cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9850t
title: Data from: A shift from exploitation to interference competition with increasing density affects population and community dynamics

description: Intraspecific competition influences population and community dynamics and
 occurs via two mechanisms. Exploitative competition is an indirect effect
 that occurs through use of a shared resource and depends on resource
 availability. Interference competition occurs by obstructing access to a
 resource and may not depend on resource availability. Our study tested
 whether the strength of interference competition changes with protozoa
 population density. We grew experimental microcosms of protozoa and
 bacteria under different combinations of protozoan density and basal
 resource availability. We then solved a dynamic predator–prey model for
 parameters of the functional response using population growth rates
 measured in our experiment. As population density increased, competition
 shifted from exploitation to interference, and competition was less
 dependent on resource levels. Surprisingly, the effect of resources was
 weakest when competition was the most intense. We found that at low
 population densities, competition was largely exploitative and resource
 availability had a large effect on population growth rates, but the effect
 of resources was much weaker at high densities. This shift in competitive
 mechanism could have implications for interspecific competition, trophic
 interactions, community diversity, and natural selection. We also tested
 whether this shift in the mechanism of competition with protozoa density
 affected the structure of the bacterial prey community. We found that both
 resources and protozoa density affected the structure of the bacterial
 prey community, suggesting that competitive mechanism may also affect
 trophic interactions.
description: InterferenceExploitative_ExperimentContains treatment metadata (resource availability in mg and initial Colpidium density in cells/mL) as well as final Colpidium density in cells/mL. Also indicates which samples were randomly selected for 16S rRNA gene sequencing ("y"=yes, sample was sequenced; "n"=no, sample was not sequenced).
DOI: 10.5061/dryad.121b453
title: Data from: Paleotropical diversification dominates the evolution of the hyperdiverse ant tribe Crematogastrini (Hymenoptera: Formicidae)

description: Levels of diversity vary strikingly among different phylogenetic lineages
 of ants. Rapid radiations in early ant evolution have often proven
 difficult to resolve with traditional Sanger-sequencing data sets of
 modest size. We provide a phylogenomic perspective on the evolution of the
 hyperdiverse ant tribe Crematogastrini by analyzing sequence data for
 nearly 1800 ultraconserved element (UCE) loci from 153 species comprising
 56 genera. We reconstruct a next-to-complete genus-level phylogeny using
 concatenated maximum-likelihood and species-tree approaches, estimate
 divergence dates and diversification rates for the tribe, and investigate
 the evolution of nest sites. Our results show ten well-supported major
 clades which we define as the Cataulacus, Carebara, Vollenhovia,
 Podomyrma, Crematogaster, Mayriella, Lordomyrma, Myrmecina, Paratopula,
 and Formicoxenus genus-groups. These lineages are estimated to have arisen
 from a Paleotropical ancestor (crown-group age ~75 Ma) over a relatively
 short time interval (50–70 Ma). The Afrotropical and especially the
 Indomalayan regions appear to have played a key role in the early
 diversification history of the tribe. Several shifts in diversification
 rates were found to be related to the evolution of large, widespread
 genera; however, associating these shifts with evolutionary innovations or
 events was not possible. Arboreal habitats have been successfully
 colonized by only few clades within Crematogastrini from ground-nesting
 ancestors, with no reversals supported. Our genus-level phylogeny for
 Crematogastrini provides insights into the diversification and evolution
 of one of the most diverse clades of ants, and our division of the tribe
 into well-supported genus-group lineages sets the stage for more detailed
 species-level investigations.
description: Trinity assembled contig
 files used for PhyluceCrematogastrini_Trinity_Assemblies.zipData matrices analyzed for this studySequenceDataMatrices.zipFinal trees presented and displayed in this studyTreefiles.zip
DOI: 10.7910/dvn/xlrgui
title: Replication Data for: From Olympic Gold to Government Approval?: Limited Evidence of Attribution Error from the 2024 Paris Games

description: This repository provides the data and code required to reproduce the analyses and figures reported in “From Olympic Gold to Government Approval? Limited Evidence of Attribution Error from the 2024 Paris Games" in *Japanese Journal of Political Science*. All scripts are written in R and are organized to mirror the structure of the paper and Supplementary Information.
DOI: 10.5061/dryad.pq54gh5
title: Data from: Artificial light at night decreases metamorphic duration and juvenile growth in a widespread amphibian

description: Artificial Light at Night (ALAN) affects over 20% of the earth’s surface
 and is estimated to increase 6% per year. Most studies of ALAN have
 focused on a single mechanism or life-stage. We tested for indirect and
 direct ALAN effects that occurred by altering American toads’ (Anaxyrus
 americanus) ecological interactions or by altering toad development and
 growth, respectively. We conducted an experiment over two life-stages
 using outdoor mesocosms and indoor terraria. In the first phase, the
 presence of ALAN reduced metamorphic duration and periphyton biomass. The
 effects of ALAN appeared to be mediated through direct effects on toad
 development, and we found no evidence for indirect effects of ALAN acting
 through altered ecological interactions or colonization. In the second
 phase, post-metamorphic toad growth was reduced by 15% in the ALAN
 treatment. Juvenile-stage ALAN also affected toad activity: in natural
 light, toads retreated into leaf litter at night whereas ALAN toads did
 not change behaviour. Carry-over effects of ALAN were also present;
 juvenile toads that had been exposed to larval ALAN exhibited marginally
 increased activity. In this time frame and system, our experiments
 suggested ALAN’s effects act primarily through direct effects, rather than
 indirect effects, and can persist across life-stages.
description: ALAN and American Toad
 DataThis data is the data
 used in the article entitled "Artificial Light at Night decreases
 metamorphic duration and increases juvenile growth in a widespread
 amphibian." There is data on illumination levels of local wetlands in
 Cleveland, Ohio, as well as measurements of all parts of the experiment
 including toad time to metamorphosis, metamorphic duration, growth,
 survival and behavior in the larval and or post-metamorphic live stages.
 We also included measurements of algal growth and colonization of our
 mesocosms.All data for
 dryad_Final_2018_05_23.xlsx
DOI: 10.5061/dryad.15cn3
title: Data from: Evolution determines how global warming and pesticide exposure will shape predator–prey interactions with vector mosquitoes

description: How evolution may mitigate the effects of global warming and pesticide
 exposure on predator–prey interactions is directly relevant for vector
 control. Using a space-for-time substitution approach, we addressed how
 4°C warming and exposure to the pesticide endosulfan shape the predation
 on Culex pipiens mosquitoes by damselfly predators from replicated low-
 and high-latitude populations. Although warming was only lethal for the
 mosquitoes, it reduced predation rates on these prey. Possibly, under
 warming escape speeds of the mosquitoes increased more than the attack
 efficiency of the predators. Endosulfan imposed mortality and induced
 behavioral changes (including increased filtering and thrashing and a
 positional shift away from the bottom) in mosquito larvae. Although the
 pesticide was only lethal for the mosquitoes, it reduced predation rates
 by the low-latitude predators. This can be explained by the combination of
 the evolution of a faster life history and associated higher
 vulnerabilities to the pesticide (in terms of growth rate and lowered
 foraging activity) in the low-latitude predators and pesticide-induced
 survival selection in the mosquitoes. Our results suggest that predation
 rates on mosquitoes at the high latitude will be reduced under warming
 unless predators evolve toward the current low-latitude phenotype or
 low-latitude predators move poleward.
description: Effects of global
 warming and pesticide exposure on mosquito-damselfly
 interactionsThis database include
 two data sheets. The first sheet contains survival, initial weight and end
 weight data of mosquitoes in different temperature-by-pesticide treatment
 combinations in the exposure experiment. The second sheet consists of data
 of latitude, population, survival, initial weight and end weight of
 damselfies in the exposure experiment, number of mosquitoes eaten and
 behaviors of both damselfly predators and mosquito prey during the
 predation experiment.Data for
 submit.xlsx
DOI: 10.5061/dryad.q2h13
title: Data from: Adenosine receptors mediate the hypoxic ventilatory response but not the hypoxic metabolic response in the naked mole rat during acute hypoxia

description: Naked mole rats are the most hypoxia-tolerant mammals identified; however,
 the mechanisms underlying this tolerance are poorly understood. Using
 whole-animal plethysmography and open-flow respirometry, we examined the
 hypoxic metabolic response (HMR), hypoxic ventilatory response (HVR) and
 hypoxic thermal response in awake, freely behaving naked mole rats exposed
 to 7% O2 for 1 h. Metabolic rate and ventilation each reversibly decreased
 70% in hypoxia (from 39.6 ± 2.9 to 12.1 ± 0.3 ml O2 min−1 kg−1, and 1412 ±
 244 to 417 ± 62 ml min−1 kg−1, respectively; p &lt; 0.05), whereas
 body temperature was unchanged and animals remained awake and active.
 Subcutaneous injection of the general adenosine receptor antagonist
 aminophylline (AMP; 100 mg kg−1, in saline), but not control saline
 injections, prevented the HVR but had no effect on the HMR. As a result,
 AMP-treated naked mole rats exhibited extreme hyperventilation in hypoxia.
 These animals were also less tolerant to hypoxia, and in some cases
 hypoxia was lethal following AMP injection. We conclude that in naked mole
 rats (i) hypoxia tolerance is partially dependent on profound hypoxic
 metabolic and ventilatory responses, which are equal in magnitude but
 occur independently of thermal changes in hypoxia, and (ii) adenosine
 receptors mediate the HVR but not the HMR.
description: Saline treated control
 NMR dataSham.zipAMP-treated NMR dataDrugs.zip
DOI: 10.5061/dryad.rj6gq
title: Data from: Evolution of cross-resistance to medical triazoles in Aspergillus fumigatus through selection pressure of environmental fungicides

description: Resistance to medical triazoles in Aspergillus fumigatus is an emerging
 problem for patients at risk of aspergillus diseases. There are currently
 two presumed routes for medical triazole-resistance selection: (i) through
 selection pressure of medical triazoles when treating patients and (ii)
 through selection pressure from non-medical sterol-biosynthesis-inhibiting
 (SI) triazole fungicides which are used in the environment. Previous
 studies have suggested that SI fungicides can induce cross-resistance to
 medical triazoles. Therefore, to assess the potential of selection of
 resistance to medical triazoles in the environment, we assessed
 cross-resistance to three medical triazoles in lineages of A. fumigatus
 from previous work where we applied an experimental evolution approach
 with one of five different SI fungicides to select for resistance. In our
 evolved lines we found widespread cross-resistance indicating that
 resistance to medical triazoles rapidly arises through selection pressure
 of SI fungicides. All evolved lineages showed similar evolutionary
 dynamics to SI fungicides and medical triazoles, which suggests that the
 mutations inducing resistance to both SI fungicides and medical triazoles
 are likely to be the same. Whole-genome sequencing revealed that a variety
 of mutations were putatively involved in the resistance mechanism, some of
 which are in known target genes.
description: dataset-JZ Cross
 evolution to medical triazole in A. fumigatusData of fitness
 measurements.
DOI: 10.5061/dryad.mn8cs
title: Data from: Sources of variability in cytosolic calcium transients triggered by stimulation of homogeneous uro-epithelial cell monolayers

description: Epithelial tissue structure is the emergent outcome of the interactions
 between large numbers of individual cells. Experimental cell biology
 offers an important tool to unravel these complex interactions, but
 current methods of analysis tend to be limited to mean field approaches or
 representation by selected subsets of cells. This may result in bias
 towards cells that respond in a particular way and/or neglect local,
 context-specific cell responses. Here, an automated algorithm was applied
 to examine in detail the individual calcium transients evoked in
 genetically homogeneous, but asynchronous populations of cultured
 non-immortalized normal human urothelial cells when subjected to either
 the global application of an external agonist or a localized scratch
 wound. The recorded calcium transients were classified automatically
 according to a set of defined metrics and distinct sub-populations of
 cells that responded in qualitatively different ways were observed. The
 nature of this variability in the homogeneous cell population was
 apportioned to two sources: intrinsic variation in individual cell
 responses and extrinsic variability due to context-specific factors of the
 environment, such as spatial heterogeneity. Statistically significant
 variation in the features of the calcium transients evoked by scratch
 wounding according to proximity to the wound edge was identified. The
 manifestation of distinct sub-populations of cells is considered central
 to the coordination of population-level response resulting in wound
 closure.
description: ATP_Exp_
 JPEG_SequenceRed, Green and Ratio
 Jpeg images forming primary dataset for ATP experiment described in
 paper.JPEG Sequences for
 Scratch Wound experimentRed, green and ratio
 immunofluorescence images captured during primary scratch wounding
 experiment described in paper.Wound_Exp_JPEG_Sequence.zip
DOI: 10.5061/dryad.bd6h3
title: Data from: Establishment of a coastal fish in the Azores: recent colonisation or sudden expansion of an ancient relict population?

description: The processes and timescales associated with ocean-wide changes in the
 distribution of marine species have intrigued biologists since Darwin’s
 earliest insights into biogeography. The Azores, a mid-Atlantic volcanic
 archipelago located &gt;1000 km off the European continental shelf,
 offers ideal opportunities to investigate phylogeographic colonisation
 scenarios. The benthopelagic sparid fish known as the common two-banded
 seabream (Diplodus vulgaris) is now relatively common along the coastline
 of the Azores archipelago, but was virtually absent before the 1990s. We
 employed a multiple genetic marker approach to test whether the successful
 establishment of the Azorean population derives from a recent colonisation
 from western continental/island populations or from the demographic
 explosion of an ancient relict population. Results from nuclear and mtDNA
 sequences show that all Atlantic and Mediterranean populations belong to
 the same phylogroup, though microsatellite data indicate significant
 genetic divergence between the Azorean sample and all other locations, as
 well as among Macaronesian, western Iberian and Mediterranean regions. The
 results from Approximate Bayesian Computation indicate that D. vulgaris
 has likely inhabited the Azores for ~40 (95% confidence interval (CI):
 5.5–83.6) to 52 (95% CI: 6.32–89.0) generations, corresponding to roughly
 80–150 years, suggesting near-contemporary colonisation, followed by a
 more recent demographic expansion that could have been facilitated by
 changing climate conditions. Moreover, the lack of previous records of
 this species over the past century, together with the absence of lineage
 separation and the presence of relatively few private alleles, do not
 exclude the possibility of an even more recent colonisation event.
description: Diplodus_vulgaris_DryadMicrosatellites' alleles
DOI: 10.5061/dryad.m9s46
title: Data from: Phenotypic and genetic divergence within a single whitefish form – detecting the potential for future divergence

description: Human-induced nutrient input can change the selection regime and lead to
 the loss of biodiversity. For example, eutrophication caused speciation
 reversal in polymorphic whitefish populations through a flattening of
 littoral-pelagic selection gradients. We investigated the current state of
 phenotypic and genetic diversity in whitefish (Coregonus macrophthalmus)
 in a newly restored lake whose nutrient load has returned to
 pre-eutrophication levels and found that whitefish spawning at different
 depths varied phenotypically and genetically: individuals spawning at
 shallower depth had fewer gill rakers, faster growth, and a morphology
 adapted to benthic-feeding and they showed higher degrees of diet
 specialization than deeper spawning individuals. Microsatellite analyses
 complemented the phenotype analyses by demonstrating reproductive
 isolation along different spawning depths. Our results indicate that
 whitefish still retain or currently re-gain phenotypic and genetic
 diversity, which was lost during eutrophication. Hence, the population
 documented here has a potential for future divergence because natural
 selection can target phenotypes specialized along re-established
 littoral-pelagic selection gradients. The biodiversity however, will have
 better chances to return if managers acknowledge the evolutionary
 potential within the local whitefish and adapt fishing and stocking
 measures.
description: basic data and stable
 isotope data of gangfisch (Coregonus macrophthalmus) caught at different
 depths in Lake ConstanceFish (n=30 each) were
 collected in the field using gill nets set at three different depths, 2,
 25 and 50m. C13 and N15 are stable isotope data δC13 and δN15.
 ID=indivdiual ID; TL = fish total length; SL = fish standard length; sex
 (f=female, m=male); GR=gill raker counts; age= fish age in
 yearsbasic
 data and stable isotope data.txtmorphological
 measurements of Coregounus macrophthalmus from Lake Constance caught at
 different depthsIndividual landmark
 coordinates calculated using the software TPSDIGlandmark coordinates from
 TPSDIG.txtmicrosatellite data for
 Coregouns macrophthalmus caught at different depths in Lake
 ConstanceRaw data of 12
 microsatellite loci used for genetic analysis of C. macrophthalmus caught
 at 3 different depths (2,5 and 50m) in Lake Constance. given are locus
 names and fragment sizes of individual microsatellite alleles in bp
 created with Genemapper.microsatellite
 data.txt
DOI: 10.5061/dryad.hs593
title: Data from: Genome-guided investigation of plant natural product biosynthesis

description: The medicinal plant Madagascar periwinkle, Catharanthus roseus (L.) G.
 Don, produces hundreds of biologically active monoterpene-derived indole
 alkaloid (MIA) metabolites and is the sole source of the potent, expensive
 anti-cancer compounds vinblastine and vincristine. Access to a genome
 sequence would enable insights into the biochemistry, control, and
 evolution of genes responsible for MIA biosynthesis. However, generation
 of a near-complete, scaffolded genome is prohibitive to small research
 communities due to the expense, time, and expertise required. In this
 study, we generated a genome assembly for C. roseus which provides a near
 comprehensive representation of the genic space that revealed the genomic
 context of key points within the MIA biosynthetic pathway including
 physically clustered genes, tandem gene duplication, expression
 subfunctionalization, and putative neofunctionalization. The genome
 sequence also facilitated high resolution coexpression analyses that
 revealed three distinct clusters of co-expression within the components of
 the MIA pathway. Coordinated biosynthesis of precursors and intermediates
 throughout the pathway appear to be a feature of vinblastine/vincristine
 biosynthesis. The C. roseus genome also revealed localization of
 enzyme-rich genic regions and transporters near known biosynthetic
 enzymes, highlighting how even a draft genome sequence can empower the
 study of high-value specialized metabolites.
description: cro_functional_annotation.final.txtcro_scaffolds.min_200bpcro_scaffolds.min_1000bpcro_std_maker_anno.final.cdscro_std_maker_anno.finalcro_std_maker_anno.final.pepcro_std_maker_anno.final.transcripts
DOI: 10.5061/dryad.ks4k2
title: Data from: Automixis in Artemia: solving a century-old controversy

description: Parthenogenesis (reproduction through unfertilized eggs) encompasses a
 variety of reproduction modes with (automixis) or without (apomixis)
 meiosis. Different modes of automixis have very different genetic and
 evolutionary consequences but can be particularly difficult to tease
 apart. In this paper, we propose a new method to discriminate different
 types of automixis from population-level genetic data. We apply this
 method to diploid Artemia parthenogenetica, a crustacean whose
 reproductive mode remains controversial despite a century of intensive
 cytogenetic observations. We focus on A. parthenogenetica from two western
 Mediterranean populations. We show that they are diploid, and that markers
 remain heterozygous in cultures maintained up to ~36 generations in the
 laboratory. Moreover, parallel patterns of population-wide heterozygosity
 levels between the two natural populations strongly support the conclusion
 that diploid A. parthenogenetica reproduce by automictic parthenogenesis
 with central fusion and low, but non-zero recombination. This settles a
 century-old controversy on Artemia, and, more generally, suggests that
 many automictic organisms harbor steep within-chromosome gradients of
 heterozygosity due to a transition from clonal transmission in
 centromere-proximal regions to a form of inbreeding similar to
 self-fertilization in centromere-distal regions. Such systems therefore
 offer a new avenue for contrasting the genomic consequences of asexuality
 and inbreeding.
description: Nougué et al 2015
 Individual Genotypic dataMicrosatellite genotypic
 individual data for the populations used in the paperData genotypes Nougue et al
 2015.txt