cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.445742d
title: Data from: Native grass ground covers provide multiple ecosystem services in Californian vineyards

description: 1. The mechanisms responsible for the success or failure of agricultural
 diversification are often unknown. Most studies of arthropod pest
 management focus on enhancing the effectiveness of natural enemies, but
 non-crop plants can also improve or hamper pest suppression by changing
 the host quality of crop plants by reducing or adding available soil
 nutrients or water. Native perennial ground covers may provide resources
 and long-term habitat to resident natural enemies and be more compatible
 than exotic annuals for crop management in terms of competition for soil
 nutrients or water. 2. A three-year study was conducted in a California
 vineyard to examine the impacts of native perennial grasses on pests,
 natural enemies, crop plant condition and soil properties. Three ground
 cover treatments were included: bare soil with a grower standard drip
 irrigation, native grasses with the drip irrigation, or native grasses
 with the drip irrigation and an additional flood irrigation to keep the
 grasses green and growing during the season. 3. Numbers of leafhopper
 pests (Erythroneura spp.) decreased in both native grass treatments, where
 parasitism rates and spider densities were higher. 4. Nitrate levels in
 vine leaf petioles were lower in grass treatments, indicating competition
 with vines for soil nitrogen, which is most often considered to be
 detrimental. Berry weight was higher in the irrigated treatment but did
 not differ between the bare soil and non-irrigated native grass
 treatments. Grape quality (brix) was similar in the bare soil and native
 grass treatments, suggesting that increased soil moisture in the presence
 of native grasses did not compromise grape quality. In fact, leaf water
 stress was lower and available soil moisture higher not only in the
 irrigated native grass treatment but, at times, in the non-irrigated
 native grass treatment, in comparison to the no ground cover treatment. 5.
 We conclude that native grasses contributed to a reduction in leafhopper
 density by reducing host quality through competition with vines for soil
 nitrogen and providing food resources and/or habitat for natural enemies.
 Native grasses also improved soil water content and may be part of a water
 conservation program for perennial crops in dry climate regions.
description: Daane et al native
 grasses leafhopper data setsEach study is provided
 as a separate worksheet in the excel file
DOI: 10.5061/dryad.rd25r
title: Data from: Are more diverse parts of the mammalian skull more labile?

description: Morphological variation is unevenly distributed within the mammalian
 skull; some of its parts have diversified more than others. It is commonly
 thought that this pattern of variation is mainly the result of the
 structural organization of the skull, as defined by the pattern and
 magnitude of trait covariation. Patterns of trait covariation can
 facilitate morphological diversification if they are aligned in the
 direction of selection, or these patterns can constrain diversification if
 oriented in a different direction. Within this theoretical framework, it
 is thought that more variable parts possess patterns of trait covariation
 that made them more capable of evolutionary change, that is, are more
 labile. However, differences in the degree of morphological variation
 among skull traits could arise despite variation in trait lability if, for
 example, some traits have evolved at a different rate and/or undergone
 stabilizing selection. Here, we test these hypotheses in the mammalian
 skull using 2D geometric morphometrics to quantify skull shape and
 estimating constraint, rates of evolution, and lability. Contrary to the
 expectations, more variable parts of the skull across mammalian species
 are less capable of evolutionary change than are less variable skull
 parts. Our results suggest that patterns of morphological variation in the
 skull could result from differences in rate of evolution and stabilizing
 selection.
description: Size-corrected
 Procrustes coordinates of the mammalian braincaseMammalian braincase
 shape (7 landmarks and 4 semi-landmarks) based on a compilation of 467 2D
 images from open online resources. Species nomenclature followed Wilson
 and Reeder's Mammals Species of the World, which was also used for
 constructing the supertree (Bininda-Emonds et al 2007). The file is a
 tab-delimited text.correctedBRAINCASE.txtSize-corrected Procrustes coordinates of the mammalian faceMammalian face shape (6 landmarks and 2 semi-landmarks) based on a compilation of 467 2D images from open online resources. Species nomenclature followed Wilson and Reeder's Mammals Species of the World, which was also used for constructing the supertree (Bininda-Emonds et al 2007). The file is a tab-delimited text.correctedFACE.txtSize-corrected Procrustes coordinates of the mammalian craniumMammalian cranium shape (13 landmarks and 6 semi-landmarks) based on a compilation of 207 2D images from open online resources. Species nomenclature followed Wilson and Reeder's Mammals Species of the World, which was also used for constructing the supertree (Bininda-Emonds et al 2007). The file is a tab-delimited text.correctedCRANIUM.txtSize-corrected Procrustes coordinates of the mammalian mandibleMammalian mandible shape (4 landmarks and 6 semi-landmarks) based on a compilation of 207 2D images from open online resources. Species nomenclature followed Wilson and Reeder's Mammals Species of the World, which was also used for constructing the supertree (Bininda-Emonds et al 2007). The file is a tab-delimited text.correctedMAND.txt
DOI: 10.5061/dryad.c377tq8
title: Data from: Forest disturbance and seasonal food availability influence a conditional seed dispersal mutualism

description: The interaction between granivorous scatter-hoarding mammals and plants is
 a conditional mutualism: scatter-hoarders consume seeds (acting as
 predators), but the movement of seed by scatter-hoarders may contribute to
 dispersal (acting as mutualists). Understanding the ecological factors
 that shape this relationship is highly relevant in anthropogenically
 disturbed tropical forests where large-bodied frugivores are extirpated.
 In such forests, large-seeded trees that once depended on these frugivores
 for dispersal may now only have scatter-hoarders as prospective
 dispersers. We studied Carapa oreophila (Meliaceae) in an Afromontane
 forest, to test the hypotheses that the proportion of seeds immediately
 consumed or hoarded (dispersed) would vary over a disturbance gradient.
 Temporal replication also afforded exploration of how habitat effects
 might vary with food availability. Using a Bayesian framework, we
 demonstrate that seeds were more likely to be hoarded in less disturbed
 forest, irrespective of temporal variation in food abundance. In contrast,
 forest disturbance only appeared to increase seed predation in temporal
 replicates that coincided with sustained food availability. These results
 highlight the potential variability in the dynamics between plants and
 scatter-hoarders over fine temporal scales, elucidating possible
 ecological scenarios where scatter-hoarders might act as mutualists
 (contributing positively to plant recruitment). Our study also fills
 important knowledge gaps about the importance of scatter-hoarders as
 dispersers in tropical forests depleted of large-bodied frugivores,
 particularly in Africa where scatter-hoarding mutualisms have not been
 extensively studied.
description: Aliyu_2017_Biotropica_CarapaCondMut_DATA_Phenology_LargeSeededSpeciesFruiting phenology of selected large-seeded and moderately large-seeded tree species in Ngel Nyaki during the 2011 sampling year of the study.Aliyu_2017_Biotropica_CarapaCondMut_CODE_Phenology_LargeSeededSpeciesCode to plot the phenology data in the file: Aliyu_2017_Biotropica_CarapaCondMut_DATA_Phenology_LargeSeededSpecies.csvAliyu_2017_Biotropica_CarapaCondMut_DATA_SeedFatesSeed fate data for the main experiment and analyses.
DOI: 10.5061/dryad.p763611
title: Data from: Effects of interspecific coexistence on laying date and clutch size in two closely related species of hole‐nesting birds

description: Coexistence between great tits Parus major and blue tits Cyanistes
 caeruleus, but also other hole‐nesting taxa, constitutes a classic example
 of species co‐occurrence resulting in potential interference and
 exploitation competition for food and for breeding and roosting sites.
 However, the spatial and temporal variations in coexistence and its
 consequences for competition remain poorly understood. We used an
 extensive database on reproduction in nest boxes by great and blue tits
 based on 87 study plots across Europe and Northern Africa during 1957–2012
 for a total of 19,075 great tit and 16,729 blue tit clutches to assess
 correlative evidence for a relationship between laying date and clutch
 size, respectively, and density consistent with effects of intraspecific
 and interspecific competition. In an initial set of analyses, we
 statistically controlled for a suite of site‐specific variables. We found
 evidence for an effect of intraspecific competition on blue tit laying
 date (later laying at higher density) and clutch size (smaller clutch size
 at higher density), but no evidence of significant effects of
 intraspecific competition in great tits, nor effects of interspecific
 competition for either species. To further control for site‐specific
 variation caused by a range of potentially confounding variables, we
 compared means and variances in laying date and clutch size of great and
 blue tits among three categories of difference in density between the two
 species. We exploited the fact that means and variances are generally
 positively correlated. If interspecific competition occurs, we predicted a
 reduction in mean and an increase in variance in clutch size in great tit
 and blue tit when density of heterospecifics is higher than the density of
 conspecifics, and for intraspecific competition, this reduction would
 occur when density of conspecifics is higher than the density of
 heterospecifics. Such comparisons of temporal patterns of means and
 variances revealed evidence, for both species, consistent with
 intraspecific competition and to a smaller extent with interspecific
 competition. These findings suggest that competition associated with
 reproductive behaviour between blue and great tits is widespread, but also
 varies across large spatial and temporal scales.
description: DensityClasses
 29072018All
 data
DOI: 10.5061/dryad.mg6jb
title: Data from: Condition dependence of female choosiness in a field cricket

description: Females generally choose mates that produce the loudest, brightest or most
 elaborate sexual displays, and these costly male displays are predicted to
 be condition dependent. However, mate choice itself is a costly behaviour
 also expected to be condition dependent. Male fall field crickets, Gryllus
 pennsylvanicus, produce a conspicuous long-distance calling song that
 attracts females and is condition dependent. In this study, we tested the
 condition dependence of female preferences (preference function and
 choosiness) for male calling effort in G. pennsylvanicus. We manipulated
 female condition by raising crickets from hatching on either a low- or
 high-quality diet. In a series of two-speaker phonotaxis trials, both low-
 and high-condition females preferred playbacks reflecting greater calling
 effort. However, relative to low-condition females, high-condition females
 took significantly longer to make a choice, were more likely to fail to
 choose within the time allotted for a phonotaxis trial and significantly
 increased their latency to choose over the course of multiple trials. We
 discuss these results with respect to the possibility that female G.
 pennsylvanicus may be foraging for direct benefits when they choose their
 mates.
description: Judgeetal2014JEB_dataTab-delimited text file of data.Judgeetal2014JEB_dataComma-separated values file of data.
DOI: 10.5061/dryad.kf132
title: Data from: Meniscus ascent by thrips (Thysanoptera)

description: Meniscus climbing using a fixed body posture has been well documented for
 various aquatic and neustonic insects, but is not known from small flying
 insects that inadvertently become trapped on water surfaces. Here, we show
 that thrips (order Thysanoptera) can ascend a meniscus by arching their
 non-wetting bodies to translate head-first and upward along a water
 surface; if initially oriented backwards, they can turn by 180° to ascend
 head-first, and climb upward on a surrounding boundary. Using
 variable-concentration sucrose solutions, we show that translational and
 climbing speeds during meniscus ascent vary inversely with fluid
 viscosity. Becoming trapped in water is a frequent event for flying
 insects, and given that most of them are very small, dedicated behaviours
 to escape water may be commonplace among pterygotes.
description: kinematic data of thrips
 during meniscus-climbingTime series of
 instantaneous body position, speed and acceleration of thrips during
 meniscus ascent on variable sucrose solutions (Brix).Dryad_Raw_data_Ortega_Jimenez_etal_2016.ods
DOI: 10.5061/dryad.6jg5g
title: Data from: Discrimination of volatiles in herbal formula Baizhu Shaoyao San before and after processing using needle trap device with multivariate data analysis

description: To characterize the chemical differences of volatile components between
 crude and processed Baizhu Shaoyao San (BSS), a classical Chinese herbal
 formula that is widely applied in the treatment of gastrointestinal
 diseases, we developed a GC–MS-based needle trap device combined with
 multivariate data analysis to globally profile volatile components and
 rapidly identify differentiating chemical markers. Using a triple-bed
 needle packed with Carbopack X, DVB, and Carboxen 1000 sorbents, we
 identified 121 and 123 compounds respectively in crude and processed BSS.
 According to the results of principal component analysis and orthogonal
 partial least squares-discriminant analysis, crude and processed BSS were
 successfully distinguished into two groups with good fitting and
 predicting parameters. Furthermore, 21 compounds were identified and
 adopted as potential markers that could be employed to quickly
 differentiate these two types of samples using S-PLOT and variable
 importance in projection analyses. The established method can be applied
 to explain the chemical transformation of Chinese medicine processing in
 BSS and further control the quality and understand the processing
 mechanism of Chinese herbal formulae. Besides, the triple-bed needle
 selected and optimized in this study can provide a valuable reference for
 other plant researches with similar components. Furthermore, the
 systematic research on compounds identification and markers discrimination
 of the complex components in crude and processed BSS could work as an
 example for other similar studies, such as composition changes in one
 plant during different growth periods, botanical characters of different
 medicinal parts in same kind of medicinal herbs, and quality
 identification of one species of medicinal herb from different regions.
description: Raw data of peak numbers
 and their corresponding areasRaw data of peak numbers
 and their corresponding areas from crude and processed samples obtained
 form GC-MS for multivariate data analysis.raw
 data.xlsxPCA and OPLS-DA
 dataThis is a simca-p type
 file, which contain the relavant parameters of PCA and OPLS-DA
 models.PCA
 and OPLS-DA.usp
DOI: 10.5061/dryad.3ft19
title: Data from: IKey+: a new single-access key generation web service

description: Single-access keys are a major tool for biologists who need to identify
 specimens. The construction process of these keys is particularly complex
 (especially if the input dataset is large) so having an automatic
 single-access key generation tool is essential. As part of the European
 project ViBRANT, our aim was to develop such a tool as a web service, thus
 allowing end-users to integrate it directly into their workflow.
 IKey+generates single-access keys on demand, for single users or research
 institutions. It receives user input data (using the standard SDD format),
 accepts several key-generation parameters (affecting the key topology and
 representation), and supports several output formats. IKey+ is freely
 available (sources and binary packages) at www.identificationkey.fr.
 Furthermore, it is deployed on our server and can be queried (for testing
 purposes) via a simple web client also available at
 www.identificationkey.fr. Finally a client plugin will be integrated to
 the Scratchpads biodiversity networking tool (scratchpads.eu).
description: Appendix1Main algorithmAppendix2Ancillary functionsAppendix3Discriminant power functionsAppendix4reference test configurationAppendix5tests setupsAppendix6This graph presents the results of the performance tests we ran on IKey+, the blue bars represent the time necessary for each test to complete, and the red curve represents the number of queries rejected by IKey+ for each test (IKey+ rejects any query received when the CPU load of the host server is greater than 80%). These results clearly show that, among the parameters available to the end-user, only the score method parameter has a significant influence on the time needed to complete the test (tests 2d & 2e) The results of tests 4a to 4c show that increasing the number of simultaneous threads querying IKey+ increases the number of rejected queries. On the other hand, the test 4d shows that adding a random delay (0-1000 ms) at the start of each thread decreases the number of rejected queries dramatically, even with a large number of simultaneous threads (100 in test 4d). This is encouraging, since we consider this setup to be the closest to a production environment.Appendix7Usability test results
DOI: 10.5061/dryad.rp3pc
title: Data from: Strong selection genome-wide enhances fitness trade-offs across environments and episodes of selection

description: Fitness trade-offs across episodes of selection and environments influence
 life-history evolution and adaptive population divergence. Documenting
 these trade-offs remains challenging as selection can vary in magnitude
 and direction through time and space. Here, we evaluate fitness trade-offs
 at the levels of the whole organism and the quantitative trait locus (QTL)
 in a multiyear field study of Boechera stricta (Brassicaceae), a
 genetically tractable mustard native to the Rocky Mountains. Reciprocal
 local adaptation was pronounced for viability, but not for reproductive
 components of fitness. Instead, local genomes had a fecundity advantage
 only in the high latitude garden. By estimating realized selection
 coefficients from individual-level data on viability and reproductive
 success and permuting the data to infer significance, we examined the
 genetic basis of fitness trade-offs. This analytical approach (Conditional
 Neutrality-Antagonistic Pleiotropy, CNAP) identified genetic trade-offs at
 a flowering phenology QTL (costs of adaptation) and revealed genetic
 trade-offs across fitness components (costs of reproduction). These
 patterns would not have emerged from traditional ANOVA-based QTL mapping.
 Our analytical framework can be applied to other systems to investigate
 fitness trade-offs. This task is becoming increasingly important as
 climate change may alter fitness landscapes, potentially disrupting
 fitness trade-offs that took many generations to evolve.
description: Fitness data at the
 family and individual level. Genotypic data for each
 family.Anderson Lee and Mitchell-Olds
 Dryad.xlsx
DOI: 10.5061/dryad.sc1pq
title: Data from: Habitat patch arrangement and metapopulation persistence of predators and prey

description: This study tests whether spatial dynamics can stabilize metapopulations
 with a small number of patches and tests the influence of patch
 arrangement. I measured persistence of predator and prey protists in
 replicated microcosms with two to four patches. Predators persisted for
 85–437 generations (26–130 d). As predicted by single-species and/or
 predator-prey metapopulation models, substantial variation in predator
 metapopulation persistence was accounted for by the amount of patches or
 habitat, number of dispersal corridors, maximum interpatch distance, and
 proportion of patches providing colonists (which depends on the explicit
 spatial arrangement of patches). Contrary to expectation, persistence was
 not influenced by loops of patches or patch similarity. Persistence was
 also shorter in four-patch loops than three-patch loops, indicating an
 interaction between patch number and arrangement, which is not predicted
 by published models. Spatial synchrony of density fluctuations was central
 to predator persistence but had complex effects on extinction-colonization
 dynamics, rescue effects, and predator-prey interaction strength. Levins’s
 model, containing only extinction-colonization dynamics, predicted patch
 occupancy for prey but not predators. Predators did, however, show rescue
 effects and changes in interaction strength. This work illustrates the
 need to combine experimentation with modeling to understand the mechanisms
 of spatial dynamics.
description: Persistence_timesPersistence time in days for each microcosm.Am_nat_2000_series_for_DryadDensities of predators and prey for all microcosms. See Key to microcosm types to relate microcosm numbers to treatments.Key_to_microcosm_typesTable relating microcosm numbers to Figure 1 in the published paper.Notes_for_Holyoak_2000Information about data files and their interpretationDiagram_of_microcosmsAdobe PDF document containing a hand-drawn diagram that includes microcosm numbers, treatments letters in caps (as in Holyoak 2000 in Am. Nat) and the label lower case letters a-d for individual bottles. The labeling scheme is also described in the plain text information file but is included here for additional clarity.