency than terrestrial animals.
 When correcting for body size, mobile and sessile terrestrial organisms
 show slower paces of life than aquatic ones. 4. Aquatic and terrestrial
 species are ruled by the same life history trade-offs, but have evolved
 different strategies, likely due to distinct environmental selective
 pressures. Such contrasting life history strategies have important
 consequences for the conservation and management of aquatic and
 terrestrial species.
DOI: 10.5061/dryad.8cz8w9gmj
title: Data from: A highly pneumatic ‘mid Cretaceous’ theropod from the British Lower Greensand

description: A series of axial elements from the Aptian Ferruginous Sandstone Formation
 of the Lower Greensand Group, discovered on the foreshore near Knock Cliff
 on the Isle of Wight, United Kingdom (UK) are – bar some isolated teeth –
 the youngest non-avian theropod remains reported from the British
 Mesozoic. These specimens have the potential to shed light on a poorly
 known section of the European dinosaur record. A consistency in size,
 appearance and adhering matrix indicate that the vertebrae belong to the
 same individual. This was a mid-sized tetanuran, the presence of several
 diagnostic characters indicating that it should be recognised as a new
 taxon, herein namedVectaerovenator inopinatus. The cervical and
 dorsal vertebrae are camerate and highly pneumatic. Tetanuran affinities
 include opisthocoelous cervicals and pneumatic foramina located within
 fossae, however assigning this specimen to a specific clade is
 problematic. Within Tetanurae, Vectaerovenatorpossesses axial
 structures and homoplastic features seen in megalosauroids,
 carcharodontosaurians and certain coelurosaurs. Not only
 is Vectaerovenatorone of the UK’s youngest non-bird dinosaurs,
 and one of few valid British Greensand taxa, it is also the first
 diagnosable theropod taxon to be named from Aptian deposits of Europe.
description: This character matrix, based upon the work of Cau (2018),
 includes 133 operational taxonomic units (OTUs) scored for 1781
 characters.
DOI: 10.5061/dryad.573n5tb4q
title: Data from: Effects of fluorescent glutamate indicators on neurotransmitter diffusion and uptake

description: Genetically encoded fluorescent glutamate indicators (iGluSnFRs) enable
 neurotransmitter release and diffusion to be visualized in intact tissue.
 Synaptic iGluSnFR signal time courses vary widely depending on
 experimental conditions, often lasting 10-100 times longer than the
 extracellular lifetime of synaptically released glutamate estimated with
 uptake measurements. iGluSnFR signals typically also decay much more
 slowly than the unbinding kinetics of the indicator. To resolve these
 discrepancies, here we have modeled synaptic glutamate diffusion, uptake
 and iGluSnFR activation to identify factors influencing iGluSnFR signal
 waveforms. Simulations suggested that iGluSnFR competes with transporters
 to bind synaptically released glutamate, delaying glutamate uptake.
 Accordingly, synaptic transporter currents recorded from
 iGluSnFR-expressing astrocytes in mouse cortex were slower than those in
 control astrocytes. Simulations also suggested that iGluSnFR reduces free
 glutamate levels in extrasynaptic spaces, likely limiting extrasynaptic
 receptor activation. iGluSnFR and lower-affinity variants nonetheless
 provide linear indications of vesicle release, underscoring their value
 for optical quantal analysis.
description: Please see methods; raw unprocessed data. Modeling.
description: Each experiment has an associated textfile for additional
 information
DOI: 10.5061/dryad.gqnk98sjq
title: Data from: Dynamic reorganization of neuronal activity patterns in parietal cortex dataset

description: Neuronal representations change as associations are learned between
 sensory stimuli and behavioral actions. However, it is poorly understood
 whether representations for learned associations stabilize in cortical
 association areas or continue to change following learning. We tracked the
 activity of posterior parietal cortex neurons for a month as mice stably
 performed a virtual-navigation task. The relationship between cells’
 activity and task features was mostly stable on single days but underwent
 major reorganization over weeks. The neurons informative about task
 features (trial type and maze locations) changed across days. Despite
 changes in individual cells, the population activity had statistically
 similar properties each day and stable information for over a week. As
 mice learned additional associations, new activity patterns emerged in the
 neurons used for existing representations without greatly affecting the
 rate of change of these representations. We propose that dynamic neuronal
 activity patterns could balance plasticity for learning and stability for
 memory.
description: This dataset contains calcium imaging data from the posterior
 parietal cortex (PPC) in mice performing a fixed association navigation
 task. The raw data consists of images, while the processed data consists
 of fluorescence transients of individual ROIs and behavioral variables
 (mouse position, view angle, velocity etc.). The data is from five animals
 and includes 182 recording sessions. Results from the experiments are
 described in: Driscoll, L. N., Pettit, N. L., Minderer,
 M., Chettih, S. N., & Harvey, C. D. (2017). Dynamic reorganization
 of neuronal activity patterns in parietal
 cortex. <i>Cell</i>, <i>170</i>(5),
 986-999
DOI: 10.5061/dryad.s1rn8pk4z
title: Data from: Being a bright snake: testing aposematism and mimicry in a Neotropical forest

description: Based on color patterns and behavioral similarities, venomous coral snake
 Micrurus corallinus (Elapidae) may act as a model for two polymorphic
 species, Erythrolamprus aesculapii (Dipsadidae) and Micrurus decoratus
 (Elapidae). Plasticine replicas were used to investigate the aposematism
 of these coloration patterns and whether these species may be part of
 mimetic complexes in two Atlantic Forest localities in South-east Brazil.
 Coral replicas were more avoided when set upon a white background,
 evincing that the pattern may act aposematically in contrast with light
 substrates. Birds attacked all four patterns equally during the mimicry
 experiments. Birds of prey, known to be effective in predating snakes, are
 quite abundant in the study areas, which may have led to this lack of
 avoidance. Accordingly, they predated more adult-sized replicas, which
 could be more dangerous. Interestingly, opossum avoided the Micrurus
 corallinus and Erythrolamprus aesculapii replicas that resembled the
 model. This suggests that opportunistic predators, as the opossum may be
 important selective agents in mimicry complexes.
DOI: 10.5061/dryad.zgmsbcc7x
title: Data-driven identification of reliable sensor species to predict regime shifts in ecological networks

description: Signals of critical slowing down are useful for predicting impending
 transitions in ecosystems. However, in a system with complex interacting
 components not all components provide the same quality of information to
 detect system-wide transitions. Identifying the best indicator species in
 complex ecosystems is a challenging task when a model of the system is not
 available. In this paper, we propose a data-driven approach to rank the
 elements of a spatially-distributed ecosystem based on their reliability
 in providing early-warning signals of critical transitions. The proposed
 method is rooted in experimental modal analysis techniques traditionally
 used to identify structural dynamical systems. We show that one could use
 natural system fluctuations and the system responses to small
 perturbations to reveal the slowest direction of the system dynamics and
 identify indicator regions that are best suited for detecting abrupt
 transitions in a network of interacting components. The approach is
 applied to several ecosystems to demonstrate how it successfully ranks
 regions based on their reliability to provide early-warning signals of
 regime shifts. The significance of identifying the indicator species and
 the challenges associated with ranking nodes in networks of interacting
 components are also discussed.
DOI: 10.5061/dryad.7pvmcvdqg
title: A target enrichment probe set for resolving the flagellate land plant tree of life

description: Premise of the Study: New sequencing technologies enable the possibility
 of generating large-scale molecular datasets for constructing the plant
 tree of life. We describe a new probe set for target enrichment sequencing
 to generate nuclear sequence data to build phylogenetic trees with any
 flagellate land plants, including hornworts, liverworts, mosses,
 lycophytes, ferns, and all gymnosperms. Methods and Results: We leveraged
 existing transcriptome and genome sequence data to design a set of 56,989
 probes for target enrichment sequencing of 451 exons, found in 248 single
 or low-copy nuclear genes, across flagellate plant lineages. We describe
 the performance of target enrichment using the probe set across flagellate
 land plants and demonstrate the potential of the data to resolve
 relationships among both distantly and closely related taxa. Conclusions:
 A target enrichment approach using the new probe set provides a relatively
 low-cost solution to obtain large-scale nuclear sequence data for
 inferring phylogenetic relationships across flagellate land plants.
description: This dataset is the result of targeted enrichment sequencing
 using a probe set corresponding to 451 nuclear loci.
description: Details about the dataset and scripts are available in the
 Breinholt_EtAl_.txt.
DOI: 10.5061/dryad.05qfttf0m
title: Better together? how intergroup associations affect energy balance and feeding behavior in wild bonobos

description: When the benefits of interacting with out-group members exceed the
 associated costs, social groups may be expected to be tolerant towards
 each other. However, in many species exhibiting intergroup tolerance, the
 nature of benefits gained from intergroup encounters remains unclear. We
 investigated the potential costs and benefits associated with intergroup
 associations in bonobos, a species with varying degrees of intergroup
 tolerance, by testing whether these associations conferred energetic
 benefits to participants under different socioecological contexts, and
 whether the consequences of these associations substantially differed from
 within-group competition. We used measures of socioecological factors
 (i.e. fruit abundance and group size), feeding and ranging behaviors, and
 a physiological marker of energy balance (i.e. urinary c-peptides of
 insulin) collected over a 19-month period from two neighboring wild
 communities in the Kokolopori Bonobo Reserve, DRC. We found that
 intergroup associations did not affect individuals’ energy balance, but
 they did alter individuals’ ranging and feeding behavior. Specifically,
 bonobos travelled longer distances, visited larger fruit patches, and
 increased the time spent feeding on fruits on days they associated with
 the neighboring group. These adaptations in feeding behavior may be
 strategies to offset the energetic costs of increased travel distances. In
 the absence of obvious energetic benefits and with clear strategies
 employed to offset energetic costs, it is likely that intergroup
 associations in bonobos provide benefits unrelated to energy acquisition,
 such as social benefits. Our study sheds light on the potential incentives
 promoting social networks to extend beyond and across groups in a tolerant
 species.
description: All information about the dataset is reported in the accompaning
 txt file named "README_Better
 together_supporting.data"