cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3xsj3txh8
title: Data from: Spatial variation in the biotic and abiotic filters of oyster recruitment: Implications for restoration

description: Attempts to restore marine ecosystems are increasing, but the success of
 projects remains variable. For marine invertebrates, the establishment of
 self-sustaining populations requires a larval supply as well as conditions
 that permit recruitment. Abiotic and biotic conditions that determine
 recruitment can vary across environmental gradients and have opposing or
 reinforcing effects. We assessed how predation and tidal inundation
 influence recruitment of the reef-forming oyster, Saccostrea glomerata, at
 15 sites, 5 estuaries and 8 degrees of latitude in eastern Australia.
 Oysters recruited to all 15 sites, but their density displayed spatially
 variable effects of tidal inundation and caging. Effects of tidal
 inundation and caging were weakest at the two lower-latitude estuaries
 where recruitment was low overall, average temperature and turbidity were
 high and dissolved oxygen low. At higher-latitude estuaries, where abiotic
 conditions were more favourable for recruitment, recruit density displayed
 tidal elevation gradients that were dependent on caging and time.
 Initially, recruit density decreased with tidal inundation (and exposure
 to finfish predators), in the uncaged but not the caged treatment.
 However, over time the elevation gradient disappeared, and recruitment and
 survival of oysters was greater in caged than uncaged treatments
 irrespective of elevation. Synthesis and applications: Our results suggest
 that both abiotic (i.e. temperature, turbidity and dissolved oxygen) and
 biotic (i.e. predation) factors can negatively influence oyster
 recruitment and, hence, restoration success. Consequently, oyster reef
 restoration projects should be planned to prioritise sites with low
 turbidity, high dissolved oxygen and low predation unless these stressors
 can be mitigated. Restoration projects that are designed with knowledge of
 local stressors are more likely to be successful.
DOI: 10.5061/dryad.d51c5b046
title: Data for: Plant diversity effects on herbivory are related to soil biodiversity and plant chemistry

description: Insect herbivory is a key process in ecosystem functioning. While theory
 predicts that plant diversity modulates herbivory, the mechanistic links
 remain unclear. We postulated that the plant metabolome mechanistically
 links plant diversity and herbivory. In late summer and in spring, we
 assessed individual plant aboveground herbivory rates and metabolomes of
 seven plant species in experimental plant communities varying in plant
 species diversity and resource acquisition strategies. In the same
 communities, we also measured plant individual biomass as well as soil
 microbial and nematode community composition. Herbivory rates decreased
 with increasing plant species richness. Path modelling revealed that plant
 species richness and community resource acquisition strategy correlated
 with soil community composition. In particular, changes in nematode
 community composition were related to plant metabolome composition and
 thereby herbivory rates. These results suggest that soil community
 composition plays an important role in reducing herbivory rates with
 increasing plant diversity by changing plant metabolomes.
DOI: 10.5061/dryad.m0cfxpp4n
title: Vegetation habitat of White-winged flufftail

description: The White-winged Flufftail is listed as critically endangered and limited
 knowledge about the species’ ecology has been identified as a limiting
 factor to effectively conserving the bird. Little is known about the
 vegetation inhabited by the White-winged Flufftail, which hampers the
 identification and management of its habitat. This study presents a
 fine-scale classification and description of the vegetation of wetland
 sites where the bird is known to be present. A plant phytosociological
 study was conducted to describe the plant communities and vegetation
 structure of the habitat. Three sites were selected at Verloren Valei
 Nature Reserve and two at Middelpunt Wetland, Mpumalanga, South Africa,
 shortly after the White-winged Flufftail breeding season. A total of 60
 sample plots were placed within the study sites, where all plant species
 present were recorded and identified. Other aspects such as plant height,
 water depth and anthropogenic influences were also documented. A modified
 TWINSPAN analysis resulted in the identification of three sub-communities
 that can be grouped into one major community. The Cyperaceae, Asteraceae
 and Poaceae families dominate the vegetation, with the sedges Carex
 austro-africana and Cyperus denudatus being dominant, and the grasses
 Leersia hexandra and Arundinella nepalensis co-dominant. The broad habitat
 structure consisted of medium to tall herbaceous plants (0.5-0.7 m) with
 shallow slow-flowing water.
DOI: 10.5061/dryad.fj6q573vt
title: The moment of tooth: rate, fate, and pattern of Pacific lingcod dentition revealed by pulse-chase

description: Tooth replacement rates of polyphyodont cartilaginous and bony fishes are
 hard to determine because of lack of obvious patterning, and maintaining
 specimens long enough to observe replacement. Pulse-chase is a fluorescent
 technique that differentially colours developing mineralized tissue. We
 present in-situ tooth replacement rate and position data
 for the oral and pharyngeal detentions of Ophiodon
 elongatus (Pacific lingcod). We assessed over 10,000 teeth, in 20
 fish, and found a daily replacement rate of about two teeth (3.6% of the
 dentition). The average tooth is in the dental battery for 27 days.
 Replacement was higher in the lower pharyngeal jaw (LPJ). We found no
 difference between replacement rates of feeding and non-feeding fish,
 suggesting feeding was not a driver of tooth replacement. Lingcod teeth
 have both a size and location fate; smaller teeth at one spot will not
 grow into larger teeth, even if a large tooth nearby is lost. We also
 found increased rates of replacement at the posterior of the LPJ relative
 to the anterior. We propose that lingcod teeth do not migrate in the jaw
 as they develop; their teeth are fated in size and location, erupting in
 their functional position.
DOI: 10.5061/dryad.qrfj6q5gz
title: Beneficial cumulative effects of old parental age on offspring fitness

description: Old parental age is commonly associated with negative effects on offspring
 life-history traits. Such parental senescence effects are predicted to
 have a cumulative detrimental effect over successive generations. However,
 old parents may benefit from producing higher quality offspring when these
 compete for seasonal resources. Thus, old parents may choose to increase
 investment in their offspring, thereby producing fewer but larger and more
 competitive progeny. We show that Caenorhabditis elegans hermaphrodites
 increase parental investment with advancing age, resulting in fitter
 offspring who reach their reproductive peak earlier. Remarkably, these
 effects increased over six successive generations of breeding from old
 parents and were subsequently reversed following a single generation of
 breeding from a young parent. Our findings support the hypothesis that
 offspring of old parents receive more resources and convert them into
 increasingly faster life-histories. These results contradict the theory
 that old parents transfer a cumulative detrimental “ageing factor” to
 their offspring.
DOI: 10.5061/dryad.ht76hdrgk
title: Untangling the molecular basis of coral response to sedimentation

description: Urbanized coral reefs are often chronically affected by sedimentation and
 reduced light levels, yet many species of corals appear to be able to
 thrive under these highly disturbed conditions. Recently, these marginal
 ecosystems have gained attention as potential climate change refugia due
 to the shading effect of suspended sediment, as well as potential
 reservoirs for stress-tolerant species. However, little research exists on
 the impact of sedimentation on coral physiology, particularly at the
 molecular level. Here, we investigated the transcriptomic response to
 sediment stress in corals of the family Merulinidae from a chronically
 turbid reef (one genet each of Goniastrea pectinata and Mycedium
 elephantotus from Singapore) and a clear-water reef (multiple genets of G.
 pectinata from the Gulf of Aqaba/Eilat). In two ex-situ experiments, we
 exposed corals to either natural sediment or artificial sediment enriched
 with organic matter and used whole-transcriptome sequencing (RNAseq) to
 quantify gene expression. Analysis revealed a shared basis for coral
 transcriptomic response to sediment stress, which involves the expression
 of genes broadly related to energy metabolism and immune response. In
 particular, sediment exposure induced upregulation of anaerobic glycolysis
 and glyoxylate bypass enzymes, as well as genes involved in hydrogen
 sulfide metabolism and in pathogen pattern recognition. Our results point
 towards hypoxia as a likely driver of this transcriptomic response,
 providing a molecular basis to previous work that identified hypoxia as a
 primary cause of tissue necrosis in sediment-stressed corals. Potential
 metabolic and immunity trade-offs of corals living under chronic
 sedimentation should be considered in future studies on the ecology and
 conservation of turbid reefs.
DOI: 10.5061/dryad.dv41ns201
title: Local phylogenetic signal in Dutch habitats and other data from Prinzing et al New Phytologist 2021

description: The functioning of present ecosystems reflects deep evolutionary history
 of locally co-occurring species if their functional traits show high
 phylogenetic signal (PS). However, we do not understand what drives local
 PS. We hypothesize that local PS is high in undisturbed and stressful
 habitats – either due to ongoing local assembly of species that maintained
 ancestral traits, or past evolutionary maintenance of ancestral traits
 within habitat species-pools, or both. We quantified PS and diversity of
 10 traits within 6704 local plant communities across 38 Dutch habitat
 types differing in disturbance or stress. Mean local PS varied 50-fold
 among habitat types, often independently of phylogenetic or trait
 diversity. Mean local PS decreased with disturbance but showed no
 consistent relationship to stress. Mean local PS exceeded species-pool PS,
 reflecting non-random subsampling from the pool. Disturbance or stress
 related more strongly to mean local than to species-pool PS. Disturbed
 habitats harbour species with evolutionary divergent trait values, likely
 driven by ongoing, local assembly of species: environmental fluctuations
 might maintain different trait values within lineages through an
 evolutionary storage effect. If functional traits do not reflect
 phylogeny, ecosystem functioning might not be contingent on the presence
 of particular lineages, and lineages might establish evolutionarily novel
 interactions.
description: Please see article in New Phytologist.
DOI: 10.5061/dryad.bzkh1899h
title: Climate-induced plasticity in leaf traits of riparian plants

description: Aim: Leaf inputs from riparian vegetation and its decomposition play a key
 role in energy and nutrients transfer in many stream ecosystems. Instream
 leaf-litter decomposition is mainly driven by leaf traits. Therefore,
 understanding and predicting leaf traits variation with current
 environmental changes and its putative effects on stream food webs is a
 critical challenge. Most studies have focused on the assumed higher
 interspecific leaf traits variability, with little research addressing an
 intraspecific perspective. Location: Andalusia, Spain Methods: We assessed
 the relative effects of climate and soil on the intraspecific variability
 in leaf traits of four common woody riparian species in permanent
 low-order Mediterranean streams along a wide aridity gradient. We used a
 space-for-time substitution approach to predict leaf traits changes and
 consequences for stream food webs in a future climate change scenario.
 Results: We found that climate had a major influence on intraspecific
 variability of leaf traits, but with opposite patterns depending on plant
 functional type. Results indicated that leaf quality—linked to
 palatability and decomposability—of Alnus glutinosa, Salix atrocinerea and
 Rubus ulmifolius (deciduous/semideciduous) will decrease with the
 forecasted aridification, whereas that of the evergreen Nerium oleander
 will increase. Main conclusions: Our findings suggest a decrease of
 intraspecific leaf-quality in riparian deciduous species with global
 warming in a relatively short term, which, in a longer term, may add to
 the forecasted dieback of deciduous species in riparian corridors of
 temperate climate zones. These forecasted changes have the potential to
 significantly impair ecosystem functioning of Mediterranean mountain
 streams currently under deciduous gallery forests.
DOI: 10.5061/dryad.37pvmcvm6
title: Predictors of individual performance and evolutionary potential of life-history traits in a hematophagous ectoparasite

description: Little is known about the intraspecific variation of parasite life-history
 traits and on how this variation may affect parasite fitness and
 evolution. We investigated how life-history traits predict success of
 individual tree-hole ticks Ixodes arboricola and estimated their
 evolutionary potential, as well as genetic correlations within stages and
 phenotypic correlations within and across stages. Ticks were followed
 individually over two generations while allowed to feed on great tits
 Parus major. After accounting for host and tick maternal effects, we found
 that short feeding times and high engorgement weights strongly increased
 moulting success. Also, moulting time was positively correlated with
 feeding success in adults. In larvae and nymphs we found negative
 phenotypic correlations between engorgement weight and both feeding and
 moulting time, the latter supported by a negative genetic correlation. We
 found sex-related differences in feeding time (longer in male nymphs) and
 moulting time (longer in male larvae but shorter in male nymphs). Also,
 time since the last feeding event (set experimentally) reduced larval and
 nymphal fitness while it increased adult female fitness. Furthermore, we
 found significant heritability and evolvability, i.e. the potential to
 respond to selection, for engorgement weight and moulting time across all
 stages but no significant heritability for feeding time. Our findings
 suggest that variation in tick fitness is shaped by consistent individual
 differences in tick quality, for which engorgement weight is a good proxy,
 rather than by life-history trade-offs.
description: Please refer to the Materials and Methods section of the related
 manuscript.
description: For description of the abbreviations used in the excel files
 please refer to the file "Description abbreviations". Missing
 values mean that the tick died or was missing before the value could be
 measured or that the information is not relevant for
 the individual.
DOI: 10.5061/dryad.9zw3r22g0
title: Data from: Facilitation enhances ecosystem function with non-random species gains

description: Facilitation, an ecological interaction assembling plant communities
 worldwide, has been shown to modulate both species richness and ecosystem
 functions. Such a Biodiversity-Ecosystem Functioning (BEF) relationship
 can be decomposed into different components not only related to species
 losses and gains but also to the identity of the species and the context
 in which they live. Using an extension of the classical BEF approach named
 CAFE (Community Assembly and the Functioning of Ecosystems), we quantified
 the contribution of these components to the BEF relationship in a Spanish
 semiarid plant community shaped by facilitation. We used species richness
 as a measure for biodiversity and plant cover as a proxy of multiple
 ecosystem functions including plant productivity, soil protection, soil
 fertility and microbial productivity. Nurse plants doubled the number of
 species that live beneath them relative to open ground, but caused a
 five-fold increase in plant cover. The disproportionate increase of plant
 cover was a consequence of the identity of the species enhanced by nurse
 plants, which were more productive than the average. We discuss these
 results in terms of sampling effects (i.e., the higher probability of
 richer communities to harbour hyperproductive species) and complementary
 effects (i.e., richer communities enhancing productivity through resource
 partitioning, abiotic facilitation, or biotic feedbacks). The enhancement
 of ecosystem functions that plant facilitation produces by incorporating
 species with high functional values to the community may reverberate among
 other trophic levels and propagate beyond the local scale where the
 ecological interaction is produced.
description: We selected 25 plots under the nurse plant (<em>Ononis
 tridentata</em>) canopy and 25 adjacent gaps of the same size to
 estimate the cover of each plant. The size of the plots varied with the
 size of the nurse plant, ranging from 11435 to 21980
 cm<sup>2</sup>. The cover of facilitated plants was estimated
 by adding the number of cm that each plant species occupied along a
 variable number of parallel linear transects established under the canopy
 of the nurse plant. To estimate the contribution of different processes to
 the BEF relationship, we followed the CAFE approach described in
 Bannar-Martin et al (2017; Ecol. Lett. 21, 167-180).
DOI: 10.5061/dryad.tx95x69zg
title: Litter–trapping tank bromeliads in five different forests: carbon and nutrient pools and fluxes

description: Bromeliads are the most abundant litter–trapping plants in Neotropical
 forest canopies. By intercepting litter, bromeliads obtain and retain
 nutrients before they reach the pedosphere. Here, we analyzed the litter
 captured and stored by tank bromeliads (TB) in five different forests
 along an elevation gradient in Mexico. Among those forests, carbon and
 nutrient pools and nitrogen fluxes in TB were estimated in a mangrove (MF)
 and a semi–deciduous tropical forest (SDTF). The composition of the litter
 trapped by TB along the gradient was similar to forest litterfall and was
 mainly composed of leaves. Most of the litter was captured in the dry
 season and we found a significant effect of projected plant area and the
 interaction between month and site on bromeliad litter capture. Moreover,
 litter stored in TB increased exponentially with projected plant area and
 differed between three studied species. In the MF (with ca. 2,700 TB
 ha-1), barely ca. 1% of annual litterfall is trapped by these plants, but
 even in the SDTF, with &gt;10,000 TB ha-1, only ca. 2.4% is captured.
 We found that carbon and nitrogen pools in TB were small and represented
 &lt; 1% of the carbon and nitrogen stored in forest aboveground
 biomass. Furthermore, the residence time of litter trapped in TB was not
 particularly large and was similar to that of litter on the forest floor.
 In light of our results, we conclude that in the studied forests the
 effect of TB on the forest carbon and nutrient cycle is negligible.
DOI: 10.5061/dryad.905qfttmb
title: Co-assembly of publicly available biocrust sequence datasets

description: The growing body of metagenomic data offers the possibility for creating
 longer consensus assemblies for ecosystems of interest as a community
 resource. We tested this concept by performing a co-assembly of metagenome
 and metatranscriptome data from five independent studies of biological
 soil crust communities in the southwestern United
 States.  
description: These are metagenomic assemblies
 made up from publicly available datasets collected over the course of
 2021. See the associated publication for a list of the datasets that went
 into the final assembly. Raw sequence reads were assembled with
 MetaHipMer and the resulting contigs were binned with MaxBin. Quality of
 the resulting bins were determined with CheckM
DOI: 10.5061/dryad.z612jm6cr
title: Single-synapse analyses of Alzheimer’s disease implicate pathologic tau, DJ1, CD47, and ApoE

description: Synaptic molecular characterization is limited for Alzheimer’s disease
 (AD). Our newly invented mass cytometry-based method, Synaptometry by Time
 of Flight (SynTOF), was used to measure 38 antibody probes in
 approximately 17 million single-synapse events from human brains without
 pathologic change or with pure AD or Lewy body disease (LBD), non-human
 primates (NHP), and PS/APP mice. Synaptic molecular integrity in humans
 and NHP was similar. Although not detected in human synapses, Aβ was in
 PS/APP mice single-synapse events. Clustering and pattern identification
 of human synapses showed expected disease-specific differences, like
 increased hippocampal pathologic tau in AD and reduced caudate dopamine
 transporter in LBD, and revealed novel findings including increased
 hippocampal CD47 and lowered DJ1 in AD and higher ApoE in AD with
 dementia. Our results were independently supported by multiplex ion beam
 imaging of intact tissue. This highlights the higher depth and breadth of
 insight on neurodegenerative diseases obtainable through SynTOF.
description: The dataset was collected using mass cytometry at The Human
 Immune Monitoring Center (HIMC) and multiplexed ion beam imaging by time
 of flight (MIBI-TOF) at Stanford University in 2019-2020 and 2020,
 respectively. The single-synapse data has been processed by arcsinh
 transformed with a cofactor of 5 to produce the results published in
 Science Advances, where a detailed experimental method and preprocessing
 can be found.
description: The readme file contains an explanation of each of the metadata
 of each file (both SynTOF and MIBI-TOF) as well as the column and value
 descriptions. Information on how the measurements were done can be found
 in the associated manuscript referenced above. We have also attached
 scripts we used to generate the results presented in the paper. The
 explanation of each of the script file is written in readme-files within
 the zip folder.