cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.85cb4
title: Data from: Decay of ecosystem differences and decoupling of tree community-soil environment relationships at ecotones

description: Ecotones are important landscape features where there is a transition
 between adjoining ecosystems. However, there are few generalized
 hypotheses about the response of communities to ecotones, except for a
 proposed increase in species richness that receives varying empirical
 support. Based on the assumption that transport of abiotic material and
 dispersal of organism propagules across ecotones are independent
 processes, we propose the new hypothesis that ecotones decouple
 community-environment relationships, increasing the importance of spatial
 structure that is independent of the environment. We tested this
 hypothesis by examining the effects of ecotones on relationships between
 trees and soil properties in a temperate deciduous forest. The study area
 included different landforms defined by topography, hydrology, and
 geomorphology, which we designated upland, bottomland, and riparian
 forests. The site also included a mowed herbaceous corridor. We found that
 soil properties and tree community composition significantly differed
 among landforms, and thus they could be treated as differing ecosystem
 types. However, inclusion of plots near ecotones significantly reduced the
 variance explained by landform due to introduction of increased noise,
 increased similarity of ecotone plots in different landforms, or both. To
 examine tree community-soil environment relationships, factorial kriging
 analysis was used to decompose variation in soil properties into
 structures associated with differing spatial scales, which were then used
 as predictors of tree composition using redundancy analysis. In agreement
 with the ecotone-decoupling hypothesis, we found that ecotones introduced
 significant unexplained variation into correlations between tree community
 composition and soil properties. In addition, spatial variation in tree
 community composition that was independent of soil properties was only
 detected when ecotones were included in the analysis, and little variation
 in tree community composition was attributed to small-scale soil property
 structures. Together, these results indicate that dispersal limitation and
 mass effects in the tree community take on increased importance near
 ecotones. We found no consistent changes in tree species richness
 associated with ecotones, and suggest that the ecotone-decoupling
 hypothesis may correspond with a more general community-level pattern that
 warrants further testing. Decoupling of community-environment
 relationships near ecotones also has important implications for accuracy
 of models predicting community distributions from abiotic information.
description: soil_data.csvr_code_soil.rtree_basal_area_rel_abundance.csvtree_stem_counts.csvr_code_trees.rr_code_trees.RReadMe_file
DOI: 10.5061/dryad.3v0p8
title: Data from: Demographic legacies of fire history in an African savanna

description: Fire is a key determinant of woody vegetation structure in savanna
 ecosystems, acting both independently and synergistically through
 interactions with herbivores. Fire influences biodiversity and ecological
 functioning, but quantifying its effects on woody structure is challenging
 at both species and community scales. Deeper insight into fire effects,
 and fire-herbivore interactions, can be gained through the examination of
 species-specific demographic and dynamic changes occurring across areas
 with different fire regimes in the presence of large herbivores. We used
 the Carnegie Airborne Observatory (an integrated LiDAR and imaging
 spectroscopy system) to map woody tree structure, species and dynamics
 over a four-year interval across two adjacent savanna landscapes with
 contrasting fire histories in Kruger National Park, South Africa. A
 history of higher fire frequency was associated with reduced woody canopy
 cover (17% vs. 23%) and an increased overall rate of treefall (27% vs.
 18%). The landscape with a history of higher fire frequency displayed a
 shift in woody canopy height distribution from a unimodal curve to a
 bimodal pattern at the community scale, with large reductions in height
 classes &lt; 7 m. Differences in tree height distributions and
 treefall rates across sites were underpinned by species-specific responses
 to fire frequency. Acacia nigrescens displayed the highest rates of
 treefall, most likely related to elephant activity, with losses exceeding
 40% in the 6-9 m height classes. Synthesis. Our findings indicate that
 fire history imparts demographic legacies not only on vegetation
 structure, but also on current vegetation dynamics. Current treefall rates
 of certain tree species are exacerbated by a history of higher fire
 frequency. Species-specific and context-conscious investigations are
 critical for elucidating the driving mechanisms underlying broader
 community patterns.
description: Savanna tree height
 class distribution under different fire management
 historiesTree height class and
 species data collected with airborne LiDAR and imaging spectroscopy across
 two savanna hill slopes with different fire histories in Kruger National
 Park, South Africa. Tree heights are in meters. Tree IDs are a random
 selection of 1000 individuals per species per fire history treatment.
 Airborne data was collected in April 2008.Levick_FE_tree_height.txt
DOI: 10.5061/dryad.7k66b
title: Data from: Genetic variation and differentiation of extant bison (Bison bison) subspecies and cattle (Bos taurus) breeds and subspecies

description: The genetic relationship of American plains bison (Bison bison bison) and
 wood bison (B. b. athabascae) was quantified and compared with that among
 breeds and subspecies of cattle. Plains bison from nine herds (N=136),
 wood bison from three herds (N=65), taurine cattle (Bos taurus taurus)
 from fourteen breeds (N=244), and indicine cattle (B. t. indicus) from two
 breeds (N=53) were genotyped for 29 polymorphic microsatellite loci.
 Bayesian cluster analyses indicate three groups, two of which are plains
 bison and one of which is wood bison with some admixture, and genetic
 distances do not show plains bison and wood bison as distinct groups.
 Differentiation of wood bison and plains bison is also significantly less
 than that of cattle breeds and subspecies. These and other genetic data
 and historical interbreeding of bison do not support recognition of extant
 plains bison and wood bison as phylogenetically distinct subspecies.
description: Genotypes for Cronin et
 al JOH bison genetics
DOI: 10.5061/dryad.363gs
title: Data from: Oil palm plantations fail to support mammal diversity

description: Agricultural expansion is the largest threat to global biodiversity. In
 particular, the rapid spread of tree plantations is a primary driver of
 deforestation in hyperdiverse tropical regions. Plantations tend to
 support considerably lower biodiversity than native forest, but it remains
 unclear whether plantation traits affect their ability to sustain native
 wildlife populations, particularly for threatened taxa. If animal
 diversity varies across plantations with different characteristics, these
 traits could be manipulated to make plantations more “wildlife friendly.”
 The degree to which plantations create edge effects that degrade habitat
 quality in adjacent forest also remains unclear, limiting our ability to
 predict wildlife persistence in mixed-use landscapes. We used systematic
 camera trapping to investigate mammal occurrence and diversity in oil palm
 plantations and adjacent forest in Sabah, Malaysian Borneo. Mammals within
 plantations were largely constrained to locations near native forest; the
 occurrence of most species and overall species richness declined abruptly
 with decreasing forest proximity from an estimated 14 species at the
 forest ecotone to ~1 species 2 km into the plantation. Neither tree height
 nor canopy cover within plantations strongly affected mammal diversity or
 occurrence, suggesting that manipulating tree spacing or planting cycles
 might not make plantations more wildlife friendly. Plantations did not
 appear to generate strong edge effects; mammal richness within forest
 remained high and consistent up to the plantation ecotone. Our results
 suggest that land-sparing strategies, as opposed to efforts to make
 plantations more wildlife-friendly, are required for regional wildlife
 conservation in biodiverse tropical ecosystems.
description: Yue et al 2015
 DataCamera trap and site
 data used for the studydryad.xls
DOI: 10.5061/dryad.6bt21
title: Data from: Effects of a multidisciplinary approach to improve volume of diagnostic material in CT-guided lung biopsies

description: Background: Recent publications have emphasized the importance of a
 multidisciplinary strategy for maximum conservation and utilization of
 lung biopsy material for advanced testing, which may determine therapy.
 This paper quantifies the effect of a multidisciplinary strategy
 implemented to optimize and increase tissue volume in CT-guided
 transthoracic needle core lung biopsies. The strategy was three-pronged:
 (1) once there was confidence diagnostic tissue had been obtained and if
 safe for the patient, additional biopsy passes were performed to further
 increase volume of biopsy material, (2) biopsy material was placed in
 multiple cassettes for processing, and (3) all tissue ribbons were
 conserved when cutting blocks in the histology laboratory. This study
 quantifies the effects of strategies #1 and #2. Design: This retrospective
 analysis comparing CT-guided lung biopsies from 2007 and 2012 (before and
 after multidisciplinary approach implementation) was performed at a single
 institution. Patient medical records were reviewed and main variables
 analyzed include biopsy sample size, radiologist, number of blocks
 submitted, diagnosis, and complications. The biopsy sample size measured
 was considered to be directly proportional to tissue volume in the block.
 Results: Biopsy sample size increased 2.5 fold with the average total
 biopsy sample size increasing from 1.0 cm (0.9–1.1 cm) in 2007 to 2.5 cm
 (2.3–2.8 cm) in 2012 (P&lt;0.0001). The improvement was statistically
 significant for each individual radiologist. During the same time, the
 rate of pneumothorax requiring chest tube placement decreased from 15% to
 7% (P = 0.065). No other major complications were identified. The
 proportion of tumor within the biopsy material was similar at 28%
 (23%–33%) and 35% (30%–40%) for 2007 and 2012, respectively. The number of
 cases with at least two blocks available for testing increased from 10.7%
 to 96.4% (P&lt;0.0001). Conclusions: The effect of this
 multidisciplinary strategy to CT-guided lung biopsies was effective in
 significantly increasing tissue volume and number of blocks available for
 advanced diagnostic testing.
description: CT biopsy study raw data
 setPrism Data
 Results
DOI: 10.5061/dryad.rf7s0
title: Data from: Inbreeding depression across a nutritional stress continuum

description: Many natural populations experience inbreeding and genetic drift as a
 consequence of nonrandom mating or low population size. Furthermore, they
 face environmental challenges that may interact synergistically with
 deleterious consequences of increased homozygosity and further decrease
 fitness. Most studies on inbreeding–environment (I-E) interactions use one
 or two stress levels, whereby the resolution of the possible stress and
 inbreeding depression interaction is low. Here we produced Drosophila
 melanogaster replicate populations, maintained at three different
 population sizes (10, 50 and a control size of 500) for 25 generations. A
 nutritional stress gradient was imposed on the replicate populations by
 exposing them to 11 different concentrations of yeast in the developmental
 medium. We assessed the consequences of nutritional stress by scoring
 egg-to-adult viability and body mass of emerged flies. We found: (1)
 unequivocal evidence for I-E interactions in egg-to-adult viability and to
 a lesser extent in dry body mass, with inbreeding depression being more
 severe under higher levels of nutritional stress; (2) a steeper increase
 in inbreeding depression for replicate populations of size 10 with
 increasing nutritional stress than for replicate populations of size 50;
 (3) a nonlinear norm of reaction between inbreeding depression and
 nutritional stress; and (4) a faster increase in number of lethal
 equivalents in replicate populations of size 10 compared with replicate
 populations of size 50 with increasing nutritional stress levels. Our data
 provide novel and strong evidence that deleterious fitness consequences of
 I-E interactions are more pronounced at higher nutritional stress and at
 higher inbreeding levels.
description: EggToAdultViabilityEgg-to-adult viability of all replicate populations across the different developmental media. "Total" is the number of emerged adults for a given vial.DryBodyMassDry body mass data. FlyN column denotes the order in which flies from the same tube/sample was asessed.
DOI: 10.5061/dryad.3gn80
title: Data from: Impacts and recovery from Severe Tropical Cyclone Yasi on the Great Barrier Reef

description: Full recovery of coral reefs from tropical cyclone (TC) damage can take
 decades, making cyclones a major driver of habitat condition where they
 occur regularly. Since 1985, 44 TCs generated gale force winds (≥17
 metres/second) within the Great Barrier Reef Marine Park (GBRMP). Of the
 hurricane strength TCs (≥H1—Saffir Simpson scale; ≥ category 3 Australian
 scale), TC Yasi (February, 2011) was the largest. In the weeks after TC
 Yasi crossed the GBRMP, participating researchers, managers and rangers
 assessed the extent and severity of reef damage via 841 Reef Health and
 Impact Surveys at 70 reefs. Records were scaled into five damage levels
 representing increasingly widespread colony-level damage (1, 2, 3) and
 reef structural damage (4, 5). Average damage severity was significantly
 affected by direction (north vs south of the cyclone track), reef shelf
 position (mid-shelf vs outer-shelf) and habitat type. More outer-shelf
 reefs suffered structural damage than mid-shelf reefs within 150 km of the
 track. Structural damage spanned a greater latitudinal range for mid-shelf
 reefs than outer-shelf reefs (400 vs 300 km). Structural damage was
 patchily distributed at all distances, but more so as distance from the
 track increased. Damage extended much further from the track than during
 other recent intense cyclones that had smaller circulation sizes. Just
 over 15% (3,834 km2) of the total reef area of the GBRMP is estimated to
 have sustained some level of coral damage, with ~4% (949 km2) sustaining a
 degree of structural damage. TC Yasi likely caused the greatest loss of
 coral cover on the GBR in a 24-hour period since 1985. Severely impacted
 reefs have started to recover; coral cover increased an average of 4%
 between 2011 and 2013 at re-surveyed reefs. The in situ assessment of
 impacts described here is the largest in scale ever conducted on the Great
 Barrier Reef following a reef health disturbance.
description: TC YASI RAW DATA
 PONE_D_14_40836Excel spreadsheet
 containing three sheets: A) Reef Health and Impact Survey data from the TC
 Yasi impact assessment conducted in February / March 2011. The sheet
 includes the data used to produce figures 2 and 7. B) Size, intensity and
 persistence data from 44 tropical cyclones between 1985 and 2014 used to
 create figure 5. C) Reef Health and Impact Survey data collected in 2011
 and 2013 recovery surveys used to produce figures 9a and
 9b.TCYASI
 RHIS RAWDATA PONE_D_14_40836.xlsx
DOI: 10.5061/dryad.kc4p4
title: Data from: Environmental conditions limit attractiveness of a complex sexual signal in the túngara frog

description: Animals choosing particular display sites often balance sexual and natural
 selection pressures. Here we assess how physical properties of display
 sites can alter this balance by influencing signal production and
 attractiveness of the túngara frog (Physalaemus pustulosus). Males that
 call from very shallow water bodies (few mm depth) benefit from reduced
 predation risk, but by manipulating water levels, we show that this comes
 at a cost of reduced attractiveness to females. Our data show that calling
 from shallower water reduces a male's ability to float, limits the
 inflation of his vocal sac, and consequently reduces signal
 conspicuousness in terms of amplitude and complexity. Our results
 demonstrate that display site properties can set limits on signal
 production and attractiveness and may hence influence signal evolution.
 Signallers may shift between sites or engineer their display location,
 which can play a crucial role in signal divergence and speciation,
 particularly in a rapidly changing world.
description: sound and video
 analyses, female choice experimentresults from the water
 depth treatment experiment and female choice
 experiments.Dryad_data_27-10-17.xlsx
DOI: 10.5061/dryad.6mc111c
title: Data from: Faberia pinnatifida (Asteraceae; Cichorieae), a new species from Sichuan, China

description: Faberia pinnatifida (Asteraceae; Cichorieae), a species occurring at high
 altitudes in Muli and Yanyuan Xian, Sichuan, China, is described as new
 based on morphological, palynological and molecular phylogenetic data. The
 ITS data indicate that F. pinnatifida is closely related to F. glaucescens
 and F. thibetica, but it is easily distinguished from F. glaucescens by
 its scapigerous stem with only one or two leaves, and from F. thibetica in
 its much taller stature and elliptic to oblanceolate leaf blade. Faberia
 pinnatifida somewhat resembles F. ceterach in the scapigerous stem and
 pinnatifid leaves, but readily differs in its corymbiform synflorescence
 and nodding capitula bearing ca. 30 florets.
description: ITS42863This dataset contained 45 sequences of the ITS region used in the following manuscript: Faberia pinnatifida (Asteraceae; Cichorieae), a New Species from Sichuan, China.cp datasetThis dataset contained 45 sequences of the combined matK, psbA-trnH, rbcL and trnL-F region used in the following manuscript: Faberia pinnatifida (Asteraceae; Cichorieae), a New Species from Sichuan, China.cp42863.fas
DOI: 10.5061/dryad.r2b1n
title: Data from: Lipid profiles and obesity as potential risk factors of sudden sensorineural hearing loss

description: Objectives: The objective of our study was to establish whether increased
 lipid profiles and obesity affect the prevalence and prognosis of sudden
 sensorineural hearing loss (SSNHL). Methods: This was a case-controlled
 study with a longitudinal design. According to our criteria, 324 patients
 with SSNHL were included in this study. To manage potential covariates,
 972 subjects with normal hearing from the Korean National Health and
 Nutrition Examination Survey were matched as control group according to
 their propensity scores. Age, level of total cholesterol (TC), high
 density lipoprotein cholesterol (HDL-C), low-density lipoprotein
 cholesterol (LDL-C), triglycerides (TG), and body mass index (BMI) were
 obtained from the clinical data. Multivariate logistic regression analysis
 was used to investigate the association between SSNHL and lipid profiles
 or obesity in the 1296 subjects. Multivariate Cox regression analysis was
 used to determine whether lipid profiles and obesity are prognostic
 factors in patients with SSNHL. Results: Mean body weight, BMI, TC, and TG
 were significantly higher in patients with SSNHL compared with control
 subjects (p&lt;0.05). However, LDL-C values did not differ
 significantly between the two groups. Subjects with elevated TC and TG
 levels had a 2.20- (95% CI 1.50–3.24) and 1.50-fold (95% CI 1.08–2.08)
 increased odds, respectively, of SSNHL compared with subjects with normal
 TC and TG levels. Subjects with grade III BMI had a 1.59-fold (95% CI
 1.17–2.16) increased odds of SSNHL. Multivariate Cox regression analyses
 revealed that BMI was an independent risk factor of treatment outcome, as
 patients with BMI ≥27.5 were less likely to achieve complete recovery than
 those with BMI &lt;27.5 (p&lt;0.05). Conclusions: The results of
 this study revealed that elevated TC and TG levels and increased BMI are
 significantly associated with the prevalence of SSNHL and its prognosis,
 indicating that vascular compromise may play an important role in the
 pathogenesis of SSNHL.
description: Data of
 SSNHL_Groupdata of sudden deafness
 patients.SSNHL_PLOS.xlsxdata_of_control_972Data of Control group
DOI: 10.5061/dryad.402c8
title: Data from: Stallion semen quality depends on MHC matching to teaser mare

description: The major histocompatibility complex (MHC) has repeatedly been found to
 influence mate choice of vertebrates, with MHC-dissimilar mates typically
 being preferred over MHC-similar mates. We used horses (Equus caballus) to
 test whether MHC matching also affects male investment into ejaculates
 after short exposure to a female. Semen characteristics varied much among
 stallions. Controlling for this variance with a full-factorial
 within-subject experimental design, we found that a short exposure to an
 MHC-dissimilar mare enhanced male plasma testosterone and led to
 ejaculates with elevated sperm numbers as compared to exposure to an
 MHC-similar mare. Sperm velocity seemed not affected by the treatment.
 Overall genetic similarity between stallions and mares (determined from
 polymorphic microsatellites on 20 different chromosomes) played no
 significant role here. The MHC type of the teaser mare also affected
 characteristics of cold-stored sperm after 24 and 48h. As expected from
 ejaculate economics, sperm viability was elevated after exposure to an
 MHC-dissimilar mare. However, oxidative stress and the percentage of sperm
 with a high DNA fragmentation was mostly increased after exposure to an
 MHC-dissimilar mare, depending also on whether the teaser mare was in
 estrous or not. We conclude that males can quickly adjust ejaculate
 quality relative to a female’s MHC, and that this male reaction to the
 social environment can also affect important characteristics of
 cold-stored semen.
description: Testosterone_ejaculatesPair combination, age of ejaculate at time of measurement ("incubation"), experimental week, estrus stage of teaser mare, Wang's coefficient of relatedness r, semen volume, total sperm number, stallion's blood testosterone before and after exposure to teaser mare (and ejaculation), further semen characteristics (as described in paper)microsatsGenotypes of all mares and stallions on 20 microsatellite loci