cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4mw6m907p
title: Data from: Biomass–density relationships of plant communities deviate from the self‐thinning rule due to age structure and abiotic stress

description: A pertinent debate in plant ecology centers around the generality of the
 self-thinning rule. However, studies focused on highly simplified settings
 such as even-aged monospecific populations or optimal conditions. This
 neglects the fact that most natural communities, to which the classical
 self-thinning slope is often applied, are age-structured, composed of
 multiple species and exposed to various types of abiotic stress. With the
 help of an individual-based model, we relax these simplified assumptions
 and systematically test for changes in the biomass–density relationships
 of uneven-aged, functionally diverse plant communities across a complete
 stress gradient, using excessive to insufficient soil water as a case
 study. We show that frequent recruitment, which resulted in an uneven-aged
 community, and stress intensity caused predictable changes in the entire
 biomass–density trajectory. Increasing stress resulted in steeper (more
 negative) slopes and increased the intercept in the classical
 self-thinning section irrespective of excessive or insufficient soil water
 as a stress type. Recruitment steepened the slope, too and enabled a novel
 section in the biomass–density trajectory. This novel section represented
 a quasi-steady state of the density-dependent dynamics of new generations
 which occurred locally within patches of recruitment. At the community
 level, the slope of the biomass–density relationship at quasi-steady state
 had a significantly flatter slope of −1.1 under optimal soil water
 conditions. Functional diversity showed little impact on density-dependent
 mortality. Namely, it resulted in an earlier onset of mortality but not in
 changes in the values of the slope and intercept. We conclude that the
 classical −3/2 slope is not useful to describe the biomass–density
 relationship in natural and semi-natural plant communities. The magnitude
 and direction of variation in the slope are related to the age–structure
 and abiotic stress intensity in the plant community.
description: Mean ± SD skewness of the
 biomass distribution of nineteen soil water scenarios across ten
 replicates over 2000 years. Changes in the biomass-density trajectory over
 time can be tracked by means of the skewness of the biomass distribution
 (Berger et al. 2002). The skewness of the biomass distribution subdivided
 the biomass-density trajectory into maximum four distinct sections.
 Logarithm of mean plant biomass of survivors <i>w</i> (mg/m²)
 and the logarithm of plant density <i>N</i> (individuals/m²)
 of nineteen soil water scenarios for all ten replicates over 2000
 years.
DOI: 10.5061/dryad.2280gb5pg
title: Data from: Spatial scale, neighbouring plants and variation in plant volatiles interactively determine the strength of host-parasitoid relationships

description: Species-specific responses to the environment can moderate the strength of
 interactions between plants, herbivores and parasitoids. However, the ways
 in which characteristics of plants, such as genotypic variation in
 herbivore induced volatiles (HIPVs) that attract parasitoids, affect
 trophic interactions in different contexts of plant patch size and plant
 neighbourhood is not well understood. We conducted a factorial field
 experiment with white cabbage (Brassica oleracea) accessions that differ
 in the attractiveness of their HIPVs for parasitoids, in the context of
 different patch sizes and presence or absence of surrounding Brassica
 nigra plants. Parasitism rates of experimentally introduced Pieris
 brassicae caterpillars and the presence of naturally occurring Pieris spp.
 caterpillars in the plots were assessed throughout the growing season. The
 abundance of Pieris caterpillars was neither affected by cabbage accession
 nor plot size. Later in the season, when B. nigra plants had senesced,
 fewer caterpillars were found on cabbage plants in plots with a B. nigra
 border. Parasitism rates fluctuated over the season, and were not affected
 by plot size. However, the B. nigra border negatively affected parasitism
 rates on the accession that is less attractive to the parasitoid Cotesia
 glomerata, but not on the more attractive accession. Our results show that
 plant variation in HIPVs can differentially influence herbivores and
 parasitoids depending on characteristics of the surrounding vegetation
 context. These findings underscore the importance of considering the
 interaction between focal plant traits and neighbourhood context to
 reliably predict trophic cascades.
description: Herbivore abundance Data belonging to the
 monitoring of naturally occuring <em>Pieris rapae</em>
 caterpillars. Count data of Pieris rapae caterpillars in different field
 cabbage plots during mid-season and late-season. See read me file for
 explanation of the columns.
 AartsmaHerbivoreAbundanceOikos.csv Parasitism
 rates Data belonging to the parasitism monitoring
 experiment, in which parasitism of experimentally introduced
 <em>Pieris brassicae</em> caterpillars by naturally occuring
 parasitoids was assessed. See read me file for explanation of the
 columns. AartsmaParasitismAnalysisOikos.csv
 Superparasitism rates Separate file in which
 egg counts of parasitized recollected <em>P. brassicae</em>
 caterpillars from the parasitism experiment are specified per individual
 caterpillar. See read me file for explanation of the columns.
 AartsmaSuperparasitismAnalysisOikos.csv
DOI: 10.5061/dryad.r7sqv9s8n
title: Data from: Local soil legacy effects in a multi-species grassland community are underlain by root foraging and soil nutrient availability

description: 1. Plant soil legacies consisting of species-specific microbial
 communities are hypothesized to play a critical, structuring role in plant
 species co-existence processes. Plant species are thought to perform worse
 on soil conditioned by the same species compared to soil of other species,
 which serves as a self-limitation mechanism and averts mono-dominance of
 strong competitors. Here we test in a multi-species community setting,
 whether root colonisation and resource utilisation of soil patches with
 distinct soil legacies, are consistent with this hypothesis. 2. We grew
 eight grassland species together in an outdoor mesocosm setup in
 unconditioned soil and created soil patches in these communities
 conditioned by one of four plant species, or a soil mixture of all four.
 During two subsequent growing seasons, we tested the effect of these
 conditioned soil patches on belowground root colonisation into the patches
 of each surrounding plant species using a novel sequencing based approach.
 In addition, we tested the effect of soil conditioning on local root
 functioning by injecting tracers into the soil patches and measuring the
 recovery in aboveground biomass. 3. Against expectations, plant species
 did not place less roots in own soil patches compared to foreign soil
 patches, nor did species take up less tracer from own compared to foreign
 soil patches. Using structural equation modelling, we found that tracer
 uptake of the plant species was to a varying degree explained by root
 densities in the various soil patches and by differing soil nutrient
 availability of the soil patches. We conclude that soil legacy effects are
 inextricably connected to soil nutrient availability, which needs to be
 taken into account in plant-soil feedback research to understand the
 processes that shape plant communities. 4. Synthesis. We found that soil
 legacy effects in complex, multi-species semi-field conditions did not
 match expectations based on theory and experiments in controlled
 conditions. Among the many complicating factors that may modify or even
 overrule soil legacy effects in semi-field settings, we identified soil
 nutrient availability as a critical force that may, together with soil
 biota, shape plant species co-existence processes.
DOI: 10.5061/dryad.cc2fqz642
title: Data from: Expressed mutational load increases towards the edge of a species’ geographic range

description: There is no general explanation for why species have restricted geographic
 distributions. One hypothesis posits that range expansion or increasing
 scarcity of suitable habitat result in accumulation of mutational load due
 to enhanced genetic drift, which constrains population performance towards
 range limits and further expansion. We tested this hypothesis in the North
 American plant, Arabidopsis lyrata. We experimentally assessed mutational
 load by crossing plants of 20 populations from across the entire species
 range and by raising the offspring of within- and between-population
 crosses at five common garden sites within and beyond the range. Offspring
 performance was tracked over three growing seasons. The heterosis effect,
 depicting expressed mutational load, was increased in populations with
 heightened genomic estimates of load, longer expansion distance or
 long-term isolation, and a selfing mating system. The decline in
 performance of within-population crosses amounted to 80%. Mutation
 accumulation due to past range expansion and long-term isolation of
 populations in the area of range margins is therefore a strong determinant
 of population-mean performance, and the magnitude of effect may be
 sufficient to cause range limits.
description: We crossed plants of 20 populations from across the entire range
 of the North American plant,<i> Arabidopsis lyrata, </i>and
 raised the offspring of within- and between-population crosses at five
 common garden sites within and beyond the range. Offspring performance was
 tracked over three growing seasons.
DOI: 10.5061/dryad.wm37pvmjz
title: Data from: The molecular basis of venom resistance in a rattlesnake-squirrel predator-prey system

description: Understanding how interspecific interactions mould the molecular basis of
 adaptations in coevolving species is a long-sought goal of evolutionary
 biology. Venom in predators and venom resistance proteins in prey are
 coevolving molecular phenotypes, and while venoms are highly complex
 mixtures it is unclear if prey respond with equally complex resistance
 traits. Here we use a novel molecular methodology based on protein
 affinity columns to capture and identify candidate blood serum resistance
 proteins (‘Venom Interactive Proteins’ – VIPs) in California Ground
 Squirrels (Otospermophilus beecheyi) that interact with venom proteins
 from their main predator, Northern Pacific Rattlesnakes (Crotalus o.
 oreganus). This assay showed that serum-based resistance is both
 population- and species-specific, with serum proteins from ground
 squirrels showing higher binding affinities for venom proteins of local
 snakes compared to allopatric individuals. Venom protein specificity
 assays identified numerous and diverse candidate prey resistance VIPs but
 also potential targets of venom in prey tissues. Many specific VIPs bind
 to multiple snake venom proteins and, conversely, single venom proteins
 bind multiple VIPs, demonstrating that a portion of the squirrel blood
 serum “resistome” involves broad-based inhibition of non-self proteins and
 suggests that resistance involves a toxin scavenging mechanism. Analyses
 of rates of evolution of VIP protein homologs in related mammals show that
 most of these proteins evolve under purifying selection possibly due to
 molecular constraints that limit the evolutionary responses of prey to
 rapidly evolving snake venom proteins. Our method represents a general
 approach to identify specific proteins involved in coevolutionary
 interactions between species at the molecular level.
description: Two datasets are included in this submission. One, a summary of
 proteomics data generated from ground squirrel serum and rattlesnake venom
 protein-based protein affinity columns (see Fig. 1 in Gibbs et al. 2020
 for a description of the experimental design used to generate these data).
 Two, a zipped file containing data and scripts used for PAML analyses of
 inferred Venom Interative Proteins (VIPs) (See enclosed README file for
 individual file descriptions).
DOI: 10.5061/dryad.sqv9s4n1r
title: Data from: The edaphic control of plant diversity

description: BACKGROUND: The central thesis of plant ecology is that climate determines
 the distribution of global vegetation. Within a vegetation type, however,
 finer-scale environmental features such as the physical and chemical
 properties of soil (edaphic variation) control plant distributions and
 diversity patterns. AIMS: Here, we review the literature to provide a
 mechanistic framework for the edaphic control of plant diversity. First,
 we review three examples where soils have known, prevalent effects on
 plant diversity: during soil formation, on unusual soils, and in regions
 with high edaphic heterogeneity. Second, we synthesize how edaphic factors
 mediate the relative importance of the four key processes of community
 assembly (speciation, ecological drift, dispersal, and niche selection).
 Third, we review the potential effects of climate change in edaphically
 heterogeneous regions. Finally, we outline key knowledge gaps for
 understanding the edaphic control of plant diversity. In our review, we
 emphasize floras of unusual edaphic areas (i.e., serpentine, limestone,
 granite), as these areas disproportionately contribute to the world’s
 biodiversity hotspots. TAXA: Terrestrial plants LOCATION: Global
 CONCLUSION: Edaphic variation is a key driver of biodiversity patterns and
 influences the relative importance of speciation, dispersal, ecological
 drift, niche selection, and interactions among these processes. Research
 is still needed to better understand the underlying mechanisms by which
 edaphic variation influences these community assembly processes, and
 unusual soils provide excellent natural systems for such tests.
 Furthermore, incorporating edaphic variation into climate change research
 will help increase the predictive power of species distribution models,
 help identify potential climate refugia, and help identify species with
 adaptations that buffer them from climate change.
description: Global distribution of serpentine outcrops compiled from Brooks
 (1987); Roberts & Proctor (1992), and other published studies. For
 some locations, the landmark represents the closest named geographical
 location (e.g., province, municipality, etc.).
DOI: 10.5061/dryad.m905qftz8
title: Data from: Age-related variation in the trophic characteristics of a marsupial carnivore, the Tasmanian devil Sarcophilus harrisii

description: Age-related changes in diet have implications for competitive interactions
 and for predator-prey dynamics, affecting individuals and groups at
 different life stages. To quantify patterns of variation and ontogenetic
 change in the diets of Tasmanian devils Sarcophilus harrisii, a threatened
 marsupial carnivore, we analysed variation in the stable isotope
 composition of whisker tissue samples taken from 91 individual devils from
 Wilmot, Tasmania from December 2014 to February 2017. Both δ¹³C and δ¹⁵N
 decreased with increasing age in weaned Tasmanian devils, indicating that
 as they age devils rely less on small mammals and birds, and more on large
 herbivores. Devils &lt;12 months old had broader group isotopic
 niches, as estimated by Bayesian standard ellipses (SEAB mode = 1.042)
 than devils from 12-23 months old (mode = 0.541) and devils ≥24 months old
 (mode = 0.532. Devils &lt;24 months old had broader individual
 isotopic niches (SEAB mode range 0.492-1.083) than devils ≥24 months old
 (mode range 0.092-0.240). A decrease in δ¹⁵N from the older whisker
 sections to the more recently grown sections in devils &lt;24 months
 old likely reflects the period of weaning in this species, as this pattern
 was not observed in devils ≥24 months old. Our data reveal changes in the
 isotopic composition of devil whiskers with increasing age, accompanied by
 a reduction in isotopic variation both among population age classes and
 within individuals, reflecting the effect of weaning in early life, and a
 likely shift from an initially diverse diet of small mammals, birds and
 invertebrates towards increasing consumption of larger herbivores in
 adulthood.
description: Stable isotope analyses of whiskers collected from wild Tasmanian
 devils Sarcophilus harrisii.
description: See ReadMe.txt file
DOI: 10.5061/dryad.r4xgxd292
title: Data from: High environmental stress and productivity increase functional diversity along a deep-sea hydrothermal vent gradient

description: Productivity and environmental stress are major drivers of multiple
 biodiversity facets and faunal community structure. Little is known on
 their interacting effects on early community assembly processes in the
 deep sea (&gt;200 m), the largest environment on Earth. However, at
 hydrothermal vents productivity correlates, at least partially, with
 environmental stress. Here, we studied the colonization of rock substrata
 deployed along a deep-sea hydrothermal vent gradient at four sites with
 and without direct influence of vent fluids at 1700 m depth in the Lucky
 Strike vent field (Mid-Atlantic Ridge, MAR). We examined in detail the
 composition of faunal communities (&gt;20 m) established after two
 years and evaluated species and functional patterns. We expected the
 stressful hydrothermal activity to (1) limit functional diversity and (2)
 filter for traits clustering functionally similar species. However, our
 observations did not support our hypotheses. On the contrary, our results
 show that hydrothermal activity enhanced functional diversity. Moreover,
 despite high species diversity, environmental conditions at surrounding
 sites appear to filter for specific traits, thereby reducing functional
 richness. In fact, diversity in ecological functions may relax the effect
 of competition allowing several species to coexist in high densities in
 the reduced space of the highly-productive vent habitats under direct
 fluid emissions. We suggest that the high productivity at fluid-influenced
 sites supports higher functional diversity and traits that are more
 energetically expensive. The presence of exclusive species and functional
 entities led to a high turnover between surrounding sites. As a result,
 some of these sites contributed more than expected to the total species
 and functional β-diversities. The observed faunal overlap and energy links
 (exported productivity) suggest that rather than operating as separate
 entities, habitats with and without influence of hydrothermal fluids may
 be considered as interconnected entities. Low functional richness and
 environmental filtering suggests that surrounding areas, with their very
 heterogeneous species and functional assemblages, may be especially
 vulnerable to environmental changes related to natural and anthropogenic
 impacts, including deep-sea mining.
description: For additional information, please refer to the corresponding
 author.
DOI: 10.15468/dl.wtwhxu
title: Occurrence Download

description: A dataset containing 402 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Baphiopsis parviflora",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 402 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002407-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.h44j0zpgx
title: Data from: Travel with your kin ship! Insights from genetic sibship among settlers of a coral damselfish

description: Coral reef fish larvae are tiny, exceedingly numerous, and hard to track.
 They are also highly capable, equipped with swimming and sensory abilities
 that may influence their dispersal trajectories. Despite the importance of
 larval input to the dynamics of a population, we remain reliant on
 indirect insights to the processes influencing larval behavior and
 transport. Here, we used genetic data (300 independent single nucleotide
 polymorphisms) derived from a light trap sample of a single recruitment
 event of Dascyllus abudafur in the Red Sea (N = 168 settlers). We analyzed
 the genetic composition of the larvae and assessed whether kinship among
 these was significantly different from random as evidence for cohesive
 dispersal during the larval phase. We used Monte Carlo simulations of
 similar‐sized recruitment cohorts to compare the expected kinship
 composition relative to our empirical data. The high number of siblings
 within the empirical cohort strongly suggests cohesive dispersal among
 larvae. This work highlights the utility of kinship analysis as a means of
 inferring dynamics during the pelagic larval phase.
description: Genotypes of recruiting <em>Dascyllus abudafur
 </em>from the Red Sea based on 300 single nucleotide polymorphisms
 (SNPs) obtained with ddRAD next generation sequencing.
DOI: 10.5061/dryad.zs7h44j63
title: Wolbachia infection in wild mosquitoes (Diptera: Culicidae): Implications for transmission modes and host-endosymbiont associations in Singapore

description: Background: Wolbachia are intracellular bacterial endosymbionts found in
 most insect lineages. In mosquitoes, the influence of these endosymbionts
 on host reproduction and arboviral transmission has spurred numerous
 studies aimed at using Wolbachia infection as a vector control technique.
 However, there are several knowledge gaps in the literature and little is
 known about natural Wolbachia infection across species, their transmission
 modes, or associations between various Wolbachia lineages and their hosts.
 This study aims to address these gaps by exploring mosquito-Wolbachia
 associations and their evolutionary implications. Methods: We conducted
 tissue-specific polymerase chain reaction screening for Wolbachia
 infection in the leg, gut and reproductive tissues of wild mosquitoes from
 Singapore using the Wolbachia surface protein gene (wsp) molecular marker.
 Mosquito-Wolbachia associations were explored using three methods—
 tanglegram, distance-based, and event-based methods—and by inferred
 instances of vertical transmission and host shifts. Results: Adult
 mosquitoes (271 specimens) representing 14 genera and 40 species were
 screened for Wolbachia. Overall, 21 species (51.2%) were found positive
 for Wolbachia, including five in the genus Aedes and five in the genus
 Culex. To our knowledge, Wolbachia infections have not been previously
 reported in seven of these 21 species: Aedes nr. fumidus, Aedes
 annandalei, Uranotaenia obscura, Uranotaenia trilineata, Verrallina
 butleri, Verrallina sp. and Zeugnomyia gracilis. Wolbachia were
 predominantly detected in the reproductive tissues, which is an indication
 of vertical transmission. However, Wolbachia infection rates varied widely
 within a mosquito host species. There was no clear signal of cophylogeny
 between the mosquito hosts and the 12 putative Wolbachia strains observed
 in this study. Host shift events were also observed. Conclusions: Our
 results suggest that the mosquito-Wolbachia relationship is complex and
 that combinations of transmission modes and multiple evolutionary events
 likely explain the observed distribution of Wolbachia diversity across
 mosquito hosts. These findings have implications for a better
 understanding of the diversity and ecology of Wolbachia and for their
 utility as biocontrol agents.