cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.077vm
title: Data from: Predator-prey dynamics and the plasticity of predator body size

description: 1. Body size is of fundamental importance to the structure and function of
 natural systems, yet the factors selecting for certain body sizes are
 still not well understood. Resource supply levels clearly play a role in
 setting size, but in current theory, optimality functions for body size
 are not tied to the population dynamics that govern resource supply,
 minimizing our ability to understand how body size evolves in response to
 ecological context. 2. We integrated the supply-demand (SD) model of body
 size evolution with a model of predator-prey dynamics to create a dynamic
 SD model that describes predator body size variation through time. We
 tested the model with experimental data on body size and abundance
 dynamics in the Didinium-Paramecium predator-prey system. We used a new
 differential equation fitting approach along with independently estimated
 parameters to determine whether the model could simultaneously capture
 both abundance and body size dynamics. 3. The dynamics were well described
 by the model, supporting the notion that body size changes to match bodily
 demand for resources with the available supply of resources. Surprisingly,
 despite the 10-fold variation in Didinium body size, we found that static
 model parameters were sufficient to describe the data, suggesting a lack
 of eco-evolutionary dynamics. 4. A pressing need in ecology is to be able
 predict changes in body size under novel scenarios, especially climate
 warming. The dynamic SD model does this by linking body size to the
 ecological context in an eco-evolutionary framework. Our approach expands
 our ability to understand rapid linked changes in traits and abundance.
description: DeLong et al Functional
 Ecology dataThis Excel file includes
 three tabs. In first tab is the population density (cells per mL) data for
 Didinium and Paramecium together and Paramecium alone (control cultures).
 In the second tab is a list of cell sizes (length, width, and volume in
 cubic microns) for Didinium through time. In the third tab is functional
 response data, with prey density, predator density, and prey eaten per
 predator per day, along with a block identifier.
DOI: 10.5061/dryad.2cm3h1q7
title: Data from: Fear of predation slows plant-litter decomposition

description: Aboveground consumers are believed to affect ecosystem functioning by
 regulating the quantity and quality of plant-litter entering the soil. We
 uncover a novel pathway whereby terrestrial predators regulate ecosystem
 processes via indirect control over soil community function. Grasshopper
 herbivores stressed by spider predators have a higher body
 carbon-to-nitrogen ratio than grasshoppers raised without spiders. This
 change in elemental content does not slow grasshopper decomposition but
 perturbs belowground community function, decelerating subsequent
 decomposition of plant-litter. This legacy effect of predation on soil
 community function appears to be regulated by the amount of
 herbivore-protein entering soil.
description: DataExcel file showing the
 cumulative mineralization of grasshopper, artificial grasshopper, or
 litter biomass mineralization of each experiment described in Hawlena et
 al.
DOI: 10.5061/dryad.7gt4m
title: Data from: Estimating effects of species interactions on populations of endangered species

description: Global change causes community composition to change considerably through
 time, with ever-new combinations of interacting species. To study the
 consequences of newly established species interactions, one available
 source of data could be observational surveys from biodiversity
 monitoring. However, approaches using observational data would need to
 account for niche differences between species and for imperfect detection
 of individuals. To estimate population sizes of interacting species, we
 extended N-mixture models that were developed to estimate true population
 sizes in single species. Simulations revealed that our model is able to
 disentangle direct effects of dominant on subordinate species from
 indirect effects of dominant species on detection probability of
 subordinate species. For illustration, we applied our model to data from a
 Swiss amphibian monitoring program and showed that sizes of expanding
 water frog populations were negatively related to population sizes of
 endangered yellow-bellied toads and common midwife toads and partly of
 natterjack toads. Unlike other studies that analyzed presence and absence
 of species, our model suggests that the spread of water frogs in Central
 Europe is one of the reasons for the decline of endangered toad species.
 Thus, studying population impacts of dominant species on population sizes
 of endangered species using data from biodiversity monitoring programs
 should help to inform conservation policy and to decide whether competing
 species should be subject to population management.
description: Amphibian monitoring
 canton Aargau, Switzerlandamphibian_monitoring_AG.xlsx
DOI: 10.5061/dryad.1m6764d
title: Data from: Neural dynamics of selective attention deficits in HIV-associated neurocognitive disorder

description: Objective: To identify the neural markers of attention dysfunction in
 patients with HIV-associated neurocognitive disorder (HAND). Methods:
 Sixty participants, including 40 HIV-infected adults (half with HAND) and
 20 demographically-matched controls performed a visual selective attention
 task while undergoing high-density magnetoencephalography (MEG). Neuronal
 activity related to selective attention processing was quantified and
 compared across the three groups, and correlated with neuro-psychological
 measures of attention and executive function. Spontaneous neural activity
 was also extracted from these attention-related cortical areas and
 examined with respect to HAND status. Results: HIV-infected participants
 with and without HAND exhibited behavioral selective attention deficits on
 the MEG task, as indicated by an increased flanker effect. Neuronal
 measures of flanker interference activity in the alpha and theta range
 revealed differential dynamics in attention-related brain areas across the
 three groups, especially in those with HAND. In addition, theta range
 flanker interference activity in the left inferior frontal and
 dorsolateral prefrontal cortex was associated with executive function and
 attention composite scores, respectively. Progressively stronger
 spontaneous alpha and theta activity were also found in unimpaired
 HIV-infected and HAND participants relative to controls across brain
 regions implicated in different components of attention processing.
 Conclusions: Behavioral and neuronal metrics of selective attention
 performance distinguish participants with HAND from controls and
 unimpaired HIV-infected participants. These metrics, along with measures
 of local spontaneous neural activity, may hold promise as early markers of
 cognitive decline in HIV-infected participants and be useful prognostic
 indicators for HAND.
description: Supplemental
 DataAppendix e-1-4, Figure
 e-1Supplement_Selective_Attention_in_HAND.docx
DOI: 10.5061/dryad.4gf1qb7
title: Data from: Population size changes and selection drive patterns of parallel evolution in a host-virus system

description: Predicting the repeatability of evolution remains elusive. Theory and
 empirical studies suggest that strong selection and large population sizes
 increase the probability for parallel evolution at the phenotypic and
 genotypic levels. However, selection and population sizes are not
 constant, but rather change continuously and directly affect each other
 even on short time scales. Here, we examine the degree of parallel
 evolution shaped through eco-evolutionary dynamics in an algal host
 population coevolving with a virus. We find high degrees of parallelism at
 the level of population size changes (ecology) and at the phenotypic level
 between replicated populations. At the genomic level, we find evidence for
 parallelism, as the same large genomic region was duplicated in all
 replicated populations, but also substantial novel sequence divergence
 between replicates. These patterns of genome evolution can be explained by
 considering population size changes as an important driver of rapid
 evolution.
description: Host_Resistance_PhenotypesHost Resistance PhenotypesVirus_Densitiesas particles per mlAlgal_Densitiesas cells per ml
DOI: 10.5061/dryad.s168r
title: Data from: How big of an effect do small dams have? Using geomorphological footprints to quantify spatial impact of low-head dams and identify patterns of across-dam variation

description: Longitudinal connectivity is a fundamental characteristic of rivers that
 can be disrupted by natural and anthropogenic processes. Dams are
 significant disruptions to streams. Over 2,000,000 low-head dams
 (&lt;7.6 m high) fragment United States rivers. Despite potential
 adverse impacts of these ubiquitous disturbances, the spatial impacts of
 low-head dams on geomorphology and ecology are largely untested. Progress
 for research and conservation is impaired by not knowing the magnitude of
 low-head dam impacts. Based on the geomorphic literature, we refined a
 methodology that allowed us to quantify the spatial extent of low-head dam
 impacts (herein dam footprint), assessed variation in dam footprints
 across low-head dams within a river network, and identified select aspects
 of the context of this variation. Wetted width, depth, and substrate size
 distributions upstream and downstream of six low-head dams within the
 Upper Neosho River, Kansas, United States of America were measured. Total
 dam footprints averaged 7.9 km (3.0-15.3 km) or 287 wetted widths (136-437
 wetted widths). Estimates included both upstream (mean: 6.7 km or 243
 wetted widths) and downstream footprints (mean: 1.2 km or 44 wetted
 widths). Altogether the six low-head dams impacted 47.3 km (about 17%) of
 the mainstem in the river network. Despite differences in age, size,
 location, and primary function, the sizes of geomorphic footprints of
 individual low-head dams in the Upper Neosho river network were relatively
 similar. The number of upstream dams and distance to upstream dams, but
 not dam height, affected the spatial extent of dam footprints. In summary,
 ubiquitous low-head dams individually and cumulatively altered lotic
 ecosystems. Both characteristics of individual dams and the context of
 neighboring dams affected low-head dam impacts within the river network.
 For these reasons, low-head dams require a different, more integrative,
 approach for research and management than the individualistic approach
 that has been applied to larger dams.
description: SubstrateContains three excel sheet tabs: "indvar_substrate_select", "indvar_riffle_character", "substrate_profile". First, "indvar_substrate_select" corresponds to the evaluation of individual sampler bias in substrate selection at a point along a transect. Second, "indvar_riffle_character" corresponds to the evaluation of individual variation in Wolman pebble counts of a riffle. Third, "substrate_profile" refers to the Wolman pebble counts downstream of each dam.substrate.xlsxWetted width and depthIncludes all field measurements of wetted width and depth.width_depth.xlsx
DOI: 10.5061/dryad.p45p4
title: Data from: Functional extinction of a desert rodent: implications for seed fate and vegetation dynamics

description: Population declines of once-abundant species have often preceded
 understanding of their roles within ecosystems. Consequently, important
 drivers of environmental change may remain undiagnosed because we simply
 do not know how species that are now rare or extinct shaped ecosystems in
 the past. Australia's desert rodents are thought to have little
 numerical impact on seed fate and vegetation recruitment when compared
 with ants or with desert rodents on other continents. However most
 research on granivory by Australian desert rodents has occurred in areas
 where rodents were rare or functionally extinct. Here we ask if the
 paradigm that rodents are relatively un-important granivores in Australian
 deserts is an artefact of their historical decline. In the Strzelecki
 Desert, the endangered rodent, Notomys fuscus is rare where introduced
 mesopredators are abundant but common where dingoes (an apex predator)
 suppress mesopredator populations. We used foraging trays to compare rates
 of seed removal for a common shrub (Dodonaea viscosa angustissima hopbush)
 between areas where N. fuscus, hopbush shrubs and their seedlings were
 rare and common and found that seed removal was consistently higher where
 rodents were common and hopbush rare. By excluding ants and rodents from
 foraging trays we show that ants removed more seeds than rodents where
 rodents were rare but rodents removed far more seeds than ants where
 rodents were common. By manipulating rodents’ access to the soil seed-bank
 we show that hopbush seeds persisted in greater numbers where rodents were
 excluded than where they had access. Our results support the hypothesis
 that granivory by rodents may once have been a far more important process
 influencing the fate of seeds and shaping plant communities in arid
 Australia and suggest that dingo extirpation has cascading effects on
 shrub seeds. Our study highlights that functional extinction of rodents
 may be an under-appreciated driver of vegetation change.
description: Gordon&Letnic2015_DataAll data from journal article
DOI: 10.5061/dryad.vv76g
title: Data from: True recognition of nestlings by hosts selects for mimetic cuckoo chicks

description: Cuckoos lay their eggs in other birds’ nests, whereafter the young cuckoo
 hatches, ejects its nestmates, and monopolizes the care of the host
 parents. Theory predicts that hosts should not evolve to recognize and
 reject cuckoo chicks because of the risk of mistakenly imprinting on a
 cuckoo chick in their first brood and thereafter always rejecting their
 own chicks. However, recent studies have revealed some hosts do reject
 cuckoo chicks from the nest, indicating that these hosts’ recognition
 systems either do not rely on first brood imprinting, or use cues that are
 independent of chick phenotype. Here, we investigate the proximate
 mechanisms of chick rejection behaviour in the large-billed gerygone
 (Gerygone magnirostris), a host of the little bronze-cuckoo (Chalcites
 minutillus). We find that gerygones use true template-based recognition
 based on at least one visual chick trait (the amount of hatchling
 down-feathers), and that this is further mediated by experience of adult
 cuckoos at the nest during egg-laying. Given the theoretical constraints
 of acquiring recognition templates via imprinting, gerygones must possess
 a template of own-chick appearance that is largely innate. This true
 recognition has facilitated the evolution of very rapid hatchling
 rejection and, in turn, striking visual mimicry of host young by
 little-bronze cuckoo chicks.
description: chick rejection data
 (full dataset)Data on the response
 (rejection behaviour) to the chicks according to 1) the chick species, 2)
 the presence or absence of down-feathers, 3) hatching order, 4) whether an
 adult cuckoo visited their nest or whether it was parasitized
 artificially, and/or 5) whether or not a cuckoo chick was in the minority
 in the nest.Noh et al_supp1 (full
 dataset).xlsxchick rejection data
 (reduced dataset)a reduced dataset
 comprising only one experimental chick per nestNoh et al_supp2 (reduced
 dataset).xlsx
DOI: 10.5061/dryad.43vg5
title: Data from: Genetic structure of the white-footed mouse in the context of the emergence of Lyme disease in southern Québec

description: [No abstract entered]
description: Microsatellite
 GenotypesA text file containing
 all the genotypes (11 loci) usedRogic et al. Microsatellite
 genotypes.txt
DOI: 10.5061/dryad.g45mc
title: Data from: Divergence maintained by climatic selection despite recurrent gene flow: a case study of Castanopsis carlesii (Fagaceae)

description: Local adaptation to different environments has the potential to maintain
 divergence between populations despite recurrent gene flow and is an
 important driver for generating biological diversity. In this study, we
 investigate the role of adaptation in the maintenance of two parapatric
 varieties of a forest tree. We used sequence variation of chloroplastic
 DNA and restriction site-associated DNA to investigate the genetic
 structure of two varieties of Castanopsis carlesii in subtropical China
 and relate it to climatic variation. We used niche reconstruction methods
 to investigate niche differentiation between the two varieties and to
 estimate the past distribution of this species. A deep divergence was
 observed between the two varieties, but evidence of introgression and
 genetic admixture was detected in two phenotypically and geographically
 intermediate populations. Niche reconstruction suggests that the
 distribution of the two varieties was disjunct during periods of global
 cooling and that the two varieties occupy significantly different niches.
 The genetic structure was mainly driven by environmental factors, and 13
 outlier loci under divergent selection were correlated with climatic
 variation. These results suggest that the two varieties evolved in
 allopatry and came back into secondary contact after the last glacial
 maximum and that they are an evolutionary example of divergence maintained
 by climatic selection despite recurrent gene flow.
description: Climate data used for
 Maxent and niche overlap analysisLongitude, latitude, and
 19 bioclimatic variables of collection points of two varieties of
 Castanopsis carlesii. Provided data include the longitude and latitude for
 each location, and bioclimatic variables ('BIO_1' to
 'BIO_19') as extracted from the 'WorldClim' database
 (for definitions see: http://www.worldclim.org/bioclim). Further
 information about WorldClim at Hijmans, R.J., S.E. Cameron, J.L. Parra,
 P.G. Jones and A. Jarvis, 2005. Very high resolution interpolated climate
 surfaces for global land areas. International Journal of Climatology 25:
 1965-1978. http://dx.doi.org/10.1002/joc.1276
DOI: 10.5061/dryad.hq701
title: Data from: Plasticity and epistasis strongly affect bacterial fitness after losing multiple metabolic genes

description: Many bacterial lineages lack seemingly essential metabolic genes. Previous
 work suggested selective benefits could drive the loss of biosynthetic
 functions from bacterial genomes when the corresponding metabolites are
 sufficiently available in the environment. However, the factors that
 govern this ‘genome streamlining’ remain poorly understood. Here we
 determine the effect of plasticity and epistasis on the fitness of
 Escherichia coli genotypes from whose genome biosynthetic genes for one,
 two, or three different amino acids have been deleted. Competitive fitness
 experiments between auxotrophic mutants and prototrophic wild type cells
 in one of two carbon environments revealed that plasticity and epistasis
 strongly affected the mutants’ fitness individually and interactively.
 Positive and negative epistatic interactions were prevalent, yet on
 average cancelled each other out. Moreover, epistasis correlated
 negatively with the expected effects of combined auxotrophy-causing
 mutations, thus producing a pattern of diminishing returns. Moreover,
 computationally analysing 1,432 eubacterial metabolic networks revealed
 that most pairs of auxotrophies co-occurred significantly more often than
 expected by chance, suggesting epistatic interactions and/ or
 environmental factors favoured these combinations. Our results demonstrate
 that both the genetic background and environmental conditions determine
 the adaptive value of a loss-of-biochemical-function mutation and that
 fitness gains decelerate, as more biochemical functions are lost.
description: Relative_fitness_Epistasis_Dsouza_et_al_2015The file consists of data showing the fitness (expected and observed) relative to the wild type and epistasis of different auxotrophic genotypes in minimal media with either fructose or succinate as the carbon source. The file also contains data of control experiments showing fitness relative to the wild type of genotypes subject to successive rounds of transduction with the same phage genotype and also the fitness (Malthusian parameter) of auxotrophic genotypes with and without the kanamycin resitance cassette.
DOI: 10.5061/dryad.vq021
title: Data from: Signaler and receiver boldness influence response to alarm calls in eastern chipmunks

description: Using social information can benefit individuals in many ways. Responding
 to alarm signals can, for instance, maximize survival under predation
 risk. However, foraging individuals should consider the reliability of
 such risk-based information to balance anti-predator behavior and resource
 acquisition. Receiver decisions could depend on personality effects, as
 individual variation in risk-taking tendencies (i.e. boldness) could not
 only affect receiver perception of the signaled threat but also signaler
 reliability. Recent theoretical models support the possibility of
 coevolution between personality and communication strategies. Using a
 playback experiment, we show that wild eastern chipmunks (Tamias striatus)
 respond to alarm calls according to their own boldness level (measured as
 consistent individual differences in basal vigilance) and that they
 increase their vigilance response to bolder callers potentially considered
 as more reliable. Further, receivers respond to the callers' boldness
 regardless of their own boldness and independently of their familiarity
 level with callers, therefore decoding this information from
 vocalizations. Such effects of individual behavioral variation on the
 perception and interpretation of social information could apply to signals
 used in a variety of ecological contexts.
description: data_dryad-Couchoux_etal-Boldness_affects_response_to_alarm_callsData for basal vigilance and for vigilance during playback of alarm calls
DOI: 10.5061/dryad.6v5g3
title: Data from: Sex-specific arrival times on the breeding grounds: hybridizing migratory skuas provide empirical support for the role of sex ratios

description: In migratory animals, protandry (earlier arrival of males on the breeding
 grounds) prevails over protogyny (females preceding males). In theory, sex
 differences in timing of arrival should be driven by the operational sex
 ratio, shifting toward protogyny in female-biased populations. However,
 empirical support for this hypothesis is, to date, lacking. To test this
 hypothesis, we analyzed arrival data from three populations of the
 long-distance migratory south polar skua (Catharacta maccormicki). These
 populations differed in their operational sex ratio caused by the
 unidirectional hybridization of male south polar skuas with female brown
 skuas (Catharacta antarctica lonnbergi). We found that arrival times were
 protandrous in allopatry, shifting toward protogyny in female-biased
 populations when breeding in sympatry. This unique observation is
 consistent with theoretical predictions that sex-specific arrival times
 should be influenced by sex ratio and that protogyny should be observed in
 populations with female-biased operational sex ratio.
description: DataArrival dates of South
 Polar Skuas and Brown Skuas at King George Island and Anvers
 IslandR codeIndividual based model
 to simulate sex specific arrival timesskua.IBM.R