cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fp11572
title: Data from: Brain size predicts behavioural plasticity in guppies (Poecilia reticulata): an experiment

description: Understanding how animal personality (consistent between-individual
 behavioural differences) arises has become a central topic in behavioural
 sciences. This endeavour is complicated by the fact that not only the mean
 behaviour of individuals (behavioural type), but also the strength of
 their reaction to environmental change (behavioural plasticity) varies
 consistently. Personality and cognitive abilities are linked and we
 suggest that behavioural plasticity could also be explained by differences
 in brain size (a proxy for cognitive abilities), since accurate decisions
 are likely essential to make behavioural plasticity beneficial. We test
 this idea in guppies (Poecilia reticulata), artificially selected for
 large and small brain size, which show clear cognitive differences between
 selection lines. To test whether those lines differed in behavioural
 plasticity, we reared them in groups in structurally enriched
 environments, and then placed adults individually into empty tanks, where
 we presented them daily with visual predator cues and monitored their
 behaviour for 20 days with video-aided motion tracking. We found that
 individuals differed consistently in activity and risk-taking, as well as
 in behavioural plasticity. In activity, only the large-brained lines
 demonstrated habituation (increased activity) to the new environment,
 while in risk-taking, we found sensitization (decreased risk-taking) in
 both brain size lines. We conclude that brain size, potentially via
 increasing cognitive abilities, may increase behavioural plasticity, which
 in turn can improve habituation to novel environments. However, the
 effects seem to be behaviour-specific. Our results suggest that brain size
 likely explain some of the variation in behavioural plasticity found at
 the intra-species level.
description: data used for
 analysesoriginal
 dataherczegetal_JEB_data.xlsx
DOI: 10.15468/dl.egdeay
title: Occurrence Download

description: A dataset containing 57 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Torreyochloa natans"
 ]
}

 The dataset includes 57 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000811-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.vg121
title: Data from: Effects of tree harvest on the stable-state dynamics of savanna and forest

description: Contemporary theory on the maintenance and stability of the savanna biome
 has focused extensively on how climate and disturbances interact to affect
 tree growth and demography. In particular, the role of fire in reducing
 tree cover from climatic maxima is now well appreciated, and in certain
 cases, herbivory also strongly affects tree cover. However, in African
 savannas and forests, harvest of trees by humans for cooking and heating
 is an oft overlooked disturbance. Thus, we incorporate tree harvest into a
 population dynamic model of grasses, savanna saplings, savanna trees, and
 forest trees. We use assumptions about the differential demographic
 responses of savanna trees and forest trees to harvest to show how tree
 harvest influences tree cover, demography, and community composition. Tree
 harvest can erode the intrinsic basin of attraction for forest and make a
 state transition via fire to savanna more likely. The savanna state is
 generally resilient to all but high levels of tree harvest because of the
 resprouting abilities of savanna trees. In the absence of active fire
 suppression, our analysis suggests that we can expect to see large and
 potentially irreversible shifts from forest to savanna as demand increases
 for charcoal in sub-Saharan Africa. On the other hand, savanna tree
 species’ traits promote savanna stability in the face of low to moderate
 harvest pressure.
description: Percent of Wood Cut
 versus GatheredSee ReadMe
 file.propWoodCutResponses.csv
DOI: 10.15468/dl.cmjw3s
title: Occurrence Download

description: A dataset containing 632 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Geometry POLYGON((105 20,170 20,170 70,105 70,105 20))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Poa glauca"
 ]
}

 The dataset includes 632 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000810-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.n3r2s
title: Data from: Genomic architecture of phenotypic divergence between two hybridizing plant species along an elevational gradient

description: Knowledge of the genetic basis of phenotypic divergence between species
 and how such divergence is caused and maintained is crucial to an
 understanding of speciation and the generation of biodiversity. The hybrid
 zone between Senecio aethnensis and S. chrysanthemifolius on Mount Etna,
 Sicily, provides a well-studied example of species divergence in response
 to conditions at different elevations, despite hybridization and gene
 flow. Here, we investigate the genetic architecture of divergence between
 these two species using a combination of quantitative trait locus (QTL)
 mapping and genetic differentiation measures based on genetic marker
 analysis. A QTL architecture characterized by physical QTL clustering,
 epistatic interactions between QTLs, and pleiotropy was identified, and is
 consistent with the presence of divergent QTL complexes resistant to gene
 flow. A role for divergent selection between species was indicated by
 significant negative associations between levels of interspecific genetic
 differentiation at mapped marker gene loci and map distance from QTLs and
 hybrid incompatibility loci. Within-species selection contributing to
 interspecific differentiation was evidenced by negative associations
 between interspecific genetic differentiation and genetic diversity within
 species. These results show that the two Senecio species, while subject to
 gene flow, maintain divergent genomic regions consistent with local
 selection within species and selection against hybrids between species
 which, in turn, contribute to the maintenance of their distinct phenotypic
 differences.
description: F2AC_mapping_family_trait_dataPhenotype trait data for an F2 mapping family from a reciprocal cross between Senecio aethnensis and S. chrysanthemifolius.F2AC_map_traits.txtEtna_Senecio_codominant_genotypesCodominant simple sequence repeat (SSR) and indel marker genotype data for wild sampled Senecio aethnensis and S. chrysanthemifolius.Etna_Senecio_dominant_genotypesDominant amplified fragment length polymorphism (AFLP) marker genotype data for wild sampled Senecio aethnensis and S. chrysanthemifolius.Etna_Senecio_trait_dataPhenotypic trait data for wild sampled Senecio aethnensis and S. chrysanthemifolius.Etna_Senecio_traits.txt
DOI: 10.5061/dryad.4b5c4
title: Data from: Association between integration structure and functional evolution in the opercular four-bar apparatus of the threespine stickleback, Gasterosteus aculeatus (Pisces: Gasterosteidae)

description: Phenotypes may evolve to become integrated in response to functional
 demands. Once evolved, integrated phenotypes, often modular, can also
 influence the trajectory of subsequent responses to selection. Clearly,
 connecting modularity and functionally adaptive evolution has been
 challenging. The teleost skull and jaw structures are useful for
 understanding this connection because of the key roles that these
 structures play in feeding in novel environments with different prey
 resources. In the present study, we examined such a structure in the
 threespine stickleback: the opercular four-bar lever that functions in jaw
 opening. Comparing oceanic and two fresh-water populations, we find marked
 phenotypic divergence in the skull opercular region, and the major axes of
 morphological and functional variation of the lever are found to be highly
 correlated. All three populations share the same global skull integration
 structure, and a conserved, strongly-supported modular organization is
 evident in the region encompassing the lever. Importantly, a boundary
 between two modules that subdivides the lever apparatus corresponds to the
 region of most prominent morphological evolution. The matched modular
 phenotypic and functional architecture of head and jaw structures of
 stickleback therefore may be important for facilitating their rapid
 adaptive transitions between highly divergent habitats.
description: whole_headRaw landmark coordinate data for whole-head landmark set for three populations of Alaskan threespine stickleback. Population Identifiers: 53=Boot Lake, 54=BearPaw Lake, 56=Rabbit Sloughfour_opsRaw landmark coordinate data for four-opercular-bone dataset for three populations of Alaskan threespine stickleback. Population Identifiers: 53=Boot Lake, 54=BearPaw Lake, 56=Rabbit Slough
DOI: 10.5061/dryad.4n0ff
title: Data from: Plant size and competitive dynamics along nutrient gradients

description: Resource competition theory in plants has focused largely on
 resource-acquisition traits that are independent of size such as traits of
 individual leaves or roots or proportional allocation to different
 functions. However plants also differ in maximum potential size which
 could outweigh differences in module-level traits. We used a
 community-ecosystem model called MONDRIAN to investigate whether larger
 size inevitably increases competitive ability and how size interacts with
 nitrogen supply. Contrary to the conventional wisdom that bigger is better
 we found that invader success and competitive ability are unimodal
 functions of maximum potential size such that plants that are too large
 %28or too small%29 are disproportionately suppressed by competition.
 Optimal size increases with nitrogen supply even when plants compete only
 for nitrogen in a size-symmetric manner although adding size-asymmetric
 competition for light does substantially increase the advantage of larger
 size at high nitrogen. These complex interactions of plant size and
 nitrogen supply lead to strong nonlinearities such that small differences
 in nitrogen can result in big differences in plant invasion success and
 the influence of competition along productivity gradients.
description: data for figs
 1-3Data are simulation
 results in plant invasion success from Mondrian (Modes Of Nonlinear
 Dynamics, Resource Interactions, And Nutrient cycling), a model that
 integrates population dynamics of clonal plants with ecosystem function in
 wetland plant communities, using richly detailed, highly mechanistic
 processes and interactions in a spatially explicit
 model.data for fig
 A1Data are supplemental
 simulation results from Mondrian (Modes Of Nonlinear Dynamics, Resource
 Interactions, And Nutrient cycling), a model that integrates population
 dynamics of clonal plants with ecosystem function in wetland plant
 communities, using richly detailed, highly mechanistic processes and
 interactions in a spatially explicit model.data for fig
 A2Data are supplemental
 simulation results from Mondrian (Modes Of Nonlinear Dynamics, Resource
 Interactions, And Nutrient cycling), a model that integrates population
 dynamics of clonal plants with ecosystem function in wetland plant
 communities, using richly detailed, highly mechanistic processes and
 interactions in a spatially explicit model. Code producing these
 simulations are provided as an on-line only supplement to Goldberg, D.E.,
 J.P. Martina, K.E. Elgersma, W.S. Currie. In press. Plant size and
 competitive dynamics along nutrient gradients. American
 Naturalist.
DOI: 10.5061/dryad.630
title: Data from: Multiple molecular data sets suggest independent origins of highly eusocial behavior in bees (Hymenoptera:Apinae)

description: Different views of the pattern of social evolution among the highly
 eusocial bees have arisen as a result of discordance between past
 molecular and morphology-based phylogenies. Here we present new data and
 taxa for four molecular data sets and reassess the morphological
 characters available to date. We show that there is no significant
 character incongruence between four molecular data sets (two nuclear and
 two mitochondrial) but that there is highly significant character
 incongruence, which leads to topological incongruence, between the
 molecular and morphological data. We investigate the effects of using
 different outgroup combinations to root the estimated tree. We also
 consider various ways in which biases in the sequence data could be
 misleading, employing several maximum likelihood models, LogDet
 corrections, and spectral analyses. Ultimately, we concede that there is
 strong discordance between the molecular and morphological data
 partitions, and that the conditional combination approach is appropriately
 applied in this case. We also find for the molecular trees that there are
 two equally well supported placements of the root, one supported by 16S
 and 28S sequences, the other supported by cyt b and opsin. The strength of
 the evidence leads us to accept two equally well supported hypotheses
 based on analyses of the molecular data sets. These are the most
 rigorously supported hypotheses of corbiculate bee relationships at this
 time, and frame our argument that highly eusocial behavior within the
 corbiculate bees evolved twice independently.
description: Apine CYTB Data
 SetApineCYTB.nexusApine DNA and Morphology Data SetApineDNA.morph.nexusApine 16S Data SetApine16S.nexusApine 28S Data SetApine28S.nexusApine OPSIN Data SetApineOPSIN.nexus
DOI: 10.5061/dryad.h5q34
title: Data from: Microbial richness and composition independently drive soil multifunctionality

description: Soil microbes provide multiple ecosystem functions such as nutrient
 cycling, decomposition and climate regulation. However, we lack a
 quantitative understanding of the relative importance of microbial
 richness and composition in controlling multifunctionality. This knowledge
 gap limits our capacity to understand the influence of biotic attributes
 in the provision of services and functions on which humans depend. We used
 two independent approaches (i.e. experimental and observational), and
 applied statistical modeling to identify the role and relative importance
 of bacterial richness and composition in driving multifunctionality (here
 defined as seven measures of respiration and enzyme activities). In the
 observational study we measured soil microbial communities and functions
 in both tree- and bare soil-dominated microsites at 22 locations across a
 1200 km transect in southeastern Australia. In the experimental study we
 used soils from two of those locations and developed gradients of
 bacterial diversity and composition through inoculation of sterilized
 soils. Microbial richness and the relative abundance of γ-Proteobacteria,
 Actinobacteria and Bacteroidetes were positively related to
 multifunctionality in both the observational and experimental approaches;
 however, only Bacteroidetes was consistently selected as a key predictor
 of multifunctionality across all experimental approaches and statistical
 models used here. Moreover, our results, from two different approaches,
 provide evidence that microbial richness and composition are both
 important, yet independent, drivers of multiple ecosystem functions.
 Overall, our findings advance our understanding of the mechanisms
 underpinning relationships between microbial diversity and ecosystem
 functionality in terrestrial ecosystems, and further suggest that
 information on microbial richness and composition needs to be considered
 when formulating sustainable management and conservation policies, and
 when predicting the effects of global change on ecosystem functions.
description: Dataset_06_08_2017There are five spreadsheets in this excel file. The spreadsheets "Microcosm soil A”, “Microcosm soil B” and “Environmental gradient" contain the raw data used in this paper. The spreadsheets "Microcosm metadata” and “Env. gradient metadata" contain the associated metadata, where a description of all the variables and units can be found.
DOI: 10.5061/dryad.rp13h
title: Data from: Extensive yellow crusts below limestone overhangs: a new taxon close to a minute epiphytic lichen

description: A conspicuous yellow crust forming extensive covers on some dry and shaded
 limestone rocks in Europe is described here as Caloplaca substerilis
 subsp. orbicularis M. Haji Moniri, Vondrák & Malíček subsp. nov.
 Based on nuITS rDNA, 28S nuLSU rDNA and mtSSU rDNA sequence data, the new
 taxon is closely related to Caloplaca sterilis and C. ulcerosa. The three
 taxa form a supported clade in the subfamily Xanthorioideae
 (Teloschistaceae), but none of the recent genera are suitable for them. In
 the ITS phylogeny, the new taxon forms a monophylum nested within C.
 substerilis. Its extensive yellow thalli and absence of vegetative
 diaspores clearly distinguish it from Caloplaca substerilis (subsp.
 substerilis). Indeed, if it had not been for the molecular evidence, we
 would have described it at the rank of species. We suggest that the
 substrate switch and accompanying processes are responsible for the
 striking phenotype difference between Caloplaca substerilis subsp.
 substerilis and C. substerilis subsp. orbicularis.
description: concatenated input to
 MrBayesNexus file used for
 Bayesian phylogeny of the concatenated datasetconcat_new_interleaved.nexITS input to MrBayesITS dataset prepared for MrBayes (in Nexus formate)orb_ITS_interleaved.nex
DOI: 10.5061/dryad.5g5rp
title: Data from: The causes of selection on flowering time through male fitness in a hermaphroditic annual plant

description: Flowering is a key life history event whose timing almost certainly
 affects both male and female fitness, but tests of selection on flowering
 time through male fitness are few. Such selection may arise from direct
 effects of flowering time, and indirect effects through covariance between
 flowering time and the environment experienced during reproduction. To
 isolate these intrinsically correlated associations, we staggered planting
 dates of Brassica rapa families with known flowering times, creating
 populations in which age at flowering (i.e. flowering time genotype) and
 Julian Date of flowering (i.e. flowering time environment) were
 positively, negatively, or uncorrelated. Genetic paternity analysis
 revealed that male fitness was not strongly influenced by seasonal
 environmental changes. Instead, when age and date were uncorrelated,
 selection through male fitness strongly favored young age at flowering.
 Strategic sampling offspring for paternity analysis rejected covariance
 between sire age at flowering and dam quality as the cause of this
 selection. Results instead suggest a negative association between age at
 flowering and pollen competitive ability. The manipulation also revealed
 that, at least in B. rapa, the often-observed correlation between
 flowering time and flowering duration is environmental, not genetic, in
 origin.
description: DRYAD
 filesZip folder containing
 phenotypic data from 2011 field experiment, genotypic data for parents and
 offspring at 8 microsatellite markers, and data used in path analysis
 (some of which was generated through paternity analysis). Also includes
 two R scripts for running paternity analysis.
DOI: 10.5061/dryad.8020
title: Data from: Genetic analysis of differentiation among breeding ponds reveals a candidate gene for local adaptation in Rana arvalis

description: One of the main questions in evolutionary and conservation biology is how
 geographical and environmental features of the landscape shape neutral and
 adaptive genetic variation in natural populations. The identification of
 genomic polymorphisms that account for adaptive variation can aid in
 finding candidate loci for local adaptation. Consequently, a comparison of
 spatial patterns in neutral markers and loci under selection may help
 disentangle the effects of gene flow, genetic drift and selection at the
 landscape scale. Many amphibians breed in wetlands, which differ in
 environmental conditions and in the degree of isolation, enhancing the
 potential for local adaptation. We used microsatellite markers to measure
 genetic differentiation among 17 local populations of Rana arvalis
 breeding in a network of wetlands. We found that locus RC08604 deviated
 from neutral expectations, suggesting that it is a good candidate for
 directional selection. We used a genetic network analysis to show that the
 allele distribution in this locus is correlated with habitat
 characteristics, whereas this was not the case at neutral markers that
 displayed a different allele distribution and population network in the
 study area. The graph approach illustrated the genomic heterogeneity
 (neutral loci vs. the candidate locus for directional selection) of gene
 exchange and genetic divergence among populations under directional
 selection. Limited gene flow between wetlands was only observed at the
 candidate genomic region under directional selection. RC08604 is partially
 located inside an up-regulated thyroid-hormone receptor (TRβ) gene
 coordinating the expression of other genes during metamorphosis and
 appears to be linked with variation in larval life-history traits found
 among R. arvalis populations. We suggest that directional selection on
 genes coding larval life-history traits is strong enough to maintain the
 divergence in these genomic regions, reducing the effective recombination
 of locally adapted alleles but not in other regions of the genome.
 Integrating this knowledge into conservation plans at the landscape scale
 will improve the design of management strategies to preserve adaptive
 genetic diversity in wetland networks.
description: Nine loci R.arvalis
 GenepopNine loci retained for
 analyses (including candidate loci under selection) in Genepop format.
 Ready to use with LOSITAN and any other programs.Nine loci retained for
 analyses R.arvalis Genetictudio formatNine loci of Rana
 arvalis in GeneticStudio format already to use in the graph
 approach.Nine loci retained for analyses
 R.arvalis.txt