cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hf83v
title: Data from: Janzen-Connell patterns can be induced by fungal-driven decomposition and offset by ectomycorrhizal fungi accumulated under a closely related canopy

description: 1. Seedlings near a conspecific adult might suffer increased mortality due
 to pressure from enemies such as belowground pathogenic fungi
 (Janzen-Connell Hypothesis), however variation exists among taxa such that
 some experience low levels of mortality. We hypothesized that seedlings
 close to adults might profit, rather than suffer, from belowground fungi,
 notably from mycorrhiza or decomposers, in particular near large adult
 trees and under a closely related canopy. 2. We planted oak seedlings in a
 temperate forest at different distances from adults and followed seedling
 mortality, budburst (early budburst permitting photosynthesis during the
 best light conditions) and leaf herbivory. We applied fungicide on half of
 the seedlings for 2 years to identify the net effect of belowground fungi
 on seedlings. We quantified seedling mycorrhization and fungal-driven
 decomposition of a neighbourhood-specific and an unspecific substrate,
 local oak leaves and cellulose, respectively. Finally, we related
 mycorrhization and decomposition to seedling performance. 3. We found
 that, in seedlings planted close to conspecific adults, belowground fungi
 had a negative net effect on seedlings: elimination of fungi,
 surprisingly, decreased herbivory. This effect could be due to oak leaf
 decomposition, which related to increased seedling herbivory and was
 higher near a conspecific adult. Under a closely related canopy, however,
 the net effect of belowground fungi on nearby seedlings became positive:
 elimination of fungi delayed budburst. This effect could be due to
 colonization by the ectomycorrhizal fungus Cortinarius sp., which related
 to accelerated budburst and was higher near a conspecific under a closely
 related canopy. Effects of belowground fungi on nearby seedlings were not
 dependent on the size of the conspecific and were species- but not
 lineage-specific. 4. Overall, our results suggest that a
 Janzen-Connell-like pattern, i.e. increased mortality of seedlings near
 conspecific adult, can be (i) induced by specialist decomposers increasing
 the nutritional quality of conspecific seedlings to herbivores, and (ii)
 offset by ectomycorrhizal fungal mutualists under a closely related
 canopy. Coexistence among closely related adult trees appears to change
 interactions between adults and nearby conspecific seedlings from
 conspecific inhibition to conspecific facilitation.
description: Janzen-Connell patterns
 can be induced by fungal-driven decomposition and offset by
 ectomycorrhizal fungi accumulated under a closely related
 canopyData collected in the
 fielddata_FEcol_Deniau.txt
DOI: 10.5061/dryad.8jk03jd
title: Data from: Type 1 interferon-inducible gene expression in QuantiFERON Gold TB-positive uveitis: a tool to stratify a high versus low risk of active tuberculosis?

description: QuantiFERON-Gold TB (QFT)-positive patients with undetermined cause of
 uveitis are problematic in terms of whether to diagnose and treat them for
 tuberculosis (TB). Here, we investigated whether peripheral blood
 expression of type 1 interferon (IFN)-inducible genes may be of use to
 stratify QFT-positive patients with uveitis into groups of high versus low
 risk of having active TB-associated uveitis. We recruited all new uveitis
 patients in Cipto Mangunkusumo Hospital, Jakarta, Indonesia for one year.
 We included 12 patients with uveitis and clinically diagnosed active
 pulmonary TB, 58 QFT-positive patients with uveitis of unknown cause, 10
 newly diagnosed sputum-positive active pulmonary TB patients without
 uveitis and 23 QFT-negative healthy controls. Expression of 35 type 1
 IFN-inducible genes was measured in peripheral blood cells from active
 pulmonary TB patients without uveitis and healthy controls. Differentially
 expressed genes were identified and used for further clustering analyses
 of the uveitis groups. A type-1 IFN gene signature score was calculated
 and the optimal cut-off value for this score to differentiate active
 pulmonary TB from healthy controls was determined and applied to
 QFT-positive patients with uveitis of unknown cause. Ten type 1
 IFN-inducible genes were differentially expressed between active pulmonary
 TB and healthy controls. Expression of these 10 genes in QFT-positive
 patients with uveitis of unknown cause revealed three groups: 1); patients
 resembling active pulmonary TB, 2); patients resembling healthy controls,
 and 3); patients displaying an in-between gene expression pattern. A type
 1 IFN gene signature score ≥5.61 displayed high sensitivity (100%) and
 specificity (91%) for identification of active TB. Application of this
 score to QFT-positive patients with uveitis of unknown cause yielded two
 groups with expected different likelihood (high vs. low) of having
 active-TB uveitis, and therefore may be useful in clinical management
 decisions.
description: Type I IFN gene
 signature - a tool to stratify high vs low-risk TB
 uveitis?The excel file contains
 all data from 103 subjects (as described in table 1 of the manuscript).
 All 2dCt value from all 35 genes are noted
DOI: 10.5061/dryad.vr454
title: Data from: Sex-specific phenotypes and metabolism-related gene expression in juvenile sticklebacks

description: To fully understand the evolution of sexual dimorphism, it is necessary to
 study how genetic and developmental systems function to generate
 sex-specific phenotype as well as sex-specific selection. Males and
 females show different patterns of energy storage and mitochondrial
 metabolism from early stages of life, and this may underlie sex-specific
 developmental pathway to shape both juvenile and adult phenotype. Here, we
 examined sex-specific relationships between juvenile morphology and
 behavior, and transcriptional profiles of 4 candidate genes related to
 mitochondrial function in the 3-spined stickleback. This study provides,
 for the first time to our knowledge, evidence for sex differences in
 melanin pigmentation and antipredator behavior as well as the expression
 of mitochondria-related genes in juvenile sticklebacks. Males were paler
 and bolder, and overexpressed genes involved in mitochondrial respiration
 and antioxidant enzymes compared to females. Relationships between
 phenotypic traits and gene expression were also sex-specific. In general,
 females showed stronger positive correlations between body size or
 pigmentation and the expression of genes involved in mitochondrial
 biogenesis and activity. In both sexes, more fearful individuals
 overexpressed those genes. Our results suggest that mitochondrial function
 may either facilitate or constrain sex-specific responses to selection on
 dimorphic phenotype, possibly generating intralocus sexual conflict on the
 transcriptional regulation of mito-nuclear genes during ontogeny. This
 study highlights that mitochondrial regulation plays an important role in
 the process of phenotypic differentiation between the 2 sexes from early
 stages of life before apparent sexual dimorphism appears.
description: Phenotypic traits and
 gene expressionThe raw Cqs of samples
 per triplicate and variables retated to individuals (family, sex,
 risk-taking behaviour, body mass and melanin colour), observation tank and
 samples (run and replicatesdata.txt
DOI: 10.5061/dryad.1p1c0fs
title: Data from: Multiple facets of stream macroinvertebrate alpha diversity are driven by different ecological factors across an extensive altitudinal gradient

description: Environmental filtering and spatial structuring are important ecological
 processes for the generation and maintenance of biodiversity. However, the
 relative importance of these ecological drivers for multiple facets of
 diversity is still poorly understood in highland streams. Here, we
 examined the responses of three facets of stream macroinvertebrate alpha
 diversity to local environmental, landscape-climate and spatial factors in
 a near-pristine highland riverine ecosystem. Taxonomic (species richness,
 Shannon diversity and evenness), functional (functional richness,
 evenness, divergence and Rao's Quadratic entropy) and a proxy of
 phylogenetic alpha diversity (taxonomic distinctness and variation in
 taxonomic distinctness) were calculated for macroinvertebrate assemblages
 in 55 stream sites. Then Pearson correlation coefficient was used to
 explore congruence of indices within and across the three diversity
 facets. Finally, multiple linear regression models and variation
 partitioning were employed to identify the relative importance of
 different ecological drivers of biodiversity. We found most correlations
 between the diversity indices within the same facet, and between
 functional richness and species richness were relatively strong. The two
 phylogenetic diversity indices were quite independent from taxonomic
 diversity but correlated with functional diversity indices to some extent.
 Taxonomic and functional diversity were more strongly determined by
 environmental variables, while phylogenetic diversity was better explained
 by spatial factors. In terms of environmental variables, habitat-scale
 variables describing habitat complexity and water physical features played
 the primary role in determining the diversity patterns of all three
 facets, whereas landscape factors appeared less influential. Our findings
 indicated that both environmental and spatial factors are important
 ecological drivers for biodiversity patterns of macroinvertebrates in
 Tibetan streams, although their relative importance was contingent on
 different facets of diversity. Such findings verified the complementary
 roles of taxonomic, functional and phylogenetic diversity, and highlighted
 the importance of comprehensively considering multiple ecological drivers
 for different facets of diversity in biodiversity assessment.
description: species data of
 macroinvertebrates in 55 stream sitesspecies
 data.xlsx
DOI: 10.5061/dryad.142m0
title: Data from: Land-use legacies and present fire regimes interact to mediate herbivory by altering the neighboring plant community

description: Past and present human activities, such as historic agriculture and fire
 suppression, are widespread and can create depauperate plant communities.
 Although many studies show that herbivory on focal plants depends on the
 density of herbivores or the composition of the surrounding plant
 community, it is unclear whether anthropogenic changes to plant
 communities alter herbivory. We tested the hypothesis that human
 activities that alter the plant community lead to subsequent changes in
 herbivory. At 20 sites distributed across 80 300 hectares, we conducted a
 field experiment that manipulated insect herbivore access (full exclosures
 and pseudo-exclosures) to four focal plant species in longleaf pine
 woodlands with different land-use histories (post-agricultural sites or
 non-agricultural sites) and degrees of fire frequency (frequent and
 infrequent). Plant cover, particularly herbaceous cover, was lower in
 post-agricultural and fire suppressed woodlands. Density of the dominant
 insect herbivore at our site (grasshoppers) was positively related to
 plant cover. Herbivore access reduced biomass of the palatable forb
 Solidago odora in frequently burned post-agricultural sites and in
 infrequently burned non-agricultural woodlands and increased mortality of
 another forb (Pityopsis graminifolia), but did not affect two other less
 palatable species (Schizachyrium scoparium and Tephrosia virginiana).
 Herbivory on S. odora exhibited a hump-shaped response to plant cover,
 with low herbivory at low and high levels of plant cover. Herbivore
 density had a weak negative effect on herbivory. These findings suggest
 that changes in plant cover related to past and present human activities
 can modify damage rates on focal S. odora plants by altering grasshopper
 foraging behavior rather than by altering local grasshopper density. The
 resulting changes in herbivory may have the potential to limit natural
 recovery or restoration efforts by reducing the establishment or
 performance of palatable plant species.
description: Hahn_Orrock_Oikos_DATAData associated with Hahn and Orrock (2015) Oikos
DOI: 10.5061/dryad.46nr8
title: Data from: Frequency-dependent fitness in gynodioecious Lobelia siphilitica

description: Selection is frequency dependent when an individual's fitness depends
 on the frequency of its phenotype. Frequency-dependent selection should be
 common in gynodioecious plants, where individuals are female or
 hermaphroditic; if the fitness of females is limited by the availability
 of pollen to fertilize their ovules, then they should have higher fitness
 when rare than when common. To test whether the fitness of females is
 frequency dependent, we manipulated the sex ratio in arrays of
 gynodioecious Lobelia siphilitica. To test whether fitness was frequency
 dependent because of variation in pollen availability, we compared
 open-pollinated and supplemental hand-pollinated plants. Open-pollinated
 females produced more seeds when they were rare than when they were
 common, as expected if fitness is negatively frequency dependent. However,
 hand-pollinated females also produced more seeds when they were rare,
 indicating that variation in pollen availability was not the cause of
 frequency-dependent fitness. Instead, fitness was frequency dependent
 because both hand- and open-pollinated females opened more flowers when
 they were rare than when they were common. This plasticity in the rate of
 anthesis could cause fitness to be frequency dependent even when
 reproduction is not pollen limited, and thus expand the conditions under
 which frequency-dependent selection operates in gynodioecious species.
description: Lobelia siphilitica
 frequency-dependent fitness dataFrequency-dependent
 fitness measures for female and hermaphrodite Lobelia siphilitica
 plants.Drayd
 Data.xlsx
DOI: 10.5061/dryad.g0v07
title: Data from: Video-fluoroscopic swallowing study scale for predicting aspiration pneumonia in Parkinson's disease

description: Introduction A number of video-fluoroscopic swallowing study (VFSS)
 abnormalities have been reported in patients with Parkinson's disease
 (PD). However, the most crucial finding of subsequent aspiration pneumonia
 has not been validated fully. We conducted a retrospective and
 case-control study to determine the clinically significant VFSS findings
 in this population, and to propose a practical scale for predicting
 aspiration pneumonia in patients with PD. Methods We enrolled 184 PD
 patients who underwent VFSS because of suspected dysphagia. The patients
 who developed aspiration pneumonia within six months of the VFSS were
 assigned as cases and the patients without aspiration pneumonia at six
 months were designated as controls. Logistic regression analysis was
 performed to determine the prognostic VFSS features based on the data of
 swallowing 3 mL of jelly, which were used to make a PD VFSS scale (PDVFS).
 The validity of the new PDVFS was evaluated by ROC analysis. Additionally,
 we used the survival time analysis to compare time to death between
 groups, stratified by the PDVFS score. Results Twenty-five patients
 developed aspiration pneumonia. Among the previously-proposed VFSS
 features, mastication, lingual motility prior to transfer, aspiration, and
 total swallow time were identified as significant prognostic factors. We
 combined these factors to form the PDVFS. The PDVFS score ranges from 0 to
 12, with 12 being the worst. ROC analysis revealed 92% sensitivity and 82%
 specificity at a cutoff point of 3. The higher PDVFS group showed shorter
 time-to-death than the lower PDVFS group (log rank P = 0.001). Conclusion
 Our newly developed VFSS severity scale (based on jelly swallowing) for
 patients with PD was easy to rate and could predict subsequent aspiration
 pneumonia and poor prognosis in patients with PD.
description: PDVFS_20170801This excel file contained the raw data of our study.
DOI: 10.5061/dryad.31sn1q0j
title: Data from: Evolutionary history of Scinax treefrogs on land-bridge islands in south-eastern Brazil

description: AIM: We investigated how Pleistocene refugia and recent (~12,000 years
 ago) sea level incursions shaped genetic differentiation in mainland and
 island populations of the Scinax perpusillus treefrog group. LOCATION:
 Brazilian Atlantic Forest, São Paulo state, southeastern Brazil. METHODS:
 Using mitochondrial and microsatellite loci, we surveyed population
 structure and genetic diversity in Scinax from five mainland populations
 and three land-bridge islands to understand the roles of Pleistocene
 forest fragmentation and sea level incursions on genetic differentiation.
 We calculated metrics of relatedness and genetic diversity to assess
 whether island populations exhibit signatures of genetic drift and
 isolation. Two of the three island populations in this study have
 previously been described as new species based on a combination of
 distinct morphological and behavioural characters, thus we used the
 molecular datasets to determine whether phenotypic change is consistent
 with genetic differentiation. RESULTS: Our analyses recovered three
 distinct lineages or demes comprised of northern mainland São Paulo
 populations, southern mainland São Paulo populations, and one divergent
 island population. The two remaining island populations clustered with
 samples from adjacent mainland populations. Estimates of allelic richness
 were significantly lower, and estimates of relatedness were significantly
 higher, in island populations relative to their mainland counterparts.
 MAIN CONCLUSIONS: Fine-scale genetic structure across mainland populations
 indicates the possible existence of local refugia within São Paulo state,
 underscoring the small geographic scale at which populations diverge in
 this species rich region of the Atlantic Coastal Forest. Variation in
 genetic signatures across the three islands indicates that the populations
 experienced different demographic processes after marine incursions
 fragmented the distribution of Scinax perpusillus. Genetic signatures of
 inbreeding and drift in some island populations indicate that small
 population sizes coupled with strong ecological selection may be important
 evolutionary forces driving speciation on land-bridge islands.
description: MicrosatellitesThis file includes the raw allele scores for eight microsatellites collected from 149 samples of the Scinax perpusillus species group (S. perpusillus, S. peixotoi, and S. faivovichi) at several localities in the Brazilian Atlantic Forest.ScinaxMicros.xls
DOI: 10.5061/dryad.vq94085
title: Data from: Quantifying the digestive fingerprints of predators on the bones of their prey using scanning electron microscopy

description: Paleoecological reconstruction relies on accurately determining the
 taphonomic origin of fossil deposits. Predation is a common mechanism by
 which skeletal remains become concentrated over time, leading to the
 formation of modern and fossil prey death assemblages. Skeletal element
 representation and breakage patterns within such death assemblages can be
 used to infer the identity of the responsible predator. However,
 assemblage-level metrics cannot be used to infer if a single fossil
 specimen is predator-derived. Microscopic digestive etching on individual
 bones can also indicate past predation events because acidic gastric
 fluids create distinctive micrometer-scale fissures in cortical bone. Here
 we establish a quantitative approach to predator identification from small
 mammal prey remains using microscopic digestive damage patterns. To do
 this, we collected mandibles from rodents digested by 13 predator species
 from local wildlife rehabilitation centers, and imaged them using an FEI
 Quanta 200 SEM. We found that bones exposed to gastric fluids showed clear
 digestive fissures, and that owl-digested specimens can be readily
 distinguished from specimens that were digested by diurnal raptors and
 mammalian carnivores. Specifically, owl-digested specimens are
 characterized by a high density of small and short digestive fissures.
 Within the owls, digestive fissure patterns appear to scale with owl body
 size. Finally, we used linear discriminant analysis to build a
 classification scheme from our modern data and applied it to Holocene
 mouse fossils from Two Ledges Chamber, Nevada. We found that the fossil
 specimens display the digestive fingerprints of owls. Quantification of
 microscopic digestive fissures thus offers a promising new approach for
 elucidating the taphonomic history of individual fossil specimens.
description: SEM Digestive Wear
 DataData on microscopic
 digestive wear incurred by prey bones during the digestion process of
 predatorsDryadDataTable-SEM.xlsx
DOI: 10.5061/dryad.b4q6q
title: Data from: Demographic influences of translocated individuals on a resident population of house sparrows

description: Translocation of individuals from source populations to augment small
 populations facing risk of extinction is an important conservation tool.
 Here we examine sex-specific differences between resident and translocated
 house sparrows Passer domesticus in reproductive success and survival, and
 the contribution of translocated individuals to the growth of a local
 population. We found evidence for assortative mating based on origin
 revealed by fewer parentages between translocated males and resident
 females than expected, and the total number of fledglings produced by such
 pairs was lower. Interestingly, the reproductive success of translocated
 males was positively related to the size of the throat badge (a sexual
 ornament), such that translocated males with a large badge size were as
 successful as resident males. However, offspring with parents of different
 origin had higher survival than offspring with parents of same origin,
 which suggests hybrid vigour. The contribution of resident and
 translocated individuals to the stochastic component of the long-run
 growth rate of the population was similar; neither the mean individual
 contributions in fitness nor the demographic variance differed between the
 two groups. Thus, this experiment shows that translocated individuals may
 have a similar demographic influence on the growth of local populations as
 resident individuals. Still, the intermixing of translocated and resident
 individuals was low, and fitness differed according to origin in relation
 to individual differences in a sexually selected trait. In addition,
 hybrid vigour with respect to offspring recruitment seemed to partially
 relax the negative fitness consequences of the assortative mating based on
 origin.
description: dryad_adindividual data (morphological and demographic) from the experimental birds (translocated and resident).dryad_chickschick data from the experimental birds (chicks of translocated and resident individuals).