cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6g635f6
title: Data from: STRUCTURE is more robust than other clustering methods in simulated mixed-ploidy populations

description: Analyses of population genetic structure has become a standard approach in
 population genetics. In polyploid complexes, clustering analyses can
 elucidate the origin of polyploid populations and patterns of admixture
 between different cytotypes. However, combining diploid and polyploid data
 can theoretically lead to biased inference with (artefactual) clustering
 by ploidy. We used simulated mixed-ploidy (diploid-autotetraploid) data to
 systematically compare the performance of k-means clustering and the
 model-based clustering methods implemented in STRUCTURE, ADMIXTURE,
 FASTSTRUCTURE and INSTRUCT under different scenarios of differentiation
 and with different marker types. Under scenarios of strong population
 differentiation, the tested applications performed equally well. However,
 when population differentiation was weak, STRUCTURE was the only method
 that allowed unbiased inference with markers with limited genotypic
 information (co-dominant markers with unknown do sage or dominant
 markers). Still, since STRUCTURE was comparably slow the much faster but
 less powerful FASTSTRUCTURE provides a reasonable alternative for large
 datasets. Finally, although bias makes k-means clustering unsuitable for
 markers with incomplete genotype information, given large numbers of loci
 (&gt;1000) with known dosage k-means clustering was superior to
 FASTSTRUCTURE in terms of power and speed. We conclude that STRUCTURE is
 the most robust method for the analysis of genetic structure in
 mixed-ploidy populations, although alternative methods should be
 considered under some specific conditions.
description: Stift_et_al_used_R_codeThis package contains the R-script used for simulating genetic data of two (or more) populations of a species with multiple ploidy levels. The script is extensively annotated using comments. The script will also perform several clustering analyses on the produced genetic data files. For this, the programs Structure, Admixture, and Instruct should be first downloaded from their respective websites, and placed in the R working directory. The package also contains the parameter files that are used for the Structure analysis; these should also be placed in the working directory.
DOI: 10.5061/dryad.s0b179p
title: Data from: Allelopathic effects of volatile organic compounds released from Pinus halepensis needles and roots

description: The Mediterranean region is recognized as a global biodiversity hotspot.
 However, over the last decades, the cessation of traditional farming in
 the north part of Mediterranean basin has given way to strong
 afforestation leading to occurrence of abandoned agricultural lands
 colonized by pioneer expansionist species like Pinus halepensis. This pine
 species is known to synthesize a wide range of secondary metabolites and
 previous studies have demonstrated strong allelopathic potentialities of
 its needle and root leachates. Pinus halepensis is also recognized to
 release significant amounts of volatile organic compounds (VOC) with
 potential allelopathic effects that has never been investigated. In this
 context, the objectives of the present study were to improve our knowledge
 about the VOC released from P. halepensis needles and roots, determine if
 these VOC affect the seed germination and root growth of two herbaceous
 target species (Lactuca sativa and Linum strictum), and evaluate if soil
 microorganisms modulate the potential allelopathic effects of these VOC.
 Thirty terpenes were detected from both needle and root emissions with
 β-caryophyllene as the major volatile. Numerous terpenes, such as
 β-caryophyllene, -terpinene or -pinene showed higher headspace
 concentrations according to the gradient green needles &lt; senescent
 needles &lt; needle litter. Seed germination and root growth of the
 two target species were mainly reduced in presence of P. halepensis VOC.
 In strong contrast with the trend reported with needle leachates in
 literature, we observed an increasing inhibitory effect of P. halepensis
 VOC with the progress of needle physiological stages (i.e. green needle
 &lt; senescent needle &lt; needle litter). Surprisingly, several
 inhibitory effects observed on filter paper were also found or even
 amplified when natural soil was used as a substrate, highlighting that
 soil microorganisms do not necessarily limit the negative effects of VOC
 released by P. halepensis on herbaceous target species.
description: Santonja et al. 2019 -
 Allelopathic effects of pine VOCEffects of the volatile
 organic compounds (VOC) released by Pinus halepensis needles and roots on
 seed germination and seedling growth of two herbaceous target species
 (Lactuca sativa and Linum strictum)Santonja et al. Ecol Evol 2019
 - Dataset.xlsx
DOI: 10.5061/dryad.3bq1qm4
title: Data from: Competitive reversal between plant species is driven by species-specific tolerance to flooding stress and nutrient acquisition during early marsh succession

description: 1. Understanding plant species interactions along successional
 trajectories are critical for managing and restoring ecosystems, as both
 resource availability and abiotic stresses change over time to affect
 competitive outcomes and species distributions. Newly created ecosystems
 experience a succession of plants species and rapid changes in resource
 availability, which may influence the outcome of biotic interactions. How
 these biotic interactions vary along abiotic gradients in early
 successional systems is not well understood. 2. Here, we tested the
 hypothesis that species-specific tolerances to flooding would influence
 their relative ability to capture resources (i.e., nutrients) and affect
 competition intensity between pioneer and secondary successional species
 in an early successional created tidal marsh. We transplanted a
 competitively dominant higher marsh species, Spartina patens, across an
 elevation gradient within and outside of clones of a pioneer
 stress-tolerant low marsh species, Spartina alterniflora. 3. Within six
 months, Spartina alterniflora had suppressed the stature and growth of S.
 patens; however, the magnitude of this competitive effect increased at
 lower marsh elevations where S. alterniflora was more efficient at
 capturing available nitrogen (N). In unvegetated areas, where S. patens
 vigor was high, the amount of available N was approximately 40 times
 greater than within S. alterniflora clones. 4. Synthesis and applications.
 Our results demonstrate that competition intensity of the stress-tolerant
 species over the competitive species depended on relative resource capture
 in response to abiotic stress. Managing for specific vegetation
 communities in marsh restoration, therefore, requires insight into these
 relationships and interactions. Specifically, marsh restoration in high
 nutrient environments will limit the succession to high density
 competitive species due to competition with stress-tolerant pioneer
 species, particularly at lower elevations.
description: Muench_Quirk_Data_2019This data was used for Muench & Elsey-Quirk 2019. the data was collected in the field and lab.
DOI: 10.5061/dryad.ts45225
title: Data from: PalmTraits 1.0, a species-level functional trait database for palms worldwide

description: Plant traits are critical to plant form and function —including growth,
 survival and reproduction— and therefore shape fundamental aspects of
 population and ecosystem dynamics as well as ecosystem services. Here, we
 present a global species-level compilation of key functional traits for
 palms (Arecaceae), a plant family with keystone importance in tropical and
 subtropical ecosystems. We derived measurements of essential functional
 traits for all (&gt;2500) palm species from key sources such as
 monographs, books, other scientific publications, as well as herbarium
 collections. This includes traits related to growth form, stems, armature,
 leaves and fruits. Although many species are still lacking trait
 information, the standardized and global coverage of the data set will be
 important for supporting future studies in tropical ecology, rainforest
 evolution, paleoecology, biogeography, macroecology, macroevolution,
 global change biology and conservation. Potential uses are comparative
 eco-evolutionary studies, ecological research on community dynamics,
 plant-animal interactions and ecosystem functioning, studies on
 plant-based ecosystem services, as well as conservation science concerned
 with the loss and restoration of functional diversity in a changing world.
description: ReferenceToSpecies_PalmTraits_1.0References per species, i.e. a tab-delimited text file containing all references that have been used for each speciestdwg_level3_shpA (zipped) shape file with all botanical countries (TDWG level 3 units) worldwide, data to be used with R scriptpalms_in_tdwg3Presence-absence data of palms at the resolution of botanical countries, data to be used with R scriptTREEPhylogenetic information of palms represented as maximum clade credibility (MCC) tree, data to be used with R scriptAllReferences_PalmTraits_1.0Full list of references used to compile the dataPalmTraitsDemoAn R script containing code that allows to combine the PalmTraits 1.0 database with species distribution and phylogenetic informationPalmTraits_1.0Dataset with palm traits, i.e. a tab-delimited text file containing taxonomic information (species, genus, tribe, subfamily) together with all trait data
DOI: 10.5061/dryad.3q80581
title: Data from: Snakehead (Teleostei: Channidae) diversity and the Eastern Himalaya biodiversity hotspot

description: The collision of Indian and Eurasian landmasses in the Cenozoic was a
 decisive factor in shaping biodiversity patterns in Southern and
 Southeastern Asia. While most studies thus far have focused on the biotic
 interchange between India and Eurasia and evolutionary diversification on
 or around the Tibetan Plateau little attention has been paid to the
 biodiversity build-up in the Eastern Himalaya biodiversity hotspot (EHH)
 which harbours over 540 freshwater fish species with a high degree of
 endemicity. An important component of the regional ichthyofauna are
 snakeheads fishes of the family Channidae comprising throughout their
 African-Asian distribution 47 valid species, but a poorly known
 species-level diversity. In order to evaluate channid intrarelationships
 and biogeography a temporal and geographical framework of channid
 evolution in conjunction with a critical reevaluation of the channid
 fossil record is warranted. Based on molecular data, we provide a
 comprehensive species-level phylogeny based on 223 channid individuals
 belonging to 37 species and one additional currently undescribed species.
 The first split within channids separates the African genus Parachanna
 from the Asian genus Channa which can be divided into eight distinct
 species groups (C. micropeltes, C. lucius , C. asiatica, C. argus, C.
 marulius, C. striata, C. punctata and C. gachua species groups). Large
 intraspecific divergences were observed within several species and
 potentially indicate additional species-level diversity. Almost 40% of the
 channid species are narrow-range endemics belonging to the C. gachua
 species group. These are found in the EHH making this area an outstanding
 hotspot for endemic channid diversity. The large majority of the EHH
 endemics are restricted to the southern foothills of the Eastern Himalaya
 and the Shillong-Mikir Hills Plateau, areas west of the Indo-Burman
 Ranges. Our results reveal complex and difficult to interpret
 biogeographic patterns indicating that both vicariance and dispersal
 events have potentially been responsible in shaping current distribution
 patterns in Asian channids. We recognize †Parachanna fayumensis as the
 oldest reliable channid fossil, and argue that the three oldest so-called
 channid fossils (i.e., †Eochanna chlorakkiensis, †Anchichanna kuldanensis,
 and †Ophiocephalus lydekkeri) lack clear diagnostic features that would
 allow them to be unequivocally placed within Channidae.
description: Rüber_et_al_Channidae_rRNA_befor_GblocksrRNA alignment of 246 taxa before GblocksRüber_et_al_ChannidaeFinal alignment of rRNA, cytb and rag1 of 246 taxa used for analysis
DOI: 10.5061/dryad.28pj314
title: Data from: Effects of kinematic complexity and number of muscles on musculoskeletal model robustness to muscle dysfunction

description: The robustness of motor outputs to muscle dysfunction has been
 investigated using musculoskeletal modeling, but with conflicting results
 owing to differences in model complexity and motor tasks. Our objective
 was to systematically study how the number of kinematic degrees of
 freedom, and the number of independent muscle actuators alter the
 robustness of motor output to muscle dysfunction. We took a detailed
 musculoskeletal model of the human leg and systematically varied the model
 complexity to create six models with either 3 or 7 kinematic degrees of
 freedom and either 14, 26, or 43 muscle actuators. We tested the
 redundancy of each model by quantifying the reduction in sagittal plane
 feasible force set area when a single muscle was removed. The robustness
 of feasible force set area to the loss of any single muscle, i.e. general
 single muscle loss increased with the number of independent muscles and
 decreased with the number of kinematic degrees of freedom, with the robust
 area varying from 1% and 52% of the intact feasible force set area. The
 maximum sensitivity of the feasible force set to the loss of any single
 muscle varied from 75% to 26% of the intact feasible force set area as the
 number of muscles increased. Additionally, the ranges of feasible muscle
 activation for maximum force production were largely unconstrained in many
 cases, indicating ample musculoskeletal redundancy even for maximal
 forces. We propose that ratio of muscles to kinematic degrees of freedom
 can be used as a rule of thumb for estimating musculoskeletal redundancy
 in both simulated and real biomechanical systems.
description: Models and Results from
 PLOS ONE Sohn Smith TingThis repository contains
 the MATLAB code and data files necessary to recreate all results and
 figures in Sohn, Smith, Ting, "Effects of kinematic complexity and
 number of muscles on musculoskeletal model robustness to muscle
 dysfunction."PLOS ONE Sohn Smith
 Ting_updated20190608.zip
DOI: 10.5061/dryad.22pk5m9
title: Data from: Evaluating adaptive, carry-over and plastic antipredator responses across a temporal gradient in Pacific chorus frogs

description: The development of antipredator traits is dependent on the frequency and
 intensity of predator exposure over evolutionary and ecological time. We
 hypothesized that prey species would respond with increasing accuracy when
 exposed to predators across generational, ontogenetic and immediate
 timescales. We assessed larval Pacific chorus frog (PSRE; Pseudacris
 regilla) individuals that varied in population sympatry, embryonic
 conditioning, and immediate exposure to stocked populations of Rainbow
 Trout (Oncorhynchus mykiss). Using PSRE populations from sites with and
 without resident Rainbow Trout, we conditioned embryos to trout odor, PSRE
 alarm cues, trout odor in combination with alarm cues, or control water.
 After being hatched and reared in control water, individuals were exposed
 to the four predator cue treatments using a fully factorial design.
 Tadpoles from populations with resident Rainbow Trout did not behave or
 develop differently than tadpoles originating from fishless sites.
 However, we found evidence that PSRE reduced predation risk with a
 combination of carry-over effect (i.e., transfer of information across
 life history stages) and within-life stage phenotypically plastic
 mechanisms. We found both developmental and behavioral carry-over effects:
 tadpoles conditioned with trout odor as embryos grew more slowly and took
 refuge more often than control animals. Within-life stage behavioral
 plasticity was observed in tadpoles from all treatment groups, responding
 to predator cues with increased refuge use. Potentially additive effects
 of predator exposure on prey response should be considered when predicting
 the ability of prey to recognize novel threats.
description: frog_scrubbed_dater_PSREdata for embryonic conditioning across populations with response variables for growth, development, and refuge use after larval exposure.
DOI: 10.5061/dryad.j5m8h10
title: Data from: Liquid chromatography-tandem mass spectrometry metabolic profiling of nazartinib reveals the formation of unexpected reactive metabolites

description: Nazartinib (EGF816, NZB) is a promising third-generation human epidermal
 growth factor receptor (EGFR) tyrosine kinase inhibitor. This novel
 irreversible mutant-selective EGFR inhibitor targets EGFR containing both
 the resistance mutation (T790M) and the activating mutations (L858R and
 Del19), while it does not affect wild-type EGFR. However, the metabolic
 pathway and bioactivation mechanisms of NZB are still unexplored. Thus,
 using liquid chromatography-tandem mass spectrometry, we screened for
 products of NZB metabolism formed in vitro by human liver microsomal
 preparations and investigated the formation of reactive intermediates
 using potassium cyanide as a nucleophile trap. Unexpectedly, the azepane
 ring was not bioactivated. Instead, the carbon atom between the aliphatic
 linear tertiary amine and electron-withdrawing system (butenoyl amide
 group) was bioactivated, generating iminium intermediates as reactive
 species. Six NZB phase I metabolites, formed by hydroxylation, oxidation,
 and N-demethylation, were characterized. Moreover, two reactive iminium
 ions were characterized and their corresponding bioactivation mechanisms
 were proposed. Based on our results, we speculate that bioactivation of
 NZB can be blocked by small sterically hindering groups, isosteric
 replacement, or a spacer. This approach might reduce the toxicity of NZB
 by avoiding the generation of reactive species.
description: NZB HLMs
 481NZB HLMs
 495NZB HLMs
 509aNZB HLMs
 509bNZB HLMs
 509cNZB HLMs
 511aNZB HLMs
 511bNZB HLMs KCN
 506NZB HLMs KCN
 520
DOI: 10.5061/dryad.2n3162c
title: Data from: Respiratory syncytial virus co-opts host mitochondrial function to favour infectious virus production

description: Although respiratory syncytial virus (RSV) is responsible for more human
 deaths each year than influenza, its pathogenic mechanisms are poorly
 understood. Here high-resolution quantitative imaging, bioenergetics
 measurements and mitochondrial membrane potential- and redox-sensitive
 dyes are used to define RSV's impact on host mitochondria for the
 first time, delineating RSV-induced microtubule/dynein-dependent
 mitochondrial perinuclear clustering, and translocation towards the
 microtubule-organizing centre. These changes are concomitant with impaired
 mitochondrial respiration, loss of mitochondrial membrane potential and
 increased production of mitochondrial reactive oxygen species (ROS).
 Strikingly, agents that target microtubule integrity the dynein motor
 protein, or inhibit mitochondrial ROS production strongly suppresses RSV
 virus production, including in a mouse model with concomitantly reduced
 virus-induced lung inflammation. The results establish RSV's unique
 ability to co-opt host cell mitochondria to facilitate viral infection,
 revealing the RSV-mitochondrial interface for the first time as a viable
 target for therapeutic intervention.
description: 28-09-2018-RA-eLife-42448_Source dataSource data including numerical data and image files28-09-2018-RA-eLife-42448 Source Data.rar
DOI: 10.5061/dryad.h0t0dk5
title: Data from: Beyond isolation by distance: what best explains functional connectivity among populations of three sympatric plant species in an ancient terrestrial island system?

description: Aim: Understanding how landscape features affect gene flow is critical to
 connectivity conservation and restoration management. Here, we examined
 the relationship between functional connectivity (gene flow) and
 structural connectivity (area and spatial configuration of habitats) in
 three co-occurring short-range plant taxa in an ancient terrestrial island
 system. Location: Low altitude mountain ranges south-western Australia
 Methods: We analysed spatial patterns of genetic differentiation at
 nuclear microsatellite loci using Bayesian clustering. Circuit theory
 modelling was used to generate all possible pathways that connect
 populations as resistance distance matrices based on two surfaces for each
 taxon. The first surface assumes a flat terrain and tests whether genetic
 similarity declines only with distance – isolation by distance (IBD). The
 second surface is habitat suitability based on species distribution
 modelling (SDM), which tests whether genetic similarity is a function of
 connected and suitable habitat. Multiple matrix regression with
 randomisation was used to test the significance of the resistance distance
 matrices at predicting two metrics of genetic differentiation (FST and
 DEST). Variance explained was partitioned using redundancy analysis.
 Results: Genetic structure for the insect-pollinated taxa - Acacia
 adinophylla, and Tetratheca aphylla subsp. aphylla was at similar spatial
 scales. Unexpectedly, a higher level of genetic structure was found in the
 wind-pollinated Lepidosperma bungalbin. IBD best explained the gene flow
 of A. adinophylla (R2 = 0.41-0.43) with partial support provided by
 habitat suitability (R2 = 0.04-0.07). In contrast, connectivity by habitat
 suitability was highest for T. aphylla subsp. aphylla (R2 = 0.56-0.59).
 Drivers of L. bungalbin connectivity were inconsistent between the two
 measures of genetic differentiation. Main conclusions: Gene flow is
 facilitated by different factors for the three taxa. Habitat fragmentation
 would most strongly impede gene flow for T. aphylla subsp. aphylla.
 Geographic distance cannot be assumed as the sole or best determinant of
 gene flow among populations, nor can findings be generalised to coexisting
 taxa.
description: Microsatellite data
 GenAIEx format Acacia adinophyllaMicrosatellite data
 GenAIEx format Acacia adinophyllaAcacia
 adinophylla.xlsxMicrosatellite data
 GenAIEx format Lepidosperma bungalbinMicrosatellite data
 GenAIEx format Lepidosperma bungalbinLepidosperma
 bungalbin.xlsxMicrosatellite data
 GenAIEx format Tetratheca aphylla subsp aphyllaMicrosatellite data
 GenAIEx format Tetratheca aphylla subsp aphyllaTetratheca aphylla subsp
 aphylla.xlsx