cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4ff07
title: Data from: To breed or not to breed: endocrine response to mercury contamination by an Arctic seabird

description: Mercury, a ubiquitous toxic element, is known to alter expression of sex
 steroids and to impair reproduction across vertebrates but the mechanisms
 underlying these effects are not clearly identified. We examined whether
 contamination by mercury predicts the probability to skip reproduction in
 black-legged kittiwakes (Rissa tridactyla) from Svalbard. We also
 manipulated the endocrine system to investigate the mechanism underlying
 this relationship. During the pre-laying period, we injected exogenous
 GnRH (gonadotropin-releasing hormone) to test the ability of the pituitary
 to release luteinizing hormone (LH, a key hormone for the release of sex
 steroids and hence breeding) in relation to mercury burden. Birds that
 skipped reproduction had significantly higher mercury concentration in
 blood than breeders. Endocrine profiles of these birds also varied based
 on breeding status (breeders versus non-breeders), mercury contamination
 and sex. Specifically, in skippers (birds that did not breed), baseline LH
 decreased with increasing mercury concentration in males, whereas it
 increased in females. GnRH-induced LH levels increased with increasing
 mercury concentration in both sexes. These results suggest that mercury
 contamination may disrupt GnRH input to the pituitary. Thus, high mercury
 concentration could affect the ability of long-lived birds to modulate
 their reproductive effort (skipping or breeding) according to ongoing
 environmental changes in the Arctic, thereby impacting population
 dynamics.
description: 2008-2011_Mercury_Breeding decision_LH_TestosteroneRaw data. For 2008 and 2011: Sex, breeding decision and mercury levels. For 2008: sex, breeding decision, mercury, GnRH treatment, LH and testosterone levels.2008-2011_Mercury_Breeding decision_Hormones.pdf
DOI: 10.5061/dryad.30qt0
title: Data from: Population genetic structure and direct observations reveal sex-reversed patterns of dispersal in a cooperative bird

description: Sex-biased dispersal is pervasive and has diverse evolutionary
 implications, but the fundamental drivers of dispersal sex biases remain
 unresolved. This is due in part to limited diversity within taxonomic
 groups in the direction of dispersal sex biases, which leaves hypothesis
 testing critically dependent upon identifying rare reversals of taxonomic
 norms. Here we use a combination of observational and genetic data to
 demonstrate a rare reversal of the avian sex-bias in dispersal in the
 cooperatively breeding white-browed sparrow weaver (Plocepasser mahali).
 Direct observations revealed that i) natal philopatry was rare, with both
 sexes typically dispersing locally to breed, and ii), unusually for birds,
 males bred at significantly greater distances from their natal group than
 females. Population genetic analyses confirmed these patterns, as i)
 corrected Assignment index (AIc), FST tests and isolation-by-distance
 metrics were all indicative of longer dispersal distances among males than
 females, and ii) spatial autocorrelation analysis indicated stronger
 within-group genetic structure among females than males. Examining the
 spatial scale of extra-group mating highlighted that the resulting ‘sperm
 dispersal’ could have acted in concert with individual dispersal to
 generate these genetic patterns, but gamete dispersal alone cannot account
 entirely for the sex differences in genetic structure observed. That
 leading hypotheses for the evolution of dispersal sex biases cannot
 readily account for these sex-reversed patterns of dispersal in
 white-browed sparrow-weavers, highlights the continued need for attention
 to alternative explanations for this enigmatic phenomenon. We highlight
 the potential importance of sex differences in the distances over which
 dispersal opportunities can be detected.
description: 33 Birds Final Dispersal
 TableRaw Data File of
 Dispersal Distances by Sex185 Birds Genalex
 Analysis by SexMicrosatellite data from
 185 birds, split by sex and group, for Genalex analysisSeparate Sex Analysis Final For
 Paper.xlsxSparrow Weaver Group
 CoordinatesGroup Coordinates for
 Dispersal Bias Correction Simulationssparrow weaver group
 coords.txtDistCalc
 FunctionR Function to calculate
 euclidean distance between groupsSex-Biased Dispersal R
 CodeR
 Code for: 1) Sex-Biased Dispersal Analysis, and 2) Simulations to Correct
 Observed Sex Bias for DetectabilityMonitored Study Bounds
 DataCoordinates to Construct
 Polygon delineating monitored spatial area for Dispersal Bias Correction
 Simulations R Script
DOI: 10.5061/dryad.8tt0411
title: Data from: VEGF-A/VEGFR-2 and FGF-2/FGFR-1 but not PDGF-BB/PDGFR-β play important roles in promoting immature and inflammatory intraplaque angiogenesis

description: Various angiogenic factors have been shown to play important roles in
 intraplaque angiogenesis, while little is known about the dynamic
 expression change and interplay between various angiogenic factors and
 intraplaque angiogenesis under high cholesterol conditions. New Zealand
 rabbits underwent balloon injury of the abdominal artery and then were
 assigned to a control group (n=15, normal chow) or high cholesterol group
 (n=25, 1% high cholesterol diet). At weeks 4, 6, 8, 10, and 12 after
 acclimation, rabbits (high cholesterol group, n=5; control group, n=3)
 were euthanized. No lesions were observed in the control group. From week
 4 to week 12, the expression of vascular endothelial growth factor A
 (VEGF-A), VEGF receptor 2 (VEGFR-2), fibroblast growth factor 2 (FGF-2),
 FGF receptor 1 (FGFR-1), platelet-derived growth factor-BB (PDGF-BB), and
 tumor necrosis factor alpha (TNF-α), the vulnerabilty index (VI) and the
 microvessel density (MVD) were significantly elevated in the high
 cholesterol group; however, PDGF receptor β (PDGFR-β) expression showed
 little change. Analysis by double-label immunofluorescence (CD31 and Ng2)
 and FITC-dextran indicated that the neovessels within the plaque were
 leaky due to a lack of pericytes. As indicated by Pearson’s correlation
 analysis, there was a highly positive correlation between the VI, MVD,
 macrophage content, and TNF-α level, and the levels of VEGF-A/VEGFR-2 and
 FGF-2/FGFR-1. However, no correlations were observed between PDGFR-β
 levels and the VI or MVD. High expression of VEGF-A/VEGFR-2 and
 FGF-2/FGFR-1 but not of PDGF-BB/PDGFR-β may contribute to immature and
 inflammatory intraplaque angiogenesis and plaque instability in a rabbit
 model of atherosclerosis
description: relevant datas for
 replication studiesrelevant data for replication
 studies .zip
DOI: 10.5061/dryad.gq246
title: Data from: Rapid genetic restoration of a keystone species exhibiting delayed demographic response

description: Genetic founder effects are often expected when animals colonize restored
 habitat in fragmented landscapes, but empirical data on genetic responses
 to restoration are limited. We examined the genetic response of
 banner-tailed kangaroo rats (Dipodomys spectabilis) to landscape-scale
 grassland restoration in the Chihuahuan Desert of New Mexico, USA. D.
 spectabilis is a grassland specialist and keystone species. At sites
 treated with herbicide to remove shrubs, colonization by D. spectabilis is
 slow and populations persist at low density for ≥10 yrs (≥6 generations).
 Persistence at low density and low gene flow may cause strong founder
 effects. We compared genetic structure of D. spectabilis populations
 between treated sites and remnant grasslands, and we examined how the
 genetic response to restoration depended on treatment age, area, and
 connectivity to source populations. Allelic richness and heterozygosity
 were similar between treated sites and remnant grasslands. Allelic
 richness at treated sites was greatest early in the restoration
 trajectory, and genetic divergence did not differ between recently
 colonized and established populations. These results indicated that
 founder effects during colonization of treated sites were weak or absent.
 Moreover, our results suggested founder effects were not mitigated by
 treatment area or connectivity. Dispersal is negatively density-dependent
 in D. spectabilis, and we hypothesize that high gene flow may occur early
 in the restoration trajectory when density is low. Our study shows genetic
 diversity can be recovered more rapidly than demographic components of
 populations after habitat restoration, and that founder effects are not
 inevitable for animals colonizing restored habitat in fragmented
 landscapes.
description: Year of sampling,
 geographic coordinates, and treatment status of sitescosentino_etal_sites.xlsxMicrosatellite genotypes"0" indicates alleles that were not scored due to failed amplification or ambiguous peak calling (0.17% of alleles).cosentino_etal_genotypes.xlsxPairwise geographic and genetic distancesLower triangle indicates genetic distance (Fst), and upper triangle indicates geographic distance (km).cosentino_etal_distance_matrix.xlsxSTRUCTURE input filesInput files for all sites and sites west of the Rio Grande are included as separate sheets in the file.cosentino_etal_structure.xlsx
DOI: 10.5061/dryad.f5t28
title: Data from: Differential high-altitude adaptation and restricted gene flow across a mid-elevation hybrid zone in Andean tit-tyrant flycatchers

description: The tropical Andes are a global hotspot of avian diversity that is
 characterized by dramatic elevational shifts in community composition and
 a preponderance of recently evolved species. Bird habitats in the Andes
 span a nearly two-fold range of atmospheric pressure that poses challenges
 for respiration, thermoregulation, water balance, and powered flight, but
 the extent to which physiological constraints limit species’ elevational
 distributions is poorly understood. We report a previously unknown hybrid
 zone between recently diverged flycatchers (Aves, Tyrannidae) with
 partially overlapping elevational ranges. The southern Anairetes
 reguloides has a broad elevational range (0-4200 m), while the northern
 Anairetes nigrocristatus is restricted to high elevations (&gt;2200
 m). We found hybrids in central Peru at elevations between ~3100-3800 m,
 with A. nigrocristatus above this elevation and A. reguloides below. We
 analyzed variation in hematology, heart mass, morphometrics, plumage, and
 one mitochondrial and three nuclear loci across an elevational transect
 that encompasses the hybrid zone. Phenotypic traits and genetic markers
 all showed steep clines across the hybrid zone. Hemoglobin concentration,
 hematocrit, mean cellular hemoglobin concentration, and relative heart
 mass each increased at altitude more strongly in A. reguloides than in A.
 nigrocristatus. These findings suggest that A. nigrocristatus is more
 resistant than A. reguloides to high-altitude hypoxic respiratory stress.
 Considering that the ancestor of the genus is suggested to have been
 restricted to high elevations, A. reguloides may be secondarily adapted to
 low-altitude. We conclude that differential respiratory specialization on
 atmospheric pressure combined with competitive exclusion maintains
 replacement along an elevational contour, despite interbreeding.
description: Myo_alignedFASTA file of aligned Myo2 sequencesMUSK_alignedFASTA file of aligned MUSK sequencesIRF2_alignedFASTA file of aligned IRF2 sequencesCytb_alignedFASTA file of aligned Cyt b sequenceswing_chord_clineClineFit 2.0a input file for wing chord measurementstail_clineClineFit 2.0a input file for white tail tip measurementsmass_clineClineFit 2.0a input file for mass measurementscrest_length_clineClineFit 2.0a input file for crest length measurementsMYO_clineClineFit 2.0a input file for Myo2 sequencesMUSK_clineClineFit 2.0a input file for MUSK sequencesmtDNAclineClineFit 2.0a input file for Cyt b sequencesIRF2_clineClineFit 2.0a input file for IRF2 sequencesStructure input fileStructure input file for 4 loci. The order of the loci in the file are: MUSK, IRF2, Myo2, Cyt b.MUSK_IRF2_Myo_mtDNA_STRUCTURE.txt
DOI: 10.5061/dryad.590j0
title: Data from: Invasion of Solanum tuberosum L. by Aspergillus terreus: a microscopic and proteomics insight on pathogenicity

description: Background: Aspergillus terreus is one of the most harmful filamentous
 fungal pathogen of humans, animals and plants. Recently, researchers have
 discovered that A. terreus can cause foliar blight disease in potato
 (Solanum tuberosum L.). We used light and scanning electron microscopy,
 and performed proteomics analysis in an attempt to dissect the invasion
 process of A. terreus in this important crop. Results: Microscopic study
 revealed that invasion of leaf tissue is marked by rapid germination of A.
 terreus phialidic conidia (PC) by 4 h after inoculation. By 8 h after
 inoculation, primary germ tubes from PC differentiated into irregular
 protuberance, often displayed stomata atropism, and failed to penetrate
 via the epidermal cells. Colonization of leaf tissues was associated with
 high rate of production of accessory conidia (AC). These analyses showed
 the occurrence of a unique opposing pattern of AC, tissue-specific and
 produced on melanized colonizing hyphae during the infection of leaf
 tissue. A significant proteome change hallmarked by differential
 expression of class I patatin, lipoxygenase, catalase-peroxidase complex,
 and cysteine proteinase inhibitor were observed during tuber colonization.
 These proteins are often involved in signal transduction pathways and
 crosstalk in pathogenic responses. Conclusion: A. terreus abundantly
 produced AC and multipolar germinating PC to invade potato leaf tissue.
 Additionally, A. terreus differentially induced enzymes in potato tuber
 during colonization which facilitates rapid disease development.
description: Figure 1-Phylogenetic
 and morpgological placement of Aspergillus terreusFigure 1 Molecular
 phylogenetic analysis by Maximum likelihood method (ML) based on the K2 +
 G substitution model. AIC is 1953.78, BIC is 2311.02; the highest log
 likelihood is -953.45 and bootstrap values ≥ 50% from 1000 iterations are
 shown. Blue highlighted strain of A. terreus (GenBank® accession number
 KC305600) causes foliar necrosis of potato. The ML analysis was performed
 in MEGA 6 [34]. Morphological characteristics of globular accessory
 conidia indicated arrows stained with Rose Bengal, broom-like conidiophore
 and colony on PDA, scale bar = 20 µm and magnification =
 1000X.Figure
 1.tifFile 1-Muscle-aligned
 cadmodulin genes of Aspergillus terreusMultiple sequence
 alignment of partial sequences of Cadmodulin gene of Aspergillus terreus.
 The sequences were aligned using Muscle software in MEGA 6.01 using
 default settings.Muscle-aligned cadmodulin genes
 of Aspergillus terreus.fas
DOI: 10.5061/dryad.011v40v
title: Data from: Prey limitation drives variation in allometric scaling of predator-prey interactions

description: Ecologists have long searched for a universal size-scaling constant that
 governs trophic interactions. Although this is an appealing theoretical
 concept, Predator-Prey Size Ratios (PPSR) vary strikingly across and
 within natural food webs, meaning that predators deviate from their
 optimal prey size by consuming relatively larger or smaller prey. Here, we
 suggest that this unexpected variation in allometric scaling of trophic
 interactions can be predicted by gradients of prey limitation consistent
 with predictions from the Optimal Foraging Theory. We analyzed
 &gt;6,000 trophic interactions of 52 populations from four tropical
 frog species along a gradient of prey limitation. Mean of PPSR and its
 variance differed up to two orders of magnitude across and within food
 webs. Importantly, as prey availability decreased across food webs, PPSR
 and its variance became more size-dependent. Thus, trophic interactions
 did not follow a fixed allometric scaling but changed predictably with the
 strength of prey limitation. Our results emphasize the importance of
 ecological contexts in arranging food webs and the need to incorporate
 ecological drivers of PPSR and its variance in food web and community
 models.
description: individual and
 population PPSRs# ind_data: Site
 (sampled site, 21 sites); ind (individual predator ID, nested within
 Site); pred_spp (predator taxonomic identity, 4 spp); prey_tax (prey
 taxonomic identity, 17 categories); log10_PredSize (log10-transformed
 predator lenght); log10_PPSRpref (Preferred individual-link Predator-Prey
 Size Ratio). # pop_data: Site (sampled site); beta (degree of
 size-dependence of average Predator-Prey Size Ratios); beta_SE (beta
 standard error); Vbeta (degree of size-dependence of the variance in
 Predator-Prey Size Ratios); Vbeta_SE (Vbeta standard
 error).data_ppsr_dryad.xlsx
DOI: 10.5061/dryad.p39r7kh
title: Data from: Pace of life syndrome under warming and pollution: integrating life history, behavior and physiology across latitudes

description: To fully comprehend and predict the impact of drivers of global change
 such as climate warming and pollution, integrated multi-trait approaches
 are needed. As organismal traits are often correlated, responses to
 stressors are expected to induce coordinated changes in many traits. A
 promising framework to study this is the pace-of-life syndrome (POLS),
 which predicts the integration of life-history, behavioral and
 physiological traits along a fast-slow continuum. Using an integrative
 multi-trait approach we evaluated the presence of a POLS both within and
 across latitudes and how POLS patterns are affected by warming and metal
 pollution. We studied this in Ischnura elegans damselfly larvae of
 replicated low-and high latitude populations that strongly differ in
 voltinism (3-4 generations per year vs. 1 every two years) reared in a
 common-garden experiment at two temperatures. Across latitudes, life
 history, behavior and physiology covaried in accordance with the POLS,
 with the fast-paced low-latitude damselflies characterized by a fast
 growth rate, high activity and more explorative and risk taking behavior,
 fast metabolic rate and low investment in immune function (activity of
 phenoloxidase). This fast POLS strategy was associated with a higher
 sensitivity to metal exposure and a higher vulnerability to predation.
 Warming caused opposite responses between the latitudes consistent with
 differential thermal adaptation in growth rate, behavior and oxidative
 stress parameters. Despite this, damselflies of both latitudes showed a
 consistent pattern in phenotypic correlations among traits that, moreover
 was not affected by warming and metal exposure. Within latitudes there was
 no full support for the POLS. More active larvae were more explorative and
 risk taking, which aligned with the fast-slow life-history axis, but less
 strong than at the across-latitude level. Physiological traits were also
 integrated within latitudes, yet there was no unambiguous coupling with
 the fast-slow life-history continuum. The consistent syndrome structure,
 if underpinned by genetic correlations, may restrict the independent
 evolution of individual traits, yet may not necessarily constrain adaptive
 evolution of integrated trait sets. This is because the covariance pattern
 was to a large extent similar across latitudes and within latitudes,
 suggesting adaptive trait integration guiding adaptive evolution of trait
 sets along the fast-slow continuum.
description: Debecker &
 Stoks_POLS data_Ecological Monographs_2018Every line is one
 subject (Ischnura elegans larva). Every column is a variable, either
 measured or manipulated. The columns "Latitude",
 "Temperature" and "Zinc" are the treatments used in
 the experiment. The endpoints used in the paper are indicated in yellow.
 Other columns are added for completeness. Please consult the paper for
 more information.Debecker & Stoks_POLS
 data_Ecological Monographs.xlsx
DOI: 10.5061/dryad.r7m52
title: Data from: Genetic differences and phenotypic plasticity in body size between high- and low-altitude populations of the ground beetle Carabus tosanus

description: The body size of a univoltine carabid beetle Carabus tosanus on Shikoku
 Island, Japan, was clearly smaller in higher-altitude populations
 (subspecies), which possibly represents incipient speciation. To explore
 the determinants of altitudinal differences in body size in this species,
 we studied the degree of phenotypic plasticity by conducting rearing
 experiments at two constant temperatures, and examined genetic differences
 through interpopulation crosses. At 15°C, C. tosanus had a longer
 developmental period and a shorter adult body than at 20°C. Nevertheless,
 variation in body size due to temperature effects (phenotypic plasticity)
 was small compared to the interpopulation differences, which suggests
 substantial genetic differences between populations (subspecies) at
 different altitudes. In F1 offspring from crosses between a low-altitude
 (subspecies tosanus) and a high-altitude population (subspecies
 ishizuchianus), adult body length was affected by the genotypes of both
 parents, with an interaction effect of parental genotype and offspring
 sex. Further analyses revealed that adult body length was affected by
 sex-linked factors in addition to autosomal factors. These genetic
 differences in body size may have resulted from adaptations to different
 altitudes and may be important for the process of incipient speciation
 because body size differences could contribute to premating reproductive
 isolation.
description: Development&TemperatureOriginal data of development and growth for different populations of Carabus tosanus at two temperatures (15C and 20C) under 16L-8D.CrossingExperimentOriginal data of development and growth of offspring from crossing between Carabus tosanus subspecies tosanus and ishizuchianus at 20C and 16L-8D.
DOI: 10.5061/dryad.7p9g464
title: Data from: Long and short-term responses of Asclepias species differ in respect to fire, grazing, and nutrient addition

description: Premise: The tallgrass prairie ecosystem has experienced a dramatic
 reduction over the last 150 years. This reduction has impacted the
 abundance of native grassland species including milkweeds (Asclepias).
 Methods: Here we use two long-term (27-year) datasets to examine how fire,
 grazing, and nutrient addition shape milkweed abundance in tallgrass
 prairie. We compare these results to a greenhouse experiment that varies
 nutrient levels in the absence competition, herbivory, and mutualistic
 relationships. Key Results: We find that Asclepias species exhibit broad
 patterns in response to burning regimes that do not include grazing, but
 experience more species-specific patterns in other combinations. Asclepias
 syriaca was the only species to increase in abundance in plots that
 included burning and nutrient addition. In the greenhouse we find that
 nitrogen significantly increases biomass while no effect of phosphorus was
 detected. Conclusions: These results indicate that A. syriaca will do best
 in settings with high nutrient loads, low competition, and no grazers.
 These characteristics define a small portion of the tallgrass prairie,
 while these conditions exemplify modern agricultural settings, which have
 replaced prairies. However, other milkweed examined did not share this
 pattern. This indicates that milkweed species will respond differently
 when exposed to agricultural settings, with some less able to cope with
 land conversion to pasture or row crop agriculture.
description: Nutrient_DataData from greenhouse nutrient experiment.