cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3754b
title: Data from: Beyond predation: the zoophytophagous predator Macrolophus pygmaeus induces tomato resistance against spider mites

description: Many predatory insects that prey on herbivores also feed on the plant, but
 it is unknown whether plants affect the performance of herbivores by
 responding to this phytophagy with defence induction. We investigate
 whether the prior presence of the omnivorous predator Macrolophus pygmaeus
 (Rambur) on tomato plants affects plant resistance against two different
 herbivore species. Besides plant-mediated effects of M. pygmaeus on
 herbivore performance, we examined whether a plant defence trait that is
 known to be inducible by herbivory, proteinase inhibitors (PI), may also
 be activated in response to the interactions of this predator with the
 tomato plant. We show that exposing tomato plants to the omnivorous
 predator M. pygmaeus reduced performance of a subsequently infesting
 herbivore, the two-spotted spider mite Tetranychus urticae Koch, but not
 of the greenhouse whitefly Trialeurodes vaporariorum (Westwood). The
 spider-mite infested tomato plants experience a lower herbivore load,
 i.e., number of eggs deposited and individuals present, when previously
 exposed to the zoophytophagous predator. This effect is not restricted to
 the exposed leaf and persists on exposed plants for at least two weeks
 after the removal of the predators. The decreased performance of spider
 mites as a result of prior exposure of the plant to M. pygmaeus is
 accompanied by a locally and systemically increased accumulation of
 transcripts and activity of proteinase inhibitors that are known to be
 involved in plant defence. Our results demonstrate that zoophytophagous
 predators can induce plant defence responses and reduce herbivore
 performance. Hence, the suppression of populations of certain herbivores
 via consumption may be strengthened by the induction of plant defences by
 zoophytophagous predators.
description: Pappas_et_al_all
 dataPappas
 et al_data.xlsx
DOI: 10.5061/dryad.25p96
title: Data from: Thrifty phenotype vs cold adaptation: trade-offs in upper limb proportions of Himalayan populations of Nepal

description: The multi-stress environment of high altitude has been associated with
 growth deficits in humans, particularly in zeugopod elements (forearm,
 lower leg). This is consistent with the thrifty phenotype hypothesis,
 which has been observed in Andeans, but has yet to be tested in other high
 altitude populations. In Himalayan populations, other factors, such as
 cold stress, may shape limb proportions. The current study investigated
 whether relative upper limb proportions of Himalayan adults (n=254) differ
 between highland and lowland populations, and whether cold adaptation or a
 thrifty phenotype mechanism may be acting here. Height, weight, humerus
 length, ulna length, hand length, and hand width were measured using
 standard methods. Relative to height, total upper limb and ulna lengths
 were significantly shorter in highlanders compared to lowlanders in both
 sexes, whilst hand and humerus length were not. Hand width did not
 significantly differ between populations. These results support the
 thrifty phenotype hypothesis, as hand and humerus proportions are
 conserved at the expense of the ulna. The reduction in relative ulna
 length could be attributed to cold adaptation, but the lack of difference
 between populations in both hand length and width indicate that cold
 adaptation is not shaping hands proportions in this case.
description: DatasetRaw data values from data collection from both highland and lowland populationsRaw Data.xlsx
DOI: 10.15468/dl.e5eh6f
title: Occurrence Download

description: A dataset containing 16878 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bemisia tabaci"
 ]
}

 The dataset includes 16878 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001108-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6p05c
title: Data from: Disentangling the contribution of sexual selection and ecology to the evolution of size dimorphism in pinnipeds

description: The positive relationship between sexual size dimorphism (SSD) and harem
 size across pinnipeds is often cited as a textbook example of sexual
 selection. It assumes that female aggregation selected for large male size
 via male-male competition. Yet, it is also conceivable that SSD evolved
 prior to polygyny due to ecological forces. We analysed eleven life
 history traits in 35 pinniped species to determine their co-evolutionary
 dynamics and infer their most likely evolutionary trajectories contrasting
 these two hypotheses. We find support for SSD having evolved prior to
 changes in the mating system, either as a consequence of niche
 partitioning during aquatic foraging or in combination with sexual
 selection on males to enforce copulations on females. Only subsequently
 did polygyny evolve, leading to further coevolution as the strength of
 sexual selection intensified. Evolutionary sequence analyses suggest a
 polar origin of pinnipeds and indicate that SSD and polygyny are
 intrinsically linked to a suite of ecological and life history traits.
 Overall, this study calls for the inclusion of ecological variables when
 studying sexual selection and argues for caution when assuming causality
 between coevolving traits. It provides novel insights into the role of
 sexual selection for the co-evolutionary dynamics of SSD and mating
 system.
description: Comparative seal paper
 raw data for dryad
DOI: 10.5061/dryad.5f88r9m
title: Data from: The EGA+GNM framework: an integrative approach to modelling behavioural syndromes

description: 1. Behavioural syndromes refer to correlated suites of behavioural traits
 exhibiting consistent among-individual variation, i.e. personality. Factor
 analysis (FA) is currently the dominant method for modelling behavioural
 syndromes in humans and animals. Although FA is useful for inferring the
 latent causes underlying trait correlations, it does not account for
 pairwise behavioural interactions that also contribute to syndrome
 structure. Given that latent factors and pairwise interactions are likely
 ubiquitous causes of trait covariation, both should be modelled
 simultaneously. Currently, however, behavioural ecologists lack an
 integrative framework for describing and inferring such behavioural
 syndromes. 2. Generalized network modelling (GNM), representing an
 integration of FA and Gaussian graphical modelling (GGM), meets this
 challenge. We provide a theoretical introduction to GNM as well as a
 method for detecting latent factors in GGMs called exploratory graph
 analysis (EGA). We then propose the novel EGA+GNM framework for modelling
 multiple sources of trait correlations and ensuring more robust causal
 inferences. To empirically demonstrate the utility of this framework, we
 compare models derived from EGA+GNM and FA using observational measures of
 social and arousal behaviour in common marmosets (Callithrix jacchus). 3.
 Using information-theoretic model comparison, we find support for the
 EGA+GNM models compared to models generated by FA. Two EGA+GNM models
 suggest that while latent factors contribute to the emergence of clustered
 sociability and arousal behaviours, correlations among these traits may
 also be partially explained by pairwise interactions. Additionally, these
 behavioural clusters are hypothesized to be causally linked by a positive
 pairwise interaction between allogrooming and activity level. 4. These
 results support our claim that EGA+GNM provides a superior and integrative
 framework for describing behavioural syndromes. Consequently, by
 simultaneously modelling both latent factors and pairwise interactions,
 behavioural ecologists can better understand the evolutionary causes and
 consequences of animal personality. A formal overview of the EGA+GNM
 framework and a R tutorial demonstrating its application are provided in
 the electronic supplementary material.
description: Martin et al MEE 2018
 marmoset dataData are provided for
 the six behavioral traits analyzed in the main paper, along with
 information on the subject, social group, series, and observation #. The
 names of these variables should be self-explanatory and facilitate
 efficient replication using the R code provided.Martin et al 2018 MEE R
 code
DOI: 10.5061/dryad.6t2c4
title: Data from: Development of nuclear microsatellite loci and mitochondrial single nucleotide polymorphisms for the natterjack toad, Bufo (Epidalea) calamita (Bufonidae), using next generation sequencing and Competitive Allele Specific PCR (KASPar)

description: Amphibians are undergoing a major decline worldwide and the steady
 increase in the number of threatened species in this particular taxa
 highlights the need for conservation genetics studies using high-quality
 molecular markers. The natterjack toad, Bufo (Epidalea) calamita, is a
 vulnerable pioneering species confined to specialized habitats in Western
 Europe. To provide efficient and cost-effective genetic resources for
 conservation biologists, we developed and characterized 22 new nuclear
 microsatellite markers using next-generation sequencing. We also used
 sequence data acquired from Sanger sequencing to develop the first
 mitochondrial markers for KASPar assay genotyping. Genetic polymorphism
 was then analyzed for 95 toads sampled from 5 populations in France. For
 polymorphic microsatellite loci, number of alleles and expected
 heterozygosity ranged from 2 to 14 and from 0.035 to 0.720, respectively.
 No significant departures from panmixia were observed (mean multilocus F
 IS = −0.015) and population differentiation was substantial (mean
 multilocus F ST = 0.222, P &lt; 0.001). From a set of 18 mitochondrial
 SNPs located in the 16S and D-loop region, we further developed a fast and
 cost-effective SNP genotyping method based on competitive allele-specific
 PCR amplification (KASPar). The combination of allelic states for these
 mitochondrial DNA SNP markers yielded 10 different haplotypes, ranging
 from 2 to 5 within populations. Populations were highly differentiated (G
 ST = 0.407, P &lt; 0.001). These new genetic resources will facilitate
 future parentage, population genetics and phylogeographical studies and
 will be useful for both evolutionary and conservation concerns, especially
 for the set-up of management strategies and the definition of distinct
 evolutionary significant units.
description: Microsatellite and mtDNA
 genotypes for Bufo calamitaPopulation coordinates
 and microsatellite and mtDNA genotypes for five populations of the
 natterjack toad (Bufo calamita). Location : France.Data-JOH-2016-102.R2.xlsx
DOI: 10.5061/dryad.1b8m917
title: Data from: Reproductive skipping as an optimal life history strategy in the southern elephant seal, Mirounga leonina

description: Intermittent breeding by which organisms skip some current reproductive
 opportunities in order to enhance future reproductive success is a common
 life history tradeoff among long-lived, iteroparous species. The southern
 elephant seal Mirounga leonina engages in intermediate breeding when body
 condition is low. While it is anticipated that this strategy may increase
 the lifetime reproductive output of this species, the conditions under
 which reproductive skipping are predicted to occur are not clear. Here I
 develop a dynamic state variable model based on published data that
 examines when southern elephant seals are predicted to optimally skip
 reproduction in order to maximize lifetime reproductive output as a
 function of current body mass, maternal age, and survivorship. I
 demonstrate that the optimal reproductive strategy for this species can
 include reproductive skipping, and that the conditions where this is
 optimal depend on patterns of mass-dependent adult female survival. I
 further show that intermittent breeding can increase lifetime reproductive
 output, and that the magnitude of this benefit increases with the ability
 of individual animals to replenish depleted body mass through foraging.
 Finally, I show that when the environment is variable and foraging is
 reduced in bad years, the benefit of adopting an optimal strategy that
 includes reproductive skipping increases asymptotically with the frequency
 of bad years. These results highlight the importance of characterizing the
 pattern of adult survival in this species, as well as the need to identify
 other factors that may influence the prevalence and benefits of
 reproductive skipping.
description: Model.v2This is the R code for implementing the model described in the paper using backward iteration. The parameters listed in the top section of the code can be modified to replicate the various results reported in the paper.Model.v3.R
DOI: 10.5061/dryad.64td7
title: Data from: Linguliform brachiopods across a Cambrian–Ordovician (Furongian–Early Ordovician) biomere boundary: the Sunwaptan/Skullrockian North American stage boundary in the Wilberns and Tanyard Formations of central Texas

description: The Cambrian-Ordovician Diversity Plateau, between the Cambrian Explosion
 and the Ordovician Radiation, is punctuated by a series of well-documented
 Laurentian trilobite extinction events. These events define the bounding
 surfaces of trilobite “biomeres” that correspond to North American stages,
 including those of the Sunwaptan and Skullrockian. Trilobites show a
 consistent pattern of recovery across these boundaries, and commonly each
 extinction and replacement of taxa is interpreted as a single event as
 changing environmental conditions spurred shoreward migration of shelf or
 oceanic faunas that displaced established cratonic faunas. Linguliform
 brachiopods are also abundant in strata of this interval, and we
 investigate their stratigraphic distribution across the
 Sunwaptan–Skullrockian Stage boundary in Texas through high-resolution
 stratigraphic sampling of subtidal sediments. We document complete genus-
 and species-level turnover of the linguliform brachiopod fauna coincident
 with trilobite extinction events, suggesting that these brachiopods were
 affected by the same factors that affected trilobites. The Skullrockian
 replacement fauna was cosmopolitan, with ties to Gondwana and Kazakhstan
 and to the Laurentian shelf environment. The timing of appearances of taxa
 suggests that the faunal migration onto the Laurentian shelf came from
 elsewhere during a transgression. The disappearance of the Sunwaptan fauna
 and the arrival of the Skullrockian fauna are distinct events. We suggest
 that “biomere” events may be complex, and the cause of the extinction is
 not necessarily the same event that facilitates the appearance of a
 replacement fauna. We describe one new species, Schizambon langei.
description: Supplemental_Data_1Supplemental Data Tables 1 and 2
DOI: 10.15468/dl.je2hya
title: Occurrence Download

description: A dataset containing 2032 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Clematoclethra scandens",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 2032 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001109-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6cs14
title: Data from: Soil fertility shapes belowground food webs across a regional climate gradient

description: Changes in soil fertility during pedogenesis affect the quantity and
 quality of resources entering the belowground subsystem. Climate governs
 pedogenesis, yet how climate modulates responses of soil food webs to soil
 ageing remains unexplored because of the paucity of appropriate model
 systems. We characterised soil food webs along each of four retrogressive
 soil chronosequences situated across a strong regional climate gradient to
 show that belowground communities are predominantly shaped by changes in
 fertility rather than climate. Basal consumers showed hump-shaped
 responses to soil ageing, which were propagated to higher-order consumers.
 There was a shift in dominance from bacterial to fungal energy channels
 with increasing soil age, while the root energy channel was most important
 in intermediate-aged soils. Our study highlights the overarching
 importance of soil fertility in regulating soil food webs, and indicates
 that belowground food webs will respond more strongly to shifts in soil
 resources than climate change.
description: Soil food webs
 chronosequences Western AustraliaBiotic and abiotic soil
 properties measured along four long-term chronosequences in Western
 Australia.Dataset.xlsx
DOI: 10.5061/dryad.4g622
title: Data from: Socio-economic impact classification of alien taxa (SEICAT)

description: Many alien taxa are known to cause socio-economic impacts by affecting the
 different constituents of human well-being (security; material and
 non-material assets; health; social, spiritual and cultural relations;
 freedom of choice and action). Attempts to quantify socio-economic impacts
 in monetary terms are unlikely to provide a useful basis for evaluating
 and comparing impacts of alien taxa because they are notoriously difficult
 to measure and important aspects of human well-being are ignored. Here, we
 propose a novel standardised method for classifying alien taxa in terms of
 the magnitude of their impacts on human well-being, based on the
 capability approach from welfare economics. The core characteristic of
 this approach is that it uses changes in peoples' activities as a
 common metric for evaluating impacts on well-being. Impacts are assigned
 to one of five levels, from Minimal Concern to Massive, according to
 semi-quantitative scenarios that describe the severity of the impacts.
 Taxa are then classified according to the highest level of deleterious
 impact that they have been recorded to cause on any constituent of human
 well-being. The scheme also includes categories for taxa that are not
 evaluated, have no alien population, or are data deficient, and a method
 for assigning uncertainty to all the classifications. To demonstrate the
 utility of the system, we classified impacts of amphibians globally. These
 showed a variety of impacts on human well-being, with the cane toad
 (Rhinella marina) scoring Major impacts. For most species, however, no
 studies reporting impacts on human well-being were found, i.e. these
 species were data deficient. The classification provides a consistent
 procedure for translating the broad range of measures and types of impact
 into ranked levels of socio-economic impact, assigns alien taxa on the
 basis of the best available evidence of their documented deleterious
 impacts, and is applicable across taxa and at a range of spatial scales.
 The system was designed to align closely with the Environmental Impact
 Classification for Alien Taxa (EICAT) and the Red List, both of which have
 been adopted by the International Union of Nature Conservation (IUCN), and
 could therefore be readily integrated into international practices and
 policies.
description: SI2 Table S1 SEICAT
 Application to AmphibiansSocio-economic impact
 classification of amphibians according to SEICAT
DOI: 10.5061/dryad.88qt1
title: Data from: Benefits of coloniality: communal defence saves anti-predator effort in cooperative breeders

description: 1. Many anti-predator benefits of group living are predicted to scale with
 prey density. Nevertheless, evidence for a general density-dependent
 increase of prey survival is scarce. A possible reason for this
 discrepancy is the reduction of costly anti-predator behaviour of prey
 with increasing density, which may offset density-dependent survival
 gains. Benefits of group living might hence accrue by saved investment
 into anti-predator behaviours rather than by increased survival rates. 2.
 Here, we experimentally presented predators in a colony of the
 cooperatively breeding cichlid fish Neolamprologus pulcher to study
 density dependence of their anti-predator defences. Predation is a driver
 of the formation and stability of breeding groups in this species, but
 potential benefits of coloniality are yet unclear. We hypothesised that
 increased density of breeding groups would either increase total
 anti-predator behaviour or allow individuals to reduce their anti-predator
 effort due to enhanced predator deterrence from neighbours. 3. Confirming
 predictions from the second hypothesis, our results show that focal groups
 invested less into anti-predator behaviour at higher densities, while
 neighbouring groups' behaviour compensated for this reduced effort.
 This resulted in stable levels of anti-predator behaviours over the entire
 range of natural densities. Thus, aggregating in colonies allows these
 fish to save investment in anti-predator behaviour. 4. These results
 suggest that the formation of both breeding groups and colonies reflects
 adaptive responses to high predation pressure in this species. Two
 different levels of sociality seem to be favoured by the same selective
 force. 5. Our study provides experimental evidence in nature for an
 important benefit of coloniality that may explain the concomitant
 existence of different levels of sociality in many highly social taxa.
description: all data underlying the
 publicationAll data were collected
 within the same natural colony in Lake Tanganyika. Each column is
 commented on, explaining what the respective data mean. Names of
 territories and fish were arbitrarily chosen.DataJungwirthFuncEcol.xlsx
DOI: 10.5061/dryad.jc71g
title: Data from: Flexible mate choice may contribute to ecotype assortative mating in pumpkinseed sunfish (Lepomis gibbosus)

description: Gene flow is expected to limit adaptive divergence but the ecological and
 behavioural factors that govern gene flow are still poorly understood,
 particularly at the earliest stages of population divergence. Reduced gene
 flow through mate choice (sexual isolation) can evolve even under
 conditions of subtle population divergence if intermediate phenotypes have
 reduced fitness. We indirectly tested the hypothesis that mate choice has
 evolved between coexisting littoral and pelagic ecotypes of polyphenic
 pumpkinseed sunfish (Lepomis gibbosus) that have diverged in morphology
 and resource use and where intermediate phenotypes have reduced
 performance. We assessed the ecotype of nesting males and females using
 stable isotope estimates of diet and a divergent male morphological trait,
 oral jaw width. We found positive assortative mating between ecotypes in a
 common spawning habitat along exposed lake shorelines, but contrary to
 expectations, assortative mating was variably expressed between two
 sampling years. Although the factors that influence variable assortative
 mating remain unclear, our results are consistent with mate choice being
 expressed by ecotypes. Despite being variably expressed, mate choice will
 reduce gene flow between ecotypes and could contribute to further adaptive
 divergence depending on its frequency and strength in the population. Our
 findings add to a growing body of evidence indicating mate choice
 behaviour can be a plastic trait, an idea that should be more explicitly
 considered in empirical studies of mate choice as well as conceptual
 frameworks of mate choice evolution and adaptive divergence.
description: Pumpkinseed Isotope
 DataStable isotope
 measurements for male pumpkinseed and progeny. Carbon d13 is lipid
 corrected where appropriate. Additionally, there is male standard length,
 jaw width, and collection site in this data set.Jarvis_etal_data.xlsx