cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5cn79808
title: Data from: What pollinates Lantana camara in the mountains of Costa Rica?

description: Lantana camara L. (Verbenaceae) is a shrub of Neotropical origin that has
 spread to at least 60 countries (Day et al. 2003), and its ability to
 rapidly occupy disturbed habitat has led to it being named one of the ten
 worst weeds on the planet (Cronk & Fuller 1995, Sharma et al.
 2005). A number of traits may have contributed to its success as an
 invasive species. For example, L. camara increases the available soil
 nitrogen in otherwise nitrogen-poor ecosystems (Sharma &
 Raghubanshi 2009), it is extremely resilient to disturbance (Gentle
 & Guggin 1997a, Hiremath & Sundram 2005), it is
 allelopathic to native plants (Achhireddy & Singh 1984, Gentle
 & Duggin 1997b) and its fruits are dispersed by a variety of birds
 (Mandon-Dalger et al. 2004, Swarbrick et al. 1998). A potentially
 unappreciated aspect of L. camara biology that may also contribute to its
 invasiveness relates to pollination ecology.
description: Lantana_data_dryad.csv file containing the number of fertilized ovules from the experimental treatments.Lantana_R_dryadR code needed to import data and conduct all statistical tests used in the ms. Note, that the data for the exact test are coded in this file and are not found in the associated data file.
DOI: 10.5061/dryad.8n344
title: Data from: Resources, key traits, and the size of fungal epidemics in Daphnia populations

description: 1. Parasites can profoundly affect host populations and ecological
 communities. Thus, it remains critical to identify mechanisms that drive
 variation in epidemics. Resource availability can drive epidemics via
 traits of hosts and parasites that govern disease spread. 2. Here, we map
 resource–trait–epidemic connections to explain variation in fungal
 outbreaks (Metschnikowia bicuspidata) in a zooplankton host (Daphnia
 dentifera) among lakes. We predicted epidemics would grow larger in lakes
 with more phytoplankton via three energetic mechanisms. First, resources
 should stimulate Daphnia reproduction, potentially elevating host density.
 Secondly, resources should boost body size of hosts, enhancing exposure to
 environmentally distributed propagules through size-dependent feeding.
 Thirdly, resources should fuel parasite reproduction within hosts. 3. To
 test these predictions, we sampled 12 natural epidemics and tracked edible
 algae, fungal infection prevalence, body size, fecundity and density of
 hosts, as well as within-host parasite loads. 4. Epidemics grew larger in
 lakes with more algal resources. Structural equation modelling revealed
 that resource availability stimulated all three traits (host fecundity,
 host size and parasite load). However, only parasite load connected
 resources to epidemic size. Epidemics grew larger in more dense Daphnia
 populations, but host density was unrelated to host fecundity (thus
 breaking its link to resources). 5. Thus, via energetic mechanisms,
 resource availability can stimulate key trait(s) governing epidemics in
 nature. A synthetic focus on resources and resource–trait links could
 yield powerful insights into epidemics.
description: Data on algal resources,
 Daphnia traits, and epidemic size in 12 lakesData on algal resources
 (log-transformed particulate carbon, nitrogen, and phosphorus), Daphnia
 traits (size, reproduction, and parasite load), and epidemic size
 (integrated prevalence) calculated from weekly sampling of 12 lakes in
 Indiana, USAgssfepidemics.csv
DOI: 10.5061/dryad.js25t
title: Data from: Stress and the microbiome: linking glucocorticoids to bacterial community dynamics in wild red squirrels

description: Bacterial diversity within animals is emerging as an essential component
 of health, but it is unknown how stress may influence the microbiome. We
 quantify a proximate link between the oral microbiome and
 hypothalamic–pituitary–adrenal (HPA) axis activity using faecal
 glucocorticoid metabolites (FGM) in wild red squirrels (Tamiasciurus
 hudsonicus). Not only was bacterial diversity lower at higher levels of
 FGM, but also between capture periods a change in bacterial relative
 abundance was related to an increase in FGM. These linkages between the
 HPA axis and microbiome communities represent a powerful capacity for
 stress to have multi-dimensional effects on health.
description: SRA
 #SRP064395Oral microbiome sequence
 dataSquirrel FGM
 concentrationsFecal glucocorticoid
 metabolite concentrationsSquirrelFGM CSV for
 Dryad.csv
DOI: 10.5061/dryad.rd7jt
title: Data from: Discrimination of signal carotenoid content using multidimensional chromatic information

description: Red, orange and yellow carotenoid-based ornaments, which are widely used
 as sexual signals in many birds, fish and reptiles, are known to exhibit
 multidimensional chromatic variation as a result of both the concentration
 and relative proportions of different constituent carotenoids with
 differing spectral properties. This is thought to reflect intrinsic
 variation in signaller quality, making it a useful basis for female
 choice. However, whether females are able to discriminate relevant
 variation in carotenoid concentration and/or composition independently of
 each other, and of other phenotypic or behaviour traits, and if so, how
 this mediates their choice, is poorly understood. Here, female
 three-spined sticklebacks (Gasterosteus aculeatus) were presented with
 computer-animated courting males that varied exclusively in the appearance
 of their carotenoid-based colouration; specifically, each male’s signal
 provided a perceptual match for carotenoid colouration expressed by live
 males with known underlying carotenoid content, thereby providing a
 biologically-relevant signal while precluding confounding traits
 influencing female choice. Females were able to discriminate between
 prospective mates solely on the basis of perceived variation in the
 allocation of carotenoids to males’ sexual signals, and exhibited a strong
 preference for males with colouration indicative of higher concentrations
 of carotenoids in their signal, rather than in response to perceived
 variation in the relative proportion of constituent carotenoids. This has
 important implications for our understanding male signalling strategies
 and the information content of carotenoid-based sexual signals.
description: DataData used in the
 analyses presented in this paper.
DOI: 10.5061/dryad.534
title: Data from: Phylogenetic taxonomy, a farewell to species, and a revision of Heteropodarke (Hesionidae, Polychaeta, Annelida)

description: Cladistic relationships between 7 parts of the hesionid polychaete group
 Heteropodarke are assessed in a parsimony analysis based on 34
 morphological characters. Taxon names are defined by apomorphy-based
 phylogenetic definitions, without reference to Linnean ranks or types.
 Species entities are omitted and denied any role in taxonomy; taxon names
 refer to monophyletic groups only. Linnean binomial species names are not
 employed, and all taxa are assigned uninomials. Previously known parts of
 Heteropodarke (Africana Hartmann-Schröder, 1974; Formalis, Perkins, 1984;
 Heteromorpha Hartmann-Schröder, 1962; Lyonsi Perkins, 1984; Xiamenensis
 Ding, Wu, and Westheide, 1997) are reexamined, and Bidentata, new taxon,
 and "Zmyrina" (informal name) are described from Papua New
 Guinea and Belize, respectively. The new taxon Crassichaetae is named for
 a subgroup of Heteropodarke, which is diagnosed by enlarged, anteriorly
 situated falcigers, and includes Africana, Heteromorpha, Lyonsi, and
 Xiamenensis. Within this group Africana and Heteromorpha are treated as
 taxa inquirendae.
description: Pleijel Data
 SetPleijel.txt
DOI: 10.5061/dryad.3m2c3
title: Data from: Predator kairomones change food web structure and function, regardless of cues from consumed prey

description: Predation risk in aquatic systems is often assessed by prey through
 chemical cues, either those released by prey or by the predator itself.
 Many studies on predation risk focus on simple pairwise interactions, with
 only a few studies examining community-level and ecosystem responses to
 predation risk in species-rich food webs. Further, of these few
 community-level studies, most assume that prey primarily assess predation
 risk through chemical cues from consumed prey, even heterospecific prey,
 rather than just those released by the predator. Here, we compared the
 effects of different predation cues (predator presence with or without
 consumed prey) on the structure and functioning of a speciose aquatic food
 web housed in tropical bromeliads. We found that the mere presence of the
 top predator (a damselfly) had a strong cascading effect on the food web,
 propagating down to nutrient cycling. This predation risk cue had no
 effect on the identity of colonizing species, but strongly reduced the
 abundance and biomass of the macroinvertebrate colonists. As a result,
 bacterial biomass and nitrogen cycling doubled, with a concomitant
 decrease in bacterial production, but CO2 flux was unaffected. These
 community and ecosystem effects of predator presence cues were not
 amplified by the addition of chemical cues from consumed prey. Our results
 show that some of the consequences of predation risk observed in
 controlled experiments with simplified food webs may be observed in a
 natural, species-rich food web.
description: predator kairomones and
 prey cuesThe file contains all
 the data used in the manuscript. The first column are the treatment names.
 The second, third and fourth columns are different descriptors of
 bromeliad morphology: these three measures (data centered and
 standardized) were used in a PCA, and the first axis of the ordination was
 used as a measure of bromeliad size (site scores were multiplied by -1, so
 that larger scores represented larger bromeliads). The other variables in
 the file are the response variables used in our study. The units of
 measurement are shown together with the variable names.
DOI: 10.5061/dryad.72f4s
title: Data from: Bacterial cooperation causes systematic errors in pathogen risk assessment due to the failure of the independent action hypothesis

description: The Independent Action Hypothesis (IAH) states that pathogenic individuals
 (cells, spores, virus particles etc.) behave independently of each other,
 so that each has an independent probability of causing systemic infection
 or death. The IAH is not just of basic scientific interest; it forms the
 basis of our current estimates of infectious disease risk in humans.
 Despite the important role of the IAH in managing disease interventions
 for food and water-borne pathogens, experimental support for the IAH in
 bacterial pathogens is indirect at best. Moreover since the IAH was first
 proposed, cooperative behaviors have been discovered in a wide range of
 microorganisms, including many pathogens. A fundamental principle of
 cooperation is that the fitness of individuals is affected by the presence
 and behaviors of others, which is contrary to the assumption of
 independent action. In this paper, we test the IAH in Bacillus
 thuringiensis (B.t), a widely occurring insect pathogen that releases
 toxins that benefit others in the inoculum, infecting the diamondback
 moth, Plutella xylostella. By experimentally separating B.t. spores from
 their toxins, we demonstrate that the IAH fails because there is an
 interaction between toxin and spore effects on mortality, where the toxin
 effect is synergistic and cannot be accommodated by independence
 assumptions. Finally, we show that applying recommended IAH dose-response
 models to high dose data leads to systematic overestimation of mortality
 risks at low doses, due to the presence of synergistic pathogen
 interactions. Our results show that cooperative secretions can easily
 invalidate the IAH, and that such mechanistic details should be
 incorporated into pathogen risk analysis.
description: WT
 dose-responseThe dose-response for
 wild type Bacillus thuringiensis in two experiments, presented in Fig. 2
 of the main text. Shown are the dead and live insect counts for a range of
 inoculum sizes in each of the experiments.WT_doseresponse.csvFixed toxins dose-responseThe dose-responses for varying quantities of spores of Bacillus thuringiensis a Cry null strain supplemented with 60 pg of toxin 180 pg of toxin (corresponding to Fig. 1A).Fixed_toxins.csvFixed spores dose-responseThe dose-response for 900 Bacillus thuringiensis spores supplemented with varying quantities of toxins in two experiments. (Corresponding to Fig. 1B).Fixed_spore.csv
DOI: 10.5061/dryad.tv854
title: Data from: Habitat fragmentation and the prevalence of parasites (Diptera, Streblidae) on three Phyllostomid bat species

description: Ectoparasitism in bats seems to be influenced strongly by the type of
 roost preferred by the hosts, and group size; however, the effect of
 habitat loss and fragmentation on the prevalence of ectoparasites in bats
 has scarcely been studied. In northeastern Yucatan, Mexico, we estimated
 the prevalence of infestation by Streblidae flies in three phyllostomid
 bat species with different roost preferences (caves, trees, or both) in
 two types of landscape matrices (tropical semi-deciduous forest and
 man-made pastures) that differed in area of forest cover and the number of
 forest fragments. Habitat fragmentation and the presence of a contrasting
 matrix may limit the availability of roosts (trees) and the movement of
 bats across the landscape. Accordingly, we hypothesized higher prevalence
 of Streblidae infestation in the pasture matrix and in the group of bats
 that roost in trees. Bat abundance was higher in the pasture matrix;
 however, the prevalence of infestation was significantly higher in the
 continuous forest matrix and in bats that roosted in caves. The prevalence
 of some species of Streblidae was affected by habitat fragmentation in
 species that roost in caves, such as Desmodus rotundus, as well as those
 using foliage and caves, such as Artibeus jamaicensis. Our results provide
 evidence that some species of Streblidae may respond differently to
 habitat fragmentation than their hosts, generating changes to
 bat-ectoparasite interactions in fragmented areas. Environmental
 variations involving roosts, not evaluated in this study, may influence
 our results, since these factors affect ectoparasite abundance and
 reproduction.
description: DATA
 BASEThis file include
 information about the three bat species studied with the number of
 individuals parasited and no parasited by sampling site. Also include
 information about landscape characteristics of each sampling
 site.
DOI: 10.5061/dryad.3c7pd3g
title: Data from: Antibiotic-driven escape of host in a parasite-induced Red Queen dynamics

description: Winnerless coevolution of hosts and parasites could exhibit Red Queen
 dynamics, which is characterized by parasite-driven cyclic switching of
 expressed host phenotypes. We hypothesize that the application of
 antibiotics to suppress the reproduction of parasites can provide
 opportunity for the hosts to escape such winnerless coevolution. Here, we
 formulate a minimal mathematical model of host-parasite interaction
 involving multiple host phenotypes that are targeted by adapting
 parasites. Our model predicts the levels of antibiotic effectiveness that
 can steer the parasite-driven cyclic switching of host phenotypes
 (oscillations) to a stable equilibrium of host survival. Our simulations
 show that uninterrupted application of antibiotic with high-level
 effectiveness (&gt;85%) is needed to escape the Red Queen dynamics.
 Interrupted and low level of antibiotic effectiveness are indeed useless
 to stop host-parasite coevolution. This study can be a guide in designing
 good practices and protocols to minimize risk of further progression of
 parasitic infections.
description: Code for the
 modelThis is a Berkeley
 Madonna file.model.mmd
DOI: 10.5061/dryad.cr6tg
title: Data from: Adaptive evolution to novel predators facilitates the evolution of damselfly species range shifts

description: Most species have evolved adaptations to reduce the chances of predation.
 In many cases adaptations to coexist with one predator generate tradeoffs
 in the ability to live with other predators. Consequently, the ability to
 live with one predator may limit the geographic distributions of species,
 such that adaptive evolution to coexist with novel predators may
 facilitate range shifts. In a case study with Enallagma damselflies, we
 used a comparative phylogenetic approach to test the hypothesis that
 adaptive evolution to live with a novel predator facilitates range size
 shifts. Our results suggest that the evolution of Enallagma shifting from
 living in ancestral lakes with fish as top predators, to living in lakes
 with dragonflies as predators, may have facilitated an increase in their
 range sizes. This increased range size likely arose because lakes with
 dragonflies were widespread, but unavailable as a habitat throughout much
 of the evolutionary history of Enallagma because they were historically
 maladapted to coexist with dragonfly predators. Additionally, the traits
 that have evolved as defenses against dragonflies also likely enhanced
 damselfly dispersal abilities. While many factors underlie the
 evolutionary history of species ranges, these results suggest a role for
 the evolution of predator-prey interactions.
description: Enallagma range size
 data setThis file contains range
 size estimates, wing length, clade designation and predator regime for
 Enallagma species used in the analysis.E.data.csv
DOI: 10.5061/dryad.b7n6h
title: Data from: Predatory dipteran larva contributes to nutrient sequestration in a carnivorous pitcher plant

description: The fluids of Nepenthes pitcher plants are habitats to many specialised
 animals known as inquilines, which facilitate the conversion of prey
 protein into pitcher-absorbable nitrogen forms such as ammonium.
 Xenoplatyura beaveri (Diptera: Mycetophilidae) is a predatory dipteran
 inquiline that inhabits the pitchers of N. ampullaria. Larvae of X.
 beaveri construct sticky webs over the fluid surface of N. ampullaria to
 ensnare emerging adult dipteran inquilines. However, the interaction
 between X. beaveri and its host has never been examined before, as it is
 not known if X. beaveri can contribute to nutrient sequestration in N.
 ampullaria. X. beaveri individuals were reared in artificial pitchers in
 the laboratory on a diet of emergent Tripteroides tenax mosquitoes, and
 the ammonium concentration of the pitcher fluids were measured over time.
 Fluid ammonium concentration in tubes containing X. beaveri were
 significantly greater than those of the controls. Furthermore, fluid
 ammonium concentrations increased greatly after X. beaveri larvae
 metamorphosed, although the cause for this increase could not be
 identified. Our results show that a terrestrial, inquiline predator can
 contribute significantly to nutrient sequestration in the phytotelma it
 inhabits, and suggest that this interaction has a net mutualistic outcome
 for both species.
description: Raw data of in vitro
 experimentsArtificial pitchers
 (Vials) are setup with two treatment conditions (Treatment = X. beaveri or
 control) in the laboratory. Each artificial pitcher is supplied with
 varying numbers of T. tenax pupae over time (moz). Amount of ammonium (NH4
 mmol) in artificial pitchers is determined at 3-week intervals over the
 course of the experiment, until X. beaveri emerge (Emergence; 1=yes,
 0=no). Vials belonging to the same Pair number were commenced on the same
 day, and supplied with the same number of mosquito pupae over the course
 of the experiment.Xeno
 data.csv
DOI: 10.5061/dryad.vb73f
title: Data from: Comparing measures of breeding inequality and opportunity for selection with sexual selection on a quantitative character in bighorn rams

description: The reliability and consistency of the many measures proposed to quantify
 sexual selection have been questioned for decades. Realized selection on
 quantitative characters measured by the selection differential i was
 approximated by metrics based on variance in breeding success, using
 either the opportunity for sexual selection Is or indices of inequality.
 There is no consensus about which metric best approximates realized
 selection on sexual characters. Recently, the opportunity for selection on
 character mean OSM was proposed to quantify the maximum potential
 selection on characters. Using 21 years of data on bighorn sheep (Ovis
 canadensis), we investigated the correlations between seven indices of
 inequality, Is, OSM and i on horn length of males. Bighorn sheep are ideal
 for this comparison because they are highly polygynous, sexually
 dimorphic, ram horn length is under strong sexual selection, and we have
 detailed knowledge of individual breeding success. Different metrics
 provided conflicting information, potentially leading to spurious
 conclusions about selection patterns. Iδ, an index of breeding inequality,
 and to a lesser extent Is, showed the highest correlation with i on horn
 length, suggesting that these indices document breeding inequality in a
 selection context. OSM on horn length was strongly correlated with i, Is,
 and indices of inequality. By integrating information on both realized
 sexual selection and breeding inequality, OSM appeared to be the best
 proxy of sexual selection and may be best suited to explore its ecological
 bases.
description: skew_indices
DOI: 10.5061/dryad.n59d1
title: Data from: Faithful or not: direct and indirect effects of climate on extra-pair paternities in a population of Alpine marmots

description: Despite being identified an area that is poorly understood regarding the
 effects of climate change, behavioural responses to climatic variability
 are seldom explored. Climatic variability is likely to cause large
 inter-annual variation in the frequency of extra-pair litters produced, a
 widespread alternative mating tactic to help prevent, correct or minimize
 the negative consequences of sub-optimal mate choice. In this study, we
 investigated how climatic variability affects the inter-annual variation
 in the proportion of extra-pair litters in a wild population of Alpine
 marmots. During 22 years of monitoring, the annual proportion of
 extra-pair litters directly increased with the onset of earlier springs
 and indirectly with increased snow in winters. Snowier winters resulted in
 a higher proportion of families with sexually mature male subordinates and
 thus, created a social context within which extra-pair paternity was
 favoured. Earlier spring snowmelt could create this pattern by relaxing
 energetic, movement and time constraints. Further, deeper snow in winter
 could also contribute by increasing litter size and juvenile survival.
 Optimal mate choice is particularly relevant to generate adaptive genetic
 diversity. Understanding the influence of environmental conditions and the
 capacity of the individuals to cope with them is crucial within the
 context of rapid climate change.
description: Annual proportion of
 extra-pair littersAnnual proportion of
 extra-pair litters, annual climatic variables and annual proportion of
 families with sexually mature male subordinatesannual_dryad.csv