cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f8q8qf5
title: Data from: Regional and local patterns of genetic variation and structure in yellow-necked mice − the roles of geographic distance, population abundance and winter severity

description: The goal of this study, conducted in seven large woodlands and three areas
 with small woodlots in north-eastern Poland in 2004-2008, was to infer
 genetic structure in yellow-necked mouse Apodemus flavicollis population
 and to evaluate the roles of environmental and population ecology
 variables in shaping the spatial pattern of genetic variation using 768
 samples genotyped at 13 microsatellite loci. Genetic variation was very
 high in all studied regions. The primal genetic subdivision was observed
 between the northern and the southern parts of the study area, which
 harboured two major clusters and the intermediate area of highly admixed
 individuals. The probability of assignment of individual mice to the
 northern cluster increased significantly with lower temperatures of
 January and July and declined in regions with higher proportion of
 deciduous and mixed forests. Despite the detected structure, genetic
 differentiation among regions was very low. Fine-scale structure was
 shaped by the population density, whereas higher level structure was
 mainly shaped by geographic distance. Genetic similarity indices were
 highly influenced by mouse abundance (which positively correlated with the
 share of deciduous forests in the studied regions) and exhibited the
 greatest change between 0 and 1 km in the forests, 0 and 5 km in small
 woodlots. Isolation by distance pattern, calculated among regions, was
 highly significant but such relationship between genetic and geographic
 distance was much weaker, and held the linearity at very fine scale (~1.5
 km), when analyses were conducted at individual level.
description: genotypes_mice.genGenotypes of 13 microsatellite markers for 768 samples.environmental_data.xlsData used for modelling the association between environmental variables and genetic variation measured as probability of each individual (n = 752) to be assigned to Cluster 1 (based on STRUCTURE with K = 2, please see Figure 3 and Table 3).
DOI: 10.5061/dryad.cg17c
title: Data from: Three-level mixed-effects logistic regression analysis reveals complex epidemiology of swine rotaviruses in diagnostic samples from North America

description: Rotaviruses (RV) are important causes of diarrhea in animals, especially
 in domestic animals. Of the 9 RV species, rotavirus A, B, and C (RVA, RVB,
 and RVC, respectively) had been established as important causes of
 diarrhea in pigs. The Minnesota Veterinary Diagnostic Laboratory receives
 swine stool samples from North America to determine the etiologic agents
 of disease. Between November 2009 and October 2011, 7,508 samples from
 pigs with diarrhea were submitted to determine if enteric pathogens,
 including RV, were present in the samples. All samples were tested for
 RVA, RVB, and RVC by real time RT-PCR. The majority of the samples (82%)
 were positive for RVA, RVB, and/or RVC. To better understand the risk
 factors associated with RV infections in swine diagnostic samples,
 three-level mixed-effects logistic regression models (3L-MLMs) were used
 to estimate associations among RV species, age, and geographical
 variability within the major swine production regions in North America.
 The conditional odds ratios (cORs) for RVA and RVB detection were lower
 for 1–3 day old pigs when compared to any other age group. However, the
 cOR of RVC detection in 1–3 day old pigs was significantly higher (p
 &lt; 0.001) than pigs in the 4–20 days old and &gt;55 day old age
 groups. Furthermore, pigs in the 21–55 day old age group had statistically
 higher cORs of RV co-detection compared to 1–3 day old pigs (p &lt;
 0.001). The 3L-MLMs indicated that RV status was more similar within
 states than among states or within each region. Our results indicated that
 3L-MLMs are a powerful and adaptable tool to handle and analyze
 large-hierarchical datasets. In addition, our results indicated that,
 overall, swine RV epidemiology is complex, and RV species are associated
 with different age groups and vary by regions in North America.
description: Metadata for 3 Level
 Mixed Effects Logistic Regression ModelsMetadata containing
 demographic and rotavirus results for each samplerrt_pcr_results_submitted.xlsx
DOI: 10.5061/dryad.16c9m51
title: Data from: Health insurance coverage with or without a nurse-led task shifting strategy for hypertension control: a pragmatic cluster randomized trial in Ghana

description: Rationale: Poor access to care and physician shortage are major barriers
 to hypertension control in sub-Saharan Africa. Implementation of
 evidence-based systems-level strategies targeted at these barriers are
 lacking. Objective: To evaluate the comparative effectiveness of provision
 of health insurance coverage (HIC) alone versus a nurse-led task-shifting
 strategy for hypertension control (TASSH) plus HIC on systolic BP
 reduction among patients with uncontrolled hypertension in Ghana. Methods
 and Findings: Using a pragmatic cluster-randomized trial, 32 community
 health centers within Ghana's public healthcare system were randomly
 assigned to either HIC alone or TASSH+HIC. A total of 757 patients with
 uncontrolled hypertension were recruited between November 28 2012 and June
 11 2014 and followed up to October 7 2016. Both intervention groups
 received health insurance coverage plus scheduled nurse visits while
 TASSH+HIC comprised cardiovascular risk assessment; lifestyle counseling,
 and initiation/titration of antihypertensive medications for 12 months
 delivered by trained nurses within the healthcare system. The primary
 outcome was change in systolic BP from baseline to 12 months. Secondary
 outcomes included lifestyle behaviors and BP control at 12 months; and
 sustainability of systolic BP reduction at 24 months. Of the 757 patients
 (389 in HIC and 368 in TASH+HIC groups), 85% had 12 month data available
 [60% women, mean BP 155.9/89.6]. In intention-to-treat analyses adjusted
 for clustering, the TASSH+HIC group had a greater SBP reduction (20.4
 mmHg; 95% CI -25.2 to -15.6) than the HIC group (16.8 mmHg; 95% CI -19.2
 to -15.6) with a statistically significant between-group difference of 3.6
 mmHg [95% CI -6.1 to -0.5; p = 0.021]. Blood pressure control improved
 significantly in both groups (55.2%; 95% CI 50.0 to 60.3 for the TASSH+HIC
 group versus 49·9; 95% CI 44.9 to 54.9 for the HIC group) with a
 non-significant between-group difference 5.2% ( 95% CI =-1.8 to 12.4;
 p=0.29). Similarly, lifestyle behaviors did not change appreciably for
 both groups. Twenty-one adverse events were reported (9 and 12 in the
 TASSH+HIC and HIC group respectively). The main study limitation is the
 lack of cost-effectiveness analysis to determine the additional
 cost-benefit, if any, of the TASSH+HIC group. Conclusions: Provision of
 health insurance coverage plus a nurse-led task-shifting strategy was
 associated with a greater reduction in systolic BP than provision of
 health insurance coverage alone, among patients with uncontrolled
 hypertension in Ghana. Future scale up of these systems-level strategies
 for hypertension control in sub-Saharan Africa requires a cost-benefit
 analysis.
description: Clinical
 DataObserved Outcome
 DataSite Characteristic
 DataDemographic
 Data
DOI: 10.5061/dryad.86vt482
title: Data from: The role of red coloration and song in peacock spiders: insights into complex signaling systems

description: Research on animal signaling enhances our understanding of links between
 sensory processing, decision-making, behavior, and evolution. Studies of
 sexually-selected signals may be particularly informative as mate choice
 provides access to decision patterns in the way that courtship leads to an
 easily observable behavioral output in choosers, i.e. mating. Male peacock
 spiders have some of the most elaborate and varied courtship displays
 known among animals. Particularly striking to human observers is the
 diversity of red, orange and yellow ornaments that males exhibit across
 the genus. The primary objective of our research was to investigate how
 these visual ornaments interact with vibratory songs to affect female
 mating behavior of one species, Maratus volans. Accordingly, we conducted
 mating trials under a series of experimentally manipulated vibratory and
 lighting conditions. Contrary to expectation, chromatic characteristics of
 longer wavelength ornaments are not driving female mate choice decisions,
 despite their extensive presence on male fans. Instead, our results
 suggest that contrast is important to females. Additionally, we found that
 vibratory signals were not necessary and did not increase mating rates.
 Our study demonstrates the intricacies inherent in complex signaling
 systems.
description: Irradiance
 dataIrradiance data for
 natural habitat and experimental treatment groupsIrradiance_volans_BE.xlsxMaratus volans fan reflectance dataHyperspectral color measurements on Maratus volans fan ornaments.Reflectance_HyperSpec_Volans_BE.xlsxMaratus volans mating dataRaw data on Maratus volans mating experiment. Data includes treatment type (full spectrum, minus red spectrum, augmented minus red spectrum), data conducted, copulation occurrence, latency, and mating duration.MatingData_volans_BE.xlsx
DOI: 10.5061/dryad.tq2f566
title: Data from: A function-valued trait approach to estimating the genetic basis of size at age and its potential role in fisheries induced evolution

description: Natural selection is inherently a multivariate phenomenon. The selection
 pressure on size (natural and artificial) and the age at which selection
 occurs is likely to induce evolutionary changes in growth rates across the
 entire life history. However, the covariance structure that will determine
 the path of evolution for size-at-age has been studied in only a few fish
 species. We therefore estimated the genetic covariance function for size
 throughout ontogeny using Atlantic silversides (Menidia menidia) as the
 model system. Over a 3-year period, a total of 542 families were used to
 estimate the genetic covariance in length at age from hatch through
 maturity. The function-valued trait approach was employed to estimate the
 genetic covariance functions. A Bayesian hierarchical model was used to
 account for the unbalanced design, unequal measurement intervals, unequal
 sample sizes, and family-aggregated data. To improve mixing, we developed
 a two-stage sampler using a Gibbs sampler to generate the posterior of a
 well-mixing approximate model followed by an importance sampler to draw
 samples from posterior of the completely specified model. We found that
 heritability of length is age-specific and there are strong genetic
 correlations in length across ages that last 30d or more. We used these
 estimates in a hypothetical model predicting the evolutionary response to
 harvesting following a single generation of selection under both sigmoidal
 and unimodal patterns of gear selectivity to illustrate the potential
 outcomes of ignoring the genetic correlations. In these scenarios genetic
 correlations were found to have a strong effect on both the direction and
 magnitude of the response to harvest selection.
description: Data of all three rounds
 of the quantitative genetics experimentRefer to the Readme file
 for variable descriptions.All_data.xlsx
DOI: 10.5061/dryad.b658g
title: Data from: The effects of food web structure on ecosystem function exceeds those of precipitation

description: Ecosystems are being stressed by climate change, but few studies have
 tested food web responses to changes in precipitation patterns and the
 consequences to ecosystem function. Fewer still have considered whether
 results from one geographic region can be applied to other regions, given
 the degree of community change over large biogeographic gradients. We
 assembled, in one field site, three types of macroinvertebrate communities
 within water-filled bromeliads. Two represented food webs containing both
 a fast filter feeder-microbial and slow detritivore energy channels found
 in Costa Rica and Puerto Rico, and one represented the structurally
 simpler food webs in French Guiana, which only contained the fast filter
 feeder-microbial channel. We manipulated the amount and distribution of
 rain entering bromeliads, and examined how food web structure mediated
 ecosystem responses to changes in the quantity and temporal distribution
 of precipitation. Food web structure affected the survival of functional
 groups in general, and ecosystem functions such as decomposition and the
 production of fine particulate organic matter. Ecosystem processes were
 more affected by decreased precipitation than were the abundance of
 microorganisms and metazoans. In our experiments, the sensitivity of the
 ecosystem to precipitation change was primarily revealed in the food web
 dominated by the single filter feeder-microbial channel because other
 top-down and bottom-up processes were weak or absent. Our results show
 stronger effects of food web structure than precipitation change per se on
 the functioning of bromeliad ecosystems. Consequently, we predict that
 ecosystem function in bromeliads throughout the Americas will be more
 sensitive to changes in the distribution of species, rather than to the
 direct effects caused by changes in precipitation.
description: Trzcinski Dryad data
 allData collected in field
 experiment on aquatic communities living within bromeliads in French
 Guiana.Dryad data
 all.xlsx
DOI: 10.5061/dryad.cr4d7
title: Data from: Wing trait-inversion associations in Drosophila subobscura can be generalized within continents, but may change through time

description: Clinal variation is one of the most emblematic examples of the action of
 natural selection at a wide geographical range. In Drosophila subobscura
 parallel clines in body size and inversions, but not in wing shape, were
 found in Europe and South and North America. Previous work has shown that
 a bottleneck effect might be largely responsible for differences in wing
 trait-inversions association between one European and one South American
 population. One question still unaddressed is if the associations found
 before are present across other populations of the European and South
 American clines. Another open question is whether evolutionary dynamics in
 a new environment can lead to relevant changes in wing traits-inversions
 association. In order to analyze geographical variation in these
 associations, we characterized three recently laboratory founded
 Drosophila subobscura populations from both the European and South
 American latitudinal clines. To address temporal variation, we also
 characterized the association at a later generation in the European
 populations. We found that wing size and shape associations can be
 generalized across populations of the same continent, but may change
 through time for wing size. The observed temporal changes are probably due
 to changes in the genetic content of inversions, derived from adaptation
 to the new, laboratory environment. Finally, we show that it is not
 possible to predict clinal variation from intrapopulation associations.
 All in all this suggests that, at least in the present, wing
 traits-inversion associations are not responsible for the maintenance of
 the latitudinal clines in wing shape and size.
description: Raw Data and Average
 statisticsIn this excel book you
 can find the raw data for the three populations analyzed in each continent
 (Europe and South America) and the two generations of the European
 populations analyzed (6 and 25). Additionally, there are also tables with
 the basic statistics (average and standard deviation) of centroid size and
 wing shape for each inversion analyzed, separated by replicate population
 and generation.Simulations and
 BootstrapR code used to generate
 the simulations of the association between centroid size and standard dose
 and the bootstrap of the observed associations.
DOI: 10.5061/dryad.jp596
title: Data from: Switching between apparently redundant iron-uptake mechanisms benefits bacteria in changeable environments

description: Bacteria often possess multiple siderophore-based iron uptake systems for
 scavenging this vital resource from their environment. However, some
 siderophores seem redundant, because they have limited iron-binding
 efficiency and are seldom expressed under iron limitation. Here, we
 investigate the conundrum of why selection does not eliminate this
 apparent redundancy. We focus on Pseudomonas aeruginosa, a bacterium that
 can produce two siderophores—the highly efficient but metabolically
 expensive pyoverdine, and the inefficient but metabolically cheap
 pyochelin. We found that the bacteria possess molecular mechanisms to
 phenotypically switch from mainly producing pyoverdine under severe iron
 limitation to mainly producing pyochelin when iron is only moderately
 limited. We further show that strains exclusively producing pyochelin grew
 significantly better than strains exclusively producing pyoverdine under
 moderate iron limitation, whereas the inverse was seen under severe iron
 limitation. This suggests that pyochelin is not redundant, but that
 switching between siderophore strategies might be beneficial to trade off
 efficiencies versus costs of siderophores. Indeed, simulations
 parameterized from our data confirmed that strains retaining the capacity
 to switch between siderophores significantly outcompeted strains defective
 for one or the other siderophore under fluctuating iron availabilities.
 Finally, we discuss how siderophore switching can be viewed as a form of
 collective decision-making, whereby a coordinated shift in behaviour at
 the group level emerges as a result of positive and negative feedback
 loops operating among individuals at the local scale.
description: Dumas_etal_2013_ProcB_Dryad_dataThis Excel file contains all raw laboratory data used for the paper.Dumas_etal_2013_ProcB_Dryad_simulationcodeThis R script file contains the code for the simulation used in the paper.
DOI: 10.15468/dl.ngtze2
title: Occurrence Download

description: A dataset containing 283 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Argentina, Brazil, United States of America)",
 "TaxonKey is Dalbulus maidis"
 ]
}

 The dataset includes 283 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000642-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.f6n8s
title: Data from: How much information is needed to infer reticulate evolutionary histories?

description: Phylogenetic networks are a generalization of evolutionary trees and are
 an important tool for analyzing reticulate evolutionary histories.
 Recently, there has been great interest in developing new methods to
 construct rooted phylogenetic networks, that is, networks whose internal
 vertices correspond to hypothetical ancestors, whose leaves correspond to
 sampled taxa, and in which vertices with more than one parent correspond
 to taxa formed by reticulate evolutionary events such as recombination or
 hybridization. Several methods for constructing evolutionary trees use the
 strategy of building up a tree from simpler building blocks (such as
 triplets or clusters), and so it is natural to look for ways to construct
 networks from smaller networks. In this paper we shall demonstrate a
 fundamental issue with this approach. Namely, we show that even if we are
 given all of the subnetworks induced on all proper subsets of the leaves
 of some rooted phylogenetic network, we still do not have all of the
 information required to completely determine that network. This implies
 that even if all of the building blocks for some reticulate evolutionary
 history were to be taken as the input for any given network building
 method, the method might still output an incorrect history. We also
 discuss some potential consequences of this result for constructing
 phylogenetic networks.
description: Supplementary
 materialSupplementary material
 for systematic biology submissionReconstruction_supp_rev.pdf
DOI: 10.15468/dl.kqzjd3
title: Occurrence Download

description: A dataset containing 5152 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Tetragonisca angustula, Puma concolor)",
 "HasCoordinate is true",
 "Country is Brazil"
 ]
}

 The dataset includes 5152 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000644-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.66f8c
title: Data from: Symbiodinium population genetics: testing for species boundaries and analyzing samples with mixed genotypes

description: Population genetic markers are increasingly being used to study the
 diversity, ecology, and evolution of Symbiodinium, a group of eukaryotic
 microbes that are often mutualistic with reef-building corals. Population
 genetic markers can resolve individual clones, or strains, from samples of
 host tissue, however samples may comprise different species that may
 confound interpretations of gene flow and genetic structure. Here we
 propose a method for resolving species from population genetic data using
 tests of genetic recombination. Assigning individuals to genetically
 recombining populations prior to further analyses avoids critical errors
 in the interpretation of gene flow and dispersal. To demonstrate the
 effectiveness of the approach we first apply this method to a simulated
 dataset. We then use the method to resolve two species of host-generalist
 Symbiodinium that commonly co-occur in reef-building corals collected from
 Indo-West Pacific reefs. We demonstrate that the method is robust even
 when some hosts contain genotypes of two distinct species. Finally, we
 examine population genetic datasets from two recently published papers in
 Molecular Ecology. We show that each strongly supports a two species
 interpretation, which significantly changes the original conclusions
 presented in these studies. When combined with available phylogenetic and
 ecological evidence, the use of population genetic data offers a robust
 method for unambiguously delimiting morphologically cryptic species.
description: Simulated.dataS1Simulated species 1 data, input to simulation R fileSimulated.dataS2Simulated species 2 file to input into R Simulation fileSimulating dataR script for processing the pure simulated genotypes into mixed sexual and clonal samples as would be sampled naturallyfdataraw unprocessed output of Simulated data processing script with mixed MLGsSimulated dataData processing of simulated dataC1and3Processed Symbiodinium C1 and C1 dataHowellsetal2013Presence/absence file from Howells et al. 2013 processed into a list of alleles observed in each sample used to create Figure 4Wirshingetal 2013 PartitionedData from Wirshing et al. 2013 after partitioning into the two species ( Figure 5c)
DOI: 10.15468/dl.4m9sb8
title: Occurrence Download

description: A dataset containing 69 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acromyrmex subterraneus",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2025",
 "DecimalLatitude is greater than or equal to -60.0",
 "DecimalLatitude is less than or equal to 40.0",
 "DecimalLongitude is greater than or equal to -90.0",
 "DecimalLongitude is less than or equal to 55.0",
 "HasCoordinate is true"
 ]
}

 The dataset includes 69 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000643-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.