cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g83f29f
title: Data from: Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community

description: Whereas the composition of the human gut microbiome is well resolved,
 predictive understanding is still lacking. Here, we followed a bottom-up
 strategy to explore human gut community dynamics: we established a
 synthetic community composed of three representative human gut isolates
 (Roseburia intestinalis L1-82, Faecalibacterium prausnitzii A2-165 and
 Blautia hydrogenotrophica S5a33) and explored their interactions under
 well-controlled conditions in vitro. Systematic mono- and pair-wise
 fermentation experiments confirmed competition for fructose and
 cross-feeding of formate. We quantified with a mechanistic model how well
 tri-culture dynamics was predicted from mono-culture data. With the model
 as reference, we demonstrated that strains grown in co-culture behaved
 differently than in mono-culture and confirmed their altered behavior at
 the transcriptional level. In addition, we showed with replicate
 tri-cultures and simulations that dominance in tri-culture sensitively
 depended on initial conditions. Our work has important implications for
 gut microbial community modeling as well as ecological interaction
 detection from batch cultures.
description: Batch fermenter data for
 three human gut bacterial strains grown in mono- and
 co-cultureThis collection of files
 contains data acquired for mono-, bi- and tri-cultures carried out for
 Faecalibacterium prausnitzii DSM 17677 (FP), Roseburia intestinalis DSM
 14610 (RI) and Blautia hydrogenotrophica DSM 10507 (BH). Fermentation
 experiments were carried out in 2-L Biostat B-DCU fermentors in batch
 mode. Anaerobic conditions during fermentations were assured by
 continuously sparging the medium with N2 at a flow rate of 70 mL min−1.
 The fermentation temperature was kept constant at 37 °C. A constant pH of
 6.8 was imposed and controlled automatically, using 1.5 M solutions of
 NaOH and H3PO4. To keep the medium homogeneous, a gentle stirring of 200
 rpm was applied.Fermenter.zipScreening data for Blautia hydrogenotrophicaThis collection of files contains data acquired for mono-cultures of Blautia hydrogenotrophica DSM 10507 (BH) without pH control. Experiments were performed in stationary glass bottles. The bottles contained 50 mL of heat-sterilized pH 6.8 mMCB medium. All bottles were incubated at 37°C in an anaerobic work station that was continuously sparged with a mixture of 80% N2, 10% CO2 and 10% H2. The consumption of the following substrates was tested at least in duplicate in two screening rounds: D-Fructose D-Glucose D-Galactose L-Fucose Sodium formate Sodium acetate trihydrate Lactate Oligofructose Inulin BH was also grown without substrate, to test autotrophic growth on CO2 in the headspace. In addition, the GC-FID results (ethanol, acetoin, acetic acid, propionic acid, butyric acid, isobutyric acid and isovaleric acid) for BH grown on formate are included.Screening.zip
DOI: 10.5061/dryad.1sn0gb4
title: Data from: Agri-environmental schemes promote ground-dwelling predators in adjacent oilseed rape fields: diversity, species traits and distance-decay functions

description: 1. Rising demands for agricultural products and high environmental costs
 of intensive agriculture reinforce the need for ecological replacements in
 agricultural management. In Europe, agri-environmental schemes (AES) are
 implemented to enhance species richness and provision of ecosystem
 services, but the effectiveness of different AES types and the spatial
 extent of possible beneficial effects are little understood. In this study
 we assessed the effects of different AES types on diversity, species
 traits and distance-decay functions of ground- dwelling predators in
 adjacent crop fields. 2. On 31 study sites with winter oilseed rape (OSR)
 adjacent to four types of AES differing in management intensity and
 habitat age we recorded ground-dwelling predators (carabid beetles,
 staphylinid beetles and spiders) during OSR growth from April to July.
 Effects of the AES on species richness, activity densities and different
 traits of these taxa were examined with transects of pitfall traps running
 along a continuous distance gradient from the AES across the habitat
 border into the OSR fields. 3. Ground-dwelling predator communities
 benefitted similarly from the different AES types. In adjacent OSR,
 activity densities, carabid species richness and the proportion of
 predatory carabid beetles declined from the field edge while mean body
 size increased. Adjacent AES increased the proportion of predatory species
 and simultaneously decreased the proportion of granivorous or frugivorous
 species in adjacent OSR fields. 4. Synthesis and applications. Our results
 indicate a beneficial effect of adjacent agri-environmental schemes (AES)
 on ground-dwelling predators in oilseed rape (OSR), mostly irrespective of
 AES type and therefore management intensity and habitat age. The
 short-ranged distance decay effects on natural enemies in OSR underpin
 that a strategic spatial placement of AES in agricultural landscapes is
 required to maximise biological pest control. This could help replace
 anthropogenic input in modern agriculture and secure adequate yields.
description: activity
 denistiessite = study site;
 position = trap position within the transect; interval = sampling
 interval; transect = transect number; setup & sorted = individuals who
 set up and sorted the tranps & trap samples; comment = loss (reason
 specified in additional_comment)carabidssite = study site; position = trap position within the transect; interval = sampling interval; transect = transect number; species_name = species name; abundance = abundance; stored = where the specimen is locatedenvironmentsite = study site; Lat & Lon_AES = latitude and longitude of the AES sites; Area_AES & Area_OSR = field sizes in [ha]; EDGE, MID & CENTRE = distances to the field edge of the transect position in [m]; SNH = percentage of SNH in 1km radius surrounding the study sites;
DOI: 10.5061/dryad.mt588k1
title: Data from: Climate change impacts on marine biodiversity, fisheries and society in the Arabian Gulf

description: Climate change - reflected in significant environmental changes such as
 warming, sea level rise, shifts in salinity, oxygen and other ocean
 conditions - is expected to impact marine organisms and associated
 fisheries. This study provides an assessment of the potential impacts on,
 and the vulnerability of, marine biodiversity and fisheries catches in the
 Arabian Gulf under climate change. To this end, using three separate niche
 modelling approaches under a 'business-as-usual' climate change
 scenario, we projected the future habitat suitability of the Arabian Gulf
 for 55 expert-identified priority species, including charismatic and
 non-fish species. Second, we conducted a vulnerability assessment of
 national economies to climate change impacts on fisheries. The modelling
 outputs suggested a high rate of local extinction (up to 35% of initial
 species richness) by 2090 relative to 2010. Spatially, projected local
 extinctions are highest in the southwestern part of the Arabian Gulf, off
 the coast of Saudi Arabia, Qatar and the United Arab Emirates (UAE). While
 the projected patterns provided useful indicators of climate change
 impacts on the region's diversity, the magnitude of changes in
 habitat suitability are more uncertain. Fisheries-specific results
 suggested reduced future catch potential for several countries on the
 western side of the Arabian Gulf, with projections differing only slightly
 between models. Qatar and the UAE were particularly affected, with more
 than a 26% drop in future fish catch potential. Integrating changes in
 catch potential with socio-economic indicators suggested the fisheries of
 Bahrain and Iran may be most vulnerable to climate change. We discuss
 limitations of the indicators and the methods used, as well as the
 implications of our overall findings for conservation and fisheries
 management policies in the region.
description: Data set for Figure
 2AFIGURE2A.csvData set for Figure 2BFIGURE2B.csvData set for Figure 2CFIGURE2C.csvData set for Figure 3FIGURE3.csvData set for Figure 5FIGURE5.csv
DOI: 10.5061/dryad.c03n4p6
title: Data from: DNA sequence variation among conspecific accessions of the legume Coursetia caribaea reveals geographically localized clades here ranked as species

description: Coursetia caribaea is geographically and morphologically the most variable
 species in the genus Coursetia and in the tribe Robinieae (Leguminosae,
 Papilionoideae). Because of potentially undetected species, we assessed
 the phylogenetic relationships among the eight taxonomic varieties of C.
 caribaea. Sampling included nuclear ribosomal internal transcribed spacer
 sequences from 489 Robinieae accessions representing all varieties of C.
 caribaea and 38 of the 40 species of Coursetia, in addition to chloroplast
 trnD-trnT sequences from 186 accessions. Separate and combined
 phylogenetic analyses resolved a clade of conspecific accessions of the
 Bolivian C. caribaea var. astragalina as sister to the central Andean
 Coursetia grandiflora clade. Also distantly related to Coursetia caribaea
 var. caribaea accessions were those of the coastal Oaxacan C. caribaea
 var. pacifica, which formed the sister clade to accessions of the central
 Andean C. caribaea var. ochroleuca. The estimated mean ages of the stem
 clades for these three lineages, 11, 7.7, and 7.7 Ma, respectively,
 contrasted to the estimated mean ages of the corresponding crown clades of
 0, 0, and 1.5 Ma. The contrasting stem and crown ages suggest that these
 taxa, appropriately ranked as species, Coursetia astragalina, Coursetia
 diversifolia, and Coursetia ochroleuca, each have persisted over
 evolutionary time frames as distinct geographically localized populations
 in seasonally dry tropical forests and woodlands.
description: Nexus files for the
 study of Coursetia caribaea.Three data sets are
 included. The first is a nrDNA ITS/5.8S data set involving a comprehensive
 sample of species in the genus Coursetia and closely related legume genera
 in the legume tribe Robinieae. The second data set is a chloroplast
 trnD-trnT data set that is comprehensively sampled mainly among species of
 the genus Coursetia. The third data set is a combined nrDNA ITS/5.8S and
 chloroplast trnD-trnT data set.Coursetia caribaea
 DataDryad.txtSupplemental Figure
 1.A
 Bayesian consensus tree derived from the analysis of 489 nrDNA ITS/5.8S
 sequences.Fig
 S1.pdfSupplemental Figure
 2.A
 Bayesian consensus tree derived from the analysis of 186 chloroplast
 trnD-trnT sequences.Fig
 S2.pdfSupplemental Figure
 3.A
 Bayesian consensus tree derived from the analysis of 181 accessions
 represented by nrDNA ITS/5.8S and chloroplast trnD-trnT
 sequences.Fig
 S3.pdfSupplemental
 MapMaps originally
 published as Fig. 110 and Fig. 111 in vol. 21 Systematic Botany
 Monographs. The Editor has granted permission to make the figures
 available here. For any subsequent use, please cite the original
 publication: Lavin M (1988) Systematics of Coursetia
 (Leguminosae-Papilionoideae). Systematic Botany Monographs, 21. Full text
 of vol 21 is available from American Society of Plant Taxonomists through
 JSTOR at https://doi.org/10.2307/25027701
DOI: 10.5061/dryad.s71c1tp
title: Data from: Soil microclimate changes affect soil fungal communities in a Mediterranean pine forest

description: • Soil microclimate is a potentially important regulator of the
 composition of plant-associated fungal communities in climates with
 significant drought periods. Here, we investigated spatio-temporal
 dynamics of soil fungal communities in a Mediterranean Pinus pinaster
 forest in relation to soil moisture and temperature. • Fungal communities
 in 336 soil samples collected monthly during a year from 28 long-term
 experimental plots were assessed by PacBio sequencing of ITS2 amplicons.
 Total fungal biomass was estimated by analysing ergosterol. Community
 changes were analysed in the context of functional traits. • Soil fungal
 biomass was lowest during summer and late winter and highest during
 autumn, concurrent with a greater relative abundance of mycorrhizal
 species. Intra-annual spatio-temporal changes in community composition
 correlated significantly with soil moisture and temperature. Mycorrhizal
 fungi were less affected by summer drought than free-living fungi. In
 particular, mycorrhizal species of the short-distance exploration type
 increased in relative abundance under dry conditions, whereas species of
 the long-distance exploration type were more abundant under wetter
 conditions. • Our observations demonstrate a potential for compositional
 and functional shifts in fungal communities in response to changing
 climatic conditions. Free-living fungi and mycorrhizal species with
 extensive mycelia may be negatively affected by increasing drought periods
 in Mediterranean forest ecosystems.
description: Community
 dataCommunity and
 environmental datacommunity
 data.xlsx
DOI: 10.5061/dryad.7pk103q
title: Data from: Juvenile divergence in adaptive traits among seven sympatric fish eco-morphs arises before moving to different lacustrine habitats

description: Identifying the mechanisms initiating sympatric diversification in
 vertebrates has remained a conceptual challenge. Here we analyze an
 assemblage of sympatric charr (Salvelinus malma) morphs from landlocked
 Lake Kronotskoe basin as a model to uncover the divergence pathways in
 freshwater fishes during the early life history stages. All morphs have
 distinct developmental biology, but a similar developmental rate
 retardation compared to the ancestor. Our study reveals that adult
 morphological differences, which acquire functionality at maturation,
 originate in the early juvenile stages due to heterochrony in
 skeletogenesis and allometric changes triggered by variation in metabolic
 activity. The craniofacial differences among the morphs result from
 asynchronous development of several skeletal modules. The accelerated
 ossification of teeth-armed bones occurs in predatory feeding morphs,
 while cranial cover ossification is promoted in benthivorous morphs. These
 contrasting growth patterns have led to seven phenotypes that span a range
 far beyond the ancestral variability. The most distinct morphs are a
 riverine-spawning, epilimnetic predator and a lacustrine-spawning,
 profundal benthic feeder. Taken together, we argue that the adaptive
 morphological differentiation in these sympatric freshwater fishes is
 driven by diverging patterns in ossification rate and metabolic activity
 against a background of uneven somatic growth. This divergence is
 primarily associated with basic environmental differences on the nursery
 grounds that might be unrelated to resource use. This non-heritable
 phenotype divergence is then exposed to natural selection that could
 result in further adaptive genetic changes.
description: bones_developmentThe skeletal elements measured were ranked by developmental rate to perform a comparative analysis of osteogenesis. A score-scale ranking was used for bones, which were classified according to Jollie (1986)biochemical characteristicsBlood glucose, hemoglobin, serum protein and muscle lipids were measured. Juveniles with a fork length of 61–100 mm (parrs with two annual rings on otoliths, age 2+) were used in the analysis.linear_morphometricsThe juveniles with a fork length of 61–124 mm (parrs with 2-3 annual rings on otoliths, age 2+ to 3+) were used to analysis of body shape. The extraction of truss distances from the digital images of seven Lake Kronotskoe morphs and Dolly Varden was conducted using tpsUtil and tpsDig2 v2.16 software platforms (Rohlf, 2010).
DOI: 10.5061/dryad.14g26j8
title: Data from: Costs and benefits of non-random seed release for long distance dispersal in wind-dispersed plant species

description: The dispersal ability of plants is a major factor driving ecological
 responses to global change. In wind-dispersed plant species, non-random
 seed release in relation to wind speeds has been identified as a major
 determinant of dispersal distances. However, little information is
 available about the costs and benefits of non-random abscission and the
 consequences of timing for dispersal distances. We asked: 1) To what
 extent is non-random abscission able to promote long-distance dispersal
 and what is the effect of potentially increased pre-dispersal risk costs?
 2) Which meteorological factors and respective timescales are important
 for maximizing dispersal? These questions were addressed by combining a
 mechanistic modelling approach and field data collection for herbaceous
 wind-dispersed species. Model optimization with a dynamic dispersal
 approach using measured hourly wind speed showed that plants can increase
 long-distance dispersal by developing a hard wind speed threshold below
 which no seeds are released. At the same time, increased risk costs limit
 the possibilities for dispersal distance gain and reduce the optimum level
 of the wind speed threshold, in our case (under representative Dutch
 meteorological conditions) to a threshold of 5-6 m s-1. The frequency and
 predictability (auto-correlation in time) of pre-dispersal seed-loss had a
 major impact on optimal non-random abscission functions and resulting
 dispersal distances. We observed a similar, but more gradual, bias towards
 higher wind speeds in six out of seven wind-dispersed species under
 natural conditions. This confirmed that non-random abscission exists in
 many species and that, under local Dutch meteorological conditions,
 abscission was biased towards winds exceeding 5-6 m s-1. We conclude that
 timing of seed release can vastly enhance dispersal distances in
 wind-dispersed species, but increased risk costs may greatly limit the
 benefits of selecting wind conditions for long-distance dispersal, leading
 to moderate seed abscission thresholds, depending on local meteorological
 conditions and disturbances.
description: Seed release model and
 field dataFolder contains: 1)
 field data of 7 species in .csv format. 2) matlabcode of the abscission
 submodel presented in the paper. 3) matlabscripts for all figures. 4)
 input data for figures and model.Oikos
 Dryad.zip
DOI: 10.5061/dryad.m40t6g7
title: Data from: Disruption of skin microbiota contributes to salamander disease

description: Escalating occurrences of emerging infectious diseases underscore the
 importance of understanding microbiome-pathogen interactions. The
 amphibian cutaneous microbiome is widely studied for its potential to
 mitigate disease-mediated amphibian declines. Other microbial interactions
 in this system, however, have been largely neglected in the context of
 disease outbreaks. European fire salamanders have suffered dramatic
 population crashes as a result of the newly emerged Batrachochytrium
 salamandrivorans(Bsal). We investigate microbial interactions on multiple
 fronts within this system. We show that wild, healthy fire salamanders
 maintain a complex skin microbiota containingBsal-inhibitory members, but
 the community is present at remarkably low abundance. Through
 experimentation, we show that increasing bacterial densities of
 Bsal-inhibiting bacteria via daily addition slowed disease progression in
 fire salamanders. Additionally, we find that experimental-Bsal infection
 elicited subtle changes in the skin microbiome, with selected
 opportunistic bacteria increasing in relative abundance resulting in
 septicemic events that coincide with extensive destruction of the
 epidermis. These results suggest that fire salamander skin, in natural
 settings, maintains bacterial communities at numbers too low to confer
 sufficient protection againstBsal,and in fact the native skin microbiota
 can constitute a source of opportunistic bacterial pathogens that
 contribute to pathogenesis.By shedding light on the complex interaction
 between the microbiome and a lethal pathogen, these data put the interplay
 between skin microbiomes and a wildlife disease in a new perspective.
description: Bacterial community,
 Bacterial Abundance, Bsal Infection, Cultured Isolate, and Metadata
 Associated with all Field Collection and ExperimentsThis file contains
 multiple tabs housing all data associated with Bacterial community,
 Bacterial Abundance, Bsal Infection, Cultured Isolate, and Metadata from
 all Field Collection and Experiments completed for this study. The first
 tab within the Excel document contains a description of the tabs and the
 figures the data is associated within the manuscript.RSPB-2018-0758_Bletz_etal_Dryad_AllData.xlsx
DOI: 10.5061/dryad.f9v3778
title: Data from: Parsimony, not Bayesian analysis, recovers more stratigraphically congruent phylogenetic trees

description: Reconstructing evolutionary histories requires accurate phylogenetic
 trees. Recent simulation studies suggest that probabilistic phylogenetic
 analyses of morphological data are more accurate than traditional
 parsimony techniques. Here we use empirical data to compare Bayesian and
 parsimony phylogenies in terms of their congruence with the distribution
 of age ranges of the component taxa. Analysis of 167 independent
 morphological data matrices of fossil tetrapods finds that Bayesian trees
 exhibit significantly lower stratigraphic congruence than the equivalent
 parsimony trees. As such, taking stratigraphic data as an independent
 benchmark indicates that parsimony analyses are more accurate for
 phylogenetic reconstruction of morphological data. The discrepancy between
 simulated and empirical studies may result from historic data peaking
 practises or some complexities of empirical data as yet unaccounted for.
description: RESULTSALLSTRAPcomb2Matrices (nexus) and age range data for the 167 datasets analysed, and final results (stratigraphic congruence scores for each tree)SansometalESM.zip