cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9js2m
title: Data from: Patterns in vertical distribution and their potential effects on transport of larval benthic invertebrates in a shallow embayment

description: Measurements of larval vertical distributions at high temporal and spatial
 resolutions as well as larval behavioural responses to environmental
 characteristics are needed to parameterize bio-physical models of larval
 dispersal or transport. We studied larval vertical distribution for 7
 taxonomic groups (gastropods, bivalves, polychaetes, bryozoans, asteroids,
 carideans and brachyurans), with different morphology, swimming abilities
 and life-history strategies, and examined whether these vary with physical
 or biological factors and periodic cycles (diel period and tidal state) in
 the field. Using a pump, we collected plankton samples at 6 depths (3, 6,
 9, 12, 18 and 24 m), over a 36 and a 26 h period. Temperature, salinity,
 fluorescence and current velocity were measured concurrently. Larval
 vertical distribution varied among taxonomic groups, but 4 patterns could
 be distinguished: (1) larvae exclusively in the mixed layer (asteroids),
 (2) larvae predominantly below the thermocline, halocline and pycnocline
 (gastropods, bivalves, polychaetes), (3) larvae associated predominantly
 with the fluorescence maximum (bryozoans and carideans) and (4) larval
 distribution varying dielly (gastropods, polychaetes, carideans and
 brachyurans). Based on flow velocities and depending on distribution,
 asteroid larvae were likely to be transported farther than those of
 bryozoans and carideans, while direction and magnitude of transport varied
 for the other larvae. For most taxonomic groups, behaviour observed in the
 field agreed with measured laboratory responses to relevant cues. For
 asteroids and bivalves, simple behavioural parameters can be generated
 that can be utilized to improve the accuracy of biophysical models.
description: Vertical distribution
 measurements of Meroplanktonic larvae and the environment. A Canadian
 Healthy Oceans Network Population Connectivity Project,
 PC-06.This dataset was
 collected in the field (using a plankton pump, CTD, fluorometer and ADCP)
 for a MSc Thesis and 1 publication. This dataset contains the standardized
 abundance (count m-3) of meroplanktonic larvae (Gastropods, Bivalves,
 Bryozoans, Brachyurans, Polychaetes, Carideans, and Asteroids),
 temperature, salinity, density, fluorescence, calculated Richardson number
 and current velocities (north-south, east-west, and vertical velocities)
 at 6 (3, 6, 9, 12, 18 and 24 m) depths, every 2 h over a 36- and 26-h
 sampling period, in St. George’s Bay, Nova Scotia, Canada. The dataset
 also included lunar cycle, diel period, tidal state, date, time, sampling
 depth, sampling depth range, and more.CHONE_PC-06_LLOYDM_dataset.csv
DOI: 10.5061/dryad.4hp5n
title: Data from: Experiments on the role of deleterious mutations as stepping stones in adaptive evolution

description: Many evolutionary studies assume that deleterious mutations necessarily
 impede adaptive evolution. However, a later mutation that is conditionally
 beneficial may interact with a deleterious predecessor before it is
 eliminated, thereby providing access to adaptations that might otherwise
 be inaccessible. It is unknown whether such sign-epistatic recoveries are
 inconsequential events or an important factor in evolution, owing to the
 difficulty of monitoring the effects and fates of all mutations during
 experiments with biological organisms. Here, we used digital organisms to
 compare the extent of adaptive evolution in populations when deleterious
 mutations were disallowed with control populations in which such mutations
 were allowed. Significantly higher fitness levels were achieved over the
 long term in the control populations because some of the deleterious
 mutations served as stepping stones across otherwise impassable fitness
 valleys. As a consequence, initially deleterious mutations facilitated the
 evolution of complex, beneficial functions. We also examined the effects
 of disallowing neutral mutations, of varying the mutation rate, and of
 sexual recombination. Populations evolving without neutral mutations were
 able to leverage deleterious and compensatory mutation pairs to overcome,
 at least partially, the absence of neutral mutations. Substantially
 raising or lowering the mutation rate reduced or eliminated the long-term
 benefit of deleterious mutations, but introducing recombination did not.
 Our work demonstrates that deleterious mutations can play an important
 role in adaptive evolution under at least some conditions.
description: Covert_et_al_2013_PNAS_dataData from the paper includes fitness values from all main experiments, all replay experiments, and lines of descent for reconstructing the analysis of sign-epistasis.
DOI: 10.5061/dryad.n6t2c
title: Data from: Defeating crypsis: detection and learning of camouflage strategies

description: Camouflage is perhaps the most widespread defence against predators in
 nature and an active area of interdisciplinary research. Recent work has
 aimed to understand what camouflage types exist (e.g. background matching,
 disruptive, and distractive patterns) and their effectiveness. However,
 work has almost exclusively focused on the efficacy of these strategies in
 preventing initial detection, despite the fact that predators often
 encounter the same prey phenotype repeatedly, affording them opportunities
 to learn to find those prey more effectively. The overall value of a
 camouflage strategy may, therefore, reflect both its ability to prevent
 detection by predators and resist predator learning. We conducted four
 experiments with humans searching for hidden targets of different
 camouflage types (disruptive, distractive, and background matching of
 various contrast levels) over a series of touch screen trials. As with
 previous work, disruptive coloration was the most successful method of
 concealment overall, especially with relatively high contrast patterns,
 whereas potentially distractive markings were either neutral or costly.
 However, high contrast patterns incurred faster decreases in detection
 times over trials compared to other stimuli. In addition, potentially
 distractive markings were sometimes learnt more slowly than background
 matching markings, despite being found more readily overall. Finally,
 learning effects were highly dependent upon the experimental paradigm,
 including the number of prey types seen and whether subjects encountered
 targets simultaneously or sequentially. Our results show that the survival
 advantage of camouflage strategies reflects both their ability to avoid
 initial detection (sensory mechanisms) and predator learning (perceptual
 mechanisms).
description: Capture
 timesCapture times for all
 experiments (1,2,3,4A,4B,4C), containing all data used for statistical
 analysis.DryadUploadedResults.xls
DOI: 10.5061/dryad.v6st3
title: Data from: From cellular characteristics to disease diagnosis: uncovering phenotypes with supercells

description: Cell heterogeneity and the inherent complexity due to the interplay of
 multiple molecular processes within the cell pose difficult challenges for
 current single-cell biology. We introduce an approach that identifies a
 disease phenotype from multiparameter single-cell measurements, which is
 based on the concept of “supercell statistics”, a single-cell-based
 averaging procedure followed by a machine learning classification scheme.
 We are able to assess the optimal tradeoff between the number of single
 cells averaged and the number of measurements needed to capture phenotypic
 differences between healthy and diseased patients, as well as between
 different diseases that are difficult to diagnose otherwise. We apply our
 approach to two kinds of single-cell datasets, addressing the diagnosis of
 a premature aging disorder using images of cell nuclei, as well as the
 phenotypes of two non-infectious uveitides (the ocular manifestations of
 Behçet's disease and sarcoidosis) based on multicolor flow cytometry.
 In the former case, one nuclear shape measurement taken over a group of 30
 cells is sufficient to classify samples as healthy or diseased, in
 agreement with usual laboratory practice. In the latter, our method is
 able to identify a minimal set of 5 markers that accurately predict
 Behçet's disease and sarcoidosis. This is the first time that a
 quantitative phenotypic distinction between these two diseases has been
 achieved. To obtain this clear phenotypic signature, about one hundred
 CD8+ T cells need to be measured. Although the molecular markers
 identified have been reported to be important players in autoimmune
 disorders, this is the first report pointing out that CD8+ T cells can be
 used to distinguish two systemic inflammatory diseases. Beyond these
 specific cases, the approach proposed here is applicable to datasets
 generated by other kinds of state-of-the-art and forthcoming single-cell
 technologies, such as multidimensional mass cytometry, single-cell gene
 expression, and single-cell full genome sequencing techniques.
description: Multicolor flow
 cytometry for healthy and uveitides patientsMulticolor flow
 cytometry datasets from 22 fresh peripheral blood patient samples. Please
 see attached ReadMe file.Candia_datasets.tar.gz
DOI: 10.5061/dryad.0dm16
title: Data from: Disentangling the effects of key innovations on the diversification of Bromelioideae (Bromeliaceae)

description: The evolution of key innovations, novel traits that promote
 diversification, is often seen as major driver for the unequal
 distribution of species richness within the tree of life. In this study,
 we aim to determine the factors underlying the extraordinary radiation of
 the subfamily Bromelioideae, one of the most diverse clades among the
 neotropical plant family Bromeliaceae. Based on an extended molecular
 phylogenetic data set, we examine the effect of two putative key
 innovations, that is, the Crassulacean acid metabolism (CAM) and the
 water-impounding tank, on speciation and extinction rates. To this aim, we
 develop a novel Bayesian implementation of the phylogenetic comparative
 method, binary state speciation and extinction, which enables hypotheses
 testing by Bayes factors and accommodates the uncertainty on model
 selection by Bayesian model averaging. Both CAM and tank habit were found
 to correlate with increased net diversification, thus fulfilling the
 criteria for key innovations. Our analyses further revealed that CAM
 photosynthesis is correlated with a twofold increase in speciation rate,
 whereas the evolution of the tank had primarily an effect on extinction
 rates that were found five times lower in tank-forming lineages compared
 to tank-less clades. These differences are discussed in the light of
 biogeography, ecology, and past climate change.
description: Bromelioideae complete
 alignmentCombined plastid and
 nuclear alignment of Bromelioideae (+ outgroups) in Nexus format with gene
 partitions defined for MrBayesBromelioideae.nexBromelioideae 100 BEAST treesRandom sample of 100 trees from the BEAST relaxed clock analyses (log-normal rates, Yule prior)Bromelioideae_BEAST.tree
DOI: 10.5061/dryad.57r3c
title: Data from: The clathrin adaptor complex AP-2 mediates endocytosis of BRASSINOSTEROID INSENSITIVE1 in Arabidopsis

description: Clathrin-mediated endocytosis (CME) regulates many aspects of plant
 development, including hormone signaling and responses to environmental
 stresses. Despite the importance of this process, the machinery that
 regulates CME in plants is largely unknown. In mammals, the
 heterotetrameric ADAPTOR PROTEIN COMPLEX-2 (AP-2) is required for the
 formation of clathrin-coated vesicles at the plasma membrane (PM).
 Although the existence of AP-2 has been predicted in Arabidopsis thaliana,
 the biochemistry and functionality of the complex is still
 uncharacterized. Here, we identified all the subunits of the Arabidopsis
 AP-2 by tandem affinity purification and found that one of the large AP-2
 subunits, AP2A1, localized at the PM and interacted with clathrin.
 Furthermore, endocytosis of the leucine-rich repeat receptor kinase,
 BRASSINOSTEROID INSENSITIVE1 (BRI1), was shown to depend on AP-2.
 Knockdown of the two Arabidopsis AP2A genes or overexpression of a
 dominant-negative version of the medium AP-2 subunit, AP2M, impaired BRI1
 endocytosis and enhanced the brassinosteroid signaling. Our data reveal
 that the CME machinery in Arabidopsis is evolutionarily conserved and that
 AP-2 functions in receptor-mediated endocytosis.
description: Supplemental
 DataSupplemental
 Data
DOI: 10.5061/dryad.10kd4
title: Data from: Estimation of the dispersal of a major pest of maize by cline analysis of a temporary contact zone between two invasive outbreaks

description: Dispersal is a key factor in invasion, and in the persistence and
 evolution of species. Despite the importance of estimates of dispersal
 distance, dispersal measurement remains a real methodological challenge.
 In this study, we characterized dispersal by exploiting a specific case of
 biological invasion, in which multiple introductions in disconnected areas
 lead to secondary contact between two differentiated expanding outbreaks.
 By applying cline theory to this ecological setting, we estimated σ, the
 standard deviation of the parent-offspring distance distribution, of the
 western corn rootworm, Diabrotica virgifera virgifera, one of the most
 destructive pests of maize. This species is currently invading Europe, and
 the two largest invasive outbreaks, in Northern Italy and Central Europe,
 have recently formed a secondary contact zone in Northern Italy. We
 identified vanishing clines at 12 microsatellite loci throughout the
 contact zone. By analyzing both the rate of change of cline slope and the
 spatial variation of linkage disequilibrium at these markers, we obtained
 two σ estimates of about 20 km.generation−1/2. Simulations indicated that
 these estimates were robust to changes in dispersal kernels and
 differences in population density between the two outbreaks, despite a
 systematic weak bias. These estimates are consistent with the results of
 direct methods for measuring dispersal applied to the same species. We
 conclude that secondary contact resulting from multiple introductions is
 very useful for the inference of dispersal parameters and should be more
 widely used in other species.
description: Genotypes_Dryadappendix_S1_Mathematica_notebook_Bermond_et_alThis file shows how we realized our analyses from genetic and genotypic data. Both methods that we used to estimate Sigma (methods of Endler and Linkage Disequilibrium) are detailed. Details on simulations are also given.appendix_S2_R_script_simulations_Bermond_et_alR script of the simulations that we used in this paper to evaluate the effect of dispersal kernel and heterogeneity of population density on the estimation of dispersal and time since contact.Appendix S2.txt
DOI: 10.5061/dryad.4dp00
title: Data from: Spatial heterogeneity in the strength of plant-herbivore interactions under predation risk: the tale of bison foraging in wolf country

description: Spatial heterogeneity in the strength of trophic interactions is a
 fundamental property of food web spatial dynamics. The feeding effort of
 herbivores should reflect adaptive decisions that only become rewarding
 when foraging gains exceed 1) the metabolic costs, 2) the missed
 opportunity costs of not foraging elsewhere, and 3) the foraging costs of
 anti-predator behaviour. Two aspects of these costs remain largely
 unexplored: the link between the strength of plant-herbivore interactions
 and the spatial scale of food-quality assessment, and the predator-prey
 spatial game. We modeled the foraging effort of free-ranging plains bison
 (Bison bison bison) in winter, within a mosaic of discrete meadows.
 Spatial patterns of bison herbivory were largely driven by a search for
 high net energy gains and, to a lesser degree, by the spatial game with
 grey wolves (Canis lupus). Bison decreased local feeding effort with
 increasing metabolic and missed opportunity costs. Bison herbivory was
 most consistent with a broad-scale assessment of food patch quality, i.e.,
 bison grazed more intensively in patches with a low missed opportunity
 cost relative to other patches available in the landscape. Bison and
 wolves had a higher probability of using the same meadows than expected
 randomly. This co-occurrence indicates wolves are ahead in the spatial
 game they play with bison. Wolves influenced bison foraging at fine scale,
 as bison tended to consume less biomass at each feeding station when in
 meadows where the risk of a wolf's arrival was relatively high. Also,
 bison left more high-quality vegetation in large than small meadows. This
 behavior does not maximize their energy intake rate, but is consistent
 with bison playing a shell game with wolves. Our assessment of bison
 foraging in a natural setting clarifies the complex nature of
 plant-herbivore interactions under predation risk, and reveals how spatial
 patterns in herbivory emerge from multi-scale landscape heterogeneity.
description: HarveyFortinDataset
 S1Field
 data
DOI: 10.5061/dryad.4k887
title: Data from: Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates

description: Synonymous codon usage (SCU) patterns are shaped by a balance between
 mutation, drift, and natural selection. To date, detection of
 translational selection in vertebrates has proven to be a challenging
 task, obscured by small long-term effective population sizes in larger
 animals and the existence of isochores in some species. The consensus is
 that, in such species, natural selection is either completely ineffective
 at overcoming mutational pressures and genetic drift or perhaps is
 effective but so weak that it is not detectable. The aim of this research
 is to understand the interplay between mutation, selection, and genetic
 drift in vertebrates. We observe that although variation in mutational
 bias is undoubtedly the dominant force influencing codon usage,
 translational selection acts as a weak additional factor influencing
 synonymous codon usage. These observations indicate that translational
 selection is a widespread phenomenon in vertebrates and is not limited to
 a few species.
description: Supplementary Figure
 1Plots of axis 1 versus
 axis 2 of correspondence analyses, using RSCU values and raw codon counts,
 respectively. Blue points indicate non­‐highly expressed genes. Red points
 indicate highly expressed genes.SupplementaryFigure1.pdfSupplementary Table 1Correspondence analysis of RSCU values and raw codon counts. The “Axis 0 inertia” column is the amount of inertia that is explained by the principal axis. The “Axis 1 inertia” column is the amount of interia that is explained by the next biggest CA axis. These results demonstrate that there is a single major trend that determines synonymous codon usage in vertebrates.SupplementaryTable1.pdfSupplementary Table 2Spearman correlations. Spearman correlation comparing Axis 1 versus GC3 , and axis 1 versus expression level.SupplementaryTable2.pdf
DOI: 10.5061/dryad.fv94v
title: Data from: Bioclimatic and physical characterization of the world's islands

description: The Earth’s islands harbor a distinct, yet highly threatened biological
 and cultural diversity that has been shaped by geographic isolation and
 unique environments. Island systems are key natural laboratories for
 testing theory in ecology and evolution. However, despite their potential
 usefulness for research, a quantitative description of island environments
 and an environmental classification are still lacking. Here, we prepare a
 standardized dataset and perform a comprehensive global environmental
 island characterization for 17,883 of the world’s marine islands &gt;1
 km² (∼98% of total island area). We consider area, temperature,
 precipitation, seasonality in temperature and precipitation, past climate
 change velocity, elevation, isolation, and past connectivity – key island
 characteristics and drivers of ecosystem processes. We find that islands
 are significantly cooler, wetter and less seasonal than mainlands.
 Constrained by their limited area, they show less elevational
 heterogeneity. Wet temperate climates are more prevalent on islands,
 whereas desert climates are comparatively rare. We use ordination and
 clustering to characterize islands in multidimensional environmental space
 and to delimit island ecoregions which provides unique insights into the
 environmental configuration and diversity of the world’s islands.
 Combining ordination and classification together with global environmental
 data in a common framework opens up avenues for a more integrative use of
 islands in biogeography, macroecology, and conservation. To showcase
 possible applications of the presented data, we predict vascular plant
 species richness for all 17,883 islands based on statistically derived
 environment-richness relationships.
description: Global island
 datasetThe data are described
 in detail in SI Materials and Methods in the supporting information of the
 paper (Weigelt et al. 2013, PNAS) and in the ReadMe
 file.Weigelt_etal_2013_PNAS_islanddata.csv
DOI: 10.5061/dryad.t30bh
title: Data from: An inordinate fondness for beetles? Variation in seasonal dietary preferences of night roosting big brown bats (Eptesicus fuscus)

description: Generalist species with numerous food web interactions are thought to
 provide stability to ecosystem dynamics; however, it is not always clear
 whether habitat generality translates into dietary diversity. Big brown
 bats are common across North America and employ a flexible foraging
 strategy over water, dense forests, forest edges and rural and urban
 settings. Despite this generalist use of habitat, they are paradoxically
 characterized as beetle specialists. However, hard carapaces may
 preferentially survive digestion leading to over-representation during
 morphological analysis of diet. This specialization has not been evaluated
 independently using molecular analysis and species-level identification of
 prey. We used next-generation sequencing to assess the diet of big brown
 bats. Beetles were consumed in the highest frequency but Lepidoptera
 species richness was highest among identified prey. The consumption of
 species showed strong seasonal and annual variation. While Coleoptera
 consumption varied, Lepidoptera and Ephemeroptera were relatively constant
 dietary components. Dietary diversity increased in late summer when insect
 diversity decreases. Our results indicate that big brown bats are dietary
 generalists and, while beetles are an important component of the diet,
 Lepidoptera are equally important, and Lepidoptera and Ephemeroptera are
 the only stable prey resource exploited. As resources become limited, big
 brown bats may respond by increasing the species richness of prey and thus
 their connectedness in the ecosystem. This characterization of diet
 corresponds well with a generalist approach to foraging, making them an
 important species in encouraging and maintaining ecosystem stability.
description: NGS data associated with
 this studyThis file contains the
 processed NGS data associated with the publication. Sequences have been
 collapsed to unique haplotypes and filtered for analysis. If you wish to
 use these files we suggest you contact the corresponding authors Elizabeth
 L Clare (e.clare@qmul.ac.uk or elclare.evol.biology@gmail.com) who can
 explain what steps have been conducted and how. She will be happy to
 answer any questions, explain the nature of the data and its
 limitations.Dryan
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