cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0vf86nb1
title: Data from: How depressed? Estimates of inbreeding effects during seed development depend on reproductive conditions

description: Inbreeding depression can reduce the performance of offspring produced by
 mating between relatives, with consequences for population dynamics and
 sexual-system evolution. In flowering plants, inbreeding depression
 commonly acts most intensely during seed development. This predispersal
 component is typically estimated by comparing seed production following
 exclusive self- and cross-pollination, but such estimates are unbiased
 only if seed production is limited by ovule availability, rather than by
 pollen receipt or seed-development resources. To overcome this problem, we
 propose experimental and statistical methods based on a model of ovule
 fertilization and seed development that accounts for differential
 fertilization by self- and cross-pollen, limited ovule viability or
 receptivity, differential survival of self- and cross-zygotes and limited
 resource availability. Simulations illustrate that the proposed methods
 eliminate bias in estimated predispersal inbreeding depression caused by
 pollen limitation and can improve estimates under resource limitation.
 Application of these methods to two orchid species further demonstrates
 their utility in identifying and estimating diverse influences on
 reproductive performance under typical conditions. Although our
 theoretical results raise questions about the reported intensity of
 predispersal inbreeding depression, our proposed methods guard against
 bias while also providing insight into plant reproduction.
description: Harder etal
 dataThe file contains two
 worksheets with data for Disa ferruginea and D. ophrydea concerning the
 proportion of outcross pollen applied to stigmas (pcmass), the number of
 ovules counted (ovule cnt), and the numbers of those ovules that were
 fertilized (fertilized) and developed into seeds (seeds). Each row
 represents the results from a single flower, with multiple flowers per
 plant. These data were used to estimate the relative success of self- and
 cross-pollen in fertilizing ovules, the relative survival of self- and
 cross-zygotes and inbreeding depression.Simulation
 modelThis spreadsheet
 implements simulations of seed production under specific conditions
 (including pollen, ovule or resource limitation) and was used to produce
 the results presented in Fig. 3e. Instructions are presented on the
 spreadsheet.
DOI: 10.5061/dryad.5h2sd
title: Data from: Growth trajectory influences temperature preference in fish through an effect on metabolic rate

description: Most animals experience temperature variations as they move through the
 environment. For ectotherms in particular, temperature has a strong
 influence on habitat choice. While well-studied at the species level, less
 is known about factors affecting the preferred temperature of individuals.
 Especially lacking is information on how physiological traits are linked
 to thermal preference and whether such relationships are affected by
 factors such feeding history and growth trajectory. This study examined
 these issues in the common minnow Phoxinus phoxinus, to determine the
 extent to which feeding history, standard metabolic rate (SMR) and aerobic
 scope (AS), interact to affect temperature preference. Individuals were
 either: 1) food-deprived for 21 days, then fed ad libitum for the next 74
 days; or 2) fed ad libitum throughout the entire period. All animals were
 then allowed to select preferred temperatures using a shuttle-box, and
 then measured for SMR and AS at 10°C, estimated by rates of oxygen uptake.
 Activity within the shuttle-box under a constant temperature regime was
 also measured. In both food-deprived and control fish, SMR was negatively
 correlated with preferred temperature. The SMR of the food-deprived fish
 was elevated compared to the controls, probably due to the effects of
 compensatory growth, and so these growth-compensated fish preferred
 temperatures that were on average 2.85°C cooler than controls fed a
 maintenance ration throughout the study. Fish experiencing compensatory
 growth also displayed a large reduction in activity. In growth-compensated
 fish and controls, activity measured at 10°C was positively correlated
 with preferred temperature. Individual fish prefer temperatures that vary
 predictably with SMR and activity level, which are both plastic in
 response to feeding history and growth trajectories. Cooler temperatures
 probably allow individuals to reduce maintenance costs and divert more
 energy towards growth. A reduction in SMR at cooler temperatures, coupled
 with a decrease in spontaneous activity, would also allow individuals to
 increase surplus aerobic scope for coping with environmental stressors. In
 warming climates, however, aquatic ectotherms could experience frequent
 fluctuations in food supply with long-lasting effects on metabolic rate
 due to compensatory growth, while simultaneously having limited access to
 preferred cooler habitats.
description: metabolic rate
 dataData on metabolic rate,
 growth rate, activity level, and final preferred temperature for each fish
 used in study.temperature preference
 dataTime course temperature
 preference data during an 8 hour period, during which the shuttle-box was
 in a dynamic mode.
DOI: 10.5061/dryad.22hn1
title: Data from: Pyramids of species richness: the determinants and distribution of species diversity across trophic levels

description: How species richness is distributed across trophic levels determines
 several dimensions of ecosystem functioning, including herbivory,
 predation, and decomposition rates. We perform a meta-analysis of 72 large
 published food webs to investigate their trophic diversity structure and
 possible endogenous, exogenous, and methodological causal variables.
 Consistent with classic theory, we found that published food webs can
 generally be described as ‘pyramids of species richness’. The food webs
 were more predator-poor, prey-rich and hierarchical than is expected by
 chance or by the niche or cascade models. The trophic species richness
 distribution also depended on centrality, latitude, ecosystem-type and
 methodological bias. Although trophic diversity structure is generally
 pyramidal, under many conditions the structure is consistently uniform or
 inverse-pyramidal. Our meta-analysis adds nuance to classic assumptions
 about food web structure: diversity decreases with trophic level, but not
 under all conditions, and the decrease may be scale-dependent.
description: supplemental food web
 dataData concerning each
 food web used in the meta-analysis.Raw
 data.csvnull
 modelsR code for producing the
 null models: random, niche, and cascadehierarchy
 measureR code for calculating
 GRCi and GRCo
DOI: 10.5061/dryad.pf064
title: Data from: Bees learn preferences for plant species that offer only pollen as a reward

description: The astonishing diversity of floral form in angiosperm plants is driven in
 large part by preferences of pollinators for various floral traits,
 including learned preferences. Remarkably, almost all of a vast literature
 on learning and memory in pollinators relates to nectar as a reward, even
 though bees and many flies, beetles, and butterflies must collect pollen.
 In this study, we asked if bees formed preferences for plant species from
 which pollen had been collected successfully. Using absolute conditioning,
 we gave pollen foraging bees experience with plant species that offered
 only pollen rewards. Naive bees generally showed modest preferences,
 whereas experienced bees adopted strong preferences for those species over
 alternative species not previously experienced. Learned preferences were
 retained for at least 24h, consistent with preferences learned with nectar
 rewards. These experience-mediated changes in preference raised the
 possibility that bees formed associations between particular floral
 features and pollen rewards. We therefore asked if learned preferences
 required that bees successfully collect pollen. Using differential
 conditioning, we determined that learned preferences were strongly
 influenced by receipt of a pollen reward. In a final experiment, we
 characterized the importance of 2 floral features, the corolla and the
 anther, in the expression of learned preferences. Although experience
 altered responses to both floral parts, responses to anthers were
 influenced more strongly. We discuss recent evidence in the literature for
 associative learning with pollen rewards and propose that learned
 preferences in the context of pollen collection have played an important
 role in floral display evolution.
description: Data and R scripts for
 bee preferenceThis zip file contains
 Excel files and R scripts that allow analysis and graphing of bee flower
 preference (rejections+acceptances only). Each R script indicates within
 it the corresponding Excel file to be analyzed. Data presented here is
 prepared for analysis. Raw data is available upon request from the
 corresponding author.SpeciesPreferenceData&Scripts_ARussell.zip
DOI: 10.5061/dryad.7rm62
title: Data from: Egg morphology fails to identify nests parasitized by conspecifics in common pochard: a test based on protein fingerprinting and including female relatedness

description: Conspecific brood parasites lay eggs in nests of other females of the same
 species. A variety of methods have been developed and used to detect
 conspecific brood parasitism (CBP). Traditional methods may be inaccurate
 in detecting CBP and in revealing its true frequency. On the other hand
 more accurate molecular methods are expensive and time consuming. Eadie
 developed a method for revealing CBP based on differences in egg
 morphology. That method is based on Euclidean distances calculated for
 pairs of eggs within a clutch using standardized egg measurements (length,
 width and weight). We tested the applicability of this method in the
 common pochard Aythya ferina using nests that were identified as
 parasitized (39 nests) or non-parasitized (16 nests) based on protein
 fingerprinting of eggs. We also analyzed whether we can distinguish
 between parasitic and host eggs in the nest. We found that variation in
 MED can be explained by parasitism but there was a huge overlap in MED
 between parasitized and non-parasitized nests. MED also increased with
 clutch size. Using discriminant function analysis (DFA) we found that only
 76.4% of nests were correctly assigned as parasitized or nonparasitized
 and only 68.3% of eggs as parasitic or host eggs. Moreover we found that
 MED in parasitized nests increased with relatedness of the females that
 laid eggs in the nest. This finding was supported by positive correlation
 between MED and estimated relatedness in female–female pairs. Although
 variation in egg morphology is associated with CBP, it does not provide a
 reliable clue for distinguishing parasitized nests from non-parasitized
 nests in common pochard.
description: Aythya ferina
 characteristics of eggsThe file contains
 information about eggs of Common pochard (Aythya ferina). Data were
 collected during 2004 - 2006 in the Třeboň Biosphere Reserve, South
 Bohemia, Czech Republic.AF_eggs_2004-2006_2.xlsx
DOI: 10.5061/dryad.dp0fc
title: Data from: Habitat fragmentation, not habitat loss, drives the prevalence of blood parasites in a Caribbean passerine

description: Habitat destruction due to human land-use activities is well recognized as
 a central threat to biodiversity. However, there is still debate about the
 relative influence of its two components, habitat loss and habitat
 fragmentation, mostly because few studies have been able to disentangle
 their respective effects. We studied mechanisms by which habitat
 destruction might influence the prevalence of vector-transmitted
 haemosporidian blood parasites of the genera Plasmodium and Haemoproteus
 the Lesser Antillean Bullfinch, Loxigilla noctis, on the Caribbean islands
 of Guadeloupe and Martinique . Starting from a large set of environmental
 descriptors (including metrics reflecting habitat loss, habitat
 fragmentation and landscape heterogeneity; as well as other variables not
 linked to habitat destruction, such as climatic conditions), we used PLS
 regression analyses to determine which variables were driving parasite
 prevalence on the islands. Our results showed that variables related to
 forest destruction were much more influential than other factors for all
 parasites analyzed on both islands. Remarkably, the effects documented
 were almost exclusively due to forest fragmentation, as opposed to habitat
 loss. This positive effect of forest fragmentation on blood parasite
 prevalence is proposed to happen through its effects on insect vectors
 and/or host biology. Increased understanding of the role of habitat
 fragmentation as a driver of parasitic diseases can help anticipate future
 effects and limit the risk of emergence and proliferation of wildlife
 pathogenic outbreaks and zoonosis through informed landscape planning.
description: Perez-Rodriguez et al.
 2018. Ecography. DATASETExcel file with data of
 parasite prevalence per sampling site, plus the climatic and habitat
 structure metrics associated to each sampling site.
DOI: 10.5061/dryad.rv71c
title: Data from: Suppression and facilitation of human neural responses

description: Efficient neural processing depends on regulating responses through
 suppression and facilitation of neural activity. Utilizing a well-known
 visual motion paradigm that evokes behavioral suppression and
 facilitation, and combining 5 different methodologies (behavioral
 psychophysics, computational modeling, functional MRI, pharmacology, and
 magnetic resonance spectroscopy), we provide evidence that challenges
 commonly held assumptions about the neural processes underlying
 suppression and facilitation. We show that: 1) both suppression and
 facilitation can emerge from a single, computational principle - divisive
 normalization; there is no need to invoke separate neural mechanisms, 2)
 neural suppression and facilitation in the motion-selective area MT mirror
 perception, but strong suppression also occurs in earlier visual areas,
 and 3) suppression is not primarily driven by GABA-mediated inhibition.
 Thus, while commonly used spatial suppression paradigms may provide
 insight into neural response magnitudes in visual areas, they should not
 be used to infer neural inhibition.
description: Schallmo_etal_2017_SuppressionFacilitationThis file contains the data for the manuscript entitled "Suppression and facilitation of human neural responses" Authors: Schallmo, M-P., Kale, A.M., Millin, R., Flevaris, A.V., Brkanac, Z., Edden, R.A.E., Bernier, R.A., Murray, S.O.
DOI: 10.5061/dryad.d87v3
title: Data from: Effects of grazing intensity on plant richness and diversity: a meta-analysis

description: Most of our knowledge of the effect of grazing on grassland structure is
 based on grazed-ungrazed contrasts. The effects of grazing in the most
 common scenario, where grazing intensity varies from low to high grazing
 intensity, are less known. The objectives of this paper were to (1)
 quantify the effect of stocking rates on species richness and diversity of
 grasslands world-wide, and (2) evaluate the response under different
 environmental and experimental conditions. We conducted a meta-analysis of
 experiments with at least two levels of controlled stocking rates and
 evaluated their effect on species richness and diversity. The results
 showed that the response of richness and diversity to either reducing or
 increasing stocking rate from a moderate level mostly fell within the
 range ± 25% or ± 5 species. Mean response of species richness and
 diversity to increasing stocking rate from moderate to high levels was
 negative. Mean response to lowering stocking rate from moderate levels was
 not different from 0. However, overall, species richness significantly
 decreased as stocking rate increased. The response of richness and
 diversity to stocking rate was not related to mean precipitation,
 productivity or aridity. However, the most negative responses of richness
 to stocking rate were larger in arid, low productivity systems than in
 subhumid and humid systems. The effects of grazing on richness and
 diversity found in this review were smaller than the effects on species
 composition shown by the literature. Thus, grazing drastically changes
 species composition, but the net change of species and diversity is much
 smaller.
description: Herrero-Jáuregui &
 Oesterheld 2017_DryadData on species richness
 and diversity under different stocking rates of domestic herbivores in 48
 studies all throughout the planetHerrero-Jáuregui &
 Oesterheld 2017_Dryad.xlsx
DOI: 10.5061/dryad.bs7rd
title: Data from: Mate choice in sticklebacks reveals that immunogenes can drive ecological speciation

description: Adaptation to ecologically contrasting niches can lead to the formation of
 new species. Theoretically, this process of ecological speciation can be
 driven by pleiotropic “magic traits” that genetically link natural and
 sexual selection. To qualify as a true magic trait, the pleiotropic
 function of a gene must be reflected in biologically relevant mechanisms
 underlying both local adaptation and mate choice. The immune genes of the
 major histocompatibility complex (MHC) contribute to parasite resistance
 and also play a major role in sexual selection. Hence, the MHC may encode
 a candidate magic trait. Using diverging 3-spined stickleback populations
 from a connected lake–river habitat, we show with mate choice experiments
 in a flow channel that polymorphic MHC genes probably underlie assortative
 mating with respect to particular habitat-adapted ecotypes, potentially
 resulting in reproductive isolation. By manipulating olfactory cues in
 controlled experiments, we show that female sticklebacks employ
 MHC-dependent male olfactory signals to select mates with which they can
 achieve a habitat-specific MHC gene structure that optimally protects
 their offspring against local parasites. By using MHC-based olfactory
 signals, females thus select individuals of their own population as mates.
 Our results demonstrate how mate choice and parasite resistance may be
 functionally linked. These findings suggest that MHC genes are pleiotropic
 and encode a true magic trait of biologically significant effect.
description: DATA for
 DRYADBehavioural experiments
 - times females have spent in front of each respective
 male.MHC
 allelse_DRYADTable with MHC alleles
 present in male and female sticklebacks used in the mate choice
 experiments.MHC
 alleles_DRYAD.docxMHC
 Alleles_sequencesMHC alllele sequences-
 complementary to MHC allele tablle.MHC_allele_Panel_DRYADIndividual MHC profiles for the fish used in the behavioural experiments
DOI: 10.5061/dryad.65p331m
title: Data from: Phylodynamic model adequacy using posterior predictive simulations

description: Rapidly evolving pathogens, such as viruses and bacteria, accumulate
 genetic change at a similar timescale over which their epidemiological
 processes occur, such that it is possible to make inferences about their
 infectious spread using phylogenetic time-trees. For this purpose it is
 necessary to choose a phylodynamic model. However, the resulting
 inferences are contingent on whether the model adequately describes key
 features of the data. Model adequacy methods allow formal rejection of a
 model if it cannot generate the main features of the data. We present
 TreeModelAdequacy (TMA), a package for the popular BEAST2 software, that
 allows assessing the adequacy of phylodynamic models. We illustrate its
 utility by analysing phylogenetic trees from two viral outbreaks of Ebola
 and H1N1 influenza. The main features of the Ebola data were adequately
 described by the coalescent exponential-growth model, whereas the H1N1
 influenza data was best described by the birth-death SIR model.
description: Supplementary_textTable S1FigS1Fig S1. Model adequacy results for Ebola virus data with four test statistics. The colours and symbols match those in Fig 2.FIgS1.pdfFigS2Fig S2. Model adequacy results for H1N1 influenza data with four test statistics. The colours and symbols match those in Fig 2. Note that the values are shown in log10 scale.
DOI: 10.5061/dryad.280t270
title: Data from: Belowground competition in forest and prairie

description: The hypothesis that the intensity of belowground competition varies with
 community standing crop was tested in forest and prairie in central
 Canada. Three plots were studied in each habitat. Forest had significantly
 higher soil nitrate, ammonium, water, and root biomass than prairie, but
 significantly lower root:shoot ratios. Transplants of a grass (Bouteloua
 gracilis) and a tree (Populus deltoides) were grown singly for one summer
 in both habitats with live neighbor roots either absent or present. Live
 neighbor roots were removed by cutting roots along the perimeter of a 10
 cm diameter circle to a depth of 15 cm and then inserting a plastic tube
 (10 cm diameter, 15 cm long) vertically into the soil. Transplants grown
 with live neighbor roots also had neighbor roots cut along the perimeter
 of a 10 cm diameter circle, but no tube was installed. There were ten
 replicates of each combination of species and root treatment in each plot.
 The aboveground biomass of transplants showed a significant interactive
 effect between habitat and competition treatment. Biomass was
 significantly lower in the presence of neighbor roots in prairie, but not
 in forest. Neighbor roots significantly decreased the survivorship of the
 tree but not the grass. Belowground competition was most intense in
 prairie, where the supply of soil resources was lowest.
description: Wilson93LightLight penetration data in prairie and aspen forest.Wilson93NitrogenSoil available nitrogen in prairie and aspen forest.Wilson93RootsRoot mass data in prairie and aspen forest.Wilson93StandingCropStanding crop and species composition data in prairie and aspen forest understory.Wilson93TransplantsTransplant biomass data in prairie and aspen forest.Wilson93TreesData describing neighboring tree sizes, used to estimate mass in aspen forest..Wilson93WaterSoil water content (gravimetric) in prairie and aspen forest.