cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r0q57k3
title: Data from: Functional response of subordinate species to intraspecific trait variability within dominant species

description: 1. Dominant species can act as a biotic filter in structuring plant
 communities by constraining the establishment and survival of subordinate
 species. The effect of intraspecific trait variability of dominant species
 on the functional response of subordinate species, however, is not well
 understood. 2. We quantified intraspecific variation in four functional
 traits of 26 subordinate species established in an experimental grassland
 established with two population sources (i.e., cultivars and local
 ecotypes) of three dominant grasses (Sorghastrum nutans, Andropogon
 gerardii, and Schizachyrium scoparium) and three pools of subordinate
 species (each from one origin) within each of the dominant grass source
 treatments. 3. Twenty of the 26 subordinate species exhibited
 intraspecific trait variability for one trait or more in response to
 dominant species population source, and variation among population sources
 of the dominant species was non-random. Dominant grass population source
 affected intraspecific variability in functional traits of multiple
 subordinate species. Cultivar sources of the dominant grasses and some of
 the subordinate species that established with them had higher and
 generally more variable functional leaf area and leaf nitrogen content
 compared to local ecotypes of the dominant grasses and the subordinate
 species that established with them. 4. Synthesis. This study provides
 evidence that intraspecific trait variability in dominant species acts as
 an inner, biotic filter to constrain niche availability and dimensionality
 affecting trait variation of subordinate species during community
 assembly.
description: Khalil_Plant traits
 dataPlant trait datafile for
 29 species growing in either cultivar or local ecotype plots. Data are
 provided for four functional traits. See the README file for
 details.Species Cover data
 2006-2015Date are % canopy cover
 for species (columns I-AK) from 2006-2015. Columns A-F (see column
 headers) specify quadrat location in the field experiment (See Methods and
 Figure S1) where column C Population indicates 1 = Cultivar plot, 2 =
 Local Ecotype plot. Column H Plot-Code is based upon entries in columns
 A-G.Khalil_Species cover data
 2006-2015-full.csv
DOI: 10.5061/dryad.252b9n4
title: Data from: Gene expression correlates of facultative predation in the blow fly Chrysomya rufifacies (Diptera: Calliphoridae)

description: Effects of intraguild predation (IGP) on omnivores and detritivores are
 relatively understudied when compared to work on predator guilds.
 Functional genetic work in IGP is even more limited, but its application
 can help answer a range of questions related to ultimate and proximate
 causes of this behavior. Here we integrate behavioral assays and
 transcriptomic analysis of facultative predation in a blow fly (Diptera:
 Calliphoridae) to evaluate the prevalence, effect, and correlated gene
 expression of facultative predation by the invasive species Chrysomya
 rufifacies. Field work observing donated human cadavers indicated
 facultative predation by C. rufifacies on the native blow fly Cochliomyia
 macellaria was rare under undisturbed conditions, owing in part to spatial
 segregation between species. Laboratory assays under conditions of
 starvation showed predation had a direct fitness benefit (i.e., survival)
 to the predator. As a genome is not available for C. rufifacies, a de novo
 transcriptome was developed and annotated using sequence similarity to
 Drosophila melanogaster. Under a variety of assembly parameters, several
 genes were identified as being differentially expressed between predators
 and non-predators of this species, including genes involved in
 cell-to-cell signaling, osmotic regulation, starvation responses, and
 dopamine regulation. Results of this work were integrated to develop a
 model of the processes and genetic regulation controlling facultative
 predation.
description: Pimsler_etal.2019.EcologyAndEvolution.DRYAD.tarTar file containing: RawAssemblyFasta.tar.gz (24 raw transcriptome assembles in fasta format), CountNode.tar.gz (Raw read count alignment tables for each node and each library for each of 24 separate assemblies), PredationAnalysis25_100.R (exemplar R script for analysis), and LaboratoryPredationData.xlsx (No-choice predation assay survival results table).
DOI: 10.5061/dryad.vn92f3j
title: Data from: Impacts of microplastic versus natural abiotic particles on the clearance rate of a marine mussel

description: In coastal habitats, mussels are exposed to microplastic (MP; plastic
 &lt;5mm) and silt, two abiotic particles that are similarly sized and
 lack nutrition. The addition of MP or silt may change the functional
 response of mussels. We measured clearance rate of Mytilus trossulus in
 three particle treatments (algae, MP + algae, and silt + algae) across
 four concentrations to 1) determine if the effects of MP and silt are
 similar and 2) disentangle the effects of particle type, particle
 concentration, and proportion of abiotic particles. Clearance rate
 decreased by 62% at high MP concentrations (&gt;1,250 particles/ml)
 but was not affected at equivalent silt concentrations. These findings
 suggest high MP concentrations inhibit mussel clearance rate, more than
 expected by changes in particle concentration or the proportion of abiotic
 particles. As plastic production increases, mussel exposure to MP will
 increase, potentially reducing energy transfer, benthic-pelagic coupling,
 and water clarity.
description: CR.Harris.DataClearance rate information for mussels fed algae, microplastic, and/or silt.MetadataMetadata corresponding to clearance rate data file
DOI: 10.5061/dryad.p7k5582
title: Data from: Acknowledging differences: number, characteristics, and distribution of marine benthic communities along Taiwan coast

description: Our knowledge of the ability of coral reefs to face contemporary
 challenges disregards the wide variety of benthic communities (BCs) that
 could be associated with contrasted dynamics when facing stressors.
 Accordingly, this study investigates the number, characteristics, and
 distribution of BCs responsible for the development of coastal
 three‐dimensional structures in Taiwan. A total of 89 transects among
 three regions (north, east, and south) and two depths (−10 and −40 m) were
 characterized using a morpho‐functional categorization of benthic
 organisms. Using an unsupervised learning algorithm, k‐means cluster, an
 optimal number of k groups were identified among transects in order to
 minimize total intra‐group variance and represent a first level of
 organization, mirroring the number of BCs. Each BC was then described into
 prevailing categories and typified by an association with significant
 indicator groups. Their distributions were further examined and tested
 among regions and depths. Seven BCs were identified as having different
 composition and indicator categories. Their distributions suggest that,
 while sea surface temperature and light regime may be associated with a
 panel of available BCs, local conditions may have the final say on whether
 a BC eventually thrives at a given location. Overall, this study proposes
 an innovative and simple analytical framework for acknowledging
 differences among BCs. Our results encourage greater consideration of
 these shades in coral reef ecology studies, as they could conceal a
 variety of roles and dynamics important for the conservation of these
 endangered ecosystems.
description: Lin&Denis_datasetBenthic data for the 89 transects surveyed at two depths at three regions around TaiwanLin&Denis_scriptR script for analysis
DOI: 10.15468/dl.qwmtj9
title: Occurrence Download

description: A dataset containing 1038 records in GBIF matching the query:
SELECT
 '416' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 37.42857426825602
 AND decimalLatitude &lt;= 41.89415215079384
 AND decimalLongitude &gt;= 74.83335833227108
 AND decimalLongitude &lt;= 83.91704653307544
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 1038 records were derived from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001777-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.hm3v1dm
title: Data from: Gaining ecological insight on dietary allocation among horseshoe bats through molecular primer combination

description: Knowledge on the trophic interactions among predators and their prey is
 important in order to understand ecology and behaviour of animals.
 Traditionally studies on the diet composition of insectivorous bats have
 been based on the morphological identification of prey remains, but the
 accuracy of the results has been hampered due to methodological
 limitations. Lately, the DNA metabarcoding and High Throughput Sequencing
 (HTS) techniques have changed the scene since they allows prey
 identification to the species level, ultimately giving more precision to
 the results. Nevertheless, the use of one single primer set to amplify
 faecal DNA produces biases in the assessed dietary composition. Three
 horseshoe bats overlap extensively in their distribution range in Europe:
 Rhinolophus euryale, R. hipposideros and R. ferrumequinum. In order to
 achieve the deepest insight on their prey list we combined two different
 primers. Results showed that the used primers were complementary at the
 order and species levels, only 22 out of 135 prey species being amplified
 by both. The most frequent prey of R. hipposideros belonged to Diptera and
 Lepidoptera, to Lepidoptera in R. euryale, and Lepidoptera, Diptera and
 Coleoptera in R. ferrumequinum. The three bats show significant resource
 partitioning, since their trophic niche overlap is not higher than 34%.
description: Gillet_otusFasta file of the OTUs built from mini-COI sequences amplified from bat faeces with Gillet primersZeale_otusFasta file of the OTUs built from mini-COI sequences got from bat faeces with Zeale primers
DOI: 10.5061/dryad.5tq5dn6
title: Data from: Warmer temperatures advance flowering in a spring plant more strongly than emergence of two solitary spring bee species

description: Climate warming has the potential to disrupt plant-pollinator interactions
 or to increase competition of co-flowering plants for pollinators, due to
 species-specific phenological responses to temperature. However, studies
 focusing on the effect of temperature on solitary bee emergence and the
 flowering onset of their food plants under natural conditions are still
 rare. We studied the effect of temperature on the phenology of the two
 spring bees Osmia cornuta and Osmia bicornis, by placing bee cocoons on
 eleven grasslands differing in mean site temperature. On seven grasslands,
 we additionally studied the effect of temperature on the phenology of the
 red-list plant Pulsatilla vulgaris, which was the first flowering plant,
 and of co-flowering plants with later flowering. With a warming of 0.1 °C,
 the abundance-weighted mean emergence of O. cornuta males advanced by 0.4
 days. Females of both species did not shift their emergence. Warmer
 temperatures advanced the abundance-weighted mean flowering of P. vulgaris
 by 1.3 days per 0.1 °C increase, but did not shift flowering onset of
 co-flowering plants. Competition for pollinators between P. vulgaris and
 co-flowering plants does not increase within the studied temperature
 range. We demonstrate that temperature advances plant flowering more
 strongly than bee emergence suggesting an increased risk of pollinator
 limitation for the first flowers of P. vulgaris.
description: Julian date of emergence
 of Osmia cornuta, Osmia bicornis and flowering of Pulsatilla
 vulgarisJulian date of first,
 abundance-weighted mean and last emergence of O. cornuta and O. bicornis
 males and females and of first, abundance-weighted mean and last flowering
 of P. vulgaris. Number of emerged O. cornuta and O. bicornis males and
 females, maximum number of P. vulgaris flowers on transect, Julian date of
 first other than P. vulgaris flowering plant and site
 temperature.Dryad_Manuscript_PLOSONE.xlsx
DOI: 10.5061/dryad.h8f22dh
title: Data from: Mycorrhizal network assembly in a community context: the presence of neighbours matters

description: 1. Understanding the factors and mechanisms driving the structure of
 ecological networks is a challenge for community ecologists. Notably, it
 remains unclear whether observed interaction patterns between two trophic
 groups are a result of (1) preferential partner selection between groups,
 or (2) species interactions within groups. 2. We conducted an experiment
 in order to disentangle these two drivers, using the plant-mycorrhizal
 symbiosis as a model system. We followed mycorrhizal colonization of plant
 roots growing either with or without neighbours. This allowed us to assess
 the relative importance of interaction within trophic groups (here,
 plant-to-plant interactions) on ecological network assembly. 3. Results
 showed that plants were not equally affected by the presence of neighbours
 and that network nestedness was higher when plants grew without
 neighbours. We also found a poor correlation between the centrality (i.e.
 standardized number of interactions) of plant species grown in communities
 and those grown without neighbours, while the reverse was true for
 mycorrhizal fungi. This suggests that the optimum level of specificity or
 generalism in mycorrhizal selection is not a fixed plant trait, but a
 plastic, context-dependent one. 4. Synthesis. Our results show that
 ecological networks are not only shaped by preferential partner selection,
 but also by interactions within a given trophic group. This finding should
 be considered in future modelling exercises on ecological network
 dynamics. Moreover, our nestedness results suggest that in the presence of
 multiple host plants, mycorrhizal fungi display preferences for specific
 interactions, suggesting that local plant diversity may shape mycorrhizal
 fungal community structure.
description: DRYAD_2019-06-13Raw interaction data between plants and AM fungi
DOI: 10.5061/dryad.2np959c
title: Data from: The invariant nature of a morphological character and character state: insights from gene regulatory networks

description: What constitutes a discrete morphological character versus character state
 has been long discussed in the systematics literature but the consensus on
 this issue is still missing. Different methods of classifying organismal
 features into characters and character states can dramatically affect the
 results of phylogenetic analyses. Here, I show that, in the framework of
 Markov models, the modular structure of the gene regulatory network (GRN)
 underlying trait development, and the hierarchical nature of GRN
 evolution, essentially remove the distinction between morphological
 character and character state, thus endowing the character and character
 state with an invariant property with respect to each other. This property
 allows the states of one character to be represented as several individual
 characters and vice versa. In practice, this means that a phenotype can be
 encoded using a set of characters or just one complex character with
 numerous states. The representation of a phenotype using one complex
 character can be implemented in Markov models of trait evolution by
 properly structuring transition rate matrix.
description: Supplementary_Materials_scriptsSupplementary materials and Appendix
DOI: 10.5061/dryad.69325t8
title: Data from: Shifts in phenological mean and synchrony interact to shape competitive outcomes

description: Climate change-induced phenological shifts are ubiquitous and have the
 potential to disrupt natural communities by changing the timing of species
 interactions. Shifts in first and/or mean phenological date are well
 documented, but recent studies indicate that shifts in synchrony
 (individual variation around these metrics) can be just as common.
 However, we know little about how both types of phenological shifts
 interact to affect species interactions and natural communities. Here, we
 experimentally manipulated the hatching phenologies of two competing
 species of larval amphibians to address this conceptual gap. Specifically,
 we manipulated the relative mean hatching time (early, same, or late
 relative to competitor) and population synchrony (high, medium, or low
 levels of variation around the mean) in a full 3x3 factorial design to
 measure independent and interactive effects of phenological mean and
 population phenological synchrony on competitive outcomes. Our results
 indicate that phenological synchrony within a population strongly
 influences intraspecific competition by changing the density of
 individuals and relative strength of early vs. late arriving individuals.
 Individuals from high synchrony populations competed symmetrically while
 individuals from low synchrony populations competed asymmetrically. At the
 community scale, shifts in population phenological synchrony interact with
 shifts in phenological mean to strongly affect key demographic rates
 (survival, biomass export, per capita mass, and emergence timing).
 Furthermore, changes in mean timing of species interactions altered
 phenological synchrony within a population at the next life stage, and
 phenological synchrony at one life stage altered the mean timing of the
 next life stage. Thus, shifts in phenological synchrony within populations
 can not only alter species interactions but species interactions in turn
 can also drive shifts in phenology.
description: CarterRudolf_Dryaddata on experimental communities of amphibians testing effects of shifts in hatching timing/phenology on competitive outcomes
DOI: 10.5061/dryad.hh7qf78
title: Data from: Widespread epigenetic changes to the enhancer landscape of mouse liver induced by a specific xenobiotic agonist ligand of the nuclear receptor CAR

description: CAR (Nr1i3), a liver nuclear receptor and xenobiotic sensor, induces drug,
 steroid and lipid metabolism and dysregulates genes linked to
 hepatocellular carcinogenesis, but its impact on the liver epigenome is
 poorly understood. TCPOBOP, a halogenated xenochemical and highly specific
 CAR agonist ligand, induces localized chromatin opening or closing at
 several thousand mouse liver genomic regions, discovered as differential
 DNase-hypersensitive sites (ΔDHS). Active enhancer and promoter histone
 marks induced by TCPOBOP were enriched at opening DHS and
 TCPOBOP-inducible genes. Enrichment of CAR binding and CAR motifs was seen
 at opening DHS and their inducible drug/lipid metabolism gene targets, and
 at many constitutively open DHS located nearby. TCPOBOP-responsive cell
 cycle and DNA replication genes co-dependent on MET/EGFR signaling for
 induction were also enriched for CAR binding. A subset of opening DHS and
 many closing DHS mapping to TCPOBOP-responsive target genes did not bind
 CAR, indicating an indirect mechanism for their changes in chromatin
 accessibility. TCPOBOP-responsive DHS were also enriched for induced
 binding of RXRA, CEBPA and CEBPB, and for motifs for liver-enriched
 factors that may contribute to liver-specific transcriptional responses to
 TCPOBOP exposure. These studies elucidate the enhancer landscape of
 TCPOBOP-exposed liver and the widespread epigenetic changes that are
 induced by both direct and indirect mechanisms linked to CAR activation.
 The global maps of thousands of environmental chemical-induced epigenetic
 changes described here constitute a rich resource for further research on
 xenochemical effects on liver chromatin states and the epigenome.
description: Supplemental_Figs_S1_to_S13_Rampersaud_ToxSci_2019Supplemental Figures S1 to S13, related to Rampersaud et al, Toxicological Sciences, 2019Table_S1_Rampersaud_ToxSci_2019Supplemental Table S1, related to Rampersaud et al, Toxicological Sciences, 2019Table_S2AB_Rampersaud_ToxSci_2019Supplemental Table S2AB, related to Rampersaud et al, Toxicological Sciences, 2019Table_S2CDE_Rampersaud_ToxSci_2019Supplemental Table S2CDE, related to Rampersaud et al, Toxicological Sciences, 2019Table_S2FGHI_Rampersaud_ToxSci_2019Supplemental Table S2FGHI, related to Rampersaud et al, Toxicological Sciences, 2019Table_S3_Rampersaud_ToxSci_2019Supplemental Table S3, related to Rampersaud et al, Toxicological Sciences, 2019Table_S4_Rampersaud_ToxSci_2019Supplemental Table S4, related to Rampersaud et al, Toxicological Sciences, 2019Table_S5_Rampersaud_ToxSci_2019Supplemental Table S5, related to Rampersaud et al, Toxicological Sciences, 2019Table_S6_Rampersaud_ToxSci_2019Supplemental Table S6, related to Rampersaud et al, Toxicological Sciences, 2019