cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.81nm9
title: Data from: Evolution of woody life form on tropical mountains in the tribe Spermacoceae (Rubiaceae)

description: Spermacoceae are mainly an herbaceous group in the Rubiaceae. However, a
 few lineages are woody, and are found in a diverse range of habitat types.
 Three of the largest woody lineages (Arcytophyllum, Hedyotis, and Kadua)
 are characterized by their distribution in the moist tropical mountains,
 and have disjunct distribution patterns with respect to their closest
 relatives. In this study, we explore the cases of derived woodiness in
 these three lineages and their diversification dynamics in the tropical
 mountains of Asia, the Pacific, and the Americas. By combining
 phylogenetic results with wood anatomical studies, we estimated timing of
 origin of the three woody groups, inferred their ancestral traits and
 ancestral distribution ranges, analyzed their associations with the
 tropical upland habitat, and elucidated their diversification across
 tropical mountains. The three woody clades originated and diversified from
 herbaceous ancestors in close association with the tropical upland habitat
 during the Miocene. The ancestral range for Asian-Pacific Hedyotis and
 Pacific Kadua is Africa/Madagascar and continental Asia respectively. The
 complex geological history of tropical Asia allowed Hedyotis to diversify
 faster and create narrow endemics near oceans in the highlands of Western
 Ghats (India), Sri Lanka, Southeast Asia including southeastern China, and
 New Guinea. The three major woody clades in Spermacoceae have gained their
 woodiness independently from one another, subsequent to colonization by
 their ancestors from a different geographic environment. The evolution and
 diversification along the tropical mountain orogeny is strongly linked
 with the formation of woody habit and many narrow endemic species.
description: BayesTraitsBayesTraits output filesBioGeoBearsBioGeoBears output filesHiSSEHiSSE output filesHISSE.zipRubiaceae Time TreeBEAST setting and output filesRubiaceaeTimeTree.zipSpecmacoceae Time TreeBEAST setting and output filesSpermacoceaeTimeTree.zip
DOI: 10.5061/dryad.hg600
title: Data from: Air-borne genotype by genotype indirect genetic effects are substantial in the filamentous fungus Aspergillus nidulans

description: Genotype by genotype indirect genetic effects (G × G IGEs) occur when the
 phenotype of an individual is influenced by an interaction between its own
 genotype and those of neighbour individuals. Little is known regarding the
 relative importance of G × G IGEs compared with other forms of direct and
 indirect genetic effects. We quantified the relative importance of IGEs in
 the filamentous fungus Aspergillus nidulans, a species in which IGEs are
 likely to be important as air-borne social interactions are known to
 affect growth. We used a collection of distantly related wild isolates,
 lab strains and a set of closely related mutation accumulation lines to
 estimate the contribution of direct and indirect genetic effects on
 mycelium growth rate, a key fitness component. We found that indirect
 genetic effects were dominated by G × G IGEs that occurred primarily
 between a focal genotype and its immediate neighbour within a vertical
 stack, and these accounted for 11% of phenotypic variation. These results
 indicate that G × G IGEs may be substantial, at least in some systems, and
 that the evolutionary importance of these interactions may be
 underappreciated, especially in microbes. We advocate for a wider use of
 the IGE framework in both applied (for example, choice of varietal
 mixtures in plant breeding) and evolutionary genetics (kin selection/kin
 competition studies).
description: Dataset used for the
 analysesMycelium growth rate
 data used of the linear mixed model analysesDataRode_et_al2017.csvScript for mixed model analysesScript for the analyses with ASReml-R (see http://www.vsni.co.uk/downloads/asreml/version-3-upgrade/)Mixed_Model_Analyses.RmdScript and figures from mixed model analysesOutput when knitting the file "Mixed_Model_Analyses.Rmd" using Rstudio (https://www.rstudio.com/) PowerAnalyses.Rmd: Code for the power analysesMixed_Model_Analyses.htmlScript for power analysesCode for power analysesPowerAnalyses.RmdScript and figures from power analysesOutput when knitting the file "PowerAnalyses.Rmd" using Rstudio (https://www.rstudio.com/)PowerAnalyses.htmlR environment for Fig. S4R environment including the 1000 simulations for Fig. S4 (can be loaded using the command: "load(SimulFigS4new.R)")SimulFigS4new.RR environment for Fig. S5R environment including the 1000 simulations for Fig. S5 (can be loaded using the command: "load(SimulFigS5new.R)")SimulFigS5new.REstimates of the direct genetic effectsEstimates of the direct genetic effects of the 41 strainsDGEGenotypicValues20170113.csvEstimates of the G x G indirect genetics effectsEstimates of the 417 GxG indirect genetic effects in the best model for dataset3 analyses (used for Fig. S6)GbyGGenotypicValues20170113.csv
DOI: 10.5061/dryad.tf7f7
title: Data from: Incorporating interspecific competition into species-distribution mapping by upward scaling of small-scale model projections to the landscape

description: There are a number of overarching questions and debate in the scientific
 community concerning the importance of biotic interactions in species
 distribution models at large spatial scales. In this paper, we present a
 framework for revising the potential distribution of tree species native
 to the Western Ecoregion of Nova Scotia, Canada, by integrating the
 long-term effects of interspecific competition into an existing
 abiotic-factor-based definition of potential species distribution (PSD).
 The PSD model is developed by combining spatially explicit data of
 individualistic species’ response to normalized incident
 photosynthetically active radiation, soil water content, and growing
 degree days. A revised PSD model adds biomass output simulated over a
 100-year timeframe with a robust forest gap model and scaled up to the
 landscape using a forestland classification technique. To demonstrate the
 method, we applied the calculation to the natural range of 16 target tree
 species as found in 1,240 provincial forest-inventory plots. The revised
 PSD model, with the long-term effects of interspecific competition
 accounted for, predicted that eastern hemlock (Tsuga canadensis), American
 beech (Fagus grandifolia), white birch (Betula papyrifera), red oak
 (Quercus rubra), sugar maple (Acer saccharum), and trembling aspen
 (Populus tremuloides) would experience a significant decline in their
 original distribution compared with balsam fir (Abies balsamea), black
 spruce (Picea mariana), red spruce (Picea rubens), red maple (Acer rubrum
 L.), and yellow birch (Betula alleghaniensis). True model accuracy
 improved from 64.2% with original PSD evaluations to 81.7% with revised
 PSD. Kappa statistics slightly increased from 0.26 (fair) to 0.41
 (moderate) for original and revised PSDs, respectively.
description: PONE-D-16-38039_FTC
 Supp. Data
DOI: 10.5061/dryad.2f050
title: Data from: Genomic patterns of diversity and divergence of two introduced salmonid species in Patagonia, South America

description: Invasive species have become widespread in aquatic environments throughout
 the world, yet there are few studies that have examined genomic variation
 of multiple introduced species in newly colonized environments. In this
 study, we contrast genomic variation in two salmonid species (anadromous
 Chinook Salmon, Oncorhynchus tshawytscha, 11,579 SNPs and resident Brook
 Charr Salvelinus fontinalis, 13,522 SNPs) with differing invasion success
 after introduction to new environments in South America relative to
 populations from their native range in North America. Estimates of genetic
 diversity were not significantly different between introduced and source
 populations for either species, indicative of propagule pressure that has
 been shown to maintain diversity in founding populations relative to their
 native range. Introduced populations also demonstrated higher connectivity
 and gene flow than those in their native range. Evidence for candidate
 loci under divergent selection was observed, but was limited to specific
 introduced populations and was not widely evident. Patterns of genomic
 variation were consistent with general dispersal potential of each species
 and therefore also the notion that life history variation may contribute
 to both invasion success and subsequent genetic structure of these two
 salmonids in Patagonia.
description: Chinook_Genotypes_11759SNPsChinook salmon genotypes for 11,759 SNPs (GenePop format)Ots_11759_genepop.txtBrook_Genotypes_13522SNPsBrook charr genotypes for 13,522 SNPs (GenePop format)Sfo_13522_genepop.txt
DOI: 10.5061/dryad.g5v64
title: Data from: Homeotic shift at the dawn of the turtle evolution

description: All derived turtles are characterized by one of the strongest reductions
 of the dorsal elements among Amniota, and have only 10 dorsal and eight
 cervical vertebrae. I demonstrate that the Late Triassic turtles, which
 represent successive stages of the shell evolution, indicate that the
 shift of the boundary between the cervical and dorsal sections of the
 vertebral column occurred over the course of several million years after
 the formation of complete carapace. The more generalized reptilian formula
 of at most seven cervicals and at least 11 dorsals is thus plesiomorphic
 for Testudinata. The morphological modifications associated with an
 anterior homeotic change of the first dorsal vertebra towards the last
 cervical vertebra in the Triassic turtles are partially recapitulated by
 the reduction of the first dorsal vertebra in crown-group Testudines, and
 they resemble the morphologies observed under laboratory conditions
 resulting from the experimental changes of Hox gene expression patterns.
 This homeotic shift hypothesis is supported by the, unique to turtles,
 restriction of Hox-5 expression domains, somitic precursors of scapula,
 and brachial plexus branches to the cervical region, by the number of the
 marginal scute-forming placodes, which was larger in the Triassic than in
 modern turtles, and by phylogenetic analyses.
description: Supplementary material -
 Szczygielski Tsupplementary
 information: extended discussion, character list, character matrix,
 phylogenetic trees, and lists of synapomorphiesSpecimen photographs -
 Szczygielski TPhotographs of
 Proterochersis porebensis (ZPAL V.39/48, ZPAL V.39/49, and ZPAL V.39/72)
 and Keuperotesta limendorsa (SMSN 17757)
DOI: 10.5061/dryad.gq3rg
title: Data from: A hybrid organic-inorganic perovskite dataset

description: Hybrid organic-inorganic perovskites (HOIPs) have been attracting a great
 deal of attention due to their versatility of electronic properties and
 fabrication methods. We prepare a dataset of 1,346 HOIPs, which features
 16 organic cations, 3 group-IV cations and 4 halide anions. Using a
 combination of an atomic structure search method and density functional
 theory calculations, the optimized structures, the bandgap, the dielectric
 constant, and the relative energies of the HOIPs are uniformly prepared
 and validated by comparing with relevant experimental and/or theoretical
 data. We make the dataset available at Dryad Digital Repository, NoMaD
 Repository, and Khazana Repository (http://khazana.uconn.edu/), hoping
 that it could be useful for future data-mining efforts that can explore
 possible structure-property relationships and phenomenological models.
 Progressive extension of the dataset is expected as new organic cations
 become appropriate within the HOIP framework, and as additional properties
 are calculated for the new compounds found.
description: A hybrid
 organic-inorganic perovskite datasetThe hybrid
 organic-inorganic dataset includes 1346 CIF files, each of them provides
 the optimized structure and the accompanied material properties calculated
 with first-principles calculations using VASP. The README.txt file
 provides details on the inputs of the runs used to calculate the
 properties reportes.HOIP_cif.tar
DOI: 10.5061/dryad.34qd7
title: Data from: Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes

description: Many anaerobic microbial parasites possess highly modified mitochondria
 known as mitochondrion-related organelles (MROs). The best-studied of
 these are the hydrogenosomes of Trichomonas vaginalis and Spironucleus
 salmonicida, which produce ATP anaerobically through substrate-level
 phosphorylation with concomitant hydrogen production; and the mitosomes of
 Giardia intestinalis, which are functionally reduced and lack any role in
 ATP production. However, to understand the metabolic specializations that
 these MROs underwent in adaptation to parasitism, data from their
 free-living relatives are needed. Here, we present a large-scale
 comparative transcriptomic study of MROs across a major eukaryotic group,
 Metamonada, examining lineage-specific gain and loss of metabolic
 functions in the MROs of Trichomonas, Giardia, Spironucleus and their
 free-living relatives. Our analyses uncover a complex history of ATP
 production machinery in diplomonads such as Giardia, and their closest
 relative, Dysnectes; and a correlation between the glycine cleavage
 machinery and lifestyles. Our data further suggest the existence of a
 previously undescribed biochemical class of MRO that generates hydrogen
 but is incapable of ATP synthesis.
description: Protein
 alignmentsAlignments of organellar
 proteinsmito_alignments.zipPhylogenomic datasetSingle gene alignments used for phylogenomic analysisPhylogenomic.zipData SourcesFasta files with assembled transcriptomes of Carpediemonas-like organismsAssemblies.zip
DOI: 10.5061/dryad.h6s54
title: Data from: Host specificity of Symbiodinium variants revealed by an ITS2 metahaplotype approach

description: Analysis of the widely used ITS region is confounded by the presence of
 intragenomic variants (IGVs). In Symbiodinium, the algal symbionts of reef
 building corals, deep-sequencing analyses are used to characterise
 communities within corals, yet these analyses largely overlook IGVs. Here
 we consider that distinct ITS2 sequences could represent IGVs rather than
 distinct symbiont types and argue that symbionts can be distinguished by
 their proportional composition of IGVs, described as their ITS2
 metahaplotype. Using our metahaplotype approach on Minimum Entropy
 Decomposition (MED) analysis of ITS2 sequences from the corals Acropora
 downingi, Cyphastrea microphthalma and Playgyra daedalea, we show the
 dominance of a single species-specific Symbiodinium C3 variant within each
 coral species. We confirm the presence of these species-specific symbionts
 using the psbA non-coding region. Our findings highlight the importance of
 accounting for IGVs in ITS2 analyses and demonstrate their capacity to
 resolve biological patterns that would otherwise be overlooked.
description: ITS2 and psbA
 sequencesThis folder contains the
 fasta files used to create the figures in our manuscript titled: Host
 specificity of Symbiodinium variants revealed by an ITS2 metahaplotype
 approach. Full description of the processing of reads is provided in
 detail in the Supplementary Information of the manuscript. Each file
 contains the sequences for a single individual and a single marker (see
 sample.key). Individuals were subsampled to 4500 and 2000 sequences for
 the ITS2 and psbAncr markers respectively. If you have any questions or
 queries, please feel free to contact Ed Smith,
 edsmith@nyu.eduMHdata.zip
DOI: 10.5061/dryad.8r0q8
title: Data from: Metapopulation patterns of additive and nonadditive genetic variance in the sea bass (Dicentrarchus labrax)

description: Describing and explaining the geographic within-species variation in
 phenotypes (“phenogeography”) in the sea over a species distribution range
 is central to our understanding of a variety of eco-evolutionary topics.
 However, phenogeographic studies that have a large potential to
 investigate adaptive variation are overcome by phylogeographic studies,
 still mainly focusing on neutral markers. How genotypic and phenotypic
 data could covary over large geographic scales remains poorly understood
 in marine species. We crossed 75 noninbred sires (five origins) and 26
 dams (two origins; each side of a hybrid zone) in a factorial diallel
 cross in order to investigate geographic variation for early survival and
 sex ratio in the metapopulation of the European sea bass (Dicentrarchus
 labrax), a highly prized marine fish species. Full-sib families (N =
 1,950) were produced and reared in a common environment. Parentage
 assignment of 7,200 individuals was performed with seven microsatellite
 markers. Generalized linear models showed significant additive effects for
 both traits and pleiotropy between traits. A significant nonadditive
 genetic effect was detected. Different expression of traits and distinct
 relative performances were found for reciprocal crosses involving
 populations located on each side of the main hybrid zone located at the
 Almeria-Oran front, illustrating asymmetric reproductive isolation. The
 poor fitness performance observed for the Western Mediterranean population
 of sea bass is discussed as it represents the main source of seed hatchery
 production, but also because it potentially illustrates nonadaptive
 introgression and maladaptation.
description: Data from Guinand et al
 (2017) Metapopulation patterns of additiveandnon-additive genetic variance
 in the sea bass (Dicentrarchus labrax)Three spreadsheets
 containing sire and dam data are reported. Spreadsheet 1 contains data (n
 = 7120 fish) used in the first model described in the paper including data
 for n = 2877 fish used in the second model ("sex-ratio model")
 in a specific column. Spreadsheets 2 and 3 are the genotypes of the
 parents (both sire and dams), and the genotypes of the offspring,
 respectivelyEcolEvol_2017_Guinand et
 al_Metapopulation-patterns-of-additive-and-non-additive
 genetic-variance-in-the
 -sea-bass-Dicentrarchus-labrax.xlsx
DOI: 10.5061/dryad.52650
title: Data from: Precipitation drives global variation in natural selection

description: Climate change has the potential to affect the ecology and evolution of
 every species on Earth. Although the ecological consequences of climate
 change are increasingly well documented, the effects of climate on the key
 evolutionary process driving adaptation—natural selection—are largely
 unknown. We report that aspects of precipitation and potential
 evapotranspiration, along with the North Atlantic Oscillation, predicted
 variation in selection across plant and animal populations throughout many
 terrestrial biomes, whereas temperature explained little variation. By
 showing that selection was influenced by climate variation, our results
 indicate that climate change may cause widespread alterations in selection
 regimes, potentially shifting evolutionary trajectories at a global scale.
description: Database S1 - Database
 of selection coefficientsDatabase of selection
 coefficients and associated trait, fitness, and location information. The
 first two columns describe the columns in the data set.Database
 S1.csvDatabase S2 - Database
 of climatic factors.Database of climatic
 factors. The first two columns describe the columns in the data
 set.Database
 S2.csv
DOI: 10.5061/dryad.5t76p
title: Data from: High nighttime humidity and dissolved organic carbon content support rapid decomposition of standing litter in a semi-arid landscape

description: 1. Litter in arid and semi-arid ecosystems usually exhibits a prolonged
 standing dead phase after senescence; however, we know little about the
 ways in which abiotic and microbial processes affect standing litter
 decomposition. 2. We conducted a 26-month (in situ) decomposition
 experiment in a steppe to investigate the potential mechanisms governing
 the decomposition of standing litter, and a 192-day laboratory incubation
 experiment to further explore the impacts of the standing dead stage on
 the subsequent litter decomposition and soil organic carbon formation
 after the litter falls to the soil surface. 3. Compared with soil surface
 litter, standing litter has higher dissolved organic carbon (DOC) content.
 Standing litter also experienced higher nighttime relative humidity on its
 surface, which enhanced litter moisture content. The higher DOC
 concentration, combined with the greater nighttime moisture content,
 stimulated more microbial activity in standing litter. The decomposition
 rate (k) of standing litter was 92% higher than that of soil surface
 litter. Moreover, the standing phase conditioned the litter, leading to
 more rapid decomposition after the litter fell to the soil surface, and
 increasing the efficiency with which the litter formed soil organic
 carbon. 4. We conclude that the long-neglected standing phase greatly
 determines litter decomposition and soil carbon storage in semi-arid
 regions. Accounting for standing litter decomposition is critical for
 accurately simulating carbon turnover in arid and semi-arid ecosystems.
description: Dataset_Wang et al.
 2017The file contains all
 the original data including the temperature, relative humidity, litter
 mass remaining, litter DOC concentrations and cumulative C
 loss.
DOI: 10.5061/dryad.3rr40
title: Data from: How well does a part represent the whole? A comparison of cranidial shape evolution with exoskeletal character evolution in the trilobite family Pterocephaliidae

description: For taphonomic and practical reasons, our understanding of morphological
 evolution within and among species is based primarily on measurements
 taken from one or a few morphological traits. However, patterns can be
 highly dependent on trait choice, making it difficult to draw conclusions
 about evolution of species or clades as a whole. In this paper, I test
 whether patterns of evolutionary change in the shape of a part are
 coincident with patterns of evolutionary change based on a more
 comprehensive description of the organism. The former is based on
 geometric morphometrics of the trilobite cranidium and the latter on
 discrete character data describing the exoskeleton, collected from species
 belonging to the Cambrian family Pterocephaliidae. Using these two
 datasets, I compare the amount of change occurring along phylogenetic
 branches, as well as changes in morphospace occupation and changes in
 different measures of disparity. Unlike previous studies, I apply as
 similar a data treatment as possible to each data set in order to
 facilitate the comparison and interpretation of discrepancies. Results
 suggest that cranidial shape is a robust proxy for species-level disparity
 and rates of evolution in this family of trilobites. This indicates that
 studies that have relied on data collected from the cranidium may be
 representative of the patterns that would be detected if more
 comprehensive description of the specimens had been available.
description: Hopkins_AppendixS1This appendix contains: Tables describing character matrix, with comparison to landmark data, and additional figures with 1) results when autapomorphic characters or gap-weighted characters are excluded; 2) deformation plots showing variation in cranidial shape described by the first two principal components shown in Figure 1; 3) results based on just the cranidial and just the non-cranidial characters.Hopkins_AppendixS2Nexus file with character matrix for reading into Claddis in R.