cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5q041fq
title: Data from: Quantifying the damage caused by fruit bats to backyard lychee trees in Mauritius and evaluating the benefits of protective netting

description: The Mauritius fruit bat (Pteropus niger) has been the subject of repeated
 culling campaigns, apparently in response to pressure from the
 fruit-growing industry concerned over damage to commercially valuable
 orchard crops such as lychees. More than 31,000 fruit-bearing lychee trees
 also exist in private backyards making this an issue pertinent to a wide
 cross-section of the Mauritian general public and not just those involved
 in commercial fruit production. The level of damage caused by bats to
 fruit crops is often debated and the low number of robust damage
 assessment studies hampers mitigation efforts. During the fruiting season
 of 2016/2017, we assessed the damage among backyard lychee trees
 attributable to fruit bats and other causes around Vacoas-Phoenix, Central
 Mauritius and evaluated the impact of using protective netting as a
 mitigation strategy. Fruit yield from panicles that were protected from
 depredation by nylon netting was approximately one third greater than that
 from unprotected panicles. We suspect that fruit bats were responsible for
 approximately 42% of the total damage but illustrate the difficulties in
 attributing damage to a single cause in such assessments. Although we
 demonstrate the value of protective netting we recognize that barriers to
 implementation exist and that a more holistic approach that incorporates
 crop protection, forest restoration strategies and addresses negative
 public attitudes towards bats in general is required to ensure the
 persistence of this endemic species.
description: Summarized raw data of
 fruit counts and damageThe Excel file contains
 summarized counts of fruits from panicles of backyard lychee trees and
 details of damaged fruit collected from the ground and the associated
 probable reason.Tollington et al 2019 Bat
 Damage_Dryad.xlsx
DOI: 10.5061/dryad.6t72p3j
title: Data from: Genetic rescue by distant trees mitigates qualitative pollen limitation imposed by fine-scale spatial genetic structure

description: Restricted seed dispersal frequently leads to fine-scale spatial genetic
 structure (i.e., FSGS) within plant populations. Depending on its spatial
 extent and the mobility of pollinators, this inflated kinship at the
 immediate neighbourhood can critically impoverish pollen quality. Despite
 the common occurrence of positive FSGS within plant populations, our
 knowledge regarding the role of long-distance pollination preventing
 reproductive failure is still limited. Using microsatellite markers, we
 examined the existence of positive FSGS in two low-density populations of
 the tree Pyrus bourgaeana. We also designed controlled crosses among trees
 differing in their kinship to investigate the effects of increased local
 kinship on plant reproduction. We used six pollination treatments and
 fully monitored fruit production, fruit and seed weight, proportion of
 mature seeds per fruit, and seed germination. Our results revealed
 positive FSGS in both study populations and lower fruit initiation in
 flowers pollinated with pollen from highly-genetically related individuals
 within the neighbourhood, with this trend intensifying as the fruit
 development progressed. Besides, open-pollinated flowers exhibited lower
 performance of compared to those pollinated by distant pollen donors,
 suggesting intense qualitative pollen limitation in natural populations.
 We found positive fine-scale spatial genetic structure is translated into
 impoverished pollen quality from nearby pollen donors which negatively
 impacts the reproductive success of trees in low-density populations.
 Under this scenario of intrapopulation genetic rescue by distant pollen
 donors, the relevance of highly-mobile pollinators for connecting
 spatially and genetically distant patches of trees may be crucial to
 safeguarding population recruitment.
description: Pyrus bourgaeana genetic
 rescue_07_15_19
DOI: 10.5061/dryad.js48f56
title: Data from: Secondary succession has surprisingly low impact on arboreal ant communities in tropical montane rainforest

description: Understanding forest regeneration processes is increasingly important as
 disturbed forests spread rapidly in tropical landscapes. While
 successional dynamics are relatively well-understood for plants, they
 remain poorly known for tropical insects, particularly in montane
 rainforests and tree canopies. We studied the effect of montane forest
 succession on arboreal ant communities in New Guinea near their natural
 elevational limit (1800 m a.s.l.). We censused ant species and nests in
 replicated 0.1 ha plots of primary, old and young secondary forests,
 destined to be felled for gardens by the local land-owners. Overall, 1249
 felled trees were dissected for all ant-associated microhabitats. We used
 rarefaction-based models manipulating vegetation structure and
 multivariate randomizations to assess the effects of tree density, tree
 size and nesting microhabitats on the ant communities. We expected
 increased ant species diversity, microhabitat specialization and species
 turnover among trees throughout the succession, with distinct community
 composition among the stages. In contrast to our expectations, ant species
 composition and diversity per plot did not change during succession, and
 species similarity among trees was significantly higher only in old
 secondary forest. The number of ant species per tree increased with forest
 age, but trees of similar size hosted only slightly more species in
 primary than secondary forests. Many ant species were associated with
 particular nesting microhabitats; however, the same microhabitat types
 occurred in all stages, and thus did not generate successional trends in
 ant communities. Secondary succession had an unexpectedly low impact on
 tree-dwelling ant communities in this montane ecosystem, in contrast with
 our previous findings from lowland rainforests. These results highlight
 the need to study successional processes along entire elevational
 gradients, as montane taxa may react differently to vegetation changes
 than their lowland counterparts.
description: Mottl-Ecosphere-TropicalArborealAnts_TreeFelling_PNG2019Datafile containing information about arboreal ants from succession series in the montane tropical forest in Papua New Guinea. Data were obtained using felling of all trees with DBH&gt;5 and collection of all foragers and nests. In total, 9 plot of 0.1ha in 3 successional stages were sampled. List AllRecords contains information about all tree and presence/absence information of ant species. In addition, there is information about environmental variables for each tree. List NestRecords contains information about the number of ant nests of each ant species in each tree and environmental variables linked to them.
DOI: 10.15468/dl.tpj4xz
title: Occurrence Download

description: A dataset containing 608523 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "DatasetKey is one of (A global database for the distributions of crop wild relatives, 2023 Contributions of Plant Specimen Data inside China, INPA - Observations, The System-wide Information Network for Genetic Resources (SINGER), Vascular Plant Specimen database of Kanagawa Prefectural Museum of Natural History, NIEK_NES, 500,000 plant Specimens from PE Herbarium in China from 1950 to 1999, Moscow University Herbarium (MW), Local floras of Russia: records from literature)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Poaceae"
 ]
}

 The dataset includes 608523 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001804-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.nr2250b
title: Data from: Soil fauna responses to invasive alien plants are determined by trophic groups and habitat structure: a global meta-analysis

description: Despite increasing frequency of invasions by alien plant species with
 widespread ecological and economic consequences, it remains unclear how
 belowground compartments of ecosystems are impacted. In order to
 synthetize current knowledge and provide future directions for research we
 performed a meta-analysis assessing the impact of invasive alien plant
 species on soil fauna abundance. Compared to previous synthesis on this
 topic, we included together in our model the trophic group of each soil
 faunal taxa (from herbivores to predators) and habitat structure, namely
 open and closed habitats (i.e. grass and shrub dominated areas versus
 forested areas). In doing so, we highlighted that both moderators strongly
 interact to determine the response of soil fauna to the presence of
 invasive alien plants. Soil fauna abundance increase in the presence of
 invasive species only in closed habitats (+18.2%). This pattern of
 habitat-dependent response (positive effect in closed habitats) was only
 found for primary consumers (i.e. herbivores +29.1% and detritivores
 +66.7%) within both detritus-based and live root-based trophic pathways.
 Abundances of predators and microbivores did not respond to the presence
 of IAS irrespective of habitat structure. For several groups, the habitat
 structure (open or closed) significantly drove their responses to the
 presence of invasive alien species. In addition, we carefully considered
 potential sources of bias (e.g. geographic, taxonomic and functional)
 within the collected data in an attempt to highlight gaps in available
 knowledge on the subject. Our findings support the conclusions of previous
 studies on the subject by demonstrating (i) that soil fauna abundance is
 impacted by biological invasions, (ii) that initial habitat structure has
 a strong influence on the outcome and (iii) that responses within the soil
 fauna differ between trophic levels a stronger response of primary
 consumers.
description: Data used in
 meta-analysis and to evaluate biasesContains the raw data
 for meta-analysis (mean soil fauna abundances with their variance for
 invaded and uninvaded plots) with all metadata and calculated effect
 sizes. Also contains data used to evaluate spatial, taxonomic and
 morphological biases within the collected dataset compared to database
 extracted values.dryad.data.OIK.06493.xlsx
DOI: 10.5061/dryad.10t7hd0
title: Data from: Acclimation temperature changes spermatozoa flagella length relative to head size in brown trout

description: Temperature is a ubiquitous environmental factor affecting physiological
 processes of ectotherms. Due to the effects of climate change on global
 air and water temperatures, predicting the impacts of changes in
 environmental thermal conditions on ecosystems is becoming increasingly
 important. This is especially crucial for migratory fish, such as the
 ecologically and economically vital salmonids, because their complex life
 histories make them particularly vulnerable. Here, we addressed the
 question whether temperature affects the morphology of brown trout, Salmo
 trutta L. spermatozoa. The fertilising ability of spermatozoa is commonly
 attributed to their morphological dimensions, thus implying direct impacts
 on the reproductive success of the male producing the cells. We show that
 absolute lengths of spermatozoa are not affected by temperature, but
 spermatozoa from warm acclimated S. trutta males have longer flagella
 relative to their head size compared to their cold acclimated
 counterparts. This did not directly affect sperm swimming speed, although
 spermatozoa from warm acclimated males may have experienced a hydrodynamic
 advantage at warmer temperatures, as suggested by our calculations of drag
 based on head size and sperm swimming speed. The results presented here
 highlight the importance of increasing our knowledge of the effects of
 temperature on all aspects of salmonid reproduction in order to secure
 their continued abundance.
description: 2019_Fenkes-et-al_BiO_S-trutta-spermatozoa_morphologyR code2019_Fenkes-et-al_BiO_S-trutta-abnormal_spermatozoaRaw data file a2019_Fenkes-et-al_BiO_S-trutta-spermatozoa_morphologyRaw data file b.2019_Fenkes-et-al_BiO_S-trutta-spermatozoa_morphology_averagedRaw data file c.2019_Fenkes-et-al_BiO_S-trutta-spermatozoa_head_dragRaw data file d.
DOI: 10.5061/dryad.8tp0900
title: Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat

description: This paper analyzes how partial selfing in a large source population
 influences its ability to colonize a new habitat via the introduction of a
 few founder individuals. Founders experience inbreeding depression due to
 partially recessive deleterious alleles as well as maladaptation to the
 new environment due to selection on a large number of additive loci. I
 first introduce a simplified version of the Inbreeding History Model
 (Kelly, 2007) in order to characterize mutation-selection balance in a
 large, partially selfing source population under selection involving
 multiple non-identical loci. I then use individual-based simulations to
 study the eco-evolutionary dynamics of founders establishing in the new
 habitat under a model of hard selection. The study explores how selfing
 rate shapes establishment probabilities of founders via effects on both
 inbreeding depression and adaptability to the new environment, and also
 distinguishes the effects of selfing on the initial fitness of founders
 from its effects on the long-term adaptive response of the populations
 they found. A high rate of (but not complete) selfing is found to aid
 establishment over a wide range of parameters, even in the absence of mate
 limitation. The sensitivity of the results to assumptions about the nature
 of polygenic selection are discussed.
description: Simulation codes in
 Fortrancodes.zip
DOI: 10.5061/dryad.9s2p177
title: Data from: Interspecific plant competition mediates the metabolic and ecological signature of a plant-herbivore interaction under warming and elevated CO2

description: 1. Biotic interactions shape community evolution, but we lack mechanistic
 insights on how metabolic and ecological processes under climate change
 are altered by biotic interactions. 2. We used a two-trophic model
 community consisting of the aphid Dysaphis plantaginea feeding on the forb
 Plantago lanceolata, and a grass competitor Lolium perenne that does not
 experience herbivory by the aphid. Monocultures and mixtures were exposed
 to the herbivory treatment and to three relevant simulated environmental
 changes as prevalent under current climate change (increased temperature,
 CO2, and increased temperature and CO2) 3. Elevated CO2 reduced the
 nitrogen content of P. lanceolata, while simultaneous increases of CO2 and
 temperature modified the plant metabolic component and the magnitude of
 these responses in different directions. Elevated CO2 enhanced defence
 systems in P. lanceolata, but these effects were not altered by warming.
 Interspecific plant competition did, however, neutralise these responses.
 There were no indirect effects of climate change on aphid population
 growth despite changes in plant defense, nutritional quality and biomass
 induced by our environmental change scenarios. 4. We thus demonstrate
 interactions between abiotic and biotic processes on plant metabolite
 profiles, but more importantly, that climate change effect on a selection
 of the metabolic pathways are altered by herbivory and competition. Our
 experiment under semi-natural conditions thus demonstrates the
 non-additive and often neutralizing effects of biotic interactions on
 plant metabolism and species performance under climate-associated
 environmental change.
description: data Functional
 EcologyAll raw data (and more)
 in EXCEL format
DOI: 10.5061/dryad.g3r3hp7
title: Data from: Identification of a dominant chlorosis phenotype through a forward screen of the Triticum turgidum cv. Kronos TILLING population

description: Durum wheat (Triticum turgidum) derives from a hybridization event
 approximately 400,000 years ago which led to the creation of an
 allotetraploid genome. The evolutionary recent origin of durum wheat means
 that its genome has not yet been fully diploidised. As a result, many of
 the genes present in the durum genome act in a redundant fashion, where
 loss-of-function mutations must be present in both gene copies to observe
 a phenotypic effect. Here we use a novel set of induced variation within
 the cv. Kronos TILLING population to identify a locus controlling a
 dominant, environmentally-dependent chlorosis phenotype. We carried out a
 forward screen of the sequenced cv. Kronos TILLING lines for senescence
 phenotypes and identified a line with a dominant early senescence and
 chlorosis phenotype. Mutant plants contained less chlorophyll throughout
 their development and displayed premature flag leaf senescence. A
 segregating population was classified into discrete phenotypic groups and
 subjected to bulked-segregant analysis using exome capture followed by
 next-generation sequencing. This allowed the identification of a single
 region on chromosome 3A, Yellow Early Senescence 1 (YES-1), which was
 associated with the mutant phenotype. While this phenotype was consistent
 across four years of field trials in the UK, the mutant phenotype was not
 observed when grown in Davis, CA (US). To obtain further SNPs for
 fine-mapping, we isolated chromosome 3A using flow sorting and sequenced
 the entire chromosome. By mapping these reads against both the cv. Chinese
 Spring reference sequence and the cv. Kronos assembly, we could identify
 high-quality, novel EMS-induced SNPs in non-coding regions within YES-1
 that were previously missed in the exome capture data. This allowed us to
 fine-map YES-1 to 4.3 Mb, containing 59 genes. Our study shows that
 populations containing induced variation can be sources of novel dominant
 variation in polyploid crop species, highlighting their importance in
 future genetic screens. We also demonstrate the value of using
 cultivar-specific genome assemblies alongside the gold-standard reference
 genomes particularly when working with non-coding regions of the genome.
 Further fine-mapping of the YES-1 locus will be pursued to identify the
 causal SNP underpinning this dominant, environmentally dependent
 phenotype.
description: Senescence Screen of the
 Kronos TILLING PopulationSenescence screen of the
 Kronos TILLING population Referred to in Harrington et al. 2019 doi:
 10.3389/fpls.2019.00963 The associated Excel file contains all phenotypic
 scores for heading, flag leaf senescence, and peduncle senescence of the
 Kronos TILLING population. The trial was carried out in 2015 at the John
 Innes Centre in Norwich, UK. Relevant information on trial design and
 field management practices are available in the associated paper
 (Harrington et al. 2019)TableforDryad.xlsx
DOI: 10.5061/dryad.89mt68q
title: Data from: Revisiting the functional response in habitat selection for large herbivores: a matter of spatial variation in resource distribution?

description: Most habitats are distributed heterogeneously in space, forcing animals to
 move according to both habitat characteristics and their needs for energy
 and safety. Animal space use should therefore vary according to habitat
 characteristics, a process known as the “functional response” in habitat
 selection. This response has often been tested vis-à-vis the proportion of
 a habitat category within areas available to individuals. Measuring
 sought-after resources in landscape where they are continuously
 distributed is a challenge and we posit here that both the mean
 availability of a resource and its spatial variation should be measured.
 Accordingly, we tested for a functional response in habitat selection
 according to these two descriptors of the resource available for a
 mountain herbivore. We hypothesized that selection should decrease with
 mean value of resources available and increase with its spatial variation.
 Based on GPS data from 50 chamois females and data on the actual foodscape
 (i.e. distribution of edible-only biomass in the landscape), we estimated
 individual selection ratio (during summer months) for biomass at the home
 range level, comparing edible biomass in individual home ranges and the
 mean and standard deviation of edible biomass in their available range.
 Chamois being a group-living species, available accessible ranges were
 shared by several individuals that formed socio-spatial groups (clusters)
 in the population. As expected, selection ratios increased with the
 standard deviation of edible resources in each cluster, but unlike our
 prediction, was unrelated to its mean. Selection of areas richer in
 resources hence did not fade away when more resources were available on
 average, a result that may be explained by the need for this capital
 breeder species to accumulate fat-reserve at a high rate during summer
 months. Low spatial variation could limit the selection of chamois, which
 highlights the importance of resource distribution in the process of
 habitat selection.
description: data_habitat selection
 for large herbivores_2019_07_15Data on habitat
 selection for food resource for 50 female chamois grouped by spatial
 clustering.
DOI: 10.5061/dryad.70q4744
title: Data from: Feedbacks between nitrogen fixation and soil organic matter increase ecosystem functions in diversified agroecosystems

description: Nitrogen (N) losses from intensified agriculture are a major cause of
 global change, due to nitrate (NO3-) export and the eutrophication of
 aquatic systems as well as emissions of nitrous oxide (N2O) into the
 atmosphere. Diversified agroecosystems with legume cover crops couple N
 and carbon (C) inputs to soil and reduce N pollution, but there is a need
 to identify controls on legume N2 fixation across ecosystems with variable
 soil conditions. Here, I tested the hypothesis that N mineralization from
 turnover of soil organic matter (SOM) regulates legume N2 fixation across
 10 farms that spanned a gradient of SOM levels. I separated soil samples
 into two SOM fractions, based on size and density, which are indicators of
 soil nutrient cycling and N availability (free particulate organic matter
 and intra-aggregate particulate organic matter (POM)). This study
 indicates downregulation of legume N2 fixation in diversified
 agroecosystems with increasing N availability in intra-aggregate POM and
 increasing N mineralization. Intercropping the legume with a grass
 weakened the relationship between N in POM and N2 fixation due to N
 assimilation by the grass. Further, mean rates of N and C mineralization
 across sites increased with two seasons of a legume-grass cover crop
 mixture, which could enhance this stabilizing feedback between soil N
 availability and N2 fixation over time. These results suggest a potential
 mechanism for the diversity-ecosystem function relationships measured in
 long-term studies of agroecosystems, in which regular use of legume cover
 crops increases total soil organic C and N and reduces the environmental
 costs of crop production.
description: Soil and N2
 FixationMerged baseline data
 from soil samples collected in fall 2014 or spring 2015 with data on
 biological nitrogen fixation by hairy vetch at biomass sampling in spring
 of 2016.Soil_2016BNF.csvN2 Fixation 2017Aboveground biomass and nitrogen content for hairy vetch and cereal rye, and biological nitrogen fixation by hairy vetch, measured in May, 2017.BNF2017.csvChange in soilEffect sizes for measured soil properties (i.e., the change in the property following two years of the cover crop mixture compared to the no cover control), calculated by subtracting the final value for each soil parameter measured in the mixture treatment from the final value measured in the no cover crop control at the May 2017 sampling.EffectSizes.csv