cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8t59p
title: Data from: A low technology emanator treated with the volatile pyrethroid transfluthrin confers long term protection against outdoor biting vectors of lymphatic filariasis, arboviruses and malaria

description: Background. The vapor phase of the volatile pyrethroid transfluthrin
 incapacitates mosquitoes and prevents them from feeding. Although existing
 emanator products for delivering volatile pyrethroids protect against
 outdoor mosquito bites, they are too short-lived to be practical or
 affordable for routine use in low-income settings. New transfluthrin
 emanators, comprised simply of treated hessian fabric strips, have
 recently proven highly protective against outdoor-biting vectors of
 lymphatic filariasis, arboviruses and malaria, but their full protective
 lifespan, minimum dose requirements, and range of protection have not
 previously been assessed. Methodology. The effects of
 transfluthrin-treated hessian strips upon mosquito biting exposure of
 users and nearby non-users, as well as dependence of protection upon
 treatment dose, were measured outdoors in rural Tanzania using human
 landing catches (HLC). Principal Findings. Strips treated with 10ml of
 transfluthrin prevented at least three quarters (p &lt; 0.001) of
 outdoor bites by Anopheles arabiensis, Culex spp. and Mansonia spp.
 mosquitoes, and &gt;90% protection against bites on warmer nights with
 higher evaporation rates, for at least one year. Strips treated with this
 high dose also reduced biting exposure of non-users at a distance of up to
 5m from the strips for An. arabiensis (p &lt; 0.001) and up to 2m for
 Mansonia spp. (p = 0.008), but provided no protection to non-users against
 Culex spp.. No evidence of increased risk for non-users, caused by
 diversion of mosquitoes to unprotected individuals, was found at any
 distance within an 80m radius. A dose of only 1ml provided equivalent
 protection to the 10ml dose against An. arabiensis, Culex spp. and
 Mansonia spp. mosquitoes over 6 months (p &lt; 0.001).
 Conclusions/Significance. Transfluthrin-treated hessian emanators provide
 safe, affordable, long-term protection against several different
 pathogen-transmitting mosquito taxa that attack humans outdoors, where
 they are usually active and cannot be protected by bed nets or residual
 sprays with conventional, solid-phase insecticides.
description: Ogoma et al 2017_A low
 tech emanator against outdoor mosquito vectors_dataThe data was collected
 in Kilombero Valley Tanzania to evaluate efficacy of a low technology
 transfluthrin emanator against outdoor biting mosquito vectors of malaria,
 dengue and arboviruses.Ogoma et al 2017_A low
 tech emanator against outdoor mosquito vectors_Temp dataThis data includes
 information on the effect of temperature on efficacy of transfluthrin
 treated emanators.
DOI: 10.5061/dryad.4p169
title: Data from: Trophic level, successional age and trait matching determine specialization of deadwood-based interaction networks of saproxylic beetles

description: The specialization of ecological networks provides important insights into
 possible consequences of biodiversity loss for ecosystem functioning.
 However, mostly mutualistic and antagonistic interactions of living
 organisms have been studied, whereas detritivore networks and their
 successional changes are largely unexplored. We studied the interactions
 of saproxylic (deadwood-dependent) beetles with their dead host trees. In
 a large-scale experiment, 764 logs of 13 tree species were exposed to
 analyse network structure of three trophic groups of saproxylic beetles
 over 3 successional years. We found remarkably high specialization of
 deadwood-feeding xylophages and lower specialization of fungivorous and
 predatory species. During deadwood succession, community composition,
 network specialization and network robustness changed differently for the
 functional groups. To reveal potential drivers of network specialization,
 we linked species' functional traits to their network roles, and
 tested for trait matching between plant (i.e. chemical compounds) and
 beetle (i.e. body size) traits. We found that both plant and animal traits
 are major drivers of species specialization, and that trait matching can
 be more important in explaining interactions than neutral processes
 reflecting species abundance distributions. High network specialization in
 the early successional stage and decreasing network robustness during
 succession indicate vulnerability of detritivore networks to reduced tree
 species diversity and beetle extinctions, with unknown consequences for
 wood decomposition and nutrient cycling.
description: Data of
 SaproxlyicBeetlesData sheet containing
 information about the sampled saproxylic beetlesData_SaproxlyicBeetles.xlsxWood ChemistryData sheet containing information about the wood compounds used for analyses in the publication.WoodChemistry.xlsx
DOI: 10.5061/dryad.8nf05
title: Data from: Risk of exposure to potential vector mosquitoes for rural workers in Northern Lao PDR

description: Background: One major consequence of economic development in South-East
 Asia has been a rapid expansion of rubber plantations, in which outbreaks
 of dengue and malaria have occurred. Here we explored the difference in
 risk of exposure to potential dengue, Japanese encephalitis (JE), and
 malaria vectors between rubber workers and those engaged in traditional
 forest activities in northern Laos PDR. Methodology/Principal findings:
 Adult mosquitoes were collected for nine months in secondary forests,
 mature and immature rubber plantations, and villages. Human behavior data
 were collected using rapid participatory rural appraisals and surveys.
 Exposure risk was assessed by combining vector and human behavior and
 calculating the basic reproduction number (R0) in different typologies.
 Compared to those that stayed in the village, the risk of dengue vector
 exposure was higher for those that visited the secondary forests during
 the day (odds ratio (OR) 36.0), for those living and working in rubber
 plantations (OR 16.2) and for those that tapped rubber (OR 3.2). Exposure
 to JE vectors was also higher in the forest (OR 1.4) and, similar when
 working (OR 1.0) and living in the plantations (OR 0.8). Exposure to
 malaria vectors was greater in the forest (OR 1.3), similar when working
 in the plantations (OR 0.9) and lower when living in the plantations (OR
 0.6). R0 for dengue was &gt;2.8 for all habitats surveyed, except
 villages where R0≤0.06. The main malaria vector in all habitats was
 Anopheles maculatus s.l. in the rainy season and An. minimus s.l. in the
 dry season. Conclusions/Significance: The highest risk of exposure to
 vector mosquitoes occurred when people visit natural forests. However,
 since rubber workers spend long periods in the rubber plantations, their
 risk of exposure is increased greatly compared to those who temporarily
 enter natural forests or remain in the village. This study highlights the
 necessity of broadening mosquito control to include rubber plantations.
description: Data file for paper:
 Potential risk of exposure to vector mosquitoesExcel sheet containing
 the mosquito data collection used for analysis within the
 paperData
 file Risk of exposure to vector
 mosquitoes.xlsx
DOI: 10.5061/dryad.7pd51
title: Data from: Winter chilling speeds spring development of temperate butterflies

description: Understanding and predicting phenology has become more important with
 ongoing climate change and has brought about great research efforts in the
 recent decades. The majority of studies examining spring phenology of
 insects have focussed on the effects of spring temperatures alone. Here we
 use citizen-collected observation data to show that winter cold duration,
 in addition to spring temperature, can affect the spring emergence of
 butterflies. Using spatial mixed models, we disentangle the effects of
 climate variables and reveal impacts of both spring and winter conditions
 for five butterfly species that overwinter as pupae across the UK, with
 data from 1976 to 2013 and one butterfly species in Sweden, with data from
 2001 to 2013. Warmer springs lead to earlier emergence in all species and
 milder winters lead to statistically significant delays in three of the
 five investigated species. We also find that the delaying effect of winter
 warmth has become more pronounced in the last decade, during which time
 winter durations have become shorter. For one of the studied species,
 Anthocharis cardamines (orange tip butterfly), we also make use of
 parameters determined from previous experiments on pupal development to
 model the spring phenology. Using daily temperatures in the UK and Sweden,
 we show that recent variation in spring temperature corresponds to 10–15
 day changes in emergence time over UK and Sweden, whereas variation in
 winter duration corresponds to 20 days variation in the south of the UK
 versus only 3 days in the south of Sweden. In summary, we show that short
 winters delay phenology. The effect is most prominent in areas with
 particularly mild winters, emphasising the importance of winter for the
 response of ectothermic animals to climate change. With climate change,
 these effects may become even stronger and apply also at higher latitudes.
description: Stalhandske_etal_JAEZip archive with five folders of script and data files for spatial mixed modelling of phenology of five butterfly species as well as modelling of phenology of Anthocharis cardamines.
DOI: 10.5061/dryad.796t8
title: Data from: Predator-mediated negative effects of overabundant snow geese on arctic-nesting shorebirds

description: Overabundant species can strongly impact ecosystem functioning through
 trophic cascades. The strong increase in several arctic geese populations,
 primarily due to changes in agricultural practices in temperate regions,
 can have severe direct impacts on tundra ecosystems through vegetation
 degradation. However, predator-mediated negative effects of goose
 overabundance on other tundra species can also be significant but are
 poorly understood. We tested the hypothesis that goose abundance
 negatively affects arctic-nesting shorebirds by increasing nest predation
 pressure. We used six years of data collected within and near a greater
 snow goose colony (Chen caerulescens atlantica) to evaluate the effect of
 geese on the spatial variation in (1) the occurrence of shorebird nest
 predators, (2) the nest predation risk (with artificial shorebird nests),
 and (3) the occurrence of nesting shorebirds. We found that the goose
 colony had a strong influence on the spatial distribution of nest
 predators and nesting shorebirds. Occurrence of predators decreased, while
 occurrence of nesting shorebirds increased with distance from the centroid
 of the colony. The strength of these effects was modulated by lemming
 density, the preferred prey for predators. Shorebird nest predation risk
 also decreased with distance from the colony. Overall, these results
 indicate that goose abundance negatively affects arctic-nesting shorebirds
 through shared predators. Therefore, we show that the current decline of
 some arctic shorebird populations may be in part mediated by a negative
 effect of an overabundant species.
description: DATA_MS#ECS16-0660Database on the impacts of overabundant Greater Snow Geese on sympatric species, with a focus on shorebirds.
DOI: 10.5061/dryad.2182n
title: Data from: An increase in immature β-cells lacking Glut2 precedes the expansion of β-cell mass in the pregnant mouse

description: A compensatory increase in β-cell mass occurs during pregnancy to counter
 the associated insulin resistance, and a failure in adaptation is thought
 to contribute to gestational diabetes. Insulin-expressing but
 glucose-transporter-2-low (Ins+Glut2LO) progenitor cells are present in
 mouse and human pancreas, being predominantly located in extra-islet
 β-cell clusters, and contribute to the regeneration of the endocrine
 pancreas following induced ablation. We therefore sought to investigate
 the contribution of Ins+Glut2LO cells to β-cell mass expansion during
 pregnancy. Female C57Bl/6 mice were time mated and pancreata were
 collected at gestational days (GD) 6, 9, 12, 15, and 18, and postpartum D7
 (n = 4/time-point) and compared to control (non-pregnant) animals. Beta
 cell mass, location, proliferation (Ki67+), and proportion of Ins+Glut2LO
 cells were measured using immunohistochemistry and bright field or
 confocal microscopy. Beta cell mass tripled by GD18 and β-cell
 proliferation peaked at GD12 in islets (≥6 β-cells) and small β-cell
 clusters (1–5 β-cells). The proportion and fraction of Ins+Glut2LO cells
 undergoing proliferation increased significantly at GD9 in both islets and
 clusters, preceding the increase in β-cell mass and proliferation, and
 their proliferation within clusters persisted until GD15. The overall
 number of clusters increased significantly at GD9. Quantitative PCR showed
 a significant increase in Pdx1 presence at GD9 vs. GD18 or control
 pancreas, and Pdx1 was visualized by immunohistochemistry within both
 Ins+Glut2LO and Ins+Glut2HI cells within clusters. These results indicate
 that Ins+Glut2LO cells are likely to contribute to β-cell mass expansion
 during pregnancy.
description: GTT
 dataPrism format
 fileGTT.pzfMafB expression dataPrism format fileMafB.pzfNkx6.1 expressionPrism format fileNkx6.1.pzfPdx1expressionPrism format filePdx1.pzfPdx1 protein levels ELISAPrism format filePdx1 ELISA minimal dat set.pzfSummary cell histology dataMicrosoft Excel fileSummary data PLos 1 subm.xlsx
DOI: 10.5061/dryad.5g205
title: Data from: Conflicting evolutionary histories of the mitochondrial and nuclear genomes in New World Myotis bats

description: The rapid diversification of Myotis bats into more than 100 species is one
 of the most extensive mammalian radiations available for study. Efforts to
 understand relationships within Myotis have primarily utilized
 mitochondrial markers and trees inferred from nuclear markers lacked
 resolution. Our current understanding of relationships within Myotis is
 therefore biased towards a set of phylogenetic markers that may not
 reflect the history of the nuclear genome. To resolve this, we sequenced
 the full mitochondrial genomes of 37 representative Myotis, primarily from
 the New World, in conjunction with targeted sequencing of 3,648
 ultraconserved elements (UCEs). We inferred the phylogeny and explored the
 effects of concatenation and summary phylogenetic methods, as well as
 combinations of markers based on informativeness or levels of missing
 data, on our results. Of the 294 phylogenies generated from the nuclear
 UCE data, all are significantly different from phylogenies inferred using
 mitochondrial genomes. Even within the nuclear data, quartet frequencies
 indicate that around half of all UCE loci conflict with the estimated
 species tree. Several factors can drive such conflict, including
 incomplete lineage sorting, introgressive hybridization, or even
 phylogenetic error. Despite the degree of discordance between nuclear UCE
 loci and the mitochondrial genome and among UCE loci themselves, the most
 common nuclear topology is recovered in one quarter of all analyses with
 strong nodal support. Based on these results, we re-examine the
 evolutionary history of Myotis to better understand the phenomena driving
 their unique nuclear, mitochondrial, and biogeographic histories.
description: Alignments of individual
 UCE lociIndividual alignments of
 UCE loci in nexus format. Loci were aligned using MAFFT and trimmed wtih
 Gblocks.uceLociAlignments.tgzIndividual gene trees from UCE lociIndividual gene trees per UCE locus were generated using RAxML's GTRGAMMA model of nucleotide evolution and fast bootstrapping options (replicates=1,000). Individual trees are in Newick format.uceGeneTrees.tgzsupFile-all_trees_2017-07-01Final trees from all analyses in nexus format.assembled_contigs_from_UCEenriched_readsAll loci assembled from baited reads (per taxa). These sequences were then compared in an all-vs-all manner to identify homologous UCE loci among taxa. As a results, there are some contigs that may not be present in the final alignments since they are not UCE loci.Sup Fig 1. Phylogenetic content of UCE loci based on length.The length of a UCE locus is correlated with the number of phylogenetically informative characters. UCE loci were sorted by length and ten bins of alignments were created so that the shortest loci were combined into one alignment, the next shortest set of loci were combined … etc. Parsimony informative characters made up a minor part of each alignment.supFigure1-informCharacters_2017-07-01.png
DOI: 10.5061/dryad.tp3j5
title: Data from: Size, age, and habitat determine effectiveness of Palau's Marine Protected Areas

description: Palau has a rich heritage of conservation that has evolved from the
 traditional moratoria on fishing, or "bul", to more western
 Marine Protected Areas (MPAs), while still retaining elements of customary
 management and tenure. In 2003, the Palau Protected Areas Network (PAN)
 was created to conserve Palau's unique biodiversity and culture, and
 is the country's mechanism for achieving the goals of the Micronesia
 Challenge (MC), an initiative to conserve ?30% of near-shore marine
 resources within the region by 2020. The PAN comprises a network of
 numerous MPAs within Palau that vary in age, size, level of management,
 and habitat, which provide an excellent opportunity to test hypotheses
 concerning MPA design and function using multiple discreet sampling units.
 Our sampling design provided a robust space for time comparison to
 evaluate the relative influence of potential drivers of MPA efficacy. Our
 results showed that no-take MPAs had, on average, nearly twice the biomass
 of resource fishes (i.e. those important commercially, culturally, or for
 subsistence) compared to nearby unprotected areas. Biomass of non-resource
 fishes showed no differences between no-take areas and areas open to
 fishing. The most striking difference between no-take MPAs and unprotected
 areas was the more than 5-fold greater biomass of piscivorous fishes in
 the MPAs compared to fished areas. The most important determinates of
 no-take MPA success in conserving resource fish biomass were MPA size and
 years of protection. Habitat and distance from shore had little effect on
 resource fish biomass. The extensive network of MPAs in Palau likely
 provides important conservation and tourism benefits to the Republic, and
 may also provide fisheries benefits by protecting spawning aggregation
 sites, and potentially through adult spillover.
description: Palau_fishdata_DryadPalau fish dataPalau_benthicdata_Dryad
DOI: 10.5061/dryad.b6d0r
title: Data from: Application of genomic estimation methods of inbreeding and population structure in an Arabian horse herd

description: Horse breeders rely heavily on pedigrees for identification of ancestry in
 breeding stock. Inaccurate pedigrees may erroneously assign individuals to
 false lineages or breed memberships resulting in wrong estimates of
 inbreeding and coancestry. Moreover, discrepancies in pedigree records can
 lead breeders seeking to limit inbreeding into making misguided breeding
 decisions. Genome-wide SNPs provide a quantitative tool to aid in the
 resolution of lineage assignments and the calculation of genomic measures
 of relatedness. The aim of this project was to pilot a comparison between
 pedigree and genomic relatedness and inbreeding measures in a herd of 36
 pedigreed Egyptian Arabian horses genotyped using the Equine SNP70
 platform (Geneseek, Inc.). Moreover, we sought to estimate the minimum
 number of markers sufficient for genomic inbreeding calculations. Pedigree
 inbreeding values were moderately correlated with genomic inbreeding
 values (r = 0.406), whereas genomic relationships and pedigree
 relationships have a high correlation (r = 0.77). Although first degree
 relationships were successfully reconstructed, more distant relationships
 were difficult to resolve. Multi-dimensional scaling and clustering
 analysis agreed with within-herd pedigree information. In comparing the
 herd to a reference sample of United States, Polish, and Egyptian Arabian
 horses, the herd's historically recorded Egyptian lineage was
 successfully recovered. We conclude that genomic estimates of inbreeding
 and relationships are superior to their pedigree counterparts. They can be
 thus utilized in conservation of valuable lines of livestock, and in
 breeds at risk for loss of genomic diversity. We also postulate a minimum
 of 2000 markers in linkage equilibrium to be used for inbreeding
 estimation.
description: Genotypic data (plink
 ped and map files) for the study herd and Arabian horses of different
 bloodlines.Genotypic
 Data.zip
DOI: 10.5061/dryad.8p9j6
title: Data from: All roads lead to weediness: patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian Oryza

description: Weedy rice (Oryza spp.), a weedy relative of cultivated rice (O. sativa),
 infests and persists in cultivated rice fields worldwide. Many weedy rice
 populations have evolved similar adaptive traits, considered part of the
 “agricultural weed syndrome,” making this an ideal model to study the
 genetic basis of parallel evolution. Understanding parallel evolution
 hinges on accurate knowledge of the genetic background and origins of
 existing weedy rice groups. Using population structure analyses of South
 Asian and US weedy rice, we show that weeds in South Asia have highly
 heterogeneous genetic backgrounds, with ancestry contributions both from
 cultivated varieties (aus and indica) and wild rice. Moreover, the two
 main groups of weedy rice in the US, which are also related to aus and
 indica cultivars, constitute a separate origin from that of Asian weeds.
 Weedy rice populations in South Asia largely converge on presence of red
 pericarps and awns and on ease of shattering. Genome-wide divergence scans
 between weed groups from the US and South Asia and their crop relatives
 are enriched for loci involved in metabolic processes. Some candidate
 genes related to iconic weedy traits and competitiveness are highly
 divergent between some weed-crop pairs, but are not shared amongst all
 weed-crop comparisons. Our results show that weedy rice is an extreme
 example of recurrent evolution, and suggest that most populations are
 evolving their weedy traits through different genetic mechanisms.
description: SNP polymorphisms among
 the Oryza populationThis hapmap file is
 generated from Genotyping-by-Sequencing, a Next-Generation-Sequencing
 method. Single nucleotide polymorphisms recorded in this file are called
 from the sequencing data with the standard Tassel pipeline. Each of the
 51934 rows is for one SNP locus, with the first 11 columns describing the
 ID, alleles, chromosome positions and other features of the locus, and the
 rest columns recording the SNP alleles of the panel of Oryza samples
 included.strictdrop_ZFS_gbs2_labID.hapmap.txt