cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.76gg2
title: Data from: Superior discrimination for hue than for saturation and an explanation in terms of correlated neural noise

description: The precision of human colour discrimination depends on the region of
 colour space in which measurements are made and on the direction in which
 the compared colours—the discriminanda—differ. Working in a
 MacLeod–Boynton chromaticity diagram scaled so that thresholds at the
 white point were equal for the two axes, we made measurements at reference
 points lying on lines that passed at 45° or −45° through the white point.
 At a given reference chromaticity, we measured thresholds either for
 saturation (i.e. for discriminanda lying radially along the line passing
 through the white point) or for hue (i.e. for discriminanda lying on a
 tangent of a circle passing through the reference point and centred on the
 white point). The discriminanda always straddled the reference point in
 chromaticity. The attraction of this arrangement is that the two
 thresholds can be expressed in common units. All that differs between
 saturation and hue measurements is the phase with which the short-wave
 signal is combined with the long-/middle-wave signal. Except for
 chromaticities very close to the white point, saturation thresholds were
 systematically higher than hue thresholds. We offer a possible explanation
 in terms of correlated neural noise.
description: RSPB-2016-0164 Danilova
 Mollon Exp1 datadata obtained for
 experiment 1RSPB-2016-0164 Danilova
 Mollon control exp datadata used in the control
 experimentRSPB-2016-0164 Danilova
 Mollon Suppl exp datadata used for p.5: Hue
 and saturation thresholds very close to the white point
DOI: 10.5061/dryad.s90j5
title: Data from: Rapid morphological divergence of a stream fish in response to changes in water flow

description: Recent evidence indicates that evolution can occur on a contemporary time
 scale. However, the precise timing and patterns of phenotypic change are
 not well known. Reservoir construction severely alters selective regimes
 in aquatic habitats due to abrupt cessation of water flow. We examined the
 spatial and temporal patterns of evolution of a widespread North American
 stream fish (Pimephales vigilax) in response to stream impoundment. Gross
 morphological changes occurred in P. vigilax populations following dam
 construction in each of seven different rivers. Significant changes in
 body depth, head shape and fin placement were observed relative to fish
 populations that occupied the rivers prior to dam construction. These
 changes occurred over a very small number of generations and independent
 populations exhibited common responses to similar selective pressures. The
 magnitude of change was observed to be greatest in the first 15
 generations post-impoundment, followed by continued but more gradual
 change thereafter. This pattern suggests early directional selection
 facilitated by phenotypic plasticity in the first 10–20 years, followed by
 potential stabilizing selection as populations reached a new adaptive peak
 (or variation became exhausted). This study provides evidence for rapid,
 apparently adaptive, phenotypic divergence of natural populations due to
 major environmental perturbations in a changing world.
description: Procrustes
 CoordinatesInformation on the
 population, habitat, stream-reservoir pair, year of collection, the number
 of years following stream impoundment, and procrustes landmarks (14 x- and
 14 y-coordinates) for each individual included in the
 study.ProcrustesCoordinates.xlsx
DOI: 10.5061/dryad.m5n5b
title: Data from: Kin recognition in a clonal fish, Poecilia formosa

description: Relatedness strongly influences social behaviors in a wide variety of
 species. For most species, the highest typical degree of relatedness is
 between full siblings with 50% shared genes. However, this is poorly
 understood in species with unusually high relatedness between individuals:
 clonal organisms. Although there has been some investigation into clonal
 invertebrates and yeast, nothing is known about kin selection in clonal
 vertebrates. We show that a clonal fish, the Amazon molly (Poecilia
 formosa), can distinguish between different clonal lineages, associating
 with genetically identical, sister clonals, and use multiple sensory
 modalities. Also, they scale their aggressive behaviors according to the
 relatedness to other females: they are more aggressive to non-related
 clones. Our results demonstrate that even in species with very small
 genetic differences between individuals, kin recognition can be adaptive.
 Their discriminatory abilities and regulation of costly behaviors provides
 a powerful example of natural selection in species with limited genetic
 diversity.
description: All Data Kin Recognition
 in AmazonsExcel file contains all
 raw data separated by each individual study
DOI: 10.5061/dryad.8gr12
title: Data from: Regional surveys of macrobenthic shelf invertebrate communities in Onslow Bay, North Carolina, U.S.A.

description: Despite its importance for quantifying ecosystem responses to
 environmental and anthropogenic drivers, our understanding of spatial
 heterogeneity in marine communities remains inadequate. Studies in coastal
 marine benthic habitats are sparse, and predominantly target single higher
 taxonomic groups. Here we describe macrobenthic marine invertebrate
 community surveys from 52 localities in Onslow Bay (Beaufort, North
 Carolina, U.S.A.), over an extensive geographic area (~200 km2). The data
 consist of 11,467 individuals, 175 species, and 7 phyla. The data include
 species abundance data for each sample at all localities, and
 corresponding species lists and locality information. The metadata
 describe the sampling protocols and localities. The data provided here
 will facilitate examination of assemblage heterogeneity with regards to
 spatial and temporal patterns, and depth gradient analyses.
description: Locality
 informtionMetadata associated with
 localities, including water depth (m), GPS location (decimal degrees),
 collection dates, dredge equipment, and dredge
 duration.NC.Localities.xlsxSpecies ListSpecies names and associated numeric codes to be used with the abundance data.NC.Species.List.xlsxNC.AbundanceThe abundance of each species per sample.
DOI: 10.5061/dryad.vk81vp8
title: Data from: Effects of host colony size and hygiene behaviors on social spider kleptoparasite loads along an elevation gradient

description: 1.Group living animals are likely to attract more parasites than solitary
 ones. Parasite loads, however, should also depend on environmental
 conditions and on host characteristics and behaviors. Previous work has
 found that social spider colonies harbor communities of kleptoparasitic
 spiders thats forego building their own web and, instead, steal prey from
 their social host. 2.We examined parasite loads and host hygiene behaviors
 in colonies of social and subsocial spiders in the genus Anelosimus along
 an elevation gradient in eastern Ecuador. 3.We found that parasite loads
 declined dramatically with increasing elevation. Host hygiene behaviors,
 such as debris removal, web repair, and interactions with the parasites,
 also declined with elevation. Within elevations, species with more
 frequent hygiene behaviors appeared more successful at keeping parasites
 at bay. Contrary to our predictions, parasite density declined with host
 nest and colony size. 4.The decline in parasite loads at higher elevations
 likely reflects a lower rate of energy exchange between colonies and their
 environments, where colder temperatures mean fewer and smaller prey for
 colonies to process. The decline in parasite density with host colony size
 may reflect a decline in the number of accessible prey in larger host
 colonies, as larger colonies should capture fewer but larger insects due
 to scaling properties of their three dimensional webs. 5.Social immunity,
 whereby a social host uses social behaviour to fight against parasites,
 has been studied in eusocial and non‐eusocial insects. This study opens up
 social spiders as a novel system in which to study how host
 characteristics interact with environmental factors to affect parasite
 loads. It also introduces the concept of group‐level immunity to social
 spiders and suggests a role for colony‐level metabolism in determining
 ecological patterns in parasitism.
description: Straus&Aviles_FuncEcol_Kleptoparasite&NestDataMain data file used for analyses and figure generation in paper.Straus&Aviles_FuncEcol2018_KleptoHygieneBehavSecondary data file used for Figure 5, Supplemental Figure S3 and corresponding analyses. This file contains raw number of observations for different nest hygiene behaviours.
DOI: 10.5061/dryad.h2p05
title: Data from: New insights into the dynamics between reef corals and their associated dinoflagellate endosymbionts from population genetic studies.

description: The mutualistic symbioses between reef-building corals and micro-algae
 form the basis of coral reef ecosystems, yet recent environmental changes
 threaten their survival. Diversity in host-symbiont pairings on the
 sub-species level could be an unrecognized source of functional variation
 in response to stress. The Caribbean elkhorn coral, Acropora palmata,
 associates predominantly with one symbiont species (Symbiodinium ‘fitti’),
 facilitating investigations of individual-level (genotype) interactions.
 Individual genotypes of both host and symbiont were resolved across the
 entire range of the species. Most colonies of a particular animal genotype
 were dominated by one symbiont genotype (or strain) that may persist in
 the host for decades or more. While Symbiodinium are primarily clonal, the
 occurrence of recombinant genotypes indicates sexual recombination is the
 source of this genetic variation, and some evidence suggests this happens
 within the host. When these data are examined at spatial scales spanning
 the entire distribution of A. palmata, gene flow among animal populations
 was an order of magnitude greater than among populations of the symbiont.
 This suggests that independent micro-evolutionary processes created
 dissimilar population genetic structures between host and symbiont. The
 lower effective dispersal exhibited by the dinoflagellate raises questions
 regarding the extent to which populations of host and symbiont can
 co-evolve during times of rapid and substantial climate change. However,
 these findings also support a growing body of evidence suggesting that
 genotype by genotype interactions may provide significant physiological
 variation; influencing the adaptive potential of symbiotic reef corals to
 severe selection.
description: Symbiodinium fitti
 multilocus genotypesThis file contains
 multilocus genotype data from 13 haploid microsatellite loci for
 Symbiodinium ITS-2 type A3, provisionally named Symbiodinium fitti. Please
 see ReadMe file for important information.BaumsEtAl_14_DRYAD_Sfitti_genotypes.xlsxSymbiodinium fitti Structure input fileThis files contains all unique, haploid Symbiodinium fitti multilocus genotypes as generated with 13 microsatellite loci by Baums et al. 2014 Mol Ecol. The file is in the format of a Structure input file.BaumsEtAl_14_DRYAD_StructureInputFileSymbiodinium fitti multilocus genotypes Structure parametersThis files contains the parameters for Structure analysis of Symbiodinium fitti multilocus genotypes by Baums et al. 2014BaumsEtAl_14_DRYAD_Structure_mainparamsBaumsEtAl_14_DRYAD_Sfitti_NetworkInputFileInput file of Symbiodinium fitti unique multilocus genotypes for Network 4.6 (Fluxus Technoloy Ltd.). Default settings were used to construct median joining network.BaumsEtAl_14_Network_InputFile.ychBaumsEtAl_14_DRYAD_NetworkOutfileMedian Joining Network for 178 unique multilocus genotypes of Symbiodinium fitti (plot with Network 6.4, Luxus Technologies Ltd).
DOI: 10.5061/dryad.1v780
title: Data from: Diversification in temporally heterogeneous environments: effect of the grain in experimental bacterial populations.

description: Although theory established the necessary conditions for diversification
 in temporally heterogeneous environments, empirical evidence remains
 controversial. One possible explanation is the difficulty of designing
 experiments including the relevant range of temporal grains and the
 appropriate environmental tradeoffs. Here, we experimentally explore the
 impact of the grain on the diversification of the bacterium Pseudomonas
 fluorescens SBW25 in a temporally fluctuating environment by including
 twenty different pairs of environments and four temporal grains. In
 general, higher levels of diversity were observed at intermediate temporal
 grains. This resulted in part from the enhanced capacity of disruptive
 selection to generate negative genotypic correlations in performance at
 intermediate grains. However, the evolution of reciprocal specialization
 was an uncommon outcome. Although temporal heterogeneity is in theory less
 powerful than spatial heterogeneity to generate and maintain diversity,
 our results show that diversification under temporal heterogeneity is
 possible provided appropriate environmental grains.
description: ETFresultsto
 OLI_new-2Complete data set for
 analyisis of Inconsistency and Genotypic variance
DOI: 10.5061/dryad.2656v
title: Data from: Mechanisms of plant–plant interactions: concealment from herbivores is more important than abiotic-stress mediation in an African savannah

description: Recent work on facilitative plant–plant interactions has emphasized the
 importance of neighbours’ amelioration of abiotic stress, but the
 facilitative effects of neighbours in reducing plant apparency to
 herbivores have received less attention. Whereas theory on stress
 reduction predicts that competition should be more important in less
 stressful conditions, with facilitation becoming more important in harsh
 environments, apparency theory suggests that facilitation should be
 greater in the presence of herbivores, where it is disadvantageous to be
 conspicuous regardless of abiotic stress level. We tested the relative
 strength of neighbours’ stress reduction versus apparency reduction on
 survival, growth, reproduction and lifetime fitness of Hibiscus meyeri, a
 common forb in central Kenya, using neighbour removals conducted inside
 and outside large-herbivore exclosures replicated in arid and mesic sites.
 In the absence of herbivores, neighbours competed with H. meyeri in mesic
 areas and facilitated H. meyeri in arid areas, as predicted by
 stress-reduction mechanisms. By contrast, neighbours facilitated H. meyeri
 in the presence of herbivory, regardless of aridity level, consistent with
 plant apparency. Our results show that the facilitative effects arising
 from plant apparency are stronger than the effects arising from abiotic
 stress reduction in this system, suggesting that plant-apparency effects
 may be particularly important in systems with extant large-herbivore
 communities.
description: Hibiscus meyeri growth,
 survival, and reproductionrepeated measurements of
 height, basal area, reproductive structure number (allrep), fruit, between
 2011 and 2012, for Hibiscus meyeri plants subject to either neighbor
 removal treatments (NR) or unmanipuated control (control; indicated in the
 trmtAL column), at a variety of aridity levels (N, arid; S, mesic;
 indicated in the level column) and herbivore exclosure treatments (open
 control, "CONT" and full exclosure, "LMH"; indicated
 in the trmtUHURU column).datafile.txt
DOI: 10.5061/dryad.th0rj
title: Data from: On the (un)predictability of a large intragenic fitness landscape

description: The study of fitness landscapes, which aims at mapping genotypes to
 fitness, is receiving ever-increasing attention. Novel experimental
 approaches combined with next-generation sequencing (NGS) methods enable
 accurate and extensive studies of the fitness effects of mutations,
 allowing us to test theoretical predictions and improve our understanding
 of the shape of the true underlying fitness landscape and its implications
 for the predictability and repeatability of evolution. Here, we present a
 uniquely large multiallelic fitness landscape comprising 640 engineered
 mutants that represent all possible combinations of 13 amino acid-changing
 mutations at 6 sites in the heat-shock protein Hsp90 in Saccharomyces
 cerevisiae under elevated salinity. Despite a prevalent pattern of
 negative epistasis in the landscape, we find that the global fitness peak
 is reached via four positively epistatic mutations. Combining traditional
 and extending recently proposed theoretical and statistical approaches, we
 quantify features of the global multiallelic fitness landscape. Using
 subsets of the data, we demonstrate that extrapolation beyond a known part
 of the landscape is difficult owing to both local ruggedness and amino
 acid-specific epistatic hotspots and that inference is additionally
 confounded by the nonrandom choice of mutations for experimental fitness
 landscapes.
description: Yeast Hsp90 fitness
 landscape from deep mutational scanningThis data was obtained
 from 1611 engineered mutations in yeast Hsp90 exposed to high salinity,
 using the EMPIRIC approach. This file contains the deep mutational
 scanning data from both replicates. Columns are A-E are named
 unambiguously. Numbers in column F-N, line 1, indicate sampling times of
 replicate 2 in generations, numbers in column O-W, line 1, indicate
 sampling times of replicate 1.data.csv
DOI: 10.5061/dryad.fj46f
title: Data from: Living in two worlds: evolutionary mechanisms act differently in the native and introduced ranges of an invasive plant

description: Identifying the factors that influence spatial genetic structure among
 populations can provide insights into the evolution of invasive plants. In
 this study, we used the common reed (Phragmites australis), a grass native
 in Europe and invading North America, to examine the relative importance
 of geographic, environmental (represented by climate here) and human
 effects on population genetic structure and its changes during invasion.
 We collected samples of P. australis from both the invaded North American
 and native European ranges and used molecular markers to investigate the
 population genetic structure within and between ranges. We used path
 analysis to identify the contributions of each of three factors -
 geographic, environmental and human-related - to the formation of spatial
 genetic patterns. Genetic differentiation was observed between the
 introduced and native populations, and their genetic structure in the
 native and introduced range was different. There were strong effects of
 geography and environment on the genetic structure of populations in the
 native range, but the human-related factors manifested through
 colonization of anthropogenic habitats in the introduced range
 counteracted the effects of environment. The between-range genetic
 differences among populations were mainly explained by the heterogeneous
 environment between the ranges, with the coefficient 2.6 times higher for
 the environment than that explained by the geographic distance. Human
 activities were the primary contributor to the genetic structure of the
 introduced populations. The significant environmental divergence between
 ranges and the strong contribution of human activities to the genetic
 structure in the introduced range suggest that invasive populations P.
 australis have evolved to adapt to a different climate and to human-made
 habitats in North America.
description: Microsatellite matrix
 and AFLP genetic matrix of samplesGuo.pa.genetic.matrix.DrYad.upload.xlsx
DOI: 10.5061/dryad.k25rq40
title: Data from: Local extinctions of obligate frugivores and patch size reduction disrupt the structure of seed dispersal networks

description: A central problem in ecology is to understand how human impacts affect
 plant-animal interactions that lead to effective seed dispersal services
 for plant communities. Seed dispersal services are the outcome of
 plant-frugivore interactions that often form local networks of interacting
 species. Recent work has shown that some frugivorous bird species are more
 critical to network organization than others. Here, we explore how patch
 size and the potential local extinctions of obligate frugivorous birds
 affect the reorganization of seed dispersal networks. We examined the
 structure of 20 empirical seed dispersal networks documented across
 tropical avian assemblages occupying widely variable habitat patch sizes,
 a surrogate of the amount of remaining habitat. Networks within small
 forest patches consistently supported both lower plant and bird species
 richness. Forest patch size was positively associated with nestedness,
 indicating that reductions in patch size disrupted the nested organization
 of seed dispersal networks. Obligate frugivores, especially large-bodied
 species, were almost entirely absent from small forest patches. Analysis
 at the species level showed that obligate frugivores formed the core of
 interacting species, connecting species within a given seed dispersal
 network. Our combined results revealed that patch size reduction erodes
 frugivorous bird diversity, thereby affecting the integrity of seed
 dispersal networks. We highlight the importance of conserving large forest
 patches to maintain tropical forest functionality.
description: Assis_et_al_2018_dataInformation about sampled fragments and species richness (plants and birds), richness of obligate frugivorous birds and number of interactions in the networks. Frugivory degree classification, bird body mass information and the 20 matrix of seed dispersal networks were also presented.Assis_etal_2018_data.xlsx
DOI: 10.5061/dryad.6708r
title: Data from: Food spoilage, storage, and transport: implications for a sustainable future

description: Human societies have always faced temporal and spatial fluctuations in
 food availability. The length of time that food remains edible and
 nutritious depends on temperature, moisture, and other factors that affect
 the growth rates of organisms that cause spoilage. Some storage
 techniques, such as drying, salting, and smoking, date back to ancient
 hunter–gatherer and early agricultural societies and use relatively low
 energy inputs. Newer technologies developed since the industrial
 revolution, such as canning and compressed-gas refrigeration, require much
 greater energy inputs. Coincident with the development of storage
 technologies, the transportation of food helped to overcome spatial and
 temporal fluctuations in productivity, culminating in today's global
 transport system, which delivers fresh and preserved foods worldwide.
 Because most contemporary humans rely on energy-intensive technologies for
 storing and transporting food, there are formidable challenges for feeding
 a growing and increasingly urbanized global population as finite supplies
 of fossil fuels rapidly deplete.
description: Transportation
 technologies over human historyDate of first
 appearance, average speed, capacity, and energy source for various air,
 land, and water transport vessels used for food and other transportation
 over human historySupplemental_3.docxFood storage technologiesFood storage technologies with historical dates of appearance, energy requirements, and shelf life of various food items with and without storage technologySupplemental2_revised.docxGrowth rates of food spoiling microbesThe temperature-dependent growth rates of various microbes causing food spoilageSupplemental_1.xlsx