cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b28p1
title: Data from: Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation

description: One of the most celebrated examples of sympatric speciation in nature are
 monophyletic radiations of cichlid fishes endemic to Cameroon crater
 lakes. However, phylogenetic inference of monophyly may not detect complex
 colonization histories involving some allopatric isolation, such as double
 invasions obscured by genome-wide gene flow. Population genomic approaches
 are better suited to test hypotheses of sympatric speciation in these
 cases. Here we use comprehensive sampling from all four sympatric crater
 lake cichlid radiations in Cameroon and outgroups across Africa combined
 with next-generation sequencing to genotype tens of thousands of SNPs. We
 find considerable evidence of gene flow between all four radiations and
 neighboring riverine populations after initial colonization. In a few
 cases, some sympatric species are more closely related to outgroups than
 others, consistent with secondary gene flow facilitating their speciation.
 Our results do not rule out sympatric speciation in Cameroon cichlids, but
 rather reveal a complex history of speciation with gene flow, including
 allopatric and sympatric phases, resulting in both reproductively isolated
 species and incipient species complexes. The best remaining non-cichlid
 examples of sympatric speciation all involve assortative mating within
 microhabitats. We speculate that this feature may be necessary to complete
 the process of sympatric speciation in nature.
description: Coptodon plink nexus
 STRUCTURE filesCoptodon population
 genetic data. PLINK formatted files, nexus phylogenetic alignments, and
 STRUCTURE formatted file.Sarotherodon plink nexus
 STRUCTURE filesSarotherodon population
 genetic data. PLINK formatted files, nexus phylogenetic alignments, and
 STRUCTURE formatted file.
DOI: 10.5061/dryad.521h5
title: Data from: Study of genetic variability in Vitis vinifera L. germplasm by high-throughput Vitis18kSNP array: the case of Georgian genetic resources

description: Background: Georgia, in the Caucasian region, is considered the first
 domestication centre of grapevine. This country is characterized by high
 morphological variability of cultivated (Vitis vinifera L. subsp. sativa
 (DC.) Hegi) and wild (Vitis vinifera L. subsp. sylvestris (Gmel.) Hegi)
 compartments. The main objective of this study was to investigate the
 level of genetic diversity obtained by the novel custom Vitis18kSNP array,
 in order to analyse 71 grapevine accessions representative of wild and
 cultivated Georgian germplasms. Results: The number of loci successfully
 amplified was 15,317 out of 18,775 SNP and 79 % of loci resulted
 polymorphic. Sixty-eight unique profiles were identified, 42 for the
 sativa and 26 for the sylvestris compartment. Cluster analysis highlighted
 two main groups, one for cultivars and another for wild individuals, while
 a genetic structure according to accession taxonomic status and cultivar
 geographical origin was revealed by multivariate analysis, differentiating
 clearly the genotypes into 3 main groups, two groups including cultivars
 and one for wild individuals, even though a considerable overlapping area
 was observed. Conclusions: Pattern of genetic diversity structure
 presented an additional proof that grapevine domestication events took
 place in the Caucasian region contributing to the crop evolution. Our
 results demonstrated a moderate differentiation between sativa and
 sylvestris compartments, even though a connection between several samples
 of both subspecies may be assumed for the occurrence of cross
 hybridization events among native wild populations and the cultivated
 accessions. Nevertheless, first degree relationships have not been
 discovered between wild and cultivated individuals.
description: Additional file Table
 S1SNP
 allelic profile of 43 grapevine cultivars and 28 putative wild individuals
 from Georgia at 15,317 SNP loci. Nucleotides were scored with Genotyping
 Module 1.9.4 of the GenomeStudio Data Analysis V2011.1 software (Illumina
 Inc.). Dataset was filtered based on SNP call quality and GenTrain score:
 samples with low SNP call quality (p50GC&lt;0.54) were removed from the
 analysis and only SNPs with a GenTrain score higher than 0.6 were
 retained. Markers with a number of NCs (non-call) higher than 20%, as well
 as the 100% NC markers, were removed.
DOI: 10.5061/dryad.8633
title: Data from: Stronger convex (stabilizing) selection on homologous sexual display traits in females than in males: a multipopulation comparison in Drosophila serrata

description: Mutual mate choice for homologous sexual display traits has been
 demonstrated in Mutual mate choice for homologous sexual display traits
 has been demonstrated in several recent studies yet little attention has
 been given to quantitative comparison of the strength and form of mate
 preferences between the sexes. Such comparisons may provide important
 insight into the evolution of mate choice for honest signals. In
 particular, because females generally provide the majority of resources
 for initial offspring development, female displays may trade-off with
 fecundity, causing preference evolution to differ between the sexes.
 Recent theory suggests that adaptive male preferences for honest displays
 in females are possible under certain conditions and may result in
 preferences that are convex (i.e. stabilizing) in form. We compared sexual
 selection on a suite of contact pheromones arising from mutual mate choice
 using nine separate geographic populations of Drosophila serrata. We show
 that the convex selection is stronger on females than on males overall in
 these populations, and that convex selection is the predominate form of
 nonlinear selection on females but not males.
description: rundle_dataSee readme.txt
DOI: 10.5518/1505
title: Inhibitors of the Small Membrane (M) Protein Viroporin Prevent Zika Virus Infection - dataset

description: Flaviviruses, including Zika virus (ZIKV), are a significant global health concern, yet no licensed antivirals exist to treat disease. The small Membrane (M) protein plays well-defined roles during viral egress and remains within virion membranes following release and maturation. However, it is unclear whether M plays a functional role in this setting. Here, we show that M forms oligomeric membrane-permeabilising channels in vitro, with increased activity at acidic pH and sensitivity to the prototypic channel-blocker, rimantadine. Accordingly, rimantadine blocked an early stage of ZIKV cell culture infection. Structure-based channel models, comprising hexameric arrangements of two trans-membrane domain protomers were shown to comprise more stable assemblages than other oligomers using molecular dynamics (MD) simulations. Models contained a predicted lumenal rimantadine binding site, as well as a second druggable target region on the membrane-exposed periphery. In silico screening enriched for repurposed drugs/compounds predicted to bind to either one site or the other. Hits displayed superior potency in vitro and in cell culture compared with rimantadine, with efficacy demonstrably linked to virion-resident channels. Finally, rimantadine effectively blocked ZIKV viraemia in preclinical models, supporting that M constitutes a physiologically relevant target. This could be explored by repurposing rimantadine, or development of new M-targeted-therapies.
DOI: 10.5061/dryad.864
title: Data from: Insect rate-temperature relationships: environmental variation and the metabolic theory of ecology

description: Much of the recent discussion concerning the form and underlying
 mechanistic basis of metabolic rate–temperature and development
 rate–temperature relationships has been precipitated by the development of
 the metabolic theory of ecology (MTE). Empirical tests of the theory’s
 fundamental equation are an essential component of establishing its
 validity. Here, we test the temperature component of the fundamental
 equation of the MTE as it applies to metabolic rate and development rate,
 using insects as model organisms. Specifically, we test (i) whether mean
 activation energies, E, approximate the 0.65 eV value proposed by the
 proponents of the MTE and whether the range of values is tightly
 constrained between 0.6 and 0.7 eV, as they have argued; (ii) whether
 phylogenetic signal is apparent in the rate‐temperature relationships;
 (iii) whether the slopes of the rate‐temperature relationships show
 consistent, directional variation associated with environmental variables;
 and (iv) whether intra‐ and interspecific rate‐temperature relationships
 differ significantly. Because the majority of activation energy values
 fell outside the predicted range and rate‐temperature relationships showed
 consistent directional variation correlated with large‐scale climatic
 variation, we conclude that data from insects provide only limited support
 for the MTE. In consequence, we consider alternative explanations for
 variation in rate‐temperature relationships.
description: Metabolic
 rate-temperature and development-rate temperature data for
 insectsAppendices
 final.doc
DOI: 10.5061/dryad.bh32c
title: Data from: Prescribed burning protects endangered tropical heathlands of the Arnhem Plateau, northern Australia

description: 1. There are concerns that frequent intense fires are reducing
 biodiversity on the Arnhem Plateau within Kakadu National Park, northern
 Australia. Since the 1980s, prescribed burning in the early dry season has
 aimed to reduce the extent of late dry season wildfires. A programme of
 more strategic prescribed burning has been undertaken since 2007, aiming
 to increase intervals between fires affecting heathland and rain forest
 communities. 2. We assess the effectiveness of prescribed burning in
 Kakadu's Stone Country using a Landsat satellite-derived fire history
 (1980–2011), in terms of achieving ‘tolerable fire intervals’ for dominant
 plant communities. 3. Our analysis indicates that fire regimes have become
 substantially more favourable for biodiversity since the early 1980s.
 Although annual extent of burning has remained unchanged, two significant
 changes in fire regimes have occurred over the long term: (i) a switch
 from late dry season dominance to early dry season dominance and (ii) an
 increase in the abundance of long-unburnt vegetation, both of which are
 likely to benefit biodiversity. Demonstrating the statistical significance
 of changes associated with recent, more strategic fire management
 (2007–2011) is limited by the short duration of this management approach,
 although there is evidence of increasing abundance of long-unburnt
 vegetation during this time. 4. The view that the Arnhem Plateau's
 fire regimes are increasingly driving biodiversity loss (due to frequent
 late dry season wildfires) is erroneous; they are in a more benign state
 now than at any time over the last three decades, most likely due to
 extensive use of prescribed burning. 5. Synthesis and applications. In
 highly fire-prone landscapes, such as savannas, prescribed burning can be
 an effective means of: (i) bringing forward peak fire activity to the time
 of year when fire conditions are relatively mild and (ii) increasing
 abundance of long-unburnt vegetation. These changes are likely to favour
 persistence of a range of fire-sensitive communities. Our case study
 supports the strategic use of prescribed burning to protect fire-sensitive
 biota within highly fire-prone landscapes throughout the world.
description: Fire history and
 vegetation type at 173,294 sample points in the stone country of Kakadu
 National ParkProvided is: (1) fire
 history (1980-2011, derived from Landsat satellite imagery), including
 whether each sample point was burnt in each year and season of burn (early
 or late dry season); and (2) vegetation type (heathland, rainforest, or
 savanna woodland).Murphy et
 al..txt
DOI: 10.4211/hs.3fedcfd19c4647afa88a80ba572d2598
title: Dissolved carbon and water quality data from a coastal Louisiana salt marsh

description: Discrete water-quality sensor data and dissolved carbon samples were collected at the USGS gage 292939089544400 (Wilkinson Bayou cutoff, north of Wilkinson Bay, LA). Field water-quality measurements were obtained using a YSI EXO2 water-quality sonde equipped with a data logger to measure water temperature, salinity, pH, fluorescent dissolved organic matter (fDOM), and dissolved oxygen (DO). Discrete samples of dissolved inorganic carbon (DIC), dissolved organic carbon (DOC), and total alkalinity (TA) were collected at the tidal creek. For both DIC and TA, water samples were passed through a 0.45 µm glass-fiber syringe filter and collected without headspace into airtight 40 mL glass vials by filling from the bottom and allowing overflow of at least one vial volume to minimize atmospheric contamination. Samples were preserved with 20 µL of saturated mercuric chloride (HgCl₂) solution. For DOC analysis, creek water was filtered through 0.45 µm filters and stored in amber bottles without the addition of chemical preservatives (He and Xu, 2017). All water samples were transported to the laboratory on ice and stored at 5 °C until analysis. DIC was analyzed following the standard protocol for the semi-automated Apollo SciTech AS-C5 Dissolved Inorganic Carbon Analyzer (Newark, DE, USA). Total alkalinity was determined using the Gran titration method (Gran, 1952) with a semi-automated Apollo SciTech AS-ALK2 Total Alkalinity Titrator (Newark, DE, USA). Dissolved organic carbon was analyzed using a Shimadzu TOC-5000A analyzer with an ASI-5000A autosampler by converting all carbon to CO₂ via high-temperature combustion.
DOI: 10.5061/dryad.dc3m7
title: Data from: RNA-directed epigenetic silencing of Periostin inhibits cell motility

description: The over-expression of Periostin, a member of the fasciclin family of
 proteins, has been reported in a number of cancers and, in particular, in
 metastatic tumours. These include breast, ovarian, lung, colon, head and
 neck, pancreatic, prostate, neuroblastoma and thyroid cancers. It is
 thought that Periostin plays a major role in the development of metastases
 owing to its apparent involvement in restructuring of the extracellular
 matrix to create a microenvironment favouring invasion and metastases,
 angiogenesis, independent proliferation, avoidance of apoptosis and the
 ability for cells to re-enter the cell cycle. As such we reasoned that
 targeted suppression of Periostin at the promoter and epigenetic level
 could result in the stable inhibition of cell motility. We find here that
 promoter-directed small antisense non-coding RNAs can induce
 transcriptional gene silencing of Periostin that results ultimately in a
 loss of cellular motility. The observations presented here suggest that
 cell motility and possibly metastasis can be controlled by transcriptional
 and epigenetic regulation of Periostin, offering a potentially new and
 novel manner to control the spread of cancerous cells.
description: Periostin_Data_FinalPeriostin data final
DOI: 10.5281/zenodo.18225927
title: ldsc-pop
DOI: 10.5061/dryad.5gg87
title: Data from: Edge effects on plant communities along power line clearings

description: 1. Power line clearings are edge-creating disturbances in landscapes
 world-wide, but there have been few studies on their bordering vegetation.
 Our aim was to quantify edge effects on plant communities along such
 clearings in Norway and to identify factors that influence these edge
 effects. 2. We surveyed understorey plant communities on either side of
 the power line clearing–forest edge at 51 sites, along four parallel
 transects at each site. Each transect had four plots located,
 respectively, in the clearing centre, clearing edge, forest edge and
 forest. We quantified the magnitude of edge effects (MEE) on either side
 by comparing edges with their corresponding ‘non-edge’ reference habitats.
 We also measured differences in species composition across the edge
 (clearing edge vs. forest edge). Habitat characteristics were sampled at
 plot and site level and from digital maps. 3. Differences in species
 composition were greater between clearing centres and clearing edges than
 between forests and forest edges. Differences in species composition
 across the edge increased with edge contrast and forest productivity. Edge
 effects on species composition into the forest were smallest along
 north-facing edges, whereas those in the clearings increased with power
 line age. 4. Species richness increased slightly towards the edge in
 forests but decreased considerably towards the edge in clearings. The
 direction and MEE on either side differed among functional groups. Edge
 contrast and edge aspect were the prime factors influencing the MEE into
 forests, whereas in clearings, these were influenced principally by tree
 regrowth in the clearings and by forest productivity. 5. Synthesis and
 applications. Edge effects on plant communities bordering power line
 clearings were determined by factors that can be influenced by planners
 and managers. For existing power lines, management plans should
 differentiate between the following: (i) clearings through high
 conservation value forests, where edge effects into the adjacent forest
 should be limited; (ii) clearings that can act as replacement habitat for
 cultural landscape species, where maintaining open-canopy habitats should
 be prioritized; and (iii) ‘business-as-usual’ clearings, where continuing
 the current practice of cutting every 5–10 years is recommended.
description: Eldegard et al community
 dataEldegard et al community
 matrix vascular plant data to GNMDS raw&weighedEldegard et al env
 dataEldegard et al
 environmental data raw site plotEldegard et al responses
 differencesEldegard et al response
 variables differences across&on either side of the edge
 (forest&clearing)Eldegard et al responses
 habitatsEldegard et al
 richness&cover in habitats C_Ce_Fe_F_Fi
DOI: 10.5281/zenodo.18225926
title: ldsc-pop
DOI: 10.5061/dryad.8646
title: Data from: Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional, and separate models for combined molecular phylogenetic analyses of multilocus sequence data

description: Proportional and separate models able to apply different combination of
 substitution rate matrix and among-site rate variation model to each locus
 are frequently used in phylogenetic studies of multilocus data. However,
 the selection from among nonpartitioned (i.e., a common combination of
 models is applied to all-loci concatenated sequences), proportional, and
 separate models is usually based on the researcher's preference
 rather than on any information criteria. The present study describes two
 programs, "Kakusan4" (for DNA sequences) and
 "Aminosan" (for amino-acid sequences), that allow the selection
 of evolutionary models based on several types of information criteria. The
 programs can handle both multilocus and single-locus data, in addition to
 providing an easy-to-use wizard interface and a non-interactive command
 line interface. In the case of multilocus data, substitution rate matrices
 and among-site rate variation models are compared at each locus and at
 all-loci concatenated sequences, after which nonpartitioned, proportional,
 and separate models are compared based on information criteria. The
 programs also provide model configuration files for MrBayes, PAUP*, PHYML,
 RAxML, and Treefinder to support further phylogenetic analysis using a
 selected model. The best-fit models were found to differ depending on the
 data set. Furthermore, differences in the information criteria among
 nonpartitioned, proportional, and separate models were much larger than
 those among the nonpartitioned models. These findings suggest that
 selecting from nonpartitioned, proportional, and separate models results
 in a better phylogenetic tree. Kakusan4 and Aminosan are available at
 http://www.fifthdimension.jp/. They are licensed under GNU GPL Ver.2, and
 are able to run on Windows, MacOS X, and Linux.
description: Sample_Kakusan4DNA sequence files from previously published papers and selection results of models for molecular evolution by Kakusan4. The specified options are able to find in the paper.Sample_AminosanAmino-acid sequence files from previously published papers and selection results of models for molecular evolution by Aminosan. The specified options are able to find in the paper.
DOI: 10.5061/dryad.nv5j5
title: Data from: Consequences of extensive habitat fragmentation in landscape-level patterns of genetic diversity and structure in the Mediterranean esparto grasshopper

description: Anthropogenic habitat fragmentation has altered the distribution and
 population sizes in many organisms worldwide. For this reason,
 understanding the demographic and genetic consequences of this process is
 necessary to predict the fate of populations and establish management
 practices aimed to ensure their viability. In this study, we analyse
 whether the spatial configuration of remnant semi-natural habitat patches
 within a chronically fragmented landscape has shaped the patterns of
 genetic diversity and structure in the habitat-specialist esparto
 grasshopper (Ramburiella hispanica). In particular, we predict that
 agricultural lands constitute barriers to gene flow and hypothesize that
 fragmentation has restricted interpopulation dispersal and reduced local
 levels of genetic diversity. Our results confirmed the expectation that
 isolation and habitat fragmentation have reduced the genetic diversity of
 local populations. Landscape genetic analyses based on circuit theory
 showed that agricultural land offers ~1000 times more resistance to gene
 flow than semi-natural habitats, indicating that patterns of dispersal are
 constrained by the spatial configuration of remnant patches of suitable
 habitat. Overall, this study shows that semi-natural habitat patches act
 as corridors for interpopulation gene flow and should be preserved due to
 the disproportionately large ecological function that they provide
 considering their insignificant area within these human-modified
 landscapes.
description: Microsatellite
 DataThis file contains the
 genotypes for 12 microsatellite loci and 352 individuals collected in 18
 populations of esparto grasshopper (Ramburiella
 hispanica)MicrosatelliteData.xlsNatural Vegetation GIS LayerGIS layer including natural vegetation habitat patches (non-cultivated areas) in the study areaNaturalVegetationGISLayer.zip
DOI: 10.5281/zenodo.18095956
title: VSL_BRAND1_60F_1_23C_0k_ELDC_single

description: Part of the Variable Temperature DataBase: Temp: 23°C
DOI: 10.5281/zenodo.18376889
title: VSL_BRAND1_60F_1_23C_0k_ELDC_single

description: Part of the Variable Temperature DataBase: Temp: 23°C