cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s6c7j
title: Data from: Edaphic properties enable facilitative and competitive interactions resulting in fairy circle formation

description: Millions of generally regularly spaced, roughly circular barren patches
 called fairy circles occur in a narrow band ca. 100 km inland of the
 south-west African coast. These generally have conspicuously taller
 peripheral grasses in a shorter grass matrix. The origins of these fairy
 circles are controversial, but one possibility is that they are
 self-organizing emergent vegetation patterns that are the consequence of
 interplay between positive (facilitative) and negative (competitive)
 interactions between grasses. We hypothesized that the coarse textured
 sand on which fairy circles occur creates a hydraulically and
 nutritionally connected landscape, in which neighbouring fairy circles
 competitively influence each other over several metres, while providing
 opportunity for focusing of resources around the peripheral grasses. To
 test our hypotheses we conducted three main groups of analyses: 1) We
 measured grass biomass to assess facilitative and competitive effects of
 the component grasses; 2) Across a region with fairy circles we measured
 the size and density of fairy circles and correlated that with water
 infiltration rates into soil; 3) We measured the capacity of soil to
 conduct water pulses and 15N tracers. We found evidence of facilitative
 interactions in the periphery of the fairy circles and competitive
 suppression of the matrix grass proximal to the periphery. Across the
 region, fairy circle size was positively correlated with soil infiltration
 rates and negatively with precipitation. This suggests that fairy circles
 emerge in soils with high capacity for water flux that enables landscape
 hydraulic connectivity. Water- and 15N-pulse experiments showed that
 edaphic resources were highly mobile, moving up to 7.5 metres over a
 period of 1–3 weeks. We concluded that the evidence is consistent with an
 emergent vegetation pattern explanation for the origins of fairy circles
 and that the circles are more closely associated with a highly connective
 edaphic environment, rather than with particular biota.
description: Edaphic_properties_fairy_circles_EcographyCompilation of data that is not publicly available and was utilised in the associated manuscript. Brief notes on each worksheet page explain the origin of data and provide a guide to interpretation. The methods used are documented in the manuscript.
DOI: 10.5061/dryad.73s0n
title: Data from: Climate, demography, and zoogeography predict introgression thresholds in Salmonid hybrid zones in Rocky Mountain streams

description: Among the many threats posed by invasions of nonnative species is
 introgressive hybridization, which can lead to the genomic extinction of
 native taxa. This phenomenon is regarded as common and perhaps inevitable
 among native cutthroat trout and introduced rainbow trout in western North
 America, despite that these taxa naturally co-occur in some locations. We
 conducted a synthetic analysis of 13,315 genotyped fish from 558 sites by
 building logistic regression models using data from geospatial stream
 databases and from 12 published studies of hybridization to assess whether
 environmental covariates could explain levels of introgression between
 westslope cutthroat trout and rainbow trout in the U.S. northern Rocky
 Mountains. A consensus model performed well (AUC, 0.78–0.86;
 classification success, 72–82%; 10-fold cross validation, 70–82%) and
 predicted that rainbow trout introgression was significantly associated
 with warmer water temperatures, larger streams, proximity to warmer
 habitats and to recent sources of rainbow trout propagules, presence
 within the historical range of rainbow trout, and locations further east.
 Assuming that water temperatures will continue to rise in response to
 climate change and that levels of introgression outside the historical
 range of rainbow trout will equilibrate with those inside that range, we
 applied six scenarios across a 55,234-km stream network that forecast
 9.5–74.7% declines in the amount of habitat occupied by westslope
 cutthroat trout populations of conservation value, but not the wholesale
 loss of such populations. We conclude that introgression between these
 taxa is predictably related to environmental conditions, many of which can
 be manipulated to foster largely genetically intact populations of
 westslope cutthroat trout and help managers prioritize conservation
 activities.
description: Young et al.
 2016_dataData used to relate
 introgression between westslope cutthroat trout and rainbow trout to a
 suite of environmental covariates in western Montana and northern
 Idaho.
DOI: 10.5061/dryad.6d09b
title: Data from: Local divergence of thermal reaction norms among amphibian populations is affected by pond temperature variation

description: While temperature variation is known to cause large-scale adaptive
 divergence, its potential role as a selective factor over microgeographic
 scales is less well understood. Here, we investigated how variation in
 breeding pond temperature affects divergence in multiple physiological
 (thermal performance curve (TPC) and critical thermal maximum (CTmax)) and
 life history (thermal developmental reaction norms (TDRN)) traits in a
 network of Rana arvalis populations. The results supported adaptive
 responses to face two main constraints limiting the evolution of thermal
 adaptation. First, we found support for the faster-slower model,
 indicating an adaptive response to compensate for the thermodynamic
 constraint of low temperatures in colder environments. Secondly, we found
 evidence for the generalist-specialist trade-off with populations from
 colder and less thermally variable environments exhibiting a specialist
 phenotype performing at higher rates but over a narrower range of
 temperatures. By contrast, the local optimal temperature for locomotor
 performance and CTmax did not match either mean or maximum pond
 temperatures. These results highlight the complexity of the adaptive
 multiple-trait thermal responses in natural populations, and the role of
 local thermal variation as a selective force driving diversity in life
 history and physiological traits in the presence of gene flow.
description: MetamorphsRLife-history traits of the seven populations measured at two different temperature treatments.Swimming PerformanceExcel table with different pages, include: table with tadpole morphological data, table with swimming performance at the different temperatures, table with repeatability for some individuals, extra table with individuals who die at higher temperature.SwimmingPerformance_def.xlsxCTmaxFile with the CTmax data of the seven populationsctmax2.txt
DOI: 10.5061/dryad.3543v
title: Data from: Allopolyploidy and the evolution of plant virus resistance

description: Background: The relationship between allopolyploidy and plant virus
 resistance is poorly understood. To determine the relationship of plant
 evolutionary history and basal virus resistance, a panel of Nicotiana
 species from diverse geographic regions and ploidy levels was assessed for
 resistance to non-coevolved viruses from the genus Nepovirus, family
 Secoviridae. The heritability of resistance was tested in a panel of
 synthetic allopolyploids. Leaves of different positions on each inoculated
 plant were tested for virus presence and a subset of plants was
 re-inoculated and assessed for systemic recovery. Results: Depending on
 the host-virus combination, plants displayed immunity, susceptibility or
 intermediate levels of resistance. Synthetic allopolyploids showed an
 incompletely dominant resistance phenotype and manifested systemic
 recovery. Plant ploidy was weakly negatively correlated with virus
 resistance in Nicotiana species, but this trend did not hold when
 synthetic allopolyploids were taken into account. Furthermore, a
 relationship between resistance and geographical origin was observed.
 Conclusion: The gradients of resistance and virulence corresponded to a
 modified matching allele model of resistance. Intermediate resistance
 responses of allopolyploids corresponded with a model of multi-allelic
 additive resistance. The variable virus resistance of extant
 allopolyploids suggested that selection-based mechanisms surpass ploidy
 with respect to evolution of basal resistance to viruses.
description: Detailed virus incidence
 reportIncidence of nepoviruses
 Grapevine fanleaf virus (GFLV) or Tomato ringspot virus (ToRSV) in an
 inoculated and successive apical leaves of inoculated panels of Nicotiana
 species.bmc
 supplement.docx
DOI: 10.5061/dryad.38204
title: Data from: A comparative study of egg recognition signature mixtures in Formica ants

description: Processing of information from the environment, such as assessing group
 membership in social contexts, is a major determinant of inclusive
 fitness. For social insects, recognizing brood origin is crucial for
 inclusive fitness in many contexts, such as social parasitism and kin
 conflicts within colonies. Whether or not a recognition signature is
 informative in kin conflicts, depends on the extent of a genetic
 contribution into the cues. We investigated colony and matriline specific
 variation in egg surface hydrocarbons in seven species of Formica ants. We
 show that chemical variance is distributed similarly to genetic variation,
 suggesting a significant genetic contribution to eggs odors in the genus.
 Significant among matriline components, and significant correlations
 between chemical and genetic similarity among individuals also indicate
 kin informative egg odors in several species. We suggest that egg odor
 surface variation could play a large role in within colony conflicts, and
 that a comparative method can reveal novel insight into communication of
 identity.
description: 14-0279-R1-cinerea-chemFormica cinerea egg surface hydrocarbon GC-MS data14-0279-R1-cinerea-genFormica cinerea queen microsatellite genotypes14-0279-R1-fusca-chemFormica fusca egg surface hydrocarbon GC-MS data14-0279-R1-fusca-genFormica fusca queen microsatellite genotypes14-0279-R1-lemani-chemFormica lemani egg surface hydrocarbon GC-MS data14-0279-R1-lemani-genFormica lemani queen microsatellite genotypes14-0279-R1-picea-chemFormica picea egg surface hydrocarbon GC-MS data14-0279-R1-picea-genFormica picea queen microsatellite genotypes14-0279-R1-fennica-chemFormica fennica egg surface hydrocarbon GC-MS data14-0279-R1-fennica-genFormica fennica queen microsatellite genotypes14-0279-R1-aquilonia-chemFormica aquilonia egg surface hydrocarbon GC-MS data14-0279-R1-aquilonia-genFormica aquilonia queen microsatellite genotypes14-0279-R1-pressilabris-chemFormica pressilabris egg surface hydrocarbon GC-MS data14-0279-R1-pressilabris-genFormica pressilabris queen microsatellite genotypes
DOI: 10.5061/dryad.cr0qh5gc
title: Data from: Testing gradual and speciational models of evolution in extant taxa: the example of ratites

description: Ever since Eldredge and Gould proposed their model of punctuated
 equilibria, evolutionary biologists have debated how often this model is
 the best description of nature and how important it is compared to the
 more gradual models of evolution expected from natural selection and the
 neo-Darwinian paradigm. Recently, Cubo proposed a method to test whether
 morphological data in extant ratites are more compatible with a gradual or
 with a speciational model (close to the punctuated equilibrium model). As
 shown by our simulations, a new method to test the mode of evolution of
 characters (involving regression of standardized contrasts on their
 expected standard deviation) is easier to implement and more powerful than
 the previously proposed method, but the Mesquite module CoMET (aimed at
 investigating evolutionary models using comparative data) performs better
 still. Uncertainties in branch length estimates are probably the largest
 source of potential error. Cubo hypothesized that heterochronic mechanisms
 may underlie morphological changes in bone shape during the evolution of
 ratites. He predicted that the outcome of these changes may be consistent
 with a speciational model of character evolution because heterochronic
 changes can be instantaneous in terms of geological time. Analysis of a
 more extensive dataset confirms his prediction despite branch length
 uncertainties: evolution in ratites has been mostly speciational for
 shape-related characters. However, it has been mostly gradual for
 size-related ones.
description: Laurin et al.
 SOM1Species-level data file
 with character data and phylogenies. In NEXUS format, but may be read by
 any text editor.Laurin et al.
 SOM2Genus-level data file
 with character data and phylogenies. In NEXUS format, but may be read by
 any text editor.Laurin et al.
 SOM3Detailed results,
 character by character, about the evolutionary model according to the
 CoMET analysis. Tab-delimited text file.Laurin et al. SOM3
 ExcelDetailed results about
 the evolutionary models, character by character, according to the CoMET
 analyses. This is a Microsoft Excel file with formulae.Laurin et al.
 SOM3.xls
DOI: 10.5061/dryad.249kj74s
title: Data from: Disentangling the genetic origins of a plant pathogen during disease spread using an original molecular epidemiology approach

description: The advent of molecular epidemiology has greatly improved our ability to
 identify population sources and track pathogen movement. Yet the wide
 spatial and temporal scales usually considered are useful only to infer
 historical migration pathways. In this study, Bayesian genetic assignments
 and a landscape epidemiology approach were combined to unravel genetic
 origin and annual spread during a single epidemic of a plant pathogen: the
 poplar rust fungus Melampsora larici-populina. The study focused on a
 particular area—the Durance River valley—which enabled inoculum sources to
 be identified and channeled spread of the epidemic along a one-dimensional
 corridor. Spatio-temporal monitoring of disease showed that the epidemic
 began in the upstream part of the valley and spread out downstream. Using
 genetic assignment tests, individuals collected at the end of the epidemic
 were sorted into two genetic groups; very few hybrids were detected,
 although individuals from both groups coexisted locally downstream in the
 valley. The epidemic originated from two genetically distinct inoculum
 sources. Individuals of each group then dispersed southwards along the
 Durance River and became mixed in poplar riparian stands. These two
 genetic groups were found previously at a wider spatial scale and proved
 to result from distinct evolutionary histories on either wild or
 cultivated poplars. This study showed that the two groups can mix during
 an epidemic but do not hybridize because they then reproduce asexually. In
 general, the methods employed here could be useful for elucidating the
 genetic origin and retracing the colonization history and migration
 pathways of recent epidemics.
description: Data-MEC-11-1115
DOI: 10.5061/dryad.7187rf5
title: Data from: Numerical ordering of zero in honey bees

description: Some vertebrates demonstrate complex numerosity concepts—including
 addition, sequential ordering of numbers, or even the concept of zero—but
 whether an insect can develop an understanding for such concepts remains
 unknown. We trained individual honey bees to the numerical concepts of
 “greater than” or “less than” using stimuli containing one to six
 elemental features. Bees could subsequently extrapolate the concept of
 less than to order zero numerosity at the lower end of the numerical
 continuum. Bees demonstrated an understanding that parallels animals such
 as the African grey parrot, nonhuman primates, and even preschool
 children.
description: Experiment 1 test
 dataThis file contains all
 bee choices for each test (learning, conflict and transfer) performed in
 Experiment 1.Experiment_1_Test_Data.csvExperiment 2 test dataThis file contains all bee choices for each test (learning, conflict and transfer) performed in Experiment 2.Experiment_2_Test_Data.csvExperiment 3 test dataThis file contains all bee choices for each test performed in Experiment 3.Experiment_3_Test_Data.csvExperiment 4 test dataThis file contains all bee choices for each test (learning, conflict and transfer) performed in Experiment 4.Experiment_4_Test_Data.csvExperiment 5 test dataThis file contains all bee choices for each test (learning and transfer) performed in Experiment 5.Experiment_5_Test_Data.csv
DOI: 10.5061/dryad.pb128
title: Data from: The pollen dispersal kernel and mating system of an insect-pollinated tropical palm, Oenocarpus bataua

description: Pollen dispersal shapes the local genetic structure of plant populations
 and determines the opportunity for local selection and genetic drift, but
 has been well-studied in few animal-pollinated plants in tropical
 rainforests. Here, we characterize pollen movement for an
 insect-pollinated Neotropical canopy palm, Oenocarpus bataua, and relate
 these data to adult mating system and population genetic structure. The
 study covers a 130 ha parcel in which all adult trees (n=185) were mapped
 and genotyped at 12 microsatellite loci, allowing us to positively
 identify the source tree for 90% of pollination events (n=287 of 318
 events). Mating system analysis showed O. bataua was effectively
 outcrossed (tm=1.02) with little biparental inbreeding (tm-ts=-0.005) and
 an average of 5.4 effective pollen donors (Nep) per female. Dispersal
 distances were relatively large for an insect-pollinated species (mean =
 303 m, max = 1263 m), and far exceeded nearest neighbour distances.
 Dispersal kernel modelling indicated a thin-tailed Weibull distribution
 offered the best fit to the genetic data, which contrasts with the
 fat-tailed kernels typically reported for pollen dispersal in trees.
 Preliminary analyses suggest that our findings may be explained, at least
 in part, by a relatively diffuse spatial and temporal distribution of
 flowering trees. Comparison with previously reported estimates of seed
 movement for O. bataua suggests that pollen and seed dispersal distances
 may be similar. These findings add to the growing body of information on
 dispersal in insect-pollinated trees, but underscore the need for
 continued research on tropical systems in general, and palms in
 particular.
description: Ottewell 2012 Oenocarpus
 genetic dataExcel file containing
 microsatellite genotypes of adult Oenocarpus bataua trees and seed progeny
 arrays collected from a study site in northwest Ecuador
DOI: 10.5061/dryad.d45g9j0
title: Data from: Morph-specific artificial selection reveals a constraint on the evolution of polyphenisms

description: Theory predicts that the evolution of polyphenic variation is facilitated
 where morphs are genetically uncoupled and free to evolve towards their
 phenotypic optima. However, the assumption that developmentally plastic
 morphs can evolve independently has not been tested directly. Using
 morph-specific artificial selection, we investigated correlated evolution
 between the sexes and male morphs of the bulb mite Rhizoglyphus echinopus.
 Large ‘fighter’ males have a thick and sharply terminating pair of legs
 used to kill rival males, while small ‘scrambler’ males have unmodified
 legs, and search for unguarded females, avoiding fights. We selected on
 the relative leg width of only the fighter male morph, tracked the
 evolutionary responses in fighters and the correlated evolutionary
 responses in scramblers and females that were untouched by direct
 selection. Fighters diverged in relative leg thickness after six
 generations; assaying scramblers and females at the ninth generation we
 observed correlated responses in relative leg width in both. Our results
 represent strong evidence for the evolution of intraspecific phenotypic
 diversity despite correlated evolution between morphs and sexes,
 challenging the idea that male morphs are genetically uncoupled and free
 to independen- tly respond to selection. We, therefore, question the
 perceived necessity for genetic independence in traits with extreme
 phenotypic plasticity.
description: Data for Buzatto et al
 2018 Proc BThis file has two tabs.
 The first one contains all the data for the selection applied on fighter
 males of the mite Rhizoglyphus echinopus. Each row contains information
 for one male measured during the experiment, and the columns contain
 information about (respectively from left to right): generation (1 to 10);
 replicate selection line; selection direction (up for thicker legs and
 down for thinner legs); the ID of the line (replicate and direction
 combined); the length of the anterior coxae suture (proxy for body size;
 see methods); the width of 3rd right leg (the fighting leg, measured at
 the base; see methods); the residual from a linear model describing the
 relationship between the last two variables (the allometry of the third
 pair of legs); whether that individual was selected as a sire for the next
 generation; and the number of offspring from this individual that mated
 and was measured in the following generation. The other tab has similar
 information, but only for generation 9, and including scramblers and
 females as well (in addition to the fighters), for investigation of the
 correlated evolution resulting from morph-specific selection. This tab
 also has the information of the family ID (since fighters, scramblers and
 females were sourced from a variety of different families within each
 line) and the sex/morph of each individual.
DOI: 10.5061/dryad.143h7b99
title: Data from: In a variable thermal environment selection favors greater plasticity of cell membranes in Drosophila melanogaster

description: Theory predicts that developmental plasticity, the capacity to change
 phenotypic trajectory during development, should evolve when the
 environment varies sufficiently among generations, owing to temporal
 (e.g., seasonal) variation or to migration among environments. We
 characterized the levels of cellular plasticity during development in
 populations of Drosophila melanogaster experimentally evolved for over
 three years in either constant or temporally variable thermal
 environments. We used two measures of the lipid composition of cell
 membranes as indices of physiological plasticity (a.k.a. acclimation): (1)
 change in the ratio of phosphatidylethanolamine (PE) to
 phosphatidylcholine (PC) and (2) change in lipid saturation (number of
 double bonds) in cool (16ºC) relative to warm (25ºC) developmental
 conditions. Flies evolved under variable environments had a greater
 capacity to acclimate the PE/PC ratio compared to flies evolved in
 constant environments, supporting the prediction that environments with
 high among-generation variance favor greater developmental plasticity. Our
 results are consistent with the selective advantage of a more
 environmentally sensitive allele which may have associated costs in
 constant environments.
description: Cooper_et_al_2012_dataProportions of each of the phospholipids in lipid extracts from each isofemale line after development at 16 and 25C. See the read me file for explicit details.All_data_submitted_dryad.txt