cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s636m
title: Data from: Decoupled diversity dynamics in green and brown webs during primary succession in a salt marsh

description: Terrestrial ecosystems are characterized by a strong functional connection
 between the green (plant–herbivore-based) and brown
 (detritus–detritivore-based) parts of the food web, which both develop
 over successional time. However, the interlinked changes in green and
 brown food web diversity patterns in relation to key ecosystem processes
 are rarely studied. Here, we demonstrate changes in species richness,
 diversity and evenness over a wide range of invertebrate green and brown
 trophic groups during 100 years of primary succession in a saltmarsh
 ecosystem, using a well-calibrated chronosequence. We contrast two
 hypotheses on the relationship between green and brown food web diversity
 across succession: (i) ‘coupled diversity hypothesis’, which predicts that
 all trophic groups covary similarly with the main drivers of successional
 ecosystem assembly vs. (ii) the ‘decoupled diversity hypothesis’, where
 green and brown trophic groups diversity respond to different drivers
 during succession. We found that, while species richness for plants and
 invertebrate herbivores (green web groups) both peaked at intermediate
 productivity and successional age, the diversity of macrodetritivores,
 microarthropod microbivores and secondary consumers (brown web groups)
 continuously increased towards the latest successional stages. These
 results suggest that green web trophic groups are mainly driven by
 vegetation parameters, such as the amount of bare soil, vegetation biomass
 production and vegetation height, while brown web trophic groups are
 mostly driven by the production and standing stock of dead organic
 material and soil development. Our results show that plant diversity
 cannot simply be used as a proxy for the diversity of all other species
 groups that drive ecosystem functioning, as brown and green diversity
 components in our ecosystem responded differently to successional
 gradients.
description: DATA_Schrama_et_al_diversityRaw data that underlies figures 2-5
DOI: 10.5061/dryad.fs950
title: Data from: Does high-dose antimicrobial chemotherapy prevent the evolution of resistance?

description: High-dose chemotherapy has long been advocated as a means of controlling
 drug resistance in infectious diseases but recent empirical studies have
 begun to challenge this view. We develop a very general framework for
 modeling and understanding resistance emergence based on principles from
 evolutionary biology. We use this framework to show how high-dose
 chemotherapy engenders opposing evolutionary processes involving the
 mutational input of resistant strains and their release from ecological
 competition. Whether such therapy provides the best approach for
 controlling resistance therefore depends on the relative strengths of
 these processes. These opposing processes typically lead to a unimodal
 relationship between drug pressure and resistance emergence. As a result,
 the optimal drug dose lies at either end of the therapeutic window of
 clinically acceptable concentrations. We illustrate our findings with a
 simple model that shows how a seemingly minor change in parameter values
 can alter the outcome from one where high-dose chemotherapy is optimal to
 one where using the smallest clinically effective dose is best. A review
 of the available empirical evidence provides broad support for these
 general conclusions. Our analysis opens up treatment options not currently
 considered as resistance management strategies, and it also simplifies the
 experiments required to determine the drug doses which best retard
 resistance emergence in patients.
description: Simulation
 CodeMathematica code for
 stochastic simulationsDataFilesResourceComp.nb
DOI: 10.15468/dl.p5csfz
title: Occurrence Download

description: A dataset containing 1879 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Schizocodon soldanelloides",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1879 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001154-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ct8j4
title: Data from: A genetic assessment of the human-facilitated colonization history of black swans in Australia and New Zealand

description: Movement of species beyond their indigenous distribution can fundamentally
 alter the conservation status of the populations involved. If
 introductions are human-facilitated, introduced species could be
 considered pests. Characterizing the colonization history of introduced
 species can, therefore, be critical to formulating the objectives and
 nature of wildlife management strategies. The black swan (Cygnus atratus)
 is native to Australia but is considered a reintroduced species in New
 Zealand, where the endemic population was reported extinct during the 19th
 century. After the re-introduction of a small number of individuals from
 Australia, the New Zealand population expanded unexpectedly rapidly, which
 was attributed to simultaneous waves of migration from Australia. An
 alternative, but hitherto unformalized, hypothesis is that local extant
 populations remained and admixed with introduced individuals. To
 contribute to our understanding of the reintroduction history of the
 species, we investigated dispersal patterns and demographic histories of
 seven populations from Australia and New Zealand, using population genetic
 inferences from a microsatellite dataset. Our results on genetic
 structure, dispersal rates, and demographic histories provide mixed
 evidence on the origin of New Zealand black swans. The hypothesis that
 reintroduced individuals mixed with remaining local individuals and that
 the subsequent dramatic population expansion may have been due to genetic
 rescue of the inbred indigenous population cannot be discarded and needs
 further investigation.
description: Swan microsatellite data
 with coordinatesComplete Microsatellite
 Dataset used in the publication with geographic coordinates and sex
 assignment of individualsBlackSwansDryad
DOI: 10.5061/dryad.bs5hn51
title: Data from: Interactions between seed traits and digestive processes determine the germinability of bird-dispersed seeds

description: Waterbirds disperse a wide range of plant seeds via their guts, promoting
 biotic connectivity between isolated habitat patches. However, the
 intensity of digestive forces encountered by seeds, and therefore their
 potential to survive digestive tract passage, varies within and between
 waterbird species. Here, we investigate under controlled conditions how
 the interaction between seed traits and digestive strategies affect the
 germinability of seeds following waterbird-mediated dispersal. We exposed
 seeds of 30 wetland plant species to the main digestive processes in the
 dabbling duck digestive system: mechanical, chemical and intestinal
 digestion. These were simulated by 1) a pressure test and scarification
 treatment, 2) incubation in simulated gastric juice, and 3) incubation in
 intestinal contents of culled mallards (Anas platyrhynchos). We evaluated
 their separate and combined effects on seed germination, and identified
 the role of seed size and seed coat traits in resisting the digestive
 forces. Seeds were generally resistant to separate digestive processes,
 but highly sensitive to a combination. Resistance to mechanical break-down
 was reduced by up to 80% by chemical pre-treatment, especially for seeds
 with permeable coats. Scarified seeds were 12–17% more vulnerable to
 chemical and intestinal digestive processes than undamaged seeds. Large
 seeds and seeds with thin, permeable coats were particularly sensitive to
 chemical and intestinal digestion. These results indicate that efficient
 digestion of seeds requires multiple digestive processes. The gizzard,
 responsible for mechanical digestion, plays a key role in seed survival.
 Omnivorous birds, which have relatively light gizzards compared to pure
 herbivores or granivores, are thus most likely to disperse seeds
 successfully. Regardless of digestive strategy, small seeds with tough
 seed coats are most resistant to digestion and may be adapted to
 endozoochorous dispersal by waterbirds.
description: Kleyheeg et al 2018 PLOS
 ONERaw seed trait and
 germination data from Kleyheeg et al. (2018) Interactions between seed
 traits and digestive processes determine the germinability of
 bird-dispersed seeds, PLOS ONE.Raw data Kleyheeg et al
 2018.xlsx
DOI: 10.5061/dryad.q609s
title: Data from: A systematic approach to evaluate the influence of environmental conditions on eDNA detection success in aquatic ecosystems

description: The use of environmental DNA (eDNA) to determine the presence and
 distribution of aquatic organisms has become an important tool to monitor
 and investigate freshwater communities. The successful application of this
 method in the field, however, is dependent on the effectiveness of
 positive DNA verification, which is influenced by site-specific
 environmental parameters. Factors affecting lower eDNA concentrations in
 aquatic ecosystems include flow conditions, and the presence of substances
 that possess DNA-binding properties or inhibitory effects. In this study
 we investigated the influence of different environmental parameters on the
 detection success of eDNA using the invasive goby Neogobius melanostomus.
 In a standardized laboratory setup, different conditions of flow,
 sediment-properties, and fish density were compared, as well as different
 potential natural inhibitors such as algae, humic substances, and
 suspended sediment particles. The presence of sediment was mainly
 responsible for lower eDNA detection in the water samples, regardless of
 flow-through or standing water conditions and a delayed release of eDNA
 was detected in the presence of sediment. Humic substances had the highest
 inhibitory effect on eDNA detection followed by algae and siliceous
 sediment particles. The results of our study highlight that a successful
 application of eDNA methods in field surveys strongly depends on
 site-specific conditions, such as water flow conditions, sediment
 composition, and suspended particles. All these factors should be
 carefully considered when sampling, analyzing, and interpreting eDNA
 detection results.
description: qPCR results
 eDNAfile contains qPCR
 results for 2 experiments: (1) abiotic and biotic factors (2)
 inhibitorsStoeckle_et_al_PLOS_ONE_2017.xlsx
DOI: 10.5061/dryad.r28v2
title: Data from: Adaptive genetic markers discriminate migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid continued gene flow

description: Neutral genetic markers are routinely used to define distinct units within
 species that warrant discrete management. Human-induced changes to gene
 flow however may reduce the power of such an approach. We tested the
 efficiency of adaptive vs. neutral genetic markers in differentiating
 temporally divergent migratory runs of Chinook salmon (Oncorhynchus
 tshawytscha) amid high gene flow owing to artificial propagation and
 habitat alteration. We compared seven putative migration timing genes to
 ten microsatellite loci in delineating three migratory groups of Chinook
 in the Feather River, CA: offspring of fall run hatchery broodstock that
 returned as adults to freshwater in fall (fall run), spring run offspring
 that returned in spring (spring run), and fall run offspring that returned
 in spring (FRS). We found evidence for significant differentiation between
 the fall and federally-listed threatened spring groups based on divergence
 at three circadian clock genes (OtsClock1b, OmyFbxw11 and Omy1009UW), but
 not neutral markers. We thus demonstrate the importance of genetic marker
 choice in resolving complex life history types. These findings directly
 impact conservation management strategies and add to previous evidence
 from Pacific and Atlantic salmon indicating that circadian clock genes
 influence migration timing.
description: DPJ_ FRH09 9Msats and 7
 genes (07 19 12)revExcel file containing
 genotype data for Feather River Chinook salmon. Individuals are identified
 by population in each row: Fall, Spring and FRS (fall return spring). Loci
 are designated by column with the nine microsatellite listed followed by
 seven adaptive markers.
DOI: 10.5061/dryad.5fn0224
title: Data from: Alcoholism gender differences in brain responsivity to emotional stimuli

description: Men and women may use alcohol to regulate emotions differently, with
 corresponding differences in neural responses. We explored how the viewing
 of different types of emotionally salient stimuli impacted brain activity
 observed through functional magnetic resonance imaging (fMRI) from 42
 long-term abstinent alcoholic (25 women) and 46 nonalcoholic (24 women)
 participants. Analyses revealed blunted brain responsivity in alcoholic
 compared to nonalcoholic groups, as well as gender differences in those
 activation patterns. Brain activation in alcoholic men (ALCM) was
 significantly lower than in nonalcoholic men (NCM) in regions including
 rostral middle and superior frontal cortex, precentral gyrus, and inferior
 parietal cortex, whereas activation was higher in alcoholic women (ALCW)
 than in nonalcoholic women (NCW) in superior frontal and supramarginal
 cortical regions. The reduced brain reactivity of ALCM, and increases for
 ALCW, highlighted divergent brain regions and gender effects, suggesting
 possible differences in the underlying basis for development of alcohol
 use disorders.
description: Code and Data for
 "Alcoholism Gender Differences in Brain Responsivity to Emotional
 Stimuli"This archive contains
 the code and preprocessed data used to generate tables and figures for:
 Sawyer KS, Maleki N, Urban T, Marinkovic K, Karson S, Ruiz SM, Harris GJ,
 Oscar-Berman M, "Alcoholism Gender Differences in Brain Responsivity
 to Emotional Stimuli"
 (https://doi.org/10.7554/eLife.41723)sawyer-iaps.zip
DOI: 10.5061/dryad.537k1
title: Data from: Facilitation by leguminous shrubs increases along a precipitation gradient

description: Combining nutrient dynamics (plant nutrient uptake and soil fertility) can
 help uncover mechanisms of shrub-grass interactions and assess the
 validity of the stress-gradient hypothesis, which predicts that
 facilitation between plants increases in stressful environments. However,
 how facilitation via shrub-mediated nutrient increases varies with
 precipitation is poorly resolved. We first synthesized a global dataset
 from 66 studies and evaluated how shrubs affected soil organic carbon (C)
 and nitrogen (N) in grasslands along a precipitation gradient. We then
 made new measurements in a single grassland type encroached by leguminous
 shrubs from the same genus (Caragana) to constrain the variations caused
 by combining different grassland types and shrubs traits in the
 meta-analysis. Specifically, we investigated how shrubs mediated N
 dynamics and how shrub-grass interactions varied along a precipitation
 gradient (147-342 mm) in a temperate steppe of China. At the global scale,
 leguminous shrub-mediated effects on soil nutrients increased with
 precipitation, while no relationship was found for non-leguminous shrub.
 For the field experiment, greater N and lower δ15N in Caragana compared to
 non-leguminous shrub (reference shrub, Salsola collina) suggested active
 N-fixation in Caragana. We found that Caragana enhanced N concentration
 and leaf quality (low C:N ratio) in neighbouring plants more on mesic
 sites than on xeric sites. Thus, facilitation increased via higher soil N
 and with decreasing environmental stress, at least along this relatively
 arid precipitation gradient. Our results highlight the importance of
 precipitation in determining the nutritional facilitation to neighbouring
 grasses from encroaching leguminous shrubs. Conceptual frameworks for
 plant facilitation may therefore need to include shrub characteristics
 (N-fixers vs. non-fixers) and positive effects of higher precipitation on
 this type of facilitation to characterize plant interactions along stress
 gradients.
description: FE-Zhang-ST1Synthesized dataset of shrub encroachment on soil C and N pool, containing informaiton of mean annual rainfall, legumes status, woody species, sites and soil (organic carbon and nitrogen) variables at the site scales for grasslands with and without shrubs.
DOI: 10.5061/dryad.q00f8
title: Data from: Inbred and furious: negative association between aggression and genetic diversity in highly inbred fish

description: Aggressive behaviour plays an important role in securing resources,
 defending against predators and shaping social interactions. Although
 aggression can have positive effects on growth and reproductive success,
 it is also energetically costly and may increase injury and compromise
 survival. Individual genetic diversity has been positively associated with
 aggression, but the cause for such an association is not clear, and it
 might be related to the ability to recognize kin. To disentangle the
 relationships between genetic diversity, kinship and aggression, we
 quantified aggressive behaviour in a wild, self-fertilizing fish
 (Kryptolebias marmoratus) with naturally variable degrees of genetic
 diversity, relatedness and familiarity. We found that in contrast to
 captive fish, levels of aggression among wild K. marmoratus are positively
 associated with individual homozygosity, but not with relatedness or
 familiarity. We suggest that the higher aggression shown by homozygous
 fish could be related to better kin discrimination and may be facilitated
 by hermaphrodite competition for scarce males, given the fitness
 advantages provided by outcrossing in terms of parasite resistance. It
 seems likely that the relationship between aggression and genetic
 diversity is largely influenced by both the environment and population
 history.
description: Agg_data_DryadMore complete data including length, burrow, familiarity, relatedness, raw behavioural data and complete genotype for individual fish.
DOI: 10.5061/dryad.07551
title: Data from: Dispersing hemipteran vectors have reduced arbovirus prevalence

description: A challenge in managing vector-borne zoonotic diseases in human and
 wildlife populations is predicting where epidemics or epizootics are
 likely to occur, and this requires knowing in part the likelihood of
 infected insect vectors dispersing pathogens from existing infection foci
 to novel areas. We measured prevalence of an arbovirus, Buggy Creek virus,
 in dispersing and resident individuals of its exclusive vector, the
 ectoparasitic swallow bug (Oeciacus vicarius), that occupies cliff swallow
 (Petrochelidon pyrrhonota) colonies in western Nebraska. Bugs colonizing
 new colony sites and immigrating into established colonies by clinging to
 the swallows’ legs and feet had significantly lower virus prevalence than
 bugs in established colonies and those that were clustering in established
 colonies before dispersing. The reduced likelihood of infected bugs
 dispersing to new colony sites indicates that even heavily infected sites
 may not always export virus to nearby foci at a high rate. Infected
 arthropods should not be assumed to exhibit the same dispersal or movement
 behaviour as uninfected individuals, and these differences in dispersal
 should perhaps be considered in the epidemiology of vector-borne pathogens
 such as arboviruses.
description: Dispersing hemipteran
 vectors have reduced arbovirus prevalenceExcel file for data
 collected from the field and analyzed in the laboratory. For key, see,
 ReadMe file.MooreBrown.xlsx
DOI: 10.5061/dryad.61f2h
title: Data from: Multiple interaction networks: towards more realistic descriptions of the web of life

description: Ecological communities are defined by species interacting dynamically in a
 given location at a given time, and can be conveniently represented as
 networks of interactions. Pairwise interactions can be ascribed to one of
 five main types, depending on their outcome for the species involved:
 amensalism, antagonism (including predation, parasitism and disease),
 commensalism, competition or mutualism. While most studies have dealt so
 far with networks involving one single type of interaction at a time,
 often focusing on a specific clade and/or guild, recent studies are being
 developed that consider networks with more than one interaction type and
 across several levels of biological organisation. We review these
 developments and suggest that three main frameworks are in use to
 investigate the properties of multiple interactions networks:
 'expanded food-webs', 'multilayer networks' and
 'equal footing networks'. They differ on how interactions are
 classified and implemented in mathematical models, and on whether the
 effect of different interaction types is expressed in the same units. We
 analyse the mathematical and ecological assumptions of these three
 approaches, and identify some of the questions that can be addressed with
 each one of them. Since the overwhelming majority of multiple interaction
 studies are theoretical and use artificially generated data, we also
 provide recommendations for the incorporation of field data in such
 studies.
description: R script for generating
 resultsThe file included is a
 self-contained R script that was used to produce the results and images of
 the manuscript. Figures obtained with this script will not exactly match
 the ones of the paper due to the type of analyses performed, based on
 random parameterizations (within given parameter intervals) of dynamic
 models.0IK-04428.R
DOI: 10.48512/xcv8518828
title: Field Visibility Data

description: This Excel file provides the data entries for fields defined and assigned numbers for survey teams. See the variable definitions in the document: Field Visibility Variables.
DOI: 10.5061/dryad.s1kg8
title: Data from: Functional coupling constrains craniofacial diversification in Lake Tanganyika cichlids

description: Functional coupling, where a single morphological trait performs multiple
 functions, is a universal feature of organismal design. Theory suggests
 that functional coupling may constrain the rate of phenotypic evolution,
 yet empirical tests of this hypothesis are rare. In fish, the evolutionary
 transition from guarding the eggs on a sandy/rocky substrate (i.e.
 substrate guarding) to mouthbrooding introduces a novel function to the
 craniofacial system and offers an ideal opportunity to test the functional
 coupling hypothesis. Using a combination of geometric morphometrics and a
 recently developed phylogenetic comparative method, we found that head
 morphology evolution was 43% faster in substrate guarding species than in
 mouthbrooding species. Furthermore, for species in which females were
 solely responsible for mouthbrooding the males had a higher rate of head
 morphology evolution than in those with bi-parental mouthbrooding. Our
 results support the hypothesis that adaptations resulting in functional
 coupling constrain phenotypic evolution.
description: Head shape data of Lake
 Tanganyika cichlidsConsensus configuration
 of head shape for 1) sex-pooled 37 species, 2) 22 species of males,
 followed by 3) 26 species of females. In NTS format.Head
 shape.rtf