cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6q573n5wr
title: Supplementary data for: Diversification in the Arctic: biogeography and systematics of the North American Micranthes (Saxifragaceae)

description: Flora endemic to the cold habitats of the Northern Hemisphere provide
 important models for investigating diversification and disjunctions, given
 both the intense climatic fluctuations of these areas in the recent past
 and the fascinating biogeographic patterns of today’s Arctic-alpine plant
 communities. Micranthes Haw. (Saxifragaceae), a clade of small-flowered
 herbaceous flowering plants comprising 80 species, is an ideal group for
 investigating the evolution and diversification of plants in montane and
 Arctic ecosystems. Micranthes has proven to be a particularly challenging
 clade to unravel taxonomically due in part to rampant auto- and
 allopolyploidy, hybridization, and cryptic speciation. With the goal of
 providing an updated conspectus for this group, we build upon a recent
 large phylogenomic analysis, to help elucidate the evolution of Micranthes
 . Here, we present new downstream analyses including diversification
 analyses, biogeographical reconstructions, and a comparison of methods for
 dating phylogenomic analyses. To complement these latest analyses, we also
 synthesize chromosomal variation, new observations regarding morphology
 and species identification, comprehensive field studies, and an extensive
 review of the literature for Saxifragaceae and Micranthes. A new
 perspective on the systematics and taxonomy of Micranthes is provided.
description: Supplementary Table 1 and Supplementary Figures 1-3.
DOI: 10.5061/dryad.tx95x69vh
title: Effects of episodic nutrients enrichments on P-limited planktonic communities: Lake Redon ENEX 2013 experiment

description: Planktonic communities are naturally subjected to episodic nutrient
 enrichments that may stress or redress the imbalances in limiting
 nutrients. Human-enhanced atmospheric nitrogen deposition has caused
 profound N:P imbalance in many remote oligotrophic lakes in which
 phosphorus has largely become limiting. These lakes offer an opportunity
 to investigate the planktonic community response to nutrient fluctuations
 in P-limited conditions. The ENEX experiment in Lake Redon (Pyrenees),
 performed during August 2013, aimed to investigate the structural and
 stoichiometric effects of pulse nutrient additions on P-limited planktonic
 communities. We performed P (PO43-), and N (NH4+ or NO3-) additions to the
 summer epilimnetic community of the ultraoligotrophic lake using
 self-filling ~100 L enclosures and analysed the response to varying P
 availability, N:P imbalance, and N source. The nutrient additions were
 gradients within the range of values seasonally found in the lake and
 other oligotrophic lakes of the Pyrenees, with a further P level typical
 of mesotrophic lakes to provided non-limiting conditions.
description: Analytical methods are
 described in the associated publication: Giménez-Grau, P., Felip, M.,
 Zufiaurre, A., Pla-Rabès, S., Camarero, L. & Catalan, J. (2020)
 Homeostasis and non-linear changes in the stoichiometry of P limited
 planktonic communities. Ecosphere,11:e03249
description:  Initial reference conditions in the lake water column were
 sampled during three dates. They are reported separately, but they should
 be amalgamated if used as initial experimental conditions. There are a few
 missing values across the biogeochemical data. Data from the enclosure
 water column and the sediment traps are reported in separated
 files.
DOI: 10.5061/dryad.cfxpnvx3g
title: Data from: Meiofauna promotes litter decomposition in stream ecosystems depending on leaf species

description: Litter decomposition, a fundamental process of nutrient cycling and energy
 flow in freshwater ecosystems, is driven by a diverse array of
 decomposers. As an important component of the heterotrophic food web,
 meiofauna can provide a trophic link between leaf-associated microbes
 (i.e., bacteria and fungi)/plant detritus and macroinvertebrates, though
 their contribution to litter decomposition is not well understood. To
 investigate the role of different decomposer communities in litter
 decomposition, especially meiofauna, we compared the litter decomposition
 of three leaf species with different lignin to nitrogen ratios in litter
 bags with different mesh sizes (0.05, 0.25, and 2 mm) in a forested
 stream, in China for 78 days. The meiofauna significantly enhanced the
 decomposition of leaves of high- and medium-quality, while decreasing
 (negative effect) or increasing (positive effect) the fungal biomass and
 diversity. Macrofauna and meiofauna together contributed to the
 decomposition of low-quality leaf species. The presence of meiofauna and
 macrofauna triggered different aspects of the microbial community, with
 their effects on litter decomposition varying as a function of leaf
 quality. This study reveals that the meiofauna increased the trophic
 complexity and modulated their interactions with microbes, highlighting
 the important yet underestimated role of meiofauna in detritus-based
 ecosystems.
description: TableS1 Benthic meiofauna and macro
DOI: 10.5061/dryad.0p2ngf1xr
title: Data from: More than meets the eye: predator-induced pupil size plasticity in a teleost fish

description: 1. Most animals are visually oriented, and their eyes provide their
 “window to the world”. Eye size correlates positively with visual
 performance, because larger eyes can house larger pupils that increase
 photon catch and contrast discrimination, particularly under dim light,
 which have positive effects on behaviours that enhance fitness, including
 predator avoidance and foraging. 2. Recent studies have linked predation
 risk to selection for larger eyes and pupils, and such changes should be
 of importance for the majority of teleost fishes as they have a pupil that
 is fixed in size (eyes lack a pupillary sphincter muscle) and, hence, do
 not respond to changes in light conditions. 3. Here, we quantify eye and
 pupil size of individual crucian carp, a common freshwater fish, following
 controlled manipulations of perceived predation risk (presence/absence).
 We also tested if crucian carp responded to increased predation risk by
 shifts in diel activity patterns. 4. We found that crucian carp show
 phenotypic plasticity with regards to pupil size, but not eye size, as
 pupil size increased when exposed to predators (pike). Predator-exposed
 crucian carp also shifted from diurnal to nocturnal activity. Using a
 modelling exercise, we moreover show that the plastically enlarged pupils
 significantly increase visual range, especially for small objects under
 dim light conditions. 5. Overall, our results provide compelling evidence
 for predator-induced pupil enlargement resulting in enhanced visual
 capabilities in a teleost fish. Pupil-size plasticity in combination with
 the observed shift towards nocturnal activity may allow for efficient
 foraging also under dark conditions when predation risk from diurnal and
 visually oriented predators is reduced. The data highlight the powerful
 role of predation risk for eye development and evolution. 03-Jul-2020
description: Data of eye and pupil sizes of crucian carp reared with or
 without a natural predator along with data of individuals diel activity
 patterns.
DOI: 10.5061/dryad.fj6q573rr
title: Data from: Incorporating capture heterogeneity in the estimation of autoregressive coefficients of animal population dynamics using capture-recapture data

description: Population dynamics models combine density-dependence and environmental
 effects. Ignoring sampling uncertainty might lead to biased estimation of
 the strength of density-dependence. This is typically addressed using
 state-space model approaches, which integrate sampling error and
 population process estimates. Such models seldom include an explicit link
 between the sampling procedures and the true abundance, which is common in
 capture-recapture settings. However, many of the models proposed to
 estimate abundance in the presence of capture heterogeneity lead to
 incomplete likelihood functions and cannot be straightforwardly included
 in state-space models. We assessed the importance of estimating sampling
 error explicitly by taking an intermediate approach between ignoring
 uncertainty in abundance estimates and fully specified state-space models
 for density-dependence estimation based on autoregressive processes.
 First, we estimated individual capture probabilities based on a
 heterogeneity model, using a conditional multinomial likelihood, followed
 by a Horvitz-Thompson estimate for abundance. Second, we estimated
 coefficients of autoregressive models for the log abundance. Inference was
 performed using the methodology of integrated nested Laplace approximation
 (INLA). We performed an extensive simulation study to compare our approach
 with estimates disregarding capture history information, and using
 R-package VGAM, for different parameter specifications. The methods were
 then applied to a real dataset of gray-sided voles Myodes rufocanusfrom
 Northern Norway. We found that density-dependence estimation was improved
 when explicitly modelling sampling error in scenarios with low process
 variances, in which differences in coverage reached up to 8% in estimating
 the coefficients of the autoregressive processes. In this case, the bias
 also increased assuming a Poisson distribution in the observational model.
 For high process variances, the differences between methods were small and
 it appeared less important to model heterogeneity.
description: See original publication for sampling details and spatial map of
 the stations. This dataset corresponds to a processed version of the raw
 dataset, after correcting for typing errors. To make it easier to analyse,
 the captures on different days for the same individual have been
 aggregated into a single row containing the capture history associated
 with that same individual, using the mean weight measured on both capture
 days for a given vole.
description: Capture recapture histories with two sampling days of gray-sided
 voles for different spatially independent locations, sampled in Spring and
 Fall, from 2000 to 2017. Some missing values present in weight and sex of
 individuals. Animals collected at different time points (6 months apart)
 are assumed to be different (no long-term memory expected).
DOI: 10.5061/dryad.83bk3j9p9
title: Data from: Latitudinal variation in norms of reaction of phenology in the greater duckweed Spirodela polyrhiza

description: Variable environments may result in the evolution of adaptive phenotypic
 plasticity when cues reliably indicate an appropriate
 phenotype-environment match. Although adaptive plasticity is well
 established for phenological traits expressed across environments, local
 differentiation in norms of reaction is less well studied. The switch from
 the production of regular fronds to overwintering “turions” in the greater
 duckweed Spirodela polyrhiza is vital to fitness and is expressed as a
 norm of reaction induced by falling temperatures associated with the onset
 of winter. However, the optimal norm of reaction to temperature is
 expected to differ across latitudes. Here, we test the hypothesis that a
 gradient in the length and predictability of growing seasons across
 latitudes results in the evolution of reaction norms characterized by
 earlier turion production at higher latitudes. We test this by collecting
 S. polyrhiza from replicate populations across seven latitudes from
 Ontario to Florida, and then assessing differentiation in thermal reaction
 norms of turion production along a common temperature gradient. As
 predicted, northern populations produce turions at lower birth order and
 earlier; a significant latitude-by-temperature interaction suggests that
 reaction norm differentiation has occurred. Our results provide evidence
 of differentiation in reaction norms across latitudes in a phenological
 trait, and we discuss how the adaptive significance of this plasticity
 might be further tested.
description: Please see Read_Me file.
DOI: 10.7272/q6dz06j3
title: Schistosoma mansoni IgG antibody response and Kato-Katz infection among pre-school aged children in Mbita, Western Kenya 2012-2014

description: We compared serological measures of transmission based on antibody
 response to S. mansoni soluble egg antigen (SEA) with stool-based measures
 of infection among 3,663 preschool-age children in an area endemic for S.
 mansoni in western Kenya. We estimated force of infection among children
 using the seroconversion rate examined how it varied geographically and by
 age.
description: The analysis included 3,663 children ages 2 months to 5.5 years
 who were originally enrolled from 30 communities that participated in a
 cluster randomized controlled trial to measure the effect of
 community-wide versus school-based mass distribution of praziquantel to
 reduce <em>S. mansoni</em> infection in Mbita, western Kenya.
 Villages were selected within 5 km of Lake Victoria from among those with
 ≥ 25% S. mansoni prevalence that had not received mass treatment with
 praziquantel. Preschool age children ≤5 years were assessed annually from
 2012-2014 in repeated cross-sectional surveys that collected blood and
 stool specimens, and samples were tested for the presence of infection (in
 stool) and for antibodies to S. mansoni soluble egg antigen
 (SEA).
description: This repository includes data and replication files to reproduce
 the analyses in the manuscript entitled <em>Fine-scale heterogeneity
 in Schistosoma mansoni force of infection measured through antibody
 response</em> The materials in this repository
 are cross-linked with the Open Science Framework (https://osf.io/rnme8/) and with
 GitHub (https://github.com/ben-arnold/mbita-schisto). The <code>data</code> subdirectory includes the datasets for the analysis. The <code>R</code> subdirectory includes all computational notebooks, organized by display item. To re-run the analyses, clone the GitHub directory (above), and create a new <code>output</code> subdirectory alongside <code>data</code> and <code>R</code> to store the output files. Each dataset includes a codebook. We have not included lon/lat village coordinates under guidance from our IRB, so the notebook that creates Figure 1, Figure S2 and Figure S3 cannot be run on the publicly available data (though the source code and HTML output are in the repo) If you have any questions about these files, please contact Ben Arnold at UCSF (ben.arnold@ucsf.edu).
DOI: 10.5061/dryad.ncjsxksrt
title: Optimization data for determination of montelukast and bambuterol as a combined medication

description: Sensitive, simple and green analytical methodology for simultaneous
 estimation of bambuterol and montelukast as a combined medication based on
 their native fluorescence character was developed. The method relies on
 synchronous spectrofluorimety to solve the problem of the overlapping
 emission spectra of the studied drugs. Where, utilizing second derivative
 synchronous spectra enabled the simultaneous quantitation of bambuterol
 and montelukast without interference. The peak amplitudes of the aqueous
 solutions at Δλ = 20 nm were estimated at 284 nm & 304 nm for
 bambuterol and at 374 nm & 384 nm for montelukast. A linear
 relationship was achieved over the concentration range of 0.2–1.00 μg/mL
 for bambuterol and 0.4–2.00 μg/mL for montelukast. All factors and
 parameters were carefully studied to obtain the highest sensitivity and
 good precision of the proposed method. Additionally, the validation
 criteria were assessed in accordance with ICH guidelines. The method was
 utilized for the estimation of both drugs in their raw materials,
 synthetic mixtures as well their combined tablets with good agreement
 between its results and those from the comparison method.
DOI: 10.5061/dryad.bzkh1896b
title: Data from: Climate change increases predation risk for a keystone species of the boreal forest

description: Canada lynx (Lynx canadensis) and snowshoe hares (Lepus americanus) form a
 keystone predator-prey cycle that has large impacts on the North-American
 boreal forest vertebrate community. Snowshoe hares and lynx are both
 well-suited for snowy winters, but climate change associated shifts in
 snow conditions could lower hare survival and alter cyclic dynamics. Using
 detailed monitoring of snowshoe hare cause-specific mortality, behaviour,
 and prevailing weather, we demonstrate that hare mortality risk is
 strongly influenced by variation in snow conditions. Although predation
 risk from lynx was largely unaffected by snow conditions, coyote (Canis
 latrans) predation increased in shallow snow. Maximum snow depth in our
 study area has decreased 33% over the last two decades and predictions
 based on prolonged shallow snow indicate future hare survival could
 resemble that seen during population declines. Our results indicate that
 climate change could disrupt cyclic dynamics in the boreal forest.
DOI: 10.5061/dryad.sf7m0cg3p
title: Relative size underlies alternative morph development in a salamander

description: Size thresholds commonly underlie the induction of alternative
 morphological states. However, the respective importance of absolute and
 relative size to such thresholds remains uncertain. If absolute size
 governs expression, morph frequency should differ among environments that
 influence absolute sizes (e.g. resources, competition), and individuals of
 the same morph should have similar average sizes across environments. If
 relative size determines expression, the frequency of each morph may not
 differ among environments, but morphs within each environment should
 differ in size relative to one another. We tested these predictions in a
 salamander (Ambystoma talpoideum) that develops into either a terrestrial
 metamorph or an aquatic paedomorph. To generate size variation within and
 among environments, we reared individuals in mesocosm ponds across three
 conspecific densities. We found that morph frequency did not differ among
 density treatments, and the morphs were not similarly sized within each
 density treatment. Instead, within each environment, relatively larger
 individuals became metamorphs and relatively smaller individuals became
 paedomorphs. Relative size therefore determined morph development,
 highlighting the importance of an individual’s social context to
 size-dependent morph induction.
description: see article
description: see meta-data files for notes on each file and article for
 analyses conducted
DOI: 10.5061/dryad.gxd2547j3
title: Zygomorphic flowers have fewer potential pollinator species

description: Botanists have long identified bilaterally symmetrical (zygomorphic)
 flowers with more specialized pollination interactions than radially
 symmetrical (actinomorphic) flowers. Zygomorphic flowers facilitate more
 precise contact with pollinators, guide pollinator behaviour, and exclude
 less effective pollinators. However, whether zygomorphic flowers are
 actually visited by a smaller subset of available pollinator species has
 not been broadly evaluated. We compiled 53,609 floral visitation records
 in 159 communities and classified the plants' floral symmetry.
 Globally and within individual communities, plants with zygomorphic
 flowers are indeed visited by fewer species. At the same time, zygomorphic
 flowers share a somewhat larger proportion of their visitor species with
 other co-occurring plants and have particularly high sharing with
 co-occurring plants that also have zygomorphic flowers. Visitation
 sub-networks for zygomorphic species also show differences that may arise
 from reduced visitor diversity, including greater connectance, greater web
 asymmetry, and lower coextinction robustness of both plants and visitor
 species—but these changes do not necessarily translate to whole
 plant-visitor communities. These results provide context for widely
 documented associations between zygomorphy and diversification and imply
 that species with zygomorphic flowers may face a greater risk of
 extinction due to pollinator loss.
description: Floral visitation data are derived from records archived in the
 Web of
 Life and Interaction
 Web DataBase repositories; original source datasets and the
 repositories where each was obtained are given in
 `data/references_all.csv`. Time-calibrated phylogeny derived from the
 "ALLMB" supertree created by Smith and Brown
 (2018). Details of compilation and processing are given in the
 paper.
DOI: 10.5061/dryad.8gtht76m8
title: SNP Data for Aedes aegypti populations in Florida and southern California

description: In the affiliated paper we compare likely the oldest populations
 of Aedes aegypti in continental North America with some of the newest to
 illuminate the range of genetic diversity and structure that can be found
 within the invasive range of this important disease vector. Aedes aegypti
 populations in Florida have likely persisted since the 1600-1700s, while
 populations in southern California derive from new invasions that occurred
 in the last ten years. For this comparison, we genotyped 1,193 individuals
 from 29 sites at 12 highly variable microsatellites and a subset of these
 individuals at 23,961 single nucleotide polymorphisms (SNPs). This dataset
 contains the SNP genetic information.
description: A total of 156 individuals from ten Florida sites and four
 southern California sites were genotyped for single-nucleotide
 polymorphisms (SNPs) using Axiom_aegypti, a high-throughput genotyping
 chip that has 50,000 probes (Evans et al. 2015). Genotyping was conducted
 by the Functional Genomics Core at University of North Carolina, Chapel
 Hill. To prune the SNPs, we first excluded 2,166 that failed a test of
 Mendelian inheritance (Evans et al. 2015) Since some analyses
 can be confounded by SNPs in linkage disequilibrium, we excluded tightly
 linked SNPs with Plink 1.9 using the command “--indep-pairwise 50 5 0.5”.
 We also excluded any SNPs that genotyped in less than 98% of the
 individuals and those with a minor allele frequency of &lt;1%, as
 these could be genotyping errors, leaving 23,961 SNPs remaining for
 analysis. Evans, B. R., A. Gloria-Soria,
 L. Hou, C. McBride, M. Bonizzoni, H. Zhao, and J. R. Powell. 2015. A
 multipurpose, high-throughput single-nucleotide polymorphism chip for the
 dengue and yellow fever mosquito, Aedes aegypti. G3 (Bethesda)
 5:711-718.
description: We include files in Plink format (ped and map). See here for more
 information on data formats: https://www.cog-genomics.org/plink/1.9/formats. The ped files show SNP calls, and no data is represented as "0." We include these files for the full, unfiltered dataset and the filtered dataset. For more information about the populations and their abbreviations, see the attached file and affiliated manuscript.