cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v0dh5
title: Data from: Taxonomic revision of Dasyphyllum sect. Macrocephala (Asteraceae: Barnadesioideae)

description: Dasyphyllum sect. Macrocephala is restricted to the Cerrado, Caatinga, and
 Atlantic Forest biomes of Brazil, spreading into similar areas in Bolivia
 and Paraguay. The six recognized species in this section are monoecious
 shrubs with erect or decumbent branches, single or paired, rarely
 fasciculate, straight or curved axillary spines, leaves with apiculate or
 aristate apices, 5–7 basally or suprabasally acrodromous veins, sessile
 capitula, usually solitary or in groups of two to four, a campanulate or
 infundibuliform involucre generally longer than 20 mm, and with
 hermaphroditic florets usually with liguliform corollas and externally
 sericeous lobes. An identification key, descriptions, comments regarding
 morphology and taxonomy, maps showing geographical distribution, and
 illustrations are presented, together with 17 new synonyms and 18
 typifications.
description: Specimens examined of
 Dasyphyllum section MacrocephalaThese data refer to the
 herbarium specimens examined in Dasyphyllum. Herbarium acronyms according
 to Holmgren et al. (1990), except to not yet indexed herbaria HST (Rural
 University of Pernambuco, Recife, Pernambuco, Brazil) and HUCS (Department
 of Biological Sciences, Natural Sciences Museum, University of Caxias do
 Sul, Caxias do Sul, Rio Grande do Sul , Brazil).suplemento Dasyphyllum
 Macrocephala.pdf
DOI: 10.5061/dryad.j81m5
title: Data from: Condition-dependent expression of carotenoid- and melanin-based plumage colour of northern flicker nestlings revealed by manipulation of brood size

description: Carotenoid-based colouration in feathers is widely accepted to be a
 reliable signal of the health of an individual, but the
 condition-dependence of melanin-based plumage ornaments has been highly
 debated. Using broods that were manipulated in size, we tested whether
 nutritional stress during rearing affected the carotenoid pigmentation in
 secondary feathers and the size, shape, and symmetry of melanin spots on
 breast plumage of northern flicker Colaptes auratus nestlings. Two
 measures of carotenoid colour (chroma and brightness) of secondary flight
 feathers did not vary according to brood size treatment, but in a larger
 dataset from the population, carotenoid chroma was positively associated
 with nestling mass. Nestlings from experimentally enlarged broods had
 smaller melanin spots than those from reduced broods, which is some of the
 first experimental evidence that melanin ornament size in growing
 nestlings is condition-dependent. However, the shape and symmetry of the
 melanin breast spots was not associated with nestling mass. Sexual
 dimorphism was apparent in both types of pigmentation and future studies
 should investigate whether there are any trade-offs for nestlings between
 investing in carotenoid colouration and melanisation and whether
 trade-offs differ between the sexes.
description: Data file for
 condition-dependent expression of carotenoid- and melanin-based plumage
 colour of northern flicker nestlings revealed by manipulation of brood
 sizeExcel document with
 three tabs.dryad_melcar.xlsx
DOI: 10.5061/dryad.mr720
title: Data from: A faster escape does not enhance survival in zebrafish larvae

description: An escape response is a rapid manoeuvre used by prey to evade predators.
 Performing this manoeuvre at greater speed, in a favourable direction, or
 from a longer distance have been hypothesized to enhance the survival of
 prey, but these ideas are difficult to test experimentally. We examined
 how prey survival depends on escape kinematics through a novel combination
 of experimentation and mathematical modelling. This approach focused on
 zebrafish (Danio rerio) larvae under predation by adults and juveniles of
 the same species. High-speed three-dimensional kinematics were used to
 track the body position of prey and predator and to determine the
 probability of behavioural actions by both fish. These measurements
 provided the basis for an agent-based probabilistic model that simulated
 the trajectories of the animals. Predictions of survivorship by this model
 were found by Monte Carlo simulations to agree with our observations and
 we examined how these predictions varied by changing individual model
 parameters. Contrary to expectation, we found that survival may not be
 improved by increasing the speed or altering the direction of the escape.
 Rather, zebrafish larvae operate with sufficiently high locomotor
 performance due to the relatively slow approach and limited range of
 suction feeding by fish predators. We did find that survival was enhanced
 when prey responded from a greater distance. This is an ability that
 depends on the capacity of the visual and lateral line systems to detect a
 looming threat. Therefore, performance in sensing, and not locomotion, is
 decisive for improving the survival of larval fish prey. These results
 offer a framework for understanding the evolution of predator–prey
 strategy that may inform prey survival in a broad diversity of animals.
description: Kinematic
 dataAll kinematic data for
 predator-prey experiments.data.zipMatlab codeAll code for the experimental analysis and mathematical simulations.simulation code.zip
DOI: 10.5061/dryad.7hf2j
title: Data from: Time series dataset of fish assemblages near thermal discharges at nuclear power plants in northern Taiwan

description: Long-term time series datasets with consistent sampling methods are rather
 rare, especially the ones of non-target coastal fishes. Here we described
 a long-term time series dataset of fish collected by trammel net fish
 sampling and observed by an underwater diving visual census near the
 thermal discharges at two nuclear power plants on the northern coast of
 Taiwan. Both experimental and control stations of these two investigations
 were monitored four times per year in the surrounding seas at both plants
 from 2000 to 2017. The underwater visual census mainly monitored reef fish
 assemblages and trammel net samples monitored pelagic or demersal fishes
 above the muddy/sandy bottom. In total, 508 samples containing 203,863
 individuals from 347 taxa were recorded in both investigations at both
 plants. These data can be used by ecologists and fishery biologists
 interested in the elucidation of the temporal patterns of species
 abundance and composition.
description: READMETrammel net
 sampling_Plant ITrammel net
 sampling_Plant IIUnderwater visual
 census_Plant IUnderwater visual
 census_Plant IIReference of
 species
DOI: 10.5061/dryad.mr076
title: Data from: A revised framework of Dryopteris subg. Nothoperanema (Dryopteridaceae) inferred from phylogenetic evidence, with descriptions of two new sections.

description: Dryopteris subgenus Nothoperanema (Dryopteridaceae) includes sections
 Acrophorus, Diacalpe, Nothoperanema, and Peranema. Phylogenetic
 relationships among these sections and their relationship to sect.
 Dryopsis (genus Dryopteris subgenus Erythrovariae, Dryopteridaceae) are
 unclear. Additionally, previous phylogenetic work has not included
 Stenolepia, which has been suggested as an important relative of Peranema
 based on morphology. In this study, we examined phylogenetic relationships
 within subgenus Nothoperanema by including Stenolepia and utilizing six
 plastid regions (∼5,500 characters). Our inferred phylogeny revealed that
 sect. Dryopsis is not monophyletic. The Nothoperanema clade is highly
 supported, and includes sect. Acrophorus, sect. Diacalpe, sect.
 Nothoperanema, sect. Peranema, certain Dryopsis species, and Stenolepia.
 By re-examining diagnostic morphological characters, we establish and
 describe two new sections under subgenus Nothoperanema: sect. Shiehia and
 sect. Stenolepia. This revision accommodates new species transferred from
 sects. Dryopsis and Stenolepia, and makes subgenus Nothoperanema and each
 of its sections natural groups. Finally, we provide a table with
 morphological comparisons and a key to sections.
description: subg. Nothoperanema
 ndhF-trnN+rps16-matK+trnL-L-F+chlL modiThe alignment for
 phylogenetic analyses. The region partition is noted within the nex
 file.subg. Nothoperanema best
 ML treeThe best ML tree in this
 study.subg.
 Nothoperanema.best.tre
DOI: 10.5061/dryad.1s138
title: Data from: 10 years of life in compost: temporal and spatial variation of North German C. elegans populations

description: The nematode Caenorhabditis elegans is a central laboratory model system
 in almost all biological disciplines, yet its natural life history and
 population biology are largely unexplored. Such information is essential
 for in-depth understanding of the nematode's biology because its
 natural ecology provides the context, in which its traits and the
 underlying molecular mechanisms evolved. We characterized natural
 phenotypic and genetic variation among North German C. elegans isolates.
 We used the unique opportunity to compare samples collected 10 years apart
 from the same compost heap and additionally included recent samples for
 this and a second site, collected across a 1.5-year period. Our analysis
 revealed significant population genetic differentiation between locations,
 across the 10-year time period, but for only one location a trend across
 the shorter time frame. Significant variation was similarly found for
 phenotypic traits of likely importance in nature, such as choice behavior
 and population growth in the presence of pathogens or naturally associated
 bacteria. Phenotypic variation was significantly influenced by C. elegans
 genotype, time of isolation, and sampling site. The here studied C.
 elegans isolates may provide a valuable, genetically variable resource for
 future dissection of naturally relevant gene functions.
description: Results of C. elegans
 choice assayRaw data for C. elegans
 choice assay. During this assay, C. elegans was given the choice between
 two bacteria, using the standardized C. elegans choice assay. The table
 includes information on strain code (first column), origin of the strain
 (second column), strain genotype as inferred with microsatellites (third
 column), year of C. elegans sampling (fourth column), replicate of choice
 assay within a particular run of the experiment (fifth column), run of
 experiment (sixth column), scoring time point (seventh column), position
 of the two bacterial strains/species (eighth and nineth columns), and the
 inferred choice index (tenth column) - always relative to the first listed
 bacterium.Results_choice_assay.xlsxResults of C. elegans population growth assayRaw data for C. elegans population growth assay. During this assay, three hermaphrodites of C. elegans were allowed to reproduce over five days on different bacteria. The table includes information on strain code (first column), origin of the strain (second column), strain genotype as inferred with microsatellites (third column), year of C. elegans sampling (fourth column), bacterial strain/species during the population growth assay (fifth column), replicate of population growth assay within a particular run of the experiment (sixth column), run of experiment (seventh column), and the inferred mean number of worms per initial hermaphrodite after the five-day period (eighth column).Results_population_growth_assay.xlsx
DOI: 10.5061/dryad.8s881
title: Data from: Fisher’s geometric model predicts the effects of random mutations when tested in the wild

description: Fisher's Geometric Model of Adaptation (FGM) has been the conceptual
 foundation for studies investigating the genetic basis of adaptation since
 the onset of the neo Darwinian synthesis. FGM describes adaptation as the
 movement of a genotype toward a fitness optimum due to beneficial
 mutations. To date, one prediction of FGM, the probability of improvement
 is related to the distance from the optimum, has only been tested in
 microorganisms under laboratory conditions. There is reason to believe
 that results might differ under natural conditions where more mutations
 likely affect fitness, and where environmental variance may obscure the
 expected pattern. We chemically induced mutations into a set of 19
 Arabidopsis thaliana accessions from across the native range of A.
 thaliana and planted them alongside the premutated founder lines in two
 habitats in the mid-Atlantic region of the USA under field conditions. We
 show that FGM is able to predict the outcome of a set of random induced
 mutations on fitness in a set of Arabidopsis thaliana accessions grown in
 the wild: mutations are more likely to be beneficial in relatively less
 fit genotypes. This finding suggests that FGM is an accurate approximation
 of the process of adaptation under more realistic ecological conditions.
description: Raw
 DataIndividual weights and
 survivorship for each line.Dryad.xlsx
DOI: 10.6084/m9.figshare.31152117
title: Prediction and modeling on bioaccumulation of chemicals in aquatic organisms: A critical review

description: Chemical bioaccumulation, which links internal exposure to hazards, plays a crucial role in ecological and human health risk assessment. Traditional bioaccumulation evaluations rely on laboratory-simulated exposure experiments and field monitoring studies, facing limitations in high cost, time constraints, and ethical concerns. Mechanistic toxicokinetic (TK) models and data-driven quantitative structure-activity relationship (QSAR) approaches have emerged as efficient alternatives. The review synthesizes decades of progress in TK and QSAR models for bioaccumulation prediction of chemicals in aquatic organisms, encompassing theoretical foundations, mathematical equations, practical applications, and current research gaps. While traditional compartmental TK models provide simplicity, physiologically-based toxicokinetic (PBTK) models enhance accuracy by incorporating species-specific physiology and chemical-dependent biochemical parameters. Existing PBTK models are currently limited to 10 fish species and 133 chemicals across 29 categories, with applications focused on internal concentration dynamics predictions, cross-species extrapolation, <i>in vitro</i> to <i>in vivo</i> extrapolation, and toxicity integration. Major limitations include a taxonomic bias toward fish, inadequate contaminant coverage, oversimplified environmental parameterization, incomplete mechanistic representations, and parameter scarcity. QSAR models have evolved from linear regression to machine learning approaches, achieving superior prediction performance through enhancing molecular representations and incorporating advanced algorithms. Nonetheless, challenges remain in TK parameter prediction and high-quality data acquisition. The review offers valuable insights and methodological advancements to support chemical risk assessment.
DOI: 10.6084/m9.figshare.31152117.v1
title: Prediction and modeling on bioaccumulation of chemicals in aquatic organisms: A critical review

description: Chemical bioaccumulation, which links internal exposure to hazards, plays a crucial role in ecological and human health risk assessment. Traditional bioaccumulation evaluations rely on laboratory-simulated exposure experiments and field monitoring studies, facing limitations in high cost, time constraints, and ethical concerns. Mechanistic toxicokinetic (TK) models and data-driven quantitative structure-activity relationship (QSAR) approaches have emerged as efficient alternatives. The review synthesizes decades of progress in TK and QSAR models for bioaccumulation prediction of chemicals in aquatic organisms, encompassing theoretical foundations, mathematical equations, practical applications, and current research gaps. While traditional compartmental TK models provide simplicity, physiologically-based toxicokinetic (PBTK) models enhance accuracy by incorporating species-specific physiology and chemical-dependent biochemical parameters. Existing PBTK models are currently limited to 10 fish species and 133 chemicals across 29 categories, with applications focused on internal concentration dynamics predictions, cross-species extrapolation, <i>in vitro</i> to <i>in vivo</i> extrapolation, and toxicity integration. Major limitations include a taxonomic bias toward fish, inadequate contaminant coverage, oversimplified environmental parameterization, incomplete mechanistic representations, and parameter scarcity. QSAR models have evolved from linear regression to machine learning approaches, achieving superior prediction performance through enhancing molecular representations and incorporating advanced algorithms. Nonetheless, challenges remain in TK parameter prediction and high-quality data acquisition. The review offers valuable insights and methodological advancements to support chemical risk assessment.
DOI: 10.5061/dryad.s8m97
title: Data from: Discriminative host sanction together with relatedness promote the cooperation in fig/fig wasp mutualism

description: 1. Sanctioning or punishing is regarded as one of the most important
 dynamics in the evolution of cooperation. However, it has not been
 empirically examined yet whether or not such enforcement selection by
 sanctioning or punishing and classical theories like kin or reciprocity
 selection are separate mechanisms contributing to the evolution of
 cooperation. In addition, it remains largely unclear what factors
 determine the intensity or effectiveness of sanction. 2. Here, we show
 that in the obligate, interspecific cooperation between figs and fig
 wasps, the hosted figs can discriminatively sanction cheating individuals
 by decreasing the offspring development ratio. Concurrently, the figs can
 reward the cooperative pollinators with a higher offspring development
 ratio. This sanction intensity and effectiveness largely depend on how
 closely the host and symbiont are related either in terms of reciprocity
 exchange or genetic similarity as measured by the reciprocal of the
 foundress number. 3. Our results imply that in asymmetric systems,
 symbionts might be forced to evolve to be cooperative or even altruistic
 through discriminative sanction against the noncooperative symbiont and
 reward to the cooperative symbiont by the host (i.e. through a game of
 ‘carrot and stick’).
description: Data_of_Figure_1_2.Number_of_offspring_of_pollen_carried_and_pollen-free_foundresses_according_to_different_foundress_numbers.xlsNumber of offspring of pollen carried and pollen-free foundresses according to different foundress numbersData_of_Figure_3_4.Number_of_the_offspring_of_pollen_and_pollen-free_foundresses_across_different_speciesNumber of the offspring of pollen and pollen-free foundresses across different speciesData_of_Figure_4.Number_of_the_foundress_and_the_fruit diameter_across_different_speciesNumber of the foundress and the fruit diameter across different speciesNotesNotes about the abbreviation of fig scientific name
DOI: 10.5061/dryad.40r16m35
title: Data from: Quantifying morphological change during an evolutionary radiation of Devonian trilobites

description: The fossil record provides an important source of data on adaptive
 radiations, and indeed some of the earliest theoretical insights on the
 nature of these radiations were made by paleontologists. Here we focus on
 the diverse Devonian Metacryphaeus group calmoniid trilobites, known from
 the Malvinokaffric Realm; these have been considered a classic example of
 an adaptive radiation preserved in the fossil record. A geometric
 morphometric analysis is used in conjunction with phylogenetic and
 biogeographic patterns and data on speciation rates. Patterns of
 morphological change are quantified using ancestral character state
 reconstruction during speciation events in order to assess the role
 ecological and geographical factors may have played in mediating this
 radiation. No significant differences were found between the amount of
 morphological change that occurred during speciation events when ancestors
 and descendents were in the same area as opposed to when they occupied
 different areas. Further, the magnitude of morphological divergence did
 not change through time or with cladogenetic rank. These patterns, in
 conjunction with the fact that the radiation occurs in a geographically
 heterogeneous region subjected to repeated episodes of sea-level rise and
 fall, suggests that at the macroevolutionary scale this radiation may have
 been motivated more by phenomena that facilitated geographic isolation
 than by competition.
description: Calmoniid_Procrustes_alignedThe TPS file generated by TPS software. This file contains Procrustes superimposed and aligned landmarks. This file also contains ancestors and is the basis for Figure 5.BigFixedRelativeWarpsIncludingAncestors.tpsEuclidean_distances_categoriesThis Excel file was the basis for the statistical analyses. It contains Euclidean distances of the different morphological transitions including the groupings used. Basis for the data file is Figures 6-8.Relative_warps_plus_nodesColumns show the first three dimensions of relative warps, and the nodes. Below is the tree with included node numbers.
DOI: 10.5061/dryad.3576v
title: Data from: Lassa virus in multimammate rats, Côte d’Ivoire, 2013

description: Lassa fever is a zoonosis caused by Lassa virus (LASV; family
 Arenaviridae, genus Lassavirus). The primary reservoir of LASV is the
 multimammate rat (Mastomys natalensis), which is found throughout
 sub-Saharan Africa. For a study investigating zoonotic pathogens in rural
 habitats, we caught small mammals in 3 ecologic zones of Côte d’Ivoire:
 dry bushland in northern Côte d’Ivoire, around Korhogo; semiarid bushland
 in central Côte d’Ivoire, around Bouake; and rainforest in southwestern
 Côte d’Ivoire, near the Taï National Park.
description: Rodent and eulipotyphlan
 partial cytochrome b sequencesFASTA file comprising
 248 sequences generated during this study.Kouadio_rodent_cyt_b.fasta