cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tj5f0
title: Data from: Age-related declines in immune response in a wild mammal are unrelated to immune cell telomere length

description: Senescence has been hypothesised to arise in part from age-related
 declines in immune performance, but the patterns and drivers of
 within-individual age-related changes in immunity remain virtually
 unexplored in natural populations. Here, using a long-term epidemiological
 study of wild European badgers (Meles meles), we (i) present evidence of a
 within-individual age-related decline in the response of a key
 immune-signalling cytokine, Interferon-gamma (IFNγ), to ex vivo lymphocyte
 stimulation, and (ii) investigate three putative drivers of individual
 variation in the rate of this decline (sex, disease and immune-cell
 telomere length; ICTL). That the within-individual rate of age-related
 decline markedly exceeded that at the population level suggests that
 individuals with weaker IFNγ responses are selectively lost from this
 population. IFNγ responses appeared to decrease with the progression of
 bovine tuberculosis infection (independent of age) and were weaker among
 males than females. However, neither sex nor disease influenced the rate
 of age-related decline in IFNγ response. Similarly, while ICTL also
 declines with age, variation in ICTL predicted neither among- nor
 within-individual variation in IFNy response. Our findings provide
 evidence of within-individual age-related declines in immune performance
 in a wild mammal and highlight the likely complexity of the mechanisms
 that generate them.
description: data_beirne et
 alID
 = Unique individual identity code; CD = focal capture date; SOCG = Social
 group of capture; AGE = Age in years (from 16th February); MEAN.AGE =
 Average age across all captures; DELTA.AGE = Deviation in age from
 MEAN.AGE; SEX = Male or Female; CONDITION = Scaled mass index condition
 estimate; DISEASE.EXCLUDED = bTB status excluding IFNγ-based ELISA test (1
 = uninfected, 2 = exposed, 4 = excretor) ; DISEASE = bTB status including
 IFNγ-based ELISA test (1 = uninfected, 2 = exposed, 4 = excretor); IFN =
 Interferon-gamma response; IFN.PLATE = IFN test plate identity; TELOMERE =
 Telomere length estimate (Kb); TELOMERE.PLATE = Telomere plate
 identity
DOI: 10.5061/dryad.f8c9165
title: Data from: Comparing the rates of speciation and extinction between phylogenetic trees

description: Over the past decade or so it has become increasingly popular to use
 reconstructed evolutionary trees to investigate questions about the rates
 of speciation and extinction. Although the methodology of this field has
 grown substantially in its sophistication in recent years, here I’ll take
 a step back to present a very simple model that is designed to investigate
 the relatively straightforward question of whether the tempo of
 diversification (speciation and extinction) differs between two or more
 phylogenetic trees, without attempting to attribute a causal basis to this
 difference. It is a likelihood method, and I demonstrate that it generally
 shows type I error that is close to the nominal level. I also demonstrate
 that parameter estimates obtained with this approach are largely unbiased.
 Since this method can be used to compare trees of unknown relationship, it
 will be particularly well-suited to problems in which a difference in
 diversification rate between clades is suspected, but in which these
 clades are not particularly closely related. Since diversification methods
 can easily take into account an incomplete sampling fraction, but missing
 lineages are assumed to be missing at random, this method is also
 appropriate for cases in which we’ve hypothesized a difference in the
 process of diversification between two or more focal clades, but in which
 many un-sampled groups separate the few of interest. The method of this
 study is by no means an attempt to replace more sophisticated models in
 which, for instance, diversification depends on the state of an observed
 or unobserved discrete or continuous trait. Rather, my intention is to
 provide a complementary approach for circumstances in which a simpler
 hypothesis is warranted and of biological interest.
description: R markdown for
 reproducible workflowR markdown file
 containing the fully reproducible workflow of the
 study.Revell-2018-Ecology_and_Evolution.RmdBuilt reproducible workflowBuilt reproducible workflow containing all analyses of the study including (low quality versions of) all figures & tables.Revell-2018-Ecology_and_Evolution.html
DOI: 10.5061/dryad.vn536
title: Data from: Elucidating the spatio-temporal dynamics of an emerging wildlife pathogen using approximate Bayesian computation

description: Emerging pathogens constitute a severe threat for human health and
 biodiversity. Determining the status (native or non-native) of emerging
 pathogens, and tracing back their spatio-temporal dynamics, is crucial to
 understand the eco-evolutionary factors promoting their emergence, to
 control their spread and mitigate their impacts. However, tracing back the
 spatio-temporal dynamics of emerging wildlife pathogens is challenging
 because (i) they are often neglected until they become sufficiently
 abundant and pose socio-economical concerns and (ii) their geographical
 range is often little known. Here, we combined classical population
 genetics tools and approximate Bayesian computation (i.e. ABC) to retrace
 the dynamics of Tracheliastes polycolpus, a poorly documented pathogenic
 ectoparasite emerging in Western Europe that threatens several freshwater
 fish species. Our results strongly suggest that populations of T.
 polycolpus in France emerged from individuals originating from a unique
 genetic pool that were most likely introduced in the 1920s in central
 France. From this initial population, three waves of colonization occurred
 into peripheral watersheds within the next two decades. We further
 demonstrated that populations remained at low densities, and hence
 undetectable, during 10 years before a major demographic expansion
 occurred, and before its official detection in France. These findings
 corroborate and expand the few historical records available for this
 emerging pathogen. More generally, our study demonstrates how ABC can be
 used to determine the status, reconstruct the colonization history and
 infer key evolutionary parameters of emerging wildlife pathogens with low
 data availability, and for which samples from the putative native area are
 inaccessible.
description: SampleDetails_Genotypes_MEC15-500This file contais three sheets. The first sheet contains information on parasite individuals used in this study (site, river and basin of origin, GPS coordinates of the sampling site, the genetic cluster to which the individuals were assigned and the probability to belong to their genetic clusters). The second sheet contains information about the sampling sites covered in this study. The third sheet contains individual multilocus genotypes at the 16 microsatellite markers used in this study.
DOI: 10.5281/zenodo.18253939
title: Supplementary Data for: GuFi phages represent the most prevalent viral family-level clusters in the human gut microbiome

description: This repository contains all supplementary data and sequence files for the manuscript "GuFi phages represent the most prevalent viral family-level clusters in the human gut microbiome".
DOI: 10.5281/zenodo.18253940
title: Supplementary Data for: GuFi phages represent the most prevalent viral family-level clusters in the human gut microbiome

description: This repository contains all supplementary data and sequence files for the manuscript "GuFi phages represent the most prevalent viral family-level clusters in the human gut microbiome".
DOI: 10.5061/dryad.st482f3
title: Data from: Beta diversity response to stress severity and heterogeneity in sensitive versus tolerant stream diatoms

description: Aim: Severity and heterogeneity of stress are major constraints of beta
 diversity, but their relative influence is poorly understood. Here, we
 addressed this question by examining the patterns of beta diversity in
 stress-sensitive versus stress-tolerant stream diatoms and their response
 to local versus regional factors along gradients of stress severity and
 heterogeneity. Location: The Adirondack region of New York. Methods: Beta
 diversity was measured as multivariate dispersion of communities across
 high stress, low stress, and high + low stress (heterogeneous)
 environments, encompassing 200 stream samples. Null models were
 implemented to assess community similarity relative to randomly assembled
 communities and the importance of local assembly processes vs. the
 regional species pool. Results: The overall beta diversity was influenced
 by a combination of severity and heterogeneity of stress, while beta
 diversity of sensitive species increased with heterogeneity. Beta
 diversity of tolerant species did not vary with either severity or
 heterogeneity of stress. Heterogeneity decreased community similarity
 relative to the null expectation in all groups of species. Stress reduced
 the importance of local assembly mechanisms for the overall beta diversity
 and sensitive species beta diversity. In contrast, the importance of local
 assembly mechanisms increased with stress regarding beta diversity of
 tolerant species. Main Conclusions: Beta diversity responded to both
 severity and heterogeneity of stress, but turnover along these gradients
 was mostly driven by sensitive species. The overall beta diversity and
 beta diversity of sensitive species became more constrained by the
 depauperate regional species pool, as opposed to local assembly
 mechanisms. While heterogeneous stress contributed to beta diversity,
 severe stress suppressed beta diversity through elimination of sensitive
 species. Therefore, an increase in beta diversity in an
 environmentally-stressed region may serve as a forewarning for future loss
 of sensitive species, should the stress continue to intensify.
description: Site information and
 species data for Pound et al. 2018Site information and
 species data, collected from streams in the Adirondacks, NY. Site
 information tab: stream ID, collection date, group classification, UTM
 coordinates based on NAD83, pH, concentration of inorganic aluminum, and
 temperature at the time of collection. Species data tab: list of species,
 acid tolerance of each species, and relative proportional abundance in
 samples across four groups of streams, LS_Aug, HS_Mar, HH_Mar, and
 HH_Aug.Pound et al
 2018.xlsx
DOI: 10.5061/dryad.b5k4s
title: Data from: From incipient to substantial: evolution of placentotrophy in a phylum of aquatic colonial invertebrates

description: Matrotrophy has long been known in invertebrates, but it is still poorly
 understood and has never been reviewed. A striking example of matrotrophy
 (namely, placentotrophy) is provided by the Bryozoa, a medium-sized phylum
 of the aquatic colonial filter feeders. Here I report on an extensive
 anatomical study of placental analogues in 21 species of the bryozoan
 order Cheilostomata, offering the first review on matrotrophy among
 aquatic invertebrates. The first anatomical description of incipient
 placentotrophy in invertebrates is presented together with the evidence
 for multiple independent origins of placental analogues in this order. The
 combinations of contrasting oocytic types (macrolecithal or oligolecithal)
 and various degrees of placental development and embryonic enlargement
 during incubation, found in different bryozoan species, are suggestive of
 a transitional series from the incipient to the substantial placentotrophy
 accompanied by an inverse change in oogenesis, a situation reminiscent of
 some vertebrates. It seems that matrotrophy could trigger the evolution of
 sexual zooidal polymorphism in some clades. The results of this study show
 that this phylum, with its wide variety of reproductive patterns,
 incubation devices and types of the simple placenta-like systems, offers a
 promising model for studying parallel evolution of placentotrophy in
 particular, and matrotrophy in general.
description: Table-DRYADData file contains a list of cheilostome bryozoan species and their reproductive patterns describing their oogenesis mode, absence and presence of brooding and its mode (placental vs non-placental)
DOI: 10.5061/dryad.51p67
title: Data from: Visual obstruction and vigilance: a natural experiment

description: Visual obstructions can cause an increase in antipredator vigilance in
 prey animals by making predator detection more difficult. However, visual
 obstructions can also skew the perception of group size and
 inter-individual distances and impair the detection of alarm signals by
 conspecifics. These changes within the group alone can cause an increase
 in vigilance. To disentangle the contribution of these various factors to
 changes in vigilance, I documented vigilance in a gregarious species, the
 semipalmated sandpiper Calidris pusilla, foraging in a habitat where a
 naturally-occurring visual barrier partially prevented predator detection
 without altering the transfer of information about predation risk within
 the group. I used a matched sampling design to collect vigilance data for
 birds using adjacent areas with and without the visual barrier. In the
 visually-obstructed area, sandpipers maintained a higher level of
 vigilance, occurred farther away from cover and in smaller flocks, and
 preferentially scanned the area of danger with one eye in particular. All
 these changes suggest that visual obstruction increased perceived
 predation risk. I conclude that it is the inability to get a good view of
 any approaching predator, rather than changes in intra-group communication
 that caused the increase in vigilance in the visually-obstructed area.
description: jab_islandData set used to analyze the data. Legends are provided for each column.
DOI: 10.5061/dryad.2r8f9
title: Data from: How and when do insects rely on endogenous protein and lipid resources during lethal bouts of starvation? a new application for 13C-breath testing

description: Most of our understanding about the physiology of fasting and starvation
 comes from studies of vertebrates; however, for ethical reasons, studies
 that monitor vertebrates through the lethal endpoint are scant. Insects
 are convenient models to characterize the comparative strategies used to
 cope with starvation because they have diverse life histories and have
 evolved under the omnipresent challenge of food limitation. Moreover, we
 can study the physiology of starvation through its natural endpoint. In
 this study we raised populations of five species of insects (adult
 grasshoppers, crickets, cockroaches, and larval beetles and moths) on
 diets labeled with either 13C-palmitic acid or 13C-leucine to isotopically
 enrich the lipids or the proteins in their bodies, respectively. The
 insects were allowed to become postabsorptive and then starved. We
 periodically measured the δ13C of the exhaled breath to characterize how
 each species adjusted their reliance on endogenous lipids and proteins as
 energy sources. We found that starving insects employ a wide range of
 strategies for regulating lipid and protein oxidation. All of the insects
 except for the beetle larvae were capable of sharply reducing reliance on
 protein oxidation; however, this protein sparing strategy was usually
 unsustainable during the entire starvation period. All insects increased
 their reliance on lipid oxidation, but while some species (grasshoppers,
 cockroaches, and beetle larvae) were still relying extensively on lipids
 at the time of death, other species (crickets and moth larvae) allowed
 rates of lipid oxidation to return to prestarvation levels. Although
 lipids and proteins are critical metabolic fuels for both vertebrates and
 insects, insects apparently exhibit a much wider range of strategies for
 rationing these limited resources during starvation.
description: Insect Starvation Raw
 DataThese are the raw 13C
 values measured in the exhaled breath of different insects at various
 times of fasting.
DOI: 10.15468/dl.gjvm3g
title: Occurrence Download

description: A dataset containing 199 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((-180 -60,-70 -60,-70 70,-180 70,-180 -60))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (e9f60bdb-217d-4b4e-a22a-2781321220a1, 28eb1a3f-1c15-4a95-931a-4af90ecb574d, c8d737e0-2ff8-42e8-b8fc-6b805d26fc5f, 9c2fe801-eae7-4325-9181-e363345ff1a1)",
 "TaxonKey is Balaenoptera borealis",
 "Year 2000-2026"
 ]
}

 The dataset includes 199 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000753-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5n7f6
title: Data from: A portrait of a sucker using landscape genetics: how colonization and life history undermine the idealized dendritic metapopulation

description: Dendritic metapopulations have been attributed unique properties by in
 silico studies, including an elevated genetic diversity relative to a
 panmictic population of equal total size. These predictions have not been
 rigorously tested in nature, nor has there been full consideration of the
 interacting effects among contemporary landscape features, colonization
 history and life history traits of the target species. We tested for the
 effects of dendritic structure as well as the relative importance of life
 history, environmental barriers and historical colonization on the neutral
 genetic structure of a longnose sucker (Catostomus catostomus)
 metapopulation in the Kogaluk watershed of northern Labrador, Canada.
 Samples were collected from eight lakes, genotyped with 17
 microsatellites, and aged using opercula. Lakes varied in differentiation,
 historical and contemporary connectivity, and life history traits.
 Isolation by distance was detected only by removing two highly genetically
 differentiated lakes, suggesting a lack of migration–drift equilibrium and
 the lingering influence of historical factors on genetic structure.
 Bayesian analyses supported colonization via the Kogaluk's
 headwaters. The historical concentration of genetic diversity in
 headwaters inferred by this result was supported by high historical and
 contemporary effective sizes of the headwater lake, T-Bone. Alternatively,
 reduced allelic richness in headwaters confirmed the dendritic
 structure's influence on gene flow, but this did not translate to an
 elevated metapopulation effective size. A lack of equilibrium and upstream
 migration may have dampened the effects of dendritic structure. We suggest
 that interacting historical and contemporary factors prevent the
 achievement of the idealized traits of a dendritic metapopulation in
 nature.
description: Salisbury et al. 2016
 Data Accession"Catostomus
 catostomus scores for Salisbury et al. 2016.xlsx" contains scores for
 869 Catostomus catostomus samples at 17 microsatellite markers. Samples
 were collected in the Kogaluk River, Labrador, Newfoundland. Row 1
 indicates markers, column A indicates individuals, column B indicates
 lake. Missing scores are denoted by "0". "Pairwise Genetic,
 Geographic, Elevation Distances for Catostomus catostomus samples from
 Salisbury et al. 2016.xlsx" contains pairwise Fsts, geographic, and
 elevation distances among Catostomus catostomus samples collected within 8
 lakes in the Kogaluk River, Labrador, Newfoundland.
DOI: 10.3535/g97-nd1-bb2
title: Corythornis cristatus nais

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.
DOI: 10.5061/dryad.mk4r5
title: Data from: Effects of nicotine on corneal wound healing following acute alkali burn

description: Epidemiological studies have indicated that smoking is a pivotal risk
 factor for the progression of several chronic diseases. Nicotine, the
 addictive component of cigarettes, has powerful pathophysiological
 properties in the body. Although the effects of cigarette smoking on
 corneal re-epithelialization have been studied, the effects of nicotine on
 corneal wound healing-related neovascularization and fibrosis have not
 been fully demonstrated. The aim of this study was to evaluate the effects
 of chronic administration of nicotine on corneal wound healing following
 acute insult induced by an alkali burn. BALB/C female mice randomly
 received either vehicle (2% saccharin) or nicotine (100 or 200 μg/ml in 2%
 saccharin) in drinking water ad libitum. After 1 week, animals were
 re-randomized and the experimental group was subjected to a corneal alkali
 burn, and then nicotine was administered until day 14 after the alkali
 burn. A corneal alkali burn model was generated by placing a piece of 2
 mm-diameter filter paper soaked in 1N NaOH on the right eye.
 Histopathological analysis and the expression level of the pro-angiogenic
 genes vascular endothelial growth factor (VEGF) and matrix
 metalloproteinase-9 (MMP9) revealed that chronic nicotine administration
 enhanced alkali burn-induced corneal neovascularization. Furthermore, the
 mRNA expression of the pro-fibrogenic factors α-smooth muscle actin
 (αSMA), transforming growth factor-β (TGF-β), and collagen α1 (Col1) was
 enhanced in the high-concentration nicotine-treated group compared with
 the vehicle group after corneal injury. Immunohistochemical analysis also
 showed that the αSMA-positive area was increased in chronic
 nicotine-treated mice after corneal alkali burn. An in vitro assay found
 that expression of the α3, α7, and β1 nicotinic acetylcholine receptor
 (nAChR) subunits was significantly increased by chemical injury in human
 corneal fibroblast cells. Moreover, alkali-induced fibrogenic gene
 expression and proliferation of fibroblast cells were further increased by
 treatment with nicotine and cotinine. The proliferation of such cells
 induced by treatment of nicotine and cotinine was reduced by inhibition of
 the PI3K and PKC pathways using specific inhibitors. In conclusion,
 chronic administration of nicotine accelerated the angiogenic and
 fibrogenic healing processes in alkali-burned corneal tissue.
description: Figure
 1Figure
 2Figure
 3Figure
 4Figure
 5
DOI: 10.3535/0zx-v1h-am3
title: Corythornis cristatus thomensis

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.
DOI: 10.3535/z1y-zsf-etb
title: Corythornis cristatus thomensis

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.
DOI: 10.3535/z6a-8qs-hej
title: Corythornis cristatus thomensis

description: Digital Specimen for the physical specimen hosted at Natural History Museum of Denmark.