cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nd779
title: Data from: Individual personalities shape task differentiation in a social spider

description: Deciphering the mechanisms involved in shaping social structure is key to
 a deeper understanding of the evolutionary processes leading to sociality.
 Individual specialization within groups can increase colony efficiency and
 consequently productivity. Here, we test the hypothesis that within-group
 variation in individual personalities (i.e. boldness and aggression) can
 shape task differentiation. The social spider Stegodyphus sarasinorum
 (Eresidae) showed task differentiation (significant unequal participation)
 in simulated prey capture events across 10-day behavioural assays in the
 field, independent of developmental stage (level of maturation),
 eliminating age polyethism. Participation in prey capture was positively
 associated with level of boldness but not with aggression. Body size
 positively correlated with being the first spider to emerge from the
 colony as a response to prey capture but not with being the first to
 attack, and dispersal distance from experimental colonies correlated with
 attacking but not with emerging. This suggests that different behavioural
 responses to prey capture result from a complex set of individual
 characteristics. Boldness and aggression correlated positively, but
 neither was associated with body size, developmental stage or dispersal
 distance. Hence, we show that personalities shape task differentiation in
 a social spider independent of age and maturation. Our results suggest
 that personality measures obtained in solitary, standardized laboratory
 settings can be reliable predictors of behaviour in a social context in
 the field. Given the wealth of organisms that show consistent individual
 behavioural differences, animal personality could play a role in social
 organization in a diversity of animals.
description: Grinsted et al. 2013
 Proceedings B online dataAll data, raw and
 summarized, used for the statistical analyses in this paper. Data was
 collected both in the field and in the laboratory in India, and all
 analyses were performed in R.
DOI: 10.5061/dryad.58060
title: Data from: Nonautosomal genetic variation in carotenoid coloration

description: Carotenoid-based coloration plays an important role in signaling, is often
 sexually dimorphic, and is potentially subject to directional and/or
 sex-specific selection. To understand the evolutionary dynamics of such
 color traits, it is essential to quantify patterns of inheritance, yet
 nonautosomal sources of genetic variation are easily overlooked by
 classical heritability analyses. Carotenoid metabolism has recently been
 linked to mitochondria, highlighting the potential for color variation to
 be explained by cytoplasmically inherited factors. In this study, we used
 quantitative genetic animal models to estimate the importance of
 mitochondrial and sex chromosome–linked sources of genetic variation in
 coloration in two songbird populations in which dietary carotenoids are
 either unmodified (great tit plumage) or metabolized into alternative
 color forms (zebra finch beak). We found no significant Z-linked genetic
 variance in great tit plumage coloration, while zebra finch beak
 coloration exhibited significant W linkage and cytoplasmic inheritance.
 Our results support cytoplasmic inheritance of color in the zebra finch, a
 trait based on endogenously metabolized carotenoids, and demonstrate the
 potential for nonautosomal sources to account for a considerable share of
 genetic variation in coloration. Although often overlooked, such
 nonautosomal genetic variation exhibits sex-dependent patterns of
 inheritance and potentially influences the evolution of sexual
 dichromatism.
description: Great tit
 datasetPhenotypic data for
 Bagley Wood great tits (2008-2012).Great tit pedigree (to
 2012)Great tit pedigree file
 used in analysesGreat tit
 analysesASReml code to run the
 analyses of great tit plumage coloration described in the main article
 (when saved as a '.as' file)Zebra finch
 datasetPhenotypic data for
 Seeweisen zebra finch population.Zebra finch
 pedigreeZebra finch pedigree
 file used for analyses in ASReml (when saved as a '.ped'
 file).Zebra finch
 analysesASReml code to run the
 analyses of zebra finch beak redness described in the main article (when
 saved as a '.as' file)
DOI: 10.15468/dl.kdsu35
title: Occurrence Download

description: A dataset containing 29787 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Gasteracantha cancriformis"
 ]
}

 The dataset includes 29787 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000550-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.g2r32
title: Data from: Honeybees (Apis mellifera) learn color discriminations via differential conditioning independent of long wavelength (green) photoreceptor modulation

description: BACKGROUND: Recent studies on colour discrimination suggest that
 experience is an important factor in how a visual system processes
 spectral signals. In insects it has been shown that differential
 conditioning is important for processing fine colour discriminations.
 However, the visual system of many insects, including the honeybee, has a
 complex set of neural pathways, in which input from the long wavelength
 sensitive (‘green’) photoreceptor may be processed either as an
 independent achromatic signal or as part of a trichromatic opponent-colour
 system. Thus, a potential confound of colour learning in insects is the
 possibility that modulation of the ‘green’ photoreceptor could underlie
 observations. METHODOLOGY/PRINCIPAL FINDINGS: We tested honeybee vision
 using light emitting diodes centered on 414 and 424 nm wavelengths, which
 limit activation to the short-wavelength-sensitive (‘UV’) and
 medium-wavelength-sensitive (‘blue’) photoreceptors. The absolute
 irradiance spectra of stimuli was measured and modelled at both receptor
 and colour processing levels, and stimuli were then presented to the bees
 in a Y-maze at a large visual angle (26°), to ensure chromatic processing.
 Sixteen bees were trained over 50 trials, using either appetitive
 differential conditioning (N = 8), or aversive-appetitive differential
 conditioning (N = 8). In both cases the bees slowly learned to
 discriminate between the target and distractor with significantly better
 accuracy than would be expected by chance. Control experiments confirmed
 that changing stimulus intensity in transfers tests does not significantly
 affect bee performance, and it was possible to replicate previous findings
 that bees do not learn similar colour stimuli with absolute conditioning.
 CONCLUSION: Our data indicate that honeybee colour vision can be tuned to
 relatively small spectral differences, independent of ‘green’
 photoreceptor contrast and brightness cues. We thus show that colour
 vision is at least partly experience dependent, and behavioural plasticity
 plays an important role in how bees exploit colour information.
description: Normal Bee data - spss
 outputReal text file
 containing touch test data in blocks of 5 trialsQuinine versus water
 1graph of quinine vs. H2O
 as aversive stimulus for differential conditioning.graph pad Q versus
 waterGraphpad file containing
 intermediate and comparison data used to generate acquisition curves for
 differential conditioning procedure.414nm_75pct_A1text file containing absolute irradiance data for 414 nm LED array obtained by Ocean Optics Spectrometer per methods.424nm_75pct_A1Text file containing absolute irradiance data for 424 nm LED array. Note that output for both spectra files include wavelengths from 177.9 - 879.5 nm obtained at 75% of peak power supply output (details in methods).
DOI: 10.5061/dryad.s1674
title: Data from: The maternal cytoplasmic environment may be involved in the viability selection of gametes and zygotes

description: Segregation distortion is the phenomenon whereby the observed genotypic
 frequencies of a locus fall outside the expected Mendelian segregation
 ratio, and it is increasingly recognised as a potentially powerful
 evolutionary force. The main reason for segregation distortion is a
 difference in the viability of gametes and zygotes caused by viability
 loci in the segregating progeny. However, the maternal cytoplasm may also
 be involved in the viability selection of gametes and zygotes. The
 objectives of this study were to map the segregation distortion loci (SDL)
 in maize and to test the hypothesis that the viability of gametes and
 zygotes may also be associated with the maternal cytoplasmic environment.
 In the present study, a reciprocal mating design was conducted to generate
 an F2-segregating population. A linkage map was constructed with 126
 microsatellite markers. A whole-genome scan was performed to detect the
 SDL in segregating populations with different maternal cytoplasm
 environments. Altogether, 14 SDL with strong LOD (logarithm (base 10) of
 odds) supports were identified in the specifically designed F2
 populations. Interestingly, we found dramatic changes in the genotypic
 frequencies of the SDL in the two maternal cytoplasmic backgrounds, which
 indicated a change in the viability of gametes and zygotes in different
 cytoplasmic environments. Furthermore, in the JB cytoplasmic background,
 most of the detected SDL and complete distortion markers exhibited similar
 bias patterns favouring the Y53 alleles. These results suggested that
 selfish cytoplasmic elements may have an important role in shaping the
 patterns of segregation distortion in F2 populations through selective
 viability of gametes and zygotes.
description: data to Heredity
 HDY-12-OR0182RRA reciprocal intercross
 of maize JB and Y53 was generated to identify segregation distortion loci
 (SDL).
DOI: 10.5061/dryad.71r61
title: Data from: Not so old Archaea - the antiquity of biogeochemical processes in the archaeal domain of life

description: Since the archaeal domain of life was first recognized, it has often been
 assumed that Archaea are ancient, and harbor primitive traits. In fact,
 the names of the major archaeal lineages reflect our assumptions regarding
 the antiquity of their traits. Ancestral state reconstruction and relaxed
 molecular clock analyses using newly articulated oxygen age constraints
 show that although the archaeal domain itself is old, tracing back to the
 Archean eon, many clades and traits within the domain are not ancient or
 primitive. Indeed many clades and traits, particularly in the
 Euryarchaeota, were inferred to be Neoproterozoic or Phanerozoic in age.
 Both Eury- and Crenarchaeota show increasing metabolic and physiological
 diversity through time. Early archaeal microbial communities were likely
 limited to sulfur reduction and hydrogenotrophic methanogenesis, and were
 confined to high-temperature geothermal environments. However, after the
 appearance of atmospheric oxygen, nodes containing a wide variety of
 traits (sulfate and thiosulfate reduction, sulfur oxidation, sulfide
 oxidation, aerobic respiration, nitrate reduction, mesophilic
 methanogenesis in sedimentary environments) appear, first in environments
 containing terrestrial Crenarchaeota in the Meso/Neoproterozoic followed
 by environments containing marine Euryarchaeota in the Neoproterozoic and
 Phanerozoic. This provides phylogenetic evidence for increasing complexity
 in the biogeochemical cycling of C, N, and S through geologic time, likely
 as a consequence of microbial evolution and the gradual oxygenation of
 various compartments within the biosphere. This work has implications not
 only for the large-scale evolution of microbial communities and
 biogeochemical processes, but also for the interpretation of microbial
 biosignatures in the ancient rock record.
description: Blank2009c.NotSoOldArchaeaMesquite file containing phylogenetic tree and character matrix.
DOI: 10.5061/dryad.90317
title: Data from: A life-cycle model of human social groups produces a u-shaped distribution in group size

description: One of the central puzzles in the study of sociocultural evolution is how
 and why transitions from small-scale human groups to large-scale,
 hierarchically more complex ones occurred. Here we develop a spatially
 explicit agent-based model as a first step towards understanding the
 ecological dynamics of small and large-scale human groups. By analogy with
 the interactions between single-celled and multicellular organisms, we
 build a theory of group lifecycles as an emergent property of single cell
 demographic and expansion behaviours. We find that once the transition
 from small-scale to large-scale groups occurs, a few large-scale groups
 continue expanding while small-scale groups gradually become scarcer, and
 large-scale groups become larger in size and fewer in number over time.
 Demographic and expansion behaviours of groups are largely influenced by
 the distribution and availability of resources. Our results conform to a
 pattern of human political change in which religions and nation states
 come to be represented by a few large units and many smaller ones. Future
 enhancements of the model should include decision-making rules and
 probabilities of fragmentation for large-scale societies. We suggest that
 the synthesis of population ecology and social evolution will generate
 increasingly plausible models of human group dynamics.
description: Results of numerical
 experiments of the agent-based model describing the life-cycle of human
 social groupsDataset
 S1.zip
DOI: 10.5061/dryad.f3n5ts4
title: Data from: Integrating quantitative morphological and qualitative molecular methods to analyze soil nematode community responses to plant range expansion

description: 1. Belowground nematodes are important for soil functioning, as they are
 ubiquitous and operate at various trophic levels in the soil food web.
 However, morphological nematode community analysis is time consuming and
 requires ample training. qPCR-based nematode identification techniques are
 well available, but high throughput sequencing (HTS) might be more
 suitable for non-targeted nematode community analysis. 2. We compared
 effectiveness of qPCR and HTS-based approaches with morphological nematode
 identification while examining how climate warming-induced plant range
 expansion may influence belowground nematode assemblages. We extracted
 nematodes from soil of Centaurea stoebe and C. jacea populations in
 Slovenia, where both plant species are native, and Germany, where C.
 stoebe is range expander and C. jacea is native. Half of each nematode
 sample was identified morphologically and the other half was analysed
 using targeted qPCR and a novel HTS approach. 3. HTS produced the highest
 taxonomic resolution of the nematode community. Nematode taxa abundances
 correlated between the methods. Therefore, especially relative HTS and
 relative morphological data revealed nearly identical ecological patterns.
 All methods showed lower numbers of plant feeding nematodes in rhizosphere
 soils of C. stoebe compared to C. jacea. However, a profound difference
 was observed between absolute and relative abundance data; both sampling
 origin and plant species affected relative abundances of bacterivorous
 nematodes, whereas there was no effect on absolute abundances. 4. Taken
 together, as HTS correlates with relative analyses of soil nematode
 communities, while providing highest taxonomic resolution and sample
 throughput, we propose a combination of HTS with microscopic counting to
 supplement important quantitative data on soil nematode communities. This
 provides the most cost-effective, in-depths methodology to study soil
 nematode community responses to changes in the environment. This
 methodology will also be applicable to nematode analyses in aquatic
 systems.
description: cleaned original
 morphological and HTS files usedReviewers supporting
 file.xlsxfile used for
 statistical analysesfor
 stats.xlsxall morphological and
 qpcr raw datamorpho and qPCR all raw data
 working files.xlsx
DOI: 10.5061/dryad.v24r8753
title: Data from: Molecular phylogeny of Aphyocharacinae (Characiformes, Characidae) with morphological diagnoses for the subfamily and recognized genera

description: The subfamily Aphyocharacinae was recently redefined to comprise eight
 genera: Aphyocharax, Prionobrama, Paragoniates, Phenagoniates,
 Leptagoniates, Xenagoniates, Rachoviscus and Inpaichthys. This new
 composition, however, is partly incongruent with results of published
 molecular studies especially with regards to the positions of Rachoviscus
 and Inpaichthys. Our goal was to investigate the monophyly of
 Aphyocharacinae and its interrelationships using three distinct
 phylogenetic methodologies: Maximum–likelihood and Bayesian analyses of
 molecular data, and also Parsimony analysis of a concatenated molecular
 and morphological dataset. All tree topologies recovered herein suggest
 that Rachoviscus, Inpaichthys and Leptagoniates pi do not belong to the
 Aphyocharacinae. The remaining aphyocharacin taxa analyzed do form a
 monophyletic group, which is itself composed of two subgroups being one
 comprised of Paragoniates, Phenagoniates, Leptagoniates and Xenagoniates,
 and the other comprised of Aphyocharax and Prionobrama. Internal
 relationships among these genera are statistically well supported and
 morphological synapomorphies are presented at the generic level. All tree
 topologies also indicate that Aphyocharacidium is closely related to
 Aphyocharacinae suggesting that it should be included in this subfamily.
 As recognized in the present study, the Aphyocharacinae is diagnosed by a
 single morphological synapomorphy: two dorsal-fin rays articulating with
 the first dorsal pterygiophore.
description: molecular data
 matrixAligned molecular data
 set of five concatenated genes including two mitochondrial and three
 nuclearMatrix_Aphyocharacinae.FAS
DOI: 10.15468/dl.bf3t5f
title: Occurrence Download

description: A dataset containing 20160 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Cedrela odorata"
 ]
}

 The dataset includes 20160 records from 600 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000553-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1138
title: Data from: Angiosperm wood structure: global patterns in vessel anatomy and their relationship to wood density and potential conductivity

description: Woody stems comprise a large biological carbon fraction and determine
 water transport between roots and leaves; their structure and function can
 influence both carbon and hydrological cycles. While angiosperm wood
 anatomy and density determine hydraulic conductivity and mechanical
 strength, little is known about interrelations across many species. We
 compiled a global dataset comprising two anatomical traits for 3005 woody
 angiosperms: mean vessel lumen area ( ) and number per unit area (N). From
 these, we calculated vessel lumen fraction (F = N) and size/number ratio
 (S = /N), a new vessel composition index. We examined extent to which F
 and S influenced potential sapwood specific stem conductivity (KS) and
 wood density (D; dry mass/fresh volume). F and S varied essentially
 independently across angiosperms. Variation in KS was driven primarily by
 S, and variation in D was virtually unrelated to F and S. Tissue density
 outside vessel lumens (DN) must predominantly influence D. High S should
 confer faster Ks but incur greater freeze-thaw embolism risk. F should
 also affect KS, and both F and DN should influence mechanical strength,
 capacitance, and construction costs. Improved theory and quantification
 are needed to better understand ecological costs and benefits of these
 three distinct dimensions.
description: GlobalVesselAnatomyDatabase.xlsThe database is a literature compilation of angiosperms vessel anatomy measures for species distributed around the world. The first worksheet defines the data use policy. The second worksheet contains the data with column headings of family, binomial, average individual vessel size (A), vessel number (N), vessel composition (S = A/N), and vessel lumen fraction (F = AN), as well as log transformed values of these 4 variables. The third worksheet contains references for these data.
DOI: 10.5061/dryad.49m52
title: Data from: Diversity dynamics of mammals in relation to tectonic and climatic history: comparison of three Neogene records from North America

description: In modern ecosystems, regions of topographic heterogeneity, when compared
 with nearby topographically homogeneous regions, support high species
 densities of mammals and other groups. This biogeographic pattern could be
 explained by either greater diversification rates or greater accommodation
 of species in topographically complex regions. In this context, we assess
 the hypothesis that changes in landscape history have stimulated
 diversification in mammals. Landscape history includes tectonic and
 climatic processes that influence topographic complexity at regional
 scales. We evaluated the influence of changes in topographic complexity
 and climate on origination and extinction rates of rodents, the most
 diverse clade of mammals. We compared the Neogene records of rodent
 diversity for three regions in North America. The Columbia Basin of the
 Pacific Northwest (Region 1) and the northern Rocky Mountains (Region 2)
 were tectonically active over much of the Cenozoic and are characterized
 by high topographic complexity today. The northern Great Plains (Region 3)
 have been tectonically quiescent, with low relief, throughout the
 Cenozoic. These three regions have distinctive geologic histories and
 substantial fossil records. All three regions showed significant changes
 in diversification and faunal composition over the Neogene. In the montane
 regions, originations and extinctions peaked at the onset and close,
 respectively, of the Miocene Climatic Optimum (17–14 Ma), with significant
 changes in faunal composition accompanying these episodes of
 diversification. In the Great Plains, rodents showed considerable turnover
 but infrequent diversification. Peak Neogene diversity in the Great Plains
 occurred during cooling after the Miocene Climatic Optimum. These
 histories suggest that climatic changes interacting with increasing
 topographic complexity intensify macroevolutionary processes. In addition,
 close tracking of diversity and fossil productivity with the stratigraphic
 record suggests either large-scale sampling biases or the mutual response
 of diversity and depositional processes to changes in landscape history.
description: Badgley
 Finarelli.TablesS1-S11Data about species
 occurrences were downloaded from NeoMAP (MIOMAP and FAUNMAP). The
 supplementary tables in this file represent the processed raw data
 (species occurrences binned into 1-myr intervals) and various diversity
 metrics calculated from the raw data. Methods in the paper explain how the
 metrics were calculated.Badgley Finarelli.Suppl
 Text FiguresIn this file, we
 describe a subsampling procedure and present two figures (Figs S1, S2)
 that depict the results of the subsampling method. Data analyzed are
 summarized in the supplementary tables in a separate
 file.