cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.35bn3
title: Data from: Post-glacial recolonization of the North American Arctic by Arctic char (Salvelinus alpinus): genetic evidence of multiple northern refugia and hybridization between glacial lineages

description: Aims: We investigated post-glacial recolonization of the North American
 Arctic by Arctic char (Salvelinus alpinus) and examined potential
 hybridization between different glacial lineages upon secondary contact.
 Location: North American Arctic and adjacent areas. Methods: We collected
 mtDNA sequence data from 1355 individuals from 110 sampling locations and
 data from nine microsatellite loci from 931 individuals from 37 locations.
 We assessed the phylogenetic relationships and geographical distribution
 of mtDNA haplotypes and conducted historical demographic analyses. We used
 a Bayesian clustering analysis method to detect potential hybridization
 between glacial lineages. Results: Two highly divergent mtDNA lineages
 were identified in the Arctic region with distinct but overlapping
 geographic distributions: one in Beringia and the other over the entire
 Arctic Archipelago and coastal mainland east of Alaska. The microsatellite
 data also implied the existence of these two lineages. Evidence of
 hybridization was detected between the Arctic lineage and an Atlantic
 lineage in eastern North America. Main conclusions: Our data suggested
 survival and recolonization from two northern glacial refugia: one in
 Beringia and another in a smaller refugium, perhaps in the Arctic
 Archipelago itself or a separate refugium within Beringia. Patterns of
 hybridization detected supported the presence of a secondary contact zone
 between glacial lineages in the eastern Canadian Arctic.
description: Salpinus_usatRawGenotypes_Moore_25June2015Raw genotypes for nine microsatellite loci from North American Arctic char samplesSTRUCTURE_project_dataDatafile ready for analysis in software STRUCTURE with all 931 samples of North American Arctic char included in the present study.project_dataSTRUCTURE_mainparamsParameter file for re-running the STRUCTURE analysis on the microsatellite data from North American Arctic char included in the present study.mainparams
DOI: 10.5061/dryad.fc3sh
title: Data from: Mitochondrial introgressive hybridization following a demographic expansion in the tomato frogs of Madagascar, genus Dyscophus

description: Madagascar is a biodiversity hotspot with a unique fauna and flora largely
 endemic at the species level and highly threatened by habitat destruction.
 The processes underlying population-level differentiation in
 Madagascar's biota are poorly understood and have been proposed to be
 related to Pleistocene climatic cycles, yet the levels of genetic
 divergence observed are often suggestive of ancient events. We combined
 molecular markers of different variability to assess the phylogeography of
 Madagascar's emblematic tomato frogs (Dyscophus guineti and D.
 antongilii) and interpret the observed pattern as resulting from ancient
 and recent processes. Our results suggest that the initial divergence
 between these taxa is probably old as reflected by protein-coding nuclear
 genes and by a strong mitochondrial differentiation of the southernmost
 population. Dramatic changes in their demography appear to have been
 triggered by the end of the last glacial period and possibly by the short
 return of glacial conditions known as the 8K event. This dramatic change
 resulted in an approximately 50-fold reduction of the effective population
 size in various populations of both species. We hypothesize these
 species' current mitochondrial DNA diversity distribution reflects a
 swamping of the mitochondrial genetic diversity of D. guineti by that of
 D. antongilii previous to the populations' bottlenecks during the
 Holocene, and probably as a consequence of D. antongilii demographic
 expansion approximately 1 million years ago. Our data support the
 continued recognition of D. antongilii and D. guineti as separate species
 and flag D. guineti as the more vulnerable species to past and probably
 also future environmental changes.
description: Orozco-terWengel_et_al_MSAmicrosatellite matrix of Dyscophus antongili and D guineiti in MSA format with an additional column reflecting sample name. Missing data is represented by under scores "_".cytb_ALIGNEDcytb Alignment in phylip formatNCX1_ALIGNEDNCX1 Alignment in phylip formatPOMC_ALIGNEDPOMC Alignment in phylip formatRag1_ALIGNEDRAG-1 Alignment in phylip format
DOI: 10.5061/dryad.bk90m
title: Data from: Fine-scale analysis of parasite resistance genes in the red flour beetle, Tribolium castaneum

description: Parasite infection impacts population dynamics through effects on fitness
 and fecundity of the individual host. In addition to the known roles of
 environmental factors, host susceptibility to parasites has a genetic
 basis that has not been well characterized. We previously mapped
 quantitative trait loci (QTL) for susceptibility to rat tapeworm
 (Hymenolepis diminuta) infection in Tribolium castaneum using dominant
 AFLP markers, but the resistance genes were not identified. In the current
 study, we refined the QTL locations and increased the marker density in
 the QTL regions using new microsatellite markers, sequence-tagged site
 markers (STS), and single-strand conformational polymorphism markers
 (SSCP). Resistance QTL in three linkage groups, (LG3, LG6 and LG8), were
 each mapped to intervals less than 1.0 cM between two codominant markers.
 The effects of 21 genes in the three QTL regions were investigated by
 using quantitative RT-PCR analysis, and transcription profiles were
 obtained from the resistant TIW1 and the susceptible cSM strains. Based on
 transcription data, 8 genes were selected for RNA interference (RNAi)
 analysis to investigate their possible roles in H. diminuta resistance,
 including cytochrome P450 (LOC657454) and toll-like receptor 13 (TLR 13,
 LOC662131). The transcription of P450 and TLR 13 genes in the resistant
 TIW1 strains was reduced more than 9-fold relative to the control.
 Moreover, the effects of gene knockdown of P450 and TLR 13 caused
 resistant beetles to become susceptible to tapeworm infection, which
 strongly suggests an important role for each in T. castaneum resistance to
 H. diminuta infection.
description: Genotyping data using
 molecular markersThis file contains the
 genotype data generated using microsatellite markers, sequence-tagged site
 markers (STS), and single-strand conformational polymorphism (SSCP)
 markers.Genotyping
 data.xlsxPhenotype
 dataThis file contains
 tapeworm parasite infection scoring data for Tribolium
 castaneum.
DOI: 10.5061/dryad.4tq73
title: Data from: Impact of point-of-care ultrasound on clinical decision-making at an urban emergency department in Tanzania

description: Background: Point of care ultrasound (PoCUS) is an efficient, inexpensive,
 safe, and portable imaging modality that can be particularly useful in
 resource-limited settings. However, its impact on clinical decision making
 in such settings has not been well studied. The objective of this study is
 to describe the utilization and impact of PoCUS on clinical decision
 making at an urban emergency department in Dar es Salaam, Tanzania.
 Methods: This was a prospective descriptive cross-sectional study of
 patients receiving PoCUS at Muhimbili National Hospital's Emergency
 Medical Department (MNH EMD). Data on PoCUS studies during a period of 10
 months at MNH EMD was collected on consecutive patients during periods
 when research assistants were available. Data collected included patient
 age and gender, indications for ultrasound, findings, interpretations, and
 provider-reported diagnostic impression and disposition plan before and
 after PoCUS. Descriptive statistics, including medians and interquartile
 ranges, and counts and percentages, are reported. Pearson chi squared
 tests and p-values were applied to categorical data to evaluate for
 significant differences. Results: PoCUS data was collected for 986 studies
 performed on 784 patients. Median patient age was 32 years; 56% of
 patients were male. Top indications for PoCUS included trauma, respiratory
 presentations, and abdomino-pelvic pain. The most frequent study types
 performed were eFAST, cardiac, and obstetric or gynaecologic studies.
 Overall, clinicians reported that the use of PoCUS changed either
 diagnostic impression or disposition plan in 29% of all cases. Rates of
 change in diagnostic impression or disposition plan increased to 45% in
 patients for whom more than one PoCUS study type was performed.
 Conclusions: In resource-limited emergency care settings, PoCUS can be
 utilized for a wide range of indications and has substantial impact on
 clinical decision making, especially when more than one study type is
 performed.
description: ultrasound_data_deidentified_2015_mayDe-identified raw data transcribed from data collection forms. This file is fully cleaned by and analyzed by Stata .do and .ado files included in the "ultrasound_do_files" and "ultrasound_ado_files" zips. See READ ME for further details.ultrasound_do_filesThis zip file contains all Stata .do files required to clean and analyze the raw data file and to produce the tables in the manuscript. See the README for instructions on how to run them on your machine.ultrasound_ado_filesThese supplementary .ado files are required by some of the .do files, and should be placed in the same folder as the .do files.
DOI: 10.5061/dryad.857dd
title: Data from: The nutritional balancing act of a large herbivore: an experiment with captive moose (Alces alces L)

description: The nutrient balancing hypothesis proposes that, when sufficient food is
 available, the primary goal of animal diet selection is to obtain a
 nutritionally balanced diet. This hypothesis can be tested using the
 Geometric Framework for nutrition (GF). The GF enables researchers to
 study patterns of nutrient intake (e.g. macronutrients; protein,
 carbohydrates, fat), interactions between the different nutrients, and how
 an animal resolves the potential conflict between over-eating one or more
 nutrients and under-eating others during periods of dietary imbalance.
 Using the moose (Alces alces L.), a model species in the development of
 herbivore foraging theory, we conducted a feeding experiment guided by the
 GF, combining continuous observations of six captive moose with analysis
 of the macronutritional composition of foods. We identified the moose’s
 self-selected macronutrient target by allowing them to compose a diet by
 mixing two nutritionally complementary pellet types plus limited access to
 Salix browse. Such periods of free choice were intermixed with periods
 when they were restricted to one of the two pellet types plus Salix
 browse. Our observations of food intake by moose given free choice lend
 support to the nutrient balancing hypothesis, as the moose combined the
 foods in specific proportions that provided a particular ratio and amount
 of macronutrients. When restricted to either of two diets comprising a
 single pellet type, the moose i) maintained a relatively stable intake of
 non-protein energy while allowing protein intakes to vary with food
 composition, and ii) increased their intake of the food item that most
 closely resembled the self-selected macronutrient intake from the free
 choice periods, namely Salix browse. We place our results in the context
 of the nutritional strategy of the moose, ruminant physiology and the
 categorization of food quality.
description: Data For Depository
 Felton et alWorksheet 1 contains
 observations of daily food intakes of six captive moose individuals
 included in the feeding experiment, which included 5 different treatments.
 The weight measurements are translated into nutrient intakes and displayed
 separately for pellets and browse items. Worksheet 2 contains daily data
 on individuals' browse and pellet intake per metabolic body weight,
 matched with the browse species offered, air temperature and browse
 availability.
DOI: 10.5061/dryad.q8v8v
title: Data from: Correlated evolution of sexual dimorphism and male dimorphism in a clade of neotropical harvestmen

description: Secondary sexual traits increase male fitness, but may be maladaptive in
 females, generating intralocus sexual conflict that is ameliorated through
 sexual dimorphism. Sexual selection on males may also lead some males to
 avoid expenditure on secondary sexual traits and achieve copulations using
 alternative reproductive tactics (ARTs). Secondary sexual traits can
 increase or decrease fitness in males, depending on which ART they employ,
 generating intralocus tactical conflict that can be ameliorated through
 male dimorphism. Due to the evolutionary forces acting against intralocus
 sexual and tactical conflicts, male dimorphism could coevolve with sexual
 dimorphism, a hypothesis that we tested by investigating these dimorphisms
 across 48 harvestman species. Using three independently derived
 phylogenies we consistently found that the evolution of sexual dimorphism
 was correlated with that of male dimorphism, and suggest that the major
 force behind this relationship is the similarity between selection against
 intralocus sexual conflict and selection against intralocus tactical
 conflict. We also found that transitions in male dimorphism were more
 likely in the presence of sexual dimorphism, indicating that if a sexually
 selected trait arises on an autosome and is expressed in both sexes, its
 suppression in females probably evolves earlier than its suppression in
 small males that adopt ARTs.
description: Measurements of all
 individualsThis file is an excel
 workbook where each spreadsheet contains all the measurements for the
 species used in the study. For some species, the inference about sexual
 and male dimorphism was based on information in the literature, and these
 species are not in this data-set. For all other species (45 spp), the
 data-set contains measurements of: (1) length of the dorsal scute
 (carapace); (2) length of the lateral apophysis on the coxa of the right
 fourth leg; and (3) length of the femur of the fourth leg. All
 measurements are in mm. Some species did not present the coxal apophysis,
 and therefore there is no data for that structure in their
 spreadsheet.
DOI: 10.5061/dryad.kp5cn
title: Data from: Identification of putative orthologous genes for the phylogenetic reconstruction of temperate woody bamboos (Poaceae: Bambusoideae)

description: The temperate woody bamboos (Arundinarieae) are highly diverse in
 morphology but lack a substantial amount of genetic variation. The
 taxonomy of this lineage is intractable, and the relationships within the
 tribe have not been well resolved. Recent studies indicated that this
 tribe could have a complex evolutionary history. Although phylogenetic
 studies of the tribe have been carried out, most of these phylogenetic
 reconstructions were based on plastid data, which provide lower
 phylogenetic resolution compared to nuclear data. In this study, we
 intended to identify a set of desirable nuclear genes for resolving the
 phylogeny of the temperate woody bamboos. Using two different
 methodologies, we identified 209 and 916 genes, respectively, as putative
 single copy orthologous genes. A total of 112 genes was successfully
 amplified and sequenced by next-generation sequencing technologies in five
 species sampled from the tribe. As most of the genes exhibited
 intra-individual allele heterozygotes (IIAHs), we investigated
 phylogenetic utility by reconstructing the phylogeny based on individual
 genes. Discordance among gene trees was observed and, to resolve the
 conflict, we performed a range of analyses using BUCKy and HybTree. While
 caution should be taken when inferring a phylogeny from multiple
 conflicting genes, our analysis indicated that 74 of the 112 investigated
 genes are potential markers for resolving the phylogeny of the temperate
 woody bamboos.
description: matrixes used for
 analysisThis contains 105
 matrixes including intra-individual allele heterozygotes (IIAHs) and 82
 matrixes excluding IIAHs.GenBank
 accessionsThis contains the
 GenBank accession numbers of all the sequences used in ths
 study.
DOI: 10.5061/dryad.cb978
title: Data from: Rapid evolution of increased vulnerability to an insecticide at the expansion front in a poleward moving damselfly

description: Many species are too slow to track their poleward moving climate niche
 under global warming. Pesticide exposure may contribute to this by
 reducing population growth and impairing flight ability. Moreover, edge
 populations at the moving range front may be more vulnerable to pesticides
 because of the rapid evolution of traits to enhance their rate of spread
 that shunt energy away from detoxification and repair. We exposed
 replicated edge and core populations of the poleward moving damselfly
 Coenagrion scitulum to the pesticide esfenvalerate at low and high
 densities. Exposure to esfenvalerate had strong negative effects on
 survival, growth rate and development time in the larval stage and
 negatively affected flight-related adult traits (mass at emergence, flight
 muscle mass and fat content) across metamorphosis. Pesticide effects did
 not differ between edge and core populations, except that at the high
 concentration the pesticide-induced mortality was 17% stronger in edge
 populations. Pesticide exposure may therefore slow down the range
 expansion by lowering population growth rates, especially because edge
 populations suffered a higher mortality, and by negatively affecting
 dispersal ability by impairing flight-related traits. These results
 emphasize the need for direct conservation efforts toward leading-edge
 populations for facilitating future range shifts under global warming.
description: MAIN
 DATAEVA-2015-167-OA
 DATA.xlsSUPPLEMENTARY DATA FOR
 APPENDICES (BIOTIC AND ABIOTIC PARAMETERS)EVA-2015-167-OA DATA FOR
 APPENDICES (BIOTIC AND ABIOTIC
 PARAMETERS).xls
DOI: 10.5061/dryad.f06k49s
title: Data from: Habitat-mediated effects of diurnal and seasonal migration strategies on juvenile salmon survival

description: Behavioral decisions during periods of vulnerability to predation risk,
 such as migrations during the juvenile life-history stage, may strongly
 affect the probability of survival. Habitats through which animals migrate
 are heterogeneous, and risk-reducing behaviors may be more important in
 some habitats than others. Using biotelemetry data, diurnal and seasonal
 riverine migration patterns of &gt;3800 juvenile salmon across four
 species, 12 watersheds, and five years were quantified to evaluate
 possible effects of migration timing on survival from lower river reaches
 to coastal waters. In small, clear rivers most salmon avoided migrating
 during daylight hours, and average survival of fish migrating at night
 (55%; 95% confidence limits 50–61%) was twice that of fish migrating in
 daylight (24%; CL 17-31%). Conversely, in the large, heavily silted Fraser
 River neither preference for nocturnal travel nor effects of diurnal
 timing on survival were observed. Early ocean survival was also influenced
 by the timing of ocean entry, but in opposite directions for fish from the
 Fraser River and smaller rivers. In the Fraser River, average survival for
 later migrants (69%; CL 60–77%) was nearly twice that of earlier migrants
 (38%; CL 33–44%), likely related to seasonal increases in river flow. In
 contrast, in smaller rivers, average survival for earlier migrants (70%;
 CL 65–74%) was 3-fold greater than survival for later migrants (19%; 95%
 CL 14–25%). Together these results demonstrate that timing decisions
 affecting survival of juvenile salmon during their migration are likely
 mediated by landscape characteristics that plausibly influence the risk of
 predation.
description: Input data for Melnychuk
 and Welch - Behavioral EcologyContains data describing
 the date and light level during detection of tagged salmon smolts in
 British Columbia Rivers, and metadata for individual tagged fish.
 Detection data are from acoustic transmitters surgically implanted into
 migrating smolts, and detected on submerged hydrophones with data loggers.
 csv file is saved with Microsoft Excel 2016. Variables are defined in
 manuscript.Melnychuk_Welch_input_data.csv
DOI: 10.5061/dryad.ts608
title: Data from: Bioerosion by pit-forming, temperate-reef sea urchins: history, rates and broader implications

description: Sea urchins are dominant members of rocky temperate reefs around the
 world. They often occur in cavities within the rock, and fit so tightly,
 it is natural to assume they sculpted these "pits." However,
 there are no experimental data demonstrating they bore pits. If they do,
 what are the rates and consequences of bioerosion to nearshore systems? We
 sampled purple sea urchins, Strongylocentrotus purpuratus, from sites with
 four rock types, three sedimentary (two sandstones and one mudstone) and
 one metamorphic (granite). A year-long experiment showed urchins excavated
 depressions on sedimentary rocks in just months. The rate of pit formation
 varied with rock type and ranged from &lt;5 yr for medium-grain
 sandstone to &gt;100 yr for granite. In the field, there were
 differences in pit size and shapes of the urchins (height:diameter ratio).
 The pits were shallow and urchins flatter at the granite site, and the
 pits were deeper and urchins taller at the sedimentary sites. Although
 overall pit sizes were larger on mudstone than on sandstone, urchin size
 accounted for this difference. A second, short-term experiment, showed the
 primary mechanism for bioerosion was ingestion of the substratum. This
 experiment eliminated potential confounding factors of the year-long
 experiment and yielded higher bioerosion rates. Given the high densities
 of urchins, large amounts of rock can be converted to sediment over short
 time periods. Urchins on sandstone can excavate as much as 11.4 kg m-2
 yr-1. On a broader geographic scale, sediment production can exceed 100 t
 ha-1 yr-1, and across their range, their combined bioerosion is comparable
 to the sediment load of many rivers. The phase shift between urchin
 barrens and kelp bed habitats in the North Pacific is controlled by the
 trophic cascade of sea otters. By limiting urchin populations, these apex
 predators also may indirectly control a substantial component of coastal
 rates of bioerosion.
description: ReadmeDescription of data
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 Readme fileS1 Table
 1See
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