cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7d092
title: Data from: Asymmetric effects of loss and gain of a floral trait on pollinator preference

description: Shifts in pollination syndromes involve coordinated changes in multiple
 floral traits. This raises the question of how plants can cope with rapid
 changes in pollinator availability by the slow process of accumulation of
 mutations in multiple genes. Here we study the transition from bee to
 hawkmoth pollination in the genus Petunia. Interspecific crosses followed
 by single locus introgressions were used to recreate putative intermediate
 evolutionary stages in the evolution of moth pollination. The effect of
 the loss/gain of petal color was asymmetric: it had no influence on the
 established pollinator but enhanced visitation by the new pollinator.
 Therefore, shifts in pollination syndromes may proceed through
 intermediate stages of reduced specialization and consequently enhanced
 reproductive assurance. The loss of petal color in moth-pollinated Petunia
 involves null mutations in a single regulatory gene, An2. Such simple
 genetic changes may be sufficiently rapid and frequent to ensure survival
 during pollinator failure.
description: Fig 1-3 raw
 dataraw data related to
 Figure 1, 2 and 3, organized by figure panelfig 1-3 raw
 data.xlsx
DOI: 10.5061/dryad.mc274
title: Data from: Closing the circle: how ecologists can prepare their own quality control material to increase confidence in stable isotope data

description: 1. Stable isotope analysis (SIA) is widely used in ecology, but is usually
 performed by specialist facilities. Consequently, the reliability of SIA
 data depends completely on the facility’s quality systems unless
 ecologists take steps themselves. Although widely recommended, practical
 advice on how to do this is lacking. 2. Here, we outline preparation of
 150 vials of an in-house quality control material, and describe data
 analysis. As a readily available and stable biogenic material, we propose
 air-dried soil. Homogeneity testing of the candidate material involves
 duplicate analysis of 10 randomly chosen vials, a Cochran test for
 outliers, and 1-way ANOVA. Given that many ecologists find SIA expensive,
 we propose that the ecologist pre-test for homogeneity using a simple
 colorimetric analysis of a soil quantity (bicarbonate-extractable P)
 sensitive to inhomogeneity. 3. Once pre-test homogeneity has been
 established, homogeneity under SIA can be tested. We obtained a 1-way
 ANOVA P value of 0.824 in our laboratory pre-test, then 0.782 (δ13C) and
 0.125 (δ15N). 4. Submission of each batch of samples for SIA should be
 accompanied by a vial of the quality control material, labelled as a
 normal sample. Control charting of the results then allows detection of
 within-batch issues encompassing any component of the analytical process
 (transport to the laboratory; sample preparation and subsampling; sample
 analysis; results calculation and reporting) and assessment of long term
 analytical control. Any issue thus identified can form the basis of a
 conversation with the SIA laboratory about the affected batch of samples.
description: Instrument outputs
 in_house QCM May_2010This file is the Excel
 spreadsheet used the stable isotope lab to report the in-house QCM data
 from May 2010. It includes all instrument outputs and the analysis
 chronology.Instrument outputs
 in_house QCM Nov_2012This file is the Excel
 spreadsheet used the stable isotope lab to report the in-house QCM data
 from November 2012. It includes all instrument outputs and the analysis
 chronology.In_house QCM summary
 data incl statisticsThis Excel file
 summarises all of the data used to calculate the target mean and standard
 deviation of the in-house QCM, along with Cochran test
 results.
DOI: 10.5061/dryad.1c045
title: Data from: Testing the niche breadth-range size hypothesis: habitat specialization versus performance in Australian alpine daisies

description: Relatively common species within a clade are expected to perform well
 across a wider range of conditions than their rarer relatives, yet
 experimental tests of this “niche breadth—range size” hypothesis remain
 surprisingly scarce. Rarity may arise due to trade-offs between
 specialization and performance across a wide range of environments. Here
 we use common garden and reciprocal transplant experiments to test the
 niche breadth—range size hypothesis, focusing on four common and three
 rare endemic alpine daisies (Brachyscome spp.) from the Australian Alps.
 We used three experimental contexts: 1) alpine reciprocal seedling
 experiment: a test of seedling survival and growth in three alpine habitat
 types differing in environmental quality and species diversity, 2) warm
 environment common garden: a test of whether common daisy species have
 higher growth rates and phenotypic plasticity, assessed in a common garden
 in a warmer climate and run simultaneously with experiment 1, and 3)
 alpine reciprocal seed experiment: a test of seed germination capacity and
 viability in the same three alpine habitat types as in experiment 1. In
 the alpine reciprocal seedling experiment, survival of all species was
 highest in the open heathland habitat where overall plant diversity is
 high, suggesting a general, positive response to a relatively productive,
 low-stress environment. We found only partial support for higher survival
 of rare species in their habitats of origin. In the warm environment
 common garden, three common daisies exhibited greater growth and biomass
 than two rare species, but the other rare species performed as well as the
 common species. In the alpine reciprocal seed experiment, common daisies
 exhibited higher germination across most habitats, but rare species
 maintained a higher proportion of viable seed in all conditions,
 suggesting different life history strategies. These results indicate that
 some but not all rare, alpine endemics exhibit stress tolerance at the
 cost of reduced growth rates in low-stress environments compared to common
 species. Finally, these findings suggest the seed stage is important in
 the persistence of rare species, and they provide only weak support at the
 seedling stage for the niche breadth-range size hypothesis.
description: dryad_submission_ecology
DOI: 10.5061/dryad.8r7cn62
title: Data from: The fabrication of the heterojunction catalyst BiVO4/P25 and its visible-light photocatalytic activities

description: A heterojunction catalyst BiVO4/P25 was successfully fabricated using a
 one-step hydrothermal method. The BiVO4/P25 samples exhibited better
 photocatalytic activities and absorption performances when compared with
 the pure BiVO4. The degradation rate of the methyl blue (MB) solution (5
 mg/L) reached up to 85% in sixty minutes under visible-light illumination
 (λ &gt; 420 nm). The nanocomposites were characterized using XPS,
 Raman spectroscopy, FT-IR, UV–visual diffuse reflectance spectroscopy, SEM
 and HR-TEM. A high-powered scanning electron microscope showed a
 polyhedron shape and a flower-like shape. The BiVO4/P25 nanocomposite was
 found to have a rougher surface, as well as a larger surface area, when
 compared with the pure BiVO4. This resulted in an improved photocatalytic
 activity, along with super absorption to a large extent.
description: All the dates of “The
 Fabrication of the Heterojunction Catalyst BiVO4/P25 and its Visible-Light
 Photocatalytic Activities”date.zip
DOI: 10.5061/dryad.3sh6d
title: Data from: The organization and evolution of the Responder satellite in species of the Drosophila melanogaster group: dynamic evolution of a target of meiotic drive

description: Background: Satellite DNA can make up a substantial fraction of eukaryotic
 genomes and has roles in genome structure and chromosome segregation. The
 rapid evolution of satellite DNA can contribute to genomic instability and
 genetic incompatibilities between species. Despite its ubiquity and its
 contribution to genome evolution, we currently know little about the
 dynamics of satellite DNA evolution. The Responder (Rsp) satellite DNA
 family is found in the pericentric heterochromatin of chromosome 2 of
 Drosophila melanogaster. Rsp is well-known for being the target of
 Segregation Distorter (SD) an autosomal meiotic drive system in D.
 melanogaster. I present an evolutionary genetic analysis of the Rsp family
 of repeats in D. melanogaster and its closely-related species in the
 melanogaster group (D. simulans, D. sechellia, D. mauritiana, D. erecta,
 and D. yakuba) using a combination of available BAC sequences, whole
 genome shotgun Sanger reads, Illumina short read deep sequencing, and
 fluorescence in situ hybridization. Results: I show that Rsp repeats have
 euchromatic locations throughout the D. melanogaster genome, that Rsp
 arrays show evidence for concerted evolution, and that Rsp repeats exist
 outside of D. melanogaster, in the melanogaster group. The repeats in
 these species are considerably diverged at the sequence level compared to
 D. melanogaster, and have a strikingly different genomic distribution,
 even between closely-related sister taxa. Conclusions: The genomic
 organization of the Rsp repeat in the D. melanogaster genome is
 complex--it exists of large blocks of tandem repeats in the
 heterochromatin and small blocks of tandem repeats in the euchromatin. My
 discovery of heterochromatic Rsp-like sequences outside of D. melanogaster
 suggests that SD evolved after its target satellite and that the evolution
 of the Rsp satellite family is highly dynamic over a short evolutionary
 time scale (&lt;240,000 years).
description: Larracuente_Supplementary_file2Maximum likelihood tree with bootstrap support of Rsp and Rsp-like repeats used in Figure 3.
DOI: 10.5061/dryad.c1090r5
title: Data from: Transmission risk predicts avoidance of infected conspecifics in Trinidadian guppies

description: 1.Associating with conspecifics afflicted with infectious diseases
 increases the risk of becoming infected, but engaging in avoidance
 behaviour incurs the cost of lost social benefits. Across systems,
 infected individuals vary in the transmission risk they pose, so natural
 selection should favour risk‐sensitive avoidance behaviour that optimally
 balances the costs and benefits of sociality. 2.Here we use the guppy
 Poecilia reticulata‐Gyrodactylus turnbulli host‐parasite system to test
 the prediction that individuals avoid infected conspecifics in proportion
 to the transmission risk they pose. 3.In dichotomous choice tests,
 uninfected fish avoided both the chemical and visual cues, presented
 separately, of infected conspecifics only in the later stages of
 infection. 4.A transmission experiment indicated that this avoidance
 behaviour accurately tracked transmission risk (quantified as both the
 speed at which transmission occurs and the number of parasites
 transmitting) through the course of infection. 5.Together, these findings
 reveal that uninfected hosts can use redundant cues across sensory systems
 to inform dynamic risk‐sensitive avoidance behaviour. This correlation
 between the transmission risk posed by infected individuals and the
 avoidance response they elicit has implications for the evolutionary
 ecology of infectious disease, and its explicit inclusion may improve the
 ability of epidemic models to predict disease spread.
description: DatasetS2Data from a behavioural experiment testing whether fish discriminate between infected and uninfected conspecifics. Details are in the online supplementary material provided with the paper.DatasetS3 - Transmission load1000 simulations of the predicted number of parasites transmitting from the stimulus fish in the behavioural experiment described in the paper.DatasetS3.csvDatasetS4 - Transmission speed1000 simulations of the predicted speed at which parasites would transmit from the stimulus fish in the behavioural experiment. More details are provided in the main paper and the online supplement.DatasetS4.csv
DOI: 10.5061/dryad.p2481134
title: Data from: Generic indicators for loss of resilience before a tipping point leading to population collapse

description: Theory predicts that the approach of catastrophic thresholds in natural
 systems (e.g., ecosystems, the climate) may result in an increasingly slow
 recovery from small perturbations, a phenomenon called critical slowing
 down. We used replicate laboratory populations of the budding yeast
 Saccharomyces cerevisiae for direct observation of critical slowing down
 before population collapse. We mapped the bifurcation diagram
 experimentally and found that the populations became more vulnerable to
 disturbance closer to the tipping point. Fluctuations of population
 density increased in size and duration near the tipping point, in
 agreement with the theory. Our results suggest that indicators of critical
 slowing down can provide advance warning of catastrophic thresholds and
 loss of resilience in a variety of dynamical systems.
description: data_bifurcationdata_saltshockdata_indicatorReadMe
DOI: 10.5061/dryad.m233m
title: Data from: Herbivory and pollen limitation at the upper elevational range limit of two forest understory plants of eastern North America

description: Studies of species’ range limits focus most often on abiotic factors,
 although the strength of biotic interactions might also vary along
 environmental gradients and have strong demographic effects. For example,
 pollinator abundance might decrease at range limits due to harsh
 environmental conditions, and reduced plant density can reduce
 attractiveness to pollinators and increase or decrease herbivory. We
 tested for variation in the strength of pollen limitation and herbivory by
 ungulates along a gradient leading to the upper elevational range limits
 of Trillium erectum (Melanthiaceae) and Erythronium americanum (Liliaceae)
 in Mont-Mégantic National Park, Québec, Canada. In T. erectum, pollen
 limitation was higher at the range limit, but seed set decreased only
 slightly with elevation and only in one of two years. In contrast,
 herbivory of T. erectum increased from &lt;10% at low elevations to
 &gt;60% at the upper elevational range limit. In E. americanum, we
 found no evidence of pollen limitation despite a significant decrease in
 seed set with elevation, and herbivory was low across the entire gradient.
 Overall, our results demonstrate the potential for relatively strong
 negative interactions (herbivory) and weak positive interactions
 (pollination) at plant range edges, although this was clearly
 species-specific. To the extent that these interactions have important
 demographic consequences – highly likely for herbivory on Trillium, based
 on previous studies – such interactions might play a role in determining
 plant species’ range limits along putatively climatic gradients.
description: Trillium_erectum_Pollen_Limitation_2016Reproductive success and leaf size of Trillium erectum for control and pollen supplemented individuals along an elevation gradient at Mont-Mégantic National Park.trillium_erectum_PL_2016.xlsxErythronium_americanum_Pollen_Limiation_2016Reproductive success and leaf size of Erythronium americanum for control and pollen supplemented individuals along an elevation gradient at Mont-Mégantic National Park.erythronium_americanum_PL_2016.xlsxTrillium_erectum_herbivory_2016Proportion of browsed Trillium erectum individuals along an elevation gradient at Mont-Mégantic National Park.trillium_erectum_herbivorie_2016.xlsxErythronium_americanum_herbivory_2016Proportion of browsed Erythronium americanum individuals along an elevation gradient at Mont-Mégantic National Park.erythronium_americanum_herbivorie_2016.xlsxNumber_of_seeds_T.erectum_E.americanum_2015_2016Reproductive success of Trillium erectum and Erythronium americanum along an elevation gradient at Mont-Mégantic National Park.nombre_de_graines_contrôles_T.erectum_E.americanum_2015_2016.xlsx
DOI: 10.5061/dryad.1dp6s
title: Data from: Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake

description: RNA viruses exist as complex mixtures of genotypes, known as quasispecies,
 where the evolution potential resides in the whole community of related
 genotypes. Quasispecies structure and dynamics have been studied in detail
 for virus infecting animals and plants but remain unexplored for those
 infecting micro-organisms in environmental samples. We report the first
 metagenomic study of RNA viruses in an Antarctic lake (Lake Limnopolar,
 Livingston Island). Similar to low-latitude aquatic environments, this
 lake harbours an RNA virome dominated by positive single-strand RNA
 viruses from the order Picornavirales probably infecting micro-organisms.
 Antarctic picorna-like virus 1 (APLV1), one of the most abundant viruses
 in the lake, does not incorporate any mutation in the consensus sequence
 from 2006 to 2010 and shows stable quasispecies with low-complexity
 indexes. By contrast, APLV2-APLV3 are detected in the lake water
 exclusively in summer samples and are major constituents of surrounding
 cyanobacterial mats. Their quasispecies exhibit low complexity in
 cyanobacterial mat, but their run-off-mediated transfer to the lake
 results in a remarkable increase of complexity that may reflect the
 convergence of different viral quasispecies from the catchment area or
 replication in a more diverse host community. This is the first example of
 viral quasispecies from natural aquatic ecosystems and points to
 ecological connectivity as a modulating factor of quasispecies complexity.
description: Contigs obtained with
 Newbler and CLC Genomic Workbench de novo assemblersContigs.zipAlignment of the RpRd domainRdRp_Alignment.faPhylogenetic tree based on RpRd domain alignmentRdRp_Tree.newickValidated SNVsValidated SNVs (CLC Genomic Workbench approach) for all APLV-quasispeciesAPLV_SNVs.xlsxPCA input for dinucleotide bias analysisDinucleotidePCA_131Picornavirales.txt
DOI: 10.5061/dryad.q4c60
title: Data from: Inaccurate color discrimination by pollinators promotes evolution of discrete color polymorphism in food-deceptive flowers

description: Many plant species employing food-deceptive pollination strategy show
 discrete or continuous floral polymorphism within their populations.
 Previous studies have suggested that negative frequency-dependent
 selection (NFDS) caused by learning behavior of pollinators was
 responsible for maintenance of floral polymorphism. However, NFDS alone
 does not explain why and when discrete or continuous polymorphism evolves.
 In this study, we use an evolutionary simulation model to propose that
 inaccurate discrimination of flower colors by pollinators results in
 evolution of discrete flower color polymorphism. Simulations showed that
 associative learning based on inaccurate discrimination in pollinators
 caused disruptive selection of flower colors. The degree of inaccuracy
 determined the number of discrete flower colors that evolved. Our results
 suggest that animal behavior based on inaccurate discrimination may be a
 general cause of disruptive selection that promotes discrete trait
 polymorphism.
description: Kagawa and Takimoto 2015
 source codes and data setsThis ZIP file contains
 Java source codes, R script, and Excel files for the individual-based
 simulation and analyses in our paper: Kagawa and Takimoto (2015)
 “Inaccurate Color Discrimination by Pollinators Promotes Evolution of
 Discrete Color Polymorphism in Food-deceptive Flowers”.Kagawa_Takimoto_2015_source_code.zip
DOI: 10.5281/zenodo.18374482
title: Pathogen-induced structural simplification drives functional erosion and trophic decoupling in forest-floor arthropods

description: All data for analyses_Ecology.xlsx:

Site-level dataset containing taxonomic (estimated richness, activity-density) and functional diversity metrics (FEve, Rao’s Q, FRic where available) for each arthropod group, spiders (spi), carabids (car), centipedes (cen), millipedes (mil), and woodlice (woo), together with environmental predictors including canopy openness (%), litter depth (cm), deadwood cover (%), herb-layer cover (%), shrub-layer cover (%), ash infestation intensity (%), and stand age category.

Models_Ecology.R:

R script used for model fitting, model selection, and plotting. For each response (stand structure: Canopy, Litter, Deadwood, Herb, Shrub; and community metrics for spiders (spi), carabids (car), centipedes (cen), millipedes (mil), and woodlice (woo)), we fitted a candidate set of GAMs testing effects of ash infestation intensity (Infestation, %) and stand age category (Young, Moderate, Mature), including additive terms and age-specific smooths s(Infestation, by = age); models were compared using AIC, and fitted relationships were visualized along the infestation gradient. Gamma(log) and negative binomial error structures were used where appropriate.
DOI: 10.5281/zenodo.18374485
title: Pathogen-induced structural simplification drives functional erosion and trophic decoupling in forest-floor arthropods

description: All data for analyses_Ecology.xlsx:

Site-level dataset containing taxonomic (estimated richness, activity-density) and functional diversity metrics (FEve, Rao’s Q, FRic where available) for each arthropod group, spiders (spi), carabids (car), centipedes (cen), millipedes (mil), and woodlice (woo), together with environmental predictors including canopy openness (%), litter depth (cm), deadwood cover (%), herb-layer cover (%), shrub-layer cover (%), ash infestation intensity (%), and stand age category.

Models_Ecology.R:

R script used for model fitting, model selection, and plotting. For each response (stand structure: Canopy, Litter, Deadwood, Herb, Shrub; and community metrics for spiders (spi), carabids (car), centipedes (cen), millipedes (mil), and woodlice (woo)), we fitted a candidate set of GAMs testing effects of ash infestation intensity (Infestation, %) and stand age category (Young, Moderate, Mature), including additive terms and age-specific smooths s(Infestation, by = age); models were compared using AIC, and fitted relationships were visualized along the infestation gradient. Gamma(log) and negative binomial error structures were used where appropriate.
DOI: 10.5061/dryad.vr815
title: Data from: Female stick insects mate multiply to find compatible mates

description: Why females of many species mate multiply in the absence of direct
 benefits remains an open question in evolutionary ecology. Interacting and
 mating with multiple males can be costly to females in terms of time,
 resources, predation risk, and disease transmission. A number of indirect
 genetic benefits have been proposed to explain such behaviors, but the
 relative importance of these mechanisms in natural systems remains
 unclear. We tested for several direct and indirect benefits of polyandry
 in the walking stick Timema cristinae. We found no evidence of direct
 benefits with respect to longevity or fecundity. However, male × female
 genotypic interactions affected egg-hatching success and offspring
 production independent of relatedness, suggesting that mating with certain
 males benefits females and that the best male may differ for each female.
 Furthermore, multiply mated females biased paternity toward one or few
 males, and the extent of this bias was positively correlated to
 egg-hatching success. Our data, therefore, provide evidence for indirect
 benefits through compatibility effects in this species. By mating
 multiply, females may improve their chances of mating with a compatible
 male if compatibility cannot be assessed before mating. Such compatibility
 effects can explain the evolution and maintenance of polyandry in Timema
 and many other species.
description: Lab Female Mating
 RateResults from experiment
 to measure female mating rate and fecundity when exposed to differing
 numbers of males in the lab.NaturalMatingsThe paternity and effective paternity of eggs laid by wild caught adult females.NaturalMatingsGenotypesThe genotypes of mothers and offspring from the NaturalMatings.csv file used to assign paternity to offspring.Polyandry MatingsResults from an experiment measuring female survival, fecundity, and egg hatching success through time when singly or multiply mated.