cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0576m4r
title: Data from: Environmental filtering underpins the island species–area relationship in a subtropical anthropogenic archipelago

description: 1. Numerous mechanisms have been proposed to explain the island
 species-area relationship (ISAR), including the passive sampling effect,
 the habitat diversity effect, ecological drift and a group of mechanisms
 jointly termed environmental filtering (or abiotic selection process).
 However, determining which of these hypotheses underpins the ISAR in a
 given system remains an open and controversial question, particularly with
 regards to the environmental filtering. 2. The effect of environmental
 filtering on the ISAR for woody plants was tested on 29 islands in a
 subtropical land-bridge archipelago. Island area had a significant effect
 on species richness, while isolation was not found to have an effect.
 After controlling for the passive sampling effect and habitat diversity
 using a systematic sampling design, we found that a positive ISAR
 remained. 3. After controlling for island area and isolation, species
 richness was significantly affected by environmental conditions (e.g.
 total phosphorus, soil depth and bulk density). 4. When a null model was
 used that randomly assigned individuals to islands from the regional pool,
 the difference between the observed and expected richness was greater for
 smaller islands relative to larger islands. 5. Synthesis. Our results
 point to an overlooked role of environmental filtering in driving the
 ISAR. Consequently, our study highlights the importance of considering
 deterministic process in future analyses of the ISAR.
description: The data of island
 attributes and species diversity on the 29 islands in the Thousand Island
 LakeIsland
 attributes and species diversity on 29
 islands.csvThe environment
 variables on 29 islands in the Thousand Island LakeEnvironment variables on 29
 islands.csv
DOI: 10.5061/dryad.sr83ph7
title: Data from: Towards a predictive framework for biocrust mediation of plant performance: a meta-analysis

description: Understanding the importance of biotic interactions in driving the
 distribution and abundance of species is a central goal of plant ecology.
 Early vascular plants likely colonized land occupied by biocrusts —
 photoautotrophic, surface-dwelling soil communities comprised of
 cyanobacteria, bryophytes, lichens, and fungi — suggesting biotic
 interactions between biocrusts and plants may have been at play for some
 2,000 million years. Today, biocrusts coexist with plants in dryland
 ecosystems worldwide, and have been shown to both facilitate or inhibit
 plant species performance depending on ecological context. Yet, the
 factors that drive the direction and magnitude of these effects remain
 largely unknown. We conducted a meta-analysis of plant responses to
 biocrusts using a global dataset encompassing 1,004 studies from six
 continents. Our meta-analysis revealed there is no simple positive or
 negative effect of biocrusts on plants. Rather, plant responses differ by
 biocrust composition and plant species traits and vary across plant
 ontogeny. Moss-dominated biocrusts facilitated, while lichen-dominated
 biocrusts inhibited overall plant performance. Plant responses also varied
 among plant functional groups: C4 grasses received greater benefits from
 biocrusts compared to C3 grasses, and plants without N-fixing symbionts
 responded more positively to biocrusts than plants with N-fixing
 symbionts. Biocrusts decreased germination but facilitated growth of
 non-native plant species. Our results suggest that interspecific variation
 in plant responses to biocrusts, contingent on biocrust type, plant
 traits, and ontogeny can have strong impacts on plant species performance.
 These findings have important implications for understanding plant
 community assembly processes and ecosystem responses to global change.
description: BSC-Plant
 DatabaseDataset used in
 multi-factor meta-analyses (i.e., overall plant performance, germination,
 survival, growth, cover) and univariate meta-regression models in Havrilla
 et al. (2019). Columns G-K indicate whether or not a particular study
 (row) was utilized in a particular analysis group. Columns L-U contain
 effect sizes (log response ratios) and variance estimates (ESTVAR3) for
 the five analyses. Full citations for each publication can be found in
 Appendix S2. Columns Z-AG contain the eight candidate explanatory
 predictor variables. See text for detailed description of each variable
 (Table 1). Columns AH-AK contain additional plant species information.
 Columns AL-AP contain geographic and climatic
 information.BSC_PLANT_Database.xlsx
DOI: 10.5061/dryad.1512pn3
title: Data from: Exploring evolution and diversity of Chinese Dipterocarpaceae using next-generation sequencing

description: Tropical forests, a key-category of land ecosystems, are faced with the
 world’s highest levels of habitat conversion and associated biodiversity
 loss. In tropical Asia, Dipterocarpaceae are one of the economically and
 ecologically most important tree families, but their genomic diversity and
 evolution remain understudied, hampered by a lack of available genetic
 resources. Southern China represents the northern limit for
 Dipterocarpaceae, and thus changes in habitat ecology, community
 composition and adaptability to climatic conditions are of particular
 interest in this group. Phylogenomics is a tool for exploring both
 biodiversity and evolutionary relationships through space and time using
 plastome, nuclear and mitochondrial genome. We generated full plastome and
 Nuclear Ribosomal Cistron (NRC) data for Chinese Dipterocarpaceae species
 as a first step to improve our understanding of their ecology and
 evolutionary relationships. We generated the plastome of Dipterocarpus
 turbinatus, the species with the widest distribution using it as a
 baseline for comparisons with other taxa. Results showed low level of
 genomic diversity among analysed range-edge species, and different
 evolutionary history of the incongruent NRC and plastome data. Genomic
 resources provided in this study will serve as a starting point for future
 studies on conservation and sustainable use of these dominant forest taxa,
 phylogenomics and evolutionary studies.
description: DNA_sequences_DipterocarpaceGFF files with annotations of the Dipterocarpaceae playtimes and NRC used in the analyses
DOI: 10.5061/dryad.fm129s7
title: Data from: Testosterone modulates status-specific patterns of cooperation in a social network

description: Stable cooperation requires plasticity whereby individuals are able to
 express competitive or cooperative behaviors depending on social context.
 To date, however, the physiological mechanisms that underlie behavioral
 variation in cooperative systems are poorly understood. We studied
 hormone-mediated behavior in the wire-tailed manakin (Pipra filicauda), a
 gregarious songbird whose cooperative partnerships are crucial for
 fitness. We used automated telemetry to monitor &gt; 36,000
 cooperative interactions among male manakins over three field seasons, and
 we examined how circulating testosterone affects cooperation using
 &gt; 500 hormone samples. Observational data show that in
 non-territorial floater males, high testosterone is associated with
 increased cooperative behaviors and subsequent ascension to territorial
 status. In territory-holding males, however, both observational and
 experimental evidence demonstrate that high testosterone antagonizes
 cooperation. Moreover, circulating testosterone explains significant
 variation (2-8%) in social behavior within each status class.
 Collectively, our findings show that the hormonal control of cooperation
 depends on a male’s social status. We propose that the status-dependent
 reorganization of hormone-regulatory pathways can facilitate stable
 cooperative partnerships, and thus provide direct fitness benefits for
 males.
description: Data files and analysis
 scriptsRaw data on social
 interactions and testosterone levels plus R scripts with annotated
 analysisdata files and
 analysis.zip
DOI: 10.5061/dryad.4mv6600
title: Data from: Scalable, semi-automated fluorescence reduction neutralization assay for qualitative assessment of Ebola virus-neutralizing antibodies in human clinical samples

description: Antibody titers against a viral pathogen are typically measured using an
 antigen binding assay, such as an enzyme-linked immunosorbent assay
 (ELISA), which only measures the ability of antibodies to identify a viral
 antigen of interest. Neutralization assays measure the presence of
 virus-neutralizing antibodies in a sample. Traditional neutralization
 assays, such as the plaque reduction neutralization test (PRNT), are often
 difficult to use on a large scale due to being both labor and resource
 intensive. Here we describe an Ebola virus fluorescence reduction
 neutralization assay (FRNA), which tests for neutralizing antibodies, that
 requires only a small volume of sample in a 96-well format and is easy to
 automate. The readout of the FRNA is the percentage of Ebola
 virus-infected cells measured with an optical reader or overall
 chemiluminescence that can be generated by multiple reading platforms and
 the readout is compatible with lytic and non-lytic viruses. Using blinded
 human clinical samples (EVD survivors or contacts) obtained in Liberia
 during the 2013–2016 Ebola virus disease outbreak, we demonstrate that
 FRNA-measured antibody titers are highly correlated with those measured by
 the Filovirus Animal Non-clinical Group (FANG) ELISA - the current
 standard for anti-EBOV antibody measurement with the important distinction
 of providing information on the neutralizing capabilities of the
 antibodies.
description: FDA-FRNA50-07MAR17_plosOperetta and chemiluminescent raw data
DOI: 10.5061/dryad.625397j
title: Data from: Anti-parasite treatment results in decreased estimated survival with increasing Pb levels in the common eider Somateria mollissima

description: Field experiments where parasites are removed through treatment and
 contaminant levels in host tissues are recorded can provide insight into
 the combined effects of parasitism and contaminants in wild populations.
 In 2013 and 2014, we treated northern common eider ducks (Somateria
 mollissima) arriving at a breeding colony with either a broad-spectrum
 antihelminthic (PANACUR®) or distilled water, and measured their blood Pb
 levels. Breeding propensity and clutch sizes were inversely related to Pb
 in both treatment groups. In comparison, a negative effect of Pb on
 resight probability the following year was observed only in the
 anti-parasitic treatment (APT) group. These contrasting patterns suggest a
 long-term benefit to survival of intestinal parasitism in eiders
 experiencing Pb exposure. Arrival date of hens explained some, but not
 all, of the effects of Pb. We weigh the merits of different hypotheses in
 explaining our results, including protective bioaccumulation of Pb by
 parasites, condition-linked thresholds to costly reproduction, and the
 direct effects of APT on eider health. We conclude that variation in
 helminth parasitism influences survival in this migratory bird in
 counterintuitive ways.
description: Raw data - Common eider
 Pb, condition, reproduction, and survival metricsRaw data upon which
 analyses are based in the study "Anti-parasite treatment results in
 decreased estimated survival with increasing Pb levels in the common eider
 Somateria mollissima." Blood Pb levels, condition measures,
 reproduction metrics, returns to the colony, and additional measures are
 provided for all common eiders in both years, and for both experimental
 treatments (PANACUR® and distilled water).Supplementary - raw
 data.csv
DOI: 10.5061/dryad.mr98sp1
title: Data from: Rainfall-dependent impacts of threatened ecosystem engineers on organic matter cycling

description: 1) Species loss is often associated with a decline in ecosystem functions.
 Globally, digging mammals (or ecosystem engineers) are functionally
 important, altering soil processes at local scales. However, their effects
 on the process of decomposition are poorly understood, particularly at
 larger scales, where the environment may moderate the magnitude of
 effects. 2) We tested the landscape-scale effects of reintroducing
 ecologically extinct digging mammals on two aspects of nutrient cycling
 over a large environmental gradient in Australia, where many digging
 mammals became extinct or ecologically extinct following the arrival of
 Europeans. 3) We measured the impacts of digging mammals on soil organic
 matter content and plant litter decomposition over a 3000 km transect,
 where annual average rainfall varied between 166 and 877 mm. We set up
 paired study plots (n = 8-10) inside and outside five reintroduction
 reserves. We took soil samples to assess soil organic matter content and
 set up litter bags to measure plant litter decomposition over 4 and 12
 months. We used macro-invertebrate exclusion and control treatments to
 determine the relative importance of macroinvertebrates in decomposition
 with and without digging mammals. 4) Soil organic matter was greater in
 re-introduction areas, but the magnitude of the effect was driven by
 productivity (average annual rainfall as a proxy), with little effect of
 digging activity at the wettest sites. Short-term plant matter
 decomposition was greater in the presence of digging mammals, and their
 effect was dependent on the amount of rain that fell during the study
 period. Long-term litter decomposition increased with annual rainfall,
 independent of digging mammals. Unexpectedly, macroinvertebrate exclusion
 increased decomposition rates over 12 months. 5) Reintroduction of digging
 mammals substantially alters soil processes and organic matter
 decomposition, but impacts are rainfall-dependent. Restoring native
 digging mammals to their historical distribution is likely to reverse
 degradation of ecosystem processes, but the magnitude of this effect
 depends on the environment.
description: decay rates and measured
 properties with descriptionExcel worksheet: sheet
 nr.1 contains the raw data and sheet nr. 2 contains the measured
 variables' descriptions. Rainfall and solar exposure data is sourced
 from the Bureau of Meteorology, Australia; all other data is measured by
 the authors.decay_rates_description.xlsx
DOI: 10.5061/dryad.k0r39vv
title: Data from: Use of normalized difference vegetation index to assess N status and predict grain yield in rice

description: Fine tuning N recommendations requires an understanding of crop N status
 and yield potential early enough in the growing season when changes to N
 management can influence yields. Recent studies have demonstrated the
 ability of Normalized Difference Vegetation Index (NDVI) to assess crop N
 status and predict yield in wheat (Tricticum aestivum L.) and maize (Zea
 mays L.); however, there has been relatively little such research on rice
 (Oryza sativa L.). The objectives of this study were to determine how well
 NDVI measured at the panicle initiation (PI) rice growth stage assesses
 crop N status and predicts final grain yield. Nitrogen response trials
 were established over a 4-yr period (10 site-years) at various locations
 throughout the Sacramento Valley rice growing region of California.
 Additionally, the relationship between NDVI and crop N status was
 characterized across 28 on-farm plots representing a range of
 environmental conditions and management practices. The NDVI at PI was best
 correlated with total N uptake (NUP, r2 = 0.66), followed by N
 concentration (NCONC, r2 = 0.54), and aboveground biomass (AGB, r2 =
 0.51). The utility of NDVI was greatest at lower values of crop N status,
 whereas at higher values, NDVI saturated. The NDVI at PI was positively
 correlated with final grain yield (r2 = 0.58) indicating utility for
 developing in-season yield predictions. While NDVI is a potentially useful
 tool to improve N fertilizer management and develop in-season yield
 predictions in rice, alternative indices that do not saturate would likely
 provide a basis for a better tool.
description: yield_dataN_trial_datagreenseeker_comparisonfarm_survey_data
DOI: 10.5061/dryad.26k70d6
title: Data from: How to estimate complementarity and selection effects from an incomplete sample of species

description: Declines in global biodiversity have inspired a generation of studies that
 seek to characterize relationships between biodiversity and ecosystem
 functioning. The metrics for complementarity and selection effects derived
 by Loreau and Hector in 2001 remain some of the most influential and
 widely used statistics for studying these relationships. These metrics
 quantify the degree to which the effect of biodiversity on a given
 ecosystem function depends on only a few species that perform well in
 monoculture and in mixture (the selection effect) or if the effect of
 biodiversity on a given ecosystem function is independent of monoculture
 performance (the complementarity effect). This distinction may be useful
 in determining the consequences of the loss of rare versus common or
 dominant species in natural systems. However, because these metrics
 require observations of all species in a community in monoculture,
 applications in natural systems have been limited. Here, we derive a
 statistical augmentation of the original partition, which can be applied
 to incomplete random samples of species drawn from a larger pool. This
 augmentation controls for the bias introduced by using only a subsample of
 species in monocultures rather than having monocultures of all species.
 Using simulated and empirical examples, we demonstrate the robustness of
 these metrics, and provide source code for calculating them. We find that
 these augmentations provide a reliable estimate of complementarity and
 selection effects as long as approximately 50% of the species present in
 mixture are present in monoculture and these species represent a random
 subset of the mixture. We foresee two primary applications for this
 method: (a) estimating complementarity and selection effects for
 experimentally assembled communities where monoculture data are lacking
 for some species, and (b) extrapolating results from biodiversity
 experiments to diverse natural systems.
description: READMEDryad_README.txtTable S1Presence/absence data for the semi-natural grasslands, from the large 0.8 x 0.8 m plots used to determine community composition. Data are from Buchmann et al. (2018). Species abbreviations match those used in the Jena Experiment by Weigelt et al. (2016). See article for details.tableS1_sng_pa.csvTable S2Aboveground biomass data for the semi-natural grasslands, from the smaller 0.4 x 0.4 m plots used to determine species abundance in mixture. Reported in gm-2 dried mass. Data are from Buchmann et al. (2018). Species abbreviations match those used in the Jena Experiment by Weigelt et al. (2016). See article for details.tableS2_sng_bm.csv
DOI: 10.5061/dryad.nd57201
title: Data from: Experimental reduction of plant abundance changes interaction frequency of a tri-trophic micro-food web: contrasting responses of generalists and specialists

description: 1. Species abundance is vulnerable to climate change and anthropogenic
 impact. Although numerous studies have examined the food web response to
 species loss, their response (e.g. in network topology and interaction
 frequency) to changes in species abundance has received little attention.
 2. We experimentally reduced the abundance (by ca. 60%) of one host plant
 species (Saussurea nigrescens) in a tri-trophic micro-food web consisting
 of two common Asteraceae species (S. nigrescens and Anaphalis flavescens),
 their pre-dispersal seed predators (tephritid flies), and the parasitoid
 wasps that feed on these seed predators. 3. The neutral process hypothesis
 posits that network topology and interaction frequency are determined by
 the relative abundances of the participating species. Accordingly, we
 hypothesized that interaction frequency (indicated by the rate of flies
 infesting plants and of parasitoid wasps parasitizing flies) would
 decrease with decreasing abundance of host plant abundance. 4. Consistent
 with the neutral process hypothesis, abundance reduction significantly
 decreased the rate of generalist flies infesting the manipulated plant
 host species, but increased the rate on unmanipulated plant species. In
 contrast, abundance reduction significantly increased the rate of
 specialist flies infesting the manipulated species, but it had no
 demonstrable effect on the specialists on the unmanipulated plant host. 5.
 Moreover, abundance reduction significantly increased the rate of
 parasitoid wasps (as a species group) parasitizing flies in the
 manipulated species but decreased the rate of the unmanipulated species.
 These results were not attributable to neutral processes, but can be
 explained only by adaptive foraging theory. In addition, experimental
 manipulation did not shift the qualitative presence/absence of the
 linkages in the micro-food web, and the change in the abundance of both
 fly and wasp species was smaller than the abundance changes of the
 manipulated plant species. 6. These observations are interpreted to
 indicate that both neutral process and/or adaptive foraging likely
 contributed to food web stability in responses to changes in species
 abundance. Because species abundance is vulnerable to abiotic and biotic
 environmental changes, we suggest more research should be conducted to
 understand how food webs respond to climate change and anthropogenic
 disturbance.
description: The difference in
 fly-plant interaction frequency and parasitoid-fly interaction frequency
 between control and abundance-reduced plotsThe fly-plant
 interaction frequency is shown in the 'fly-plant' sheet, and the
 parasitoid-fly interaction frequency is shown in the
 'parasitoid-fly' sheet. In each sheet, the abundance of each
 partner species is presented.Density reduced
 experiment_Rawdata.xlsx