cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tn9775r
title: Data from: Non-linear effects of phenological shifts link inter-annual variation to species interactions

description: 1. The vast majority of species interactions are seasonally structured and
 depend on species’ relative phenologies. However, differences in the
 phenologies of species naturally vary across years and are altered by
 ongoing climate change around the world. 2. By combining experiments that
 shifted the relative hatching of two competing tadpole species across a
 productivity gradient with simulations of inter-annual variation in
 arrival times I tested how phenological variation across years can alter
 the strength and outcome of interspecific competition. 3. Shifting the
 relative timing of hatching (phenology) of a species fundamentally altered
 interspecific competition, and the effect of shifting the timing on
 competition was highly non-linear for most demographic rates. Furthemore,
 this relationship varied with productivity of the system. As a
 consequence, (i) shifts in relative timing of phenologies had small or
 large effects depending on the average natural timing of interactions, and
 (ii) changes in the inter-annual variation in onset of interaction alone
 can alter species interactions in simulations even when mean phenologies
 (timing) remain unchanged across years. 4. Traditionally, studies on
 phenologies focus on directional shifts in the mean of phenologies, but
 our results suggest that we also need to consider inter-annual variation
 in phenologies of interacting species to predict dynamics of natural
 communities and how they will be modified by climate change.
description: Emergence, survival and
 biomass as function of arrival time of two competing tadpole
 speciesCSV viles with
 Emergence, survival and biomass and growth rates as function of relative
 arrival time of two competing tadpole species, including simple R code for
 simulation variation in arrival time to estimate expected
 survival.Variance Arrival
 Data.zip
DOI: 10.5061/dryad.2j4vj
title: Data from: Direct and indirect effects of nursery habitats on coral-reef fish assemblages, grazing pressure, and benthic dynamics

description: Migrating species are common within seascapes, but the potential for these
 movements to alter the populations and functional roles of non-migrating
 species (e.g. by increasing predation) is rarely investigated. This study
 considers whether the presence of nursery habitats (mangroves and
 seagrass) simply enhances the abundance of nursery-using parrotfishes and
 piscivores on nearby coral reefs, or also affects other parrotfishes. Data
 from 131 reef sites and multiple seascape configurations across 13 degrees
 of latitude were used to model correlations between biophysical variables,
 including nursery habitat connectivity, and the abundance and grazing
 pressure of both nursery-using species and other parrotfishes and
 piscivore biomass. Connectivity to mangroves and dense seagrass was
 positively correlated with the biomass of nursery-using species, but was
 also negatively correlated with non-nursery parrotfish populations. This
 reduction may be caused indirectly by nursery habitats increasing
 confamilial competition and predation by nursery-using piscivores,
 particularly affecting small parrotfishes settling directly onto reefs. As
 key reef grazers, parrotfishes affect coral demographics. Consequently, a
 spatial simulation model predicted the impacts after five years of changes
 in grazing pressure because of nursery habitat connectivity. The model
 demonstrated that high nursery connectivity was correlated to changes in
 grazing pressure on nearby reefs that could potentially lead to
 differences in coral cover of ∼3–4% when compared to low connectivity
 reefs. However, the direction of this change depended on the seascapes’
 characteristics. Historically, large-bodied, nursery-using parrotfish
 would have increased grazing in all nursery-rich seascapes. Overfishing
 means that nursery availability may have spatially variable impacts on
 coral cover, influencing reserve design. This study suggests that nursery
 availability may directly and indirectly modify an ecological process, and
 alter an ecological cascade (migrating species increase predator and
 competitor abundances, affecting other grazers and consequently corals).
 Therefore, elucidating the multi-species impacts of animal movements is
 required to better understand ecosystem functioning.
description: Dryad data Harborne et
 al Oikos OIK-02602The spreadsheet contains
 three worksheets. The first two sheets provide the raw field data that was
 input into the linear mixed-effects models to generate Table 1 and 2 and
 Figs 2 and 3. Variables are separated into explanatory and response
 variables, and the labels are self-explanatory. Collection methods are
 described in the paper. The third sheet provides the outputs of the
 simulation model that was plotted to create Fig 4. Model design and
 parameterisation are described in the paper.
DOI: 10.5061/dryad.gk15b
title: Data from: Behavioural flexibility in spider mites: oviposition site shifts based on past and present stimuli from conspecifics and predators

description: Predator-experienced individuals often change their predation avoidance
 response when they re-encounter the same predators or their cues. Recent
 reports show that behavioural change sometimes occurs even before the
 re-encounter. To function as an adaptive strategy in the wild, such
 prospective experience-induced behaviour should change flexibly in
 response to changing situations. We assessed flexibility of
 experience-induced oviposition site shift in two closely related species
 of spider mites, Tetranychus kanzawai and T. urticae, from the viewpoint
 of reducing future predation risk on their eggs. We found that: (i)
 individuals of T. kanzawai shifted oviposition site depending on the
 presence of conspecific eggs; (ii) after experiencing predation threat T.
 kanzawai females shifted oviposition site even in the absence of any
 current predation threat; (iii) this experience-induced shift of
 oviposition site was weakened in the presence of conspecific males; and
 (iv) experience-induced behaviour was retained for a shorter period in T.
 urticae than in T. kanzawai, possibly because the demand for learning may
 differ with regard to biological conditions encountered in the wild.
description: Supplementary dataset
 1The
 number of eggs laid on the web or on the leaf surface by each replicate in
 Exp. 1.ESM1
 Dataset.xlsxSupplementary dataset
 2The
 number of eggs laid on the web or on the leaf surface by each replicate in
 Exp. 2.ESM2
 Dataset.xlsxSupplementary dataset
 3The
 number of eggs laid on the web or on the leaf surface by each replicate in
 Exp. 3.ESM3
 Dataset.xlsxSupplementary dataset
 4The
 number of eggs laid on the web or on the leaf surface by each replicate in
 Exp. 4.ESM4
 Dataset.xlsx
DOI: 10.5061/dryad.486155q
title: Data from: The shortfall of sociality: group-living affects hunting performance of individual social spiders

description: Ineffective hunters in cooperative foraging groups may be shielded from
 natural selection by their more effective group mates, whereas those
 living solitarily would starve and thus be removed from the population.
 The problem may be exacerbated in large groups where it may be easier for
 individuals to withhold participation. Group foragers may thus be
 ineffective individual hunters or exhibit greater inter-individual
 variation in hunting abilities, in particular when living in large groups.
 We test these hypotheses in spider species of the genus Anelosimus that
 differ in their level of sociality and, among social species, in colonies
 of different sizes. We found that individuals from the more social
 species, and those from larger groups, reacted more slowly to prey than
 those from solitary species or small groups. Individuals from these
 categories also had greater inter-individual variation in reaction times.
 Individuals from large social groups also had lower prey capture success
 than those from small ones. These differences may have been driven by the
 size of the group from which the social individuals were taken, as those
 from small colonies behaved similarly to individuals of the two less
 social species. This finding suggests that hunting ability may develop as
 a phenotypically plastic trait.
description: Individual hunt data -
 summarizedDemographic and prey
 capture data on each spider tested. Data include female size, colony size
 and population, average web volume and average capture rate over three
 feeding trials.Individual hunt data -
 trial dataTrial data for each of
 the 3 trials that each spider was subjected to. Data include reaction
 times, outcomes, and size of webbing.
DOI: 10.5061/dryad.dh3h417
title: Data from: Exposure to predators does not lead to the evolution of larger brains in experimental populations of threespine stickleback

description: Natural selection is often invoked to explain differences in brain size
 among vertebrates. However, the particular agents of selection that shape
 brain size variation remain obscure. Recent studies suggest that predators
 may select for larger brains because increased cognitive and sensory
 abilities allow prey to better elude predators. Yet, there is little
 direct evidence that exposure to predators causes the evolution of larger
 brains in prey species. We experimentally tested this prediction by
 exposing families of 1000-2000 F2 hybrid benthic-limnetic threespine
 stickleback to predators under naturalistic conditions, along with matched
 controls. After two generations of selection, we found that fish from the
 predator addition treatment had significantly smaller brains (specifically
 smaller telencephalons and optic lobes) than fish from the control
 treatment. After an additional generation of selection, we reared
 experimental fish in a common environment and found that this difference
 in brain size was maintained in the offspring of fish from the predator
 addition treatment. Our results provide direct experimental evidence that
 (a) predators can indeed drive the evolution of brain size – but not in
 the fashion commonly expected and (b) that the tools of experimental
 evolution can be used to the study the evolution of the vertebrate brain.
description: Experimental pond brain
 size measurementsMeasurements of the size
 of four different parts of the brain in threespine sticklebacks collected
 from experimental ponds. See readme for complete breakdown of columns
 etc.experimental_pond_brain_size_samuk_et_al_2018.txtCommon garden brain size measurementsMeasurements of the size of four different parts of the brain in threespine sticklebacks collected from experimental ponds as fry and reared in a common laboratory environment. See readme for complete breakdown of columns etc.common_garden_brain_size_samuk et_al_2018.txt
DOI: 10.5061/dryad.8qp00
title: Data from: Experimental evidence that brighter males sire more extra-pair young in tree swallows

description: Across taxa, extra-pair mating is widespread among socially monogamous
 species, but few studies have identified male ornamental traits associated
 with extra-pair mating success, and even fewer studies have experimentally
 manipulated male traits to determine whether they are related directly to
 paternity. As a consequence, there is little experimental evidence to
 support the widespread hypothesis that females choose more ornamented
 males as extra-pair mates. Here, we conducted an experimental study of the
 relationship between male plumage colour and fertilization success in tree
 swallows (Tachycineta bicolor), which have one of the highest levels of
 extra-pair mating in birds. In this study, we experimentally dulled the
 bright blue plumage on the back of males (with nontoxic ink markers) early
 in the breeding season prior to most mating. Compared with control males,
 dulled males sired fewer extra-pair young, and, as a result, fewer young
 overall. Among untreated males, brighter blue males also sired more
 extra-pair young, and in paired comparisons, extra-pair sires had brighter
 blue plumage than the within-pair male they cuckolded. These results,
 together with previous work on tree swallows, suggest that extra-pair
 mating behaviour is driven by benefits to both males and females.
description: Explanation of
 variablesThis file provides an
 explanation for variables used in all other data files associated with
 this manuscript.ALL Males
 RSReproductive success
 data for all males in the study.Exptl Males Before After
 TreatmentData for experimental
 males before and after plumage treatmentUntreated Males RS &
 PlumageData for male
 reproductive success and plumage color of untreated
 males.WPS vs EPS Paired
 PlumagePlumage data paired for
 within-pair sires and the extra-pair sire(s) that cuckolded
 them.
DOI: 10.5061/dryad.c0g7r
title: Data from: The whitefly-associated facultative symbiont Hamiltonella defensa suppresses induced plant defences in tomato

description: 1. Maternally inherited bacterial symbionts are present in many, if not
 most, insect species. While there is rapidly accumulating evidence that
 facultative, heritable symbionts often protect insect hosts from natural
 enemies, there have been few clear examples where facultative symbionts
 mediate herbivore–plant interactions. 2. The phloem-feeding whitefly,
 Bemisia tabaci, is a major agricultural pest that frequently harbours
 facultative symbionts, including Hamiltonella defensa. While H. defensa
 and other facultative symbionts have been shown to improve whitefly
 performance on particular food plants, no direct and specific roles for
 symbiont-mediated interactions with food plants have been identified. 3.
 Here, we conducted a series of assays to determine whether infection with
 H. defensa improved whitefly performance on tomato (Solanum lycopersicum)
 and whether this benefit was associated with symbiont effects on induced
 plant defences. Finally, we tested whether impacts on induced defences
 involved in the modulation of a salivary factor. 4. The downregulation of
 plant defences was associated with increased whitefly fecundity and
 survival. Feeding by H. defensa-infected whiteflies suppressed JA and
 JA-related anti-herbivore-induced defences in tomato relative to
 uninfected controls. That saliva-only treatments of damaged tomato leaves
 from H. defensa-infected whiteflies suppressed induced plant defences
 compared to saliva from uninfected controls, suggesting that elicitors in
 saliva were responsible. Characterization of the putative salivary
 factor(s) revealed they are likely small (&lt; 3-kDa) and
 nonproteinaceous. 5. Interestingly, suppression of defences was not
 observed in SA-deficient NahG plants, indicating that suppression of
 JA-regulated defences depends on the SA signalling pathway. This finding
 reveals an intriguing example of the crosstalk between SA and JA
 signalling pathways and suggests that infection with facultative symbionts
 can result in the manipulation of induced plant defences to the benefit of
 the insect host and heritable symbiont. 6. Our results show that the
 bacterial symbiont H. defensa mediates whitefly–plant interactions by
 suppressing induced plant defences in tomato. This finding is among the
 first showing a direct role for facultative symbionts in mediating
 plant–herbivore interactions and demonstrates a novel tactic for insect
 herbivores to circumvent plant defences. Symbiont-mediated suppression of
 plant defences may enhance the deleterious effects of insect pests feeding
 on important crops.
description: symbiont-mediated
 suppression of induced-defenses
DOI: 10.5061/dryad.pk8hp
title: Data from: A meta-analysis of nestedness and turnover components of beta diversity across organisms and ecosystems

description: The number of studies investigating the nestedness and turnover components
 of beta diversity has increased substantially, but our general
 understanding of the drivers of turnover and nestedness remains elusive.
 Here, we examined the effects of species traits, spatial extent, latitude
 and ecosystem type on the nestedness and turnover components of beta
 diversity. From the 99 studies that partition total beta diversity into
 its turnover and nestedness components, we assembled 269 and 259 data
 points for the pairwise and multiple site beta-diversity metrics,
 respectively. Our data covered a broad variation in species dispersal
 type, body size and trophic position. The data were from freshwater,
 marine and terrestrial realms, and encompassed geographical areas from the
 tropics to near polar regions. We used linear modelling as a
 meta-regression tool to analyse the data.Pairwise turnover, multiple site
 turnover and total beta diversity all decreased significantly with
 latitude. In contrast, multiple site nestedness showed a positive
 relationship with latitude. Beta-diversity components did not generally
 differ among the realms. The turnover component and total beta diversity
 increased with spatial extent, whereas nestedness was scale invariant for
 pairwise metrics. Multiple site beta-diversity components did not vary
 with spatial extent. Surprisingly, passively dispersed organisms had lower
 turnover and total beta diversity than flying organisms. Body size showed
 a relatively weak relationship with beta diversity but had important
 interactions with trophic position, thus also affecting beta diversity via
 interactive effects. Producers had significantly higher average pairwise
 turnover and total beta diversity than carnivores. The present results
 provide evidence that species turnover, being consistently the larger
 component of total beta diversity, and nestedness are related to the
 latitude of the study area and intrinsic organismal features. We showed
 that two beta-diversity components had generally opposing patterns with
 regard to latitude. We highlight that beta-diversity partition may give
 additional insights into the underlying causes of spatial variability in
 biotic communities compared with total beta diversity alone.
description: data for pairwise site
 beta diversitypairwise.txtdata for multiple site beta diversitymultiple.txt
DOI: 10.5061/dryad.8075
title: Data from: Distinct niche divergence characterizes the homoploid hybrid speciation of Pinus densata on the Tibetan Plateau

description: Ecological divergence and selection for novel adaptations to new habitats
 have been theoretically proposed to play important roles in promoting
 homoploid hybrid speciation (HHS). The successful establishment of Pinus
 densata on the Tibetan Plateau is one of the few known examples of HHS. In
 this study, we carried out extensive field expeditions to obtain
 representative coverage of occurrence sites of P. densata and its two
 putative parents. We then applied a series of GIS-based analyses to define
 the patterns of environmental variation within and among the three pine
 species, to remove potentially confounding effects of spatial
 autocorrelation in the environmental data due to allopatric ranges, and to
 build species distribution models. All results consistently indicated that
 the ecological preferences of P. densata and its parental species have
 diverged, and identified candidate ecological factors associated with
 habitat-specific adaptation. Projections from niche modelling indicated
 that P. densata could extend across a vast range along the parallel valley
 systems of the SE Tibetan Plateau. Our findings provide evidence of a
 distinct niche shift in P. densata, and support the hypothesis that local
 adaptation and geographic isolation help maintain and reinforce
 between-species differences and reproductive isolation in the species
 complex.
description: Locality_dataTo obtain general information relating to the occurrence of the three pine species and facilitate representative sampling of occurrence points from their whole ranges, we first referenced their distributions described by the Flora of China and the Chinese Virtual Herbarium (CVH) (http://www.cvh.org.cn/englishindex.asp) database. Many of the occurrence records for pine species in the CVH database lack exact geo-coordinates, so we used the information available in the database as a guide, and carried out extensive field surveys to assess the distribution of the three pines in the period 2003 - 2010. In total, we collected 412 geo-referenced occurrence records; 115 for Pinus densata, 149 for P. tabuliformis, and 148 for P. yunnanensis.Environmental variablesTo obtain information about the local niches of the three pines, we initially compiled information about 34 environmental variables. The detailed information is listed in this data file.environmental_variables.txt
DOI: 10.5061/dryad.37c1m
title: Data from: An approach to estimate short-term, long-term, and reaction norm repeatability

description: Evolutionary ecologists increasingly study reaction norms that are
 expressed repeatedly within the same individual's lifetime. For
 example, foragers continuously alter anti-predator vigilance in response
 to moment-to-moment changes in predation risk. Variation in this form of
 plasticity occurs both among and within individuals. Among-individual
 variation in plasticity (individual by environment interaction or I×E) is
 commonly studied; by contrast, despite increasing interest in its
 evolution and ecology, within-individual variation in phenotypic
 plasticity is not. We outline a study design based on repeated measures
 and a multi-level extension of random regression models that enables
 quantification of variation in reaction norms at different hierarchical
 levels (such as among- and within-individuals). The approach enables the
 calculation of repeatability of reaction norm intercepts (average
 phenotype) and slopes (level of phenotypic plasticity); these indices are
 not specific to measurement or scaling and are readily comparable across
 data sets. The proposed study design also enables calculation of
 repeatability at different temporal scales (such as short- and long-term
 repeatability) thereby answering calls for the development of approaches
 enabling scale-dependent repeatability calculations. We introduce a
 simulation package in the R statistical language to assess power,
 imprecision and bias for multi-level random regression that may be
 utilised for realistic datasets (unequal sample sizes across individuals,
 missing data, etc). We apply the idea to a worked example to illustrate
 its utility. We conclude that consideration of multi-level variation in
 reaction norms deepens our understanding of the hierarchical structuring
 of labile characters and helps reveal the biology in heterogeneous
 patterns of within-individual variance that would otherwise remain
 ‘unexplained’ residual variance.
description: Simulated data used in
 the worked exampleSimulatedDataWorkedExample.csv