cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f58gt56
title: Data from: GxG epistasis in growth and condition and the maintenance of genetic polymorphism in Gambusia holbrooki

description: Theory on indirect genetic effects (IGEs) indicates that variation in the
 genetic composition of social groups can generate GxG epistasis that may
 promote the evolution of stable polymorphisms. Using a livebearing fish
 with a genetic polymorphism in coloration and associated behavioral
 differences, we tested whether genotypes of social partners interacted
 with focal individual genotypes to influence growth and condition over 16
 weeks of development. We found that IGEs had a significant influence on
 patterns of feeding, regardless of focal fish genotype. There was no
 influence of social environment on juvenile length, but there was
 significant GxG epistasis for body condition. Each focal juvenile was in
 better condition when its own genotype was not present in adult social
 partners. These data are consistent with negative frequency-dependent
 selection in which each morph performs better when it is rare. Neither
 variation in feeding nor activity-related behaviors explained variation in
 body condition, suggesting that GxG epistasis for condition was caused by
 physiological differences between the two genotypes. These findings
 indicate that GxG epistasis in a given polymorphism can generate selection
 that contributes to the maintenance of that polymorphism and to
 maintenance of genetic variation for additional fitness-related traits.
description: EVO13474Data on mass, length and feeding rates.
DOI: 10.5061/dryad.j16p2
title: Data from: A novel multi-scale assessment of community assembly across time, space, and functional niche

description: A basic ecological tenet is that organisms in a community occupy different
 niches and have different traits, but how consistently competition,
 selection, and phylogenetic effects structure communities remains
 uncertain. Are all communities created equal? We examine how mammalian
 carnivoran communities are assembled with regard to mass, diet, and
 locomotion. Here, we use a multivariate nearest-neighbor framework to
 examine multiple North American localities spanning 3 million years to
 determine whether community assembly is consistent through time and four
 modern localities around the world to assess the effects of habitat.
 Additionally, we examined how trait patterns differ among families and how
 family-level evolutionary effects affect them. We found some broadly
 consistent patterns, although differences are more pronounced than
 similarities. Diet is more affected by evolutionary constraints than by
 time or place. Locomotion is most affected by habitat, and the ability to
 partition niches is related to habitat heterogeneity. Mass is influenced
 by family, but also by habitat and the mass-selective extinction events at
 the end-Pleistocene. These findings indicate that assembly patterns are
 not largely determined by within-community interactions but instead show
 that each community is a product of its independent variables.
description: Extant carnivore
 indicesExtant carnivore dietary
 and postcranial indices used in this study.Fossil carnivore
 indicesFossil carnivore dietary
 and locomotor indices used in this study.carnivores.multi.scaled.functions.setup.finalFINAL VERSIONS OF R CODE FROM START TO FINISH, WITH DOCUMENTATIONcarnivores.multi.scaled.graphs.runfile.finalR code for graphs shown in this publicationcarnivores.multi.scaled.runcode.finalsimulation distributions and family-space analyses in R.new pretty histograms nov2013Histogram code for R and rough simulations of raw data for R
DOI: 10.5061/dryad.6nd54
title: Data from: Assessing conservation risks to populations of an anadromous Arctic salmonid, the northern Dolly Varden (Salvelinus malma malma), via estimates of effective and census population sizes and approximate Bayesian computation

description: Census population size (Nc) is crucial to the development of resource
 management strategies, however, monitoring the effective population size
 (Ne) of managed populations has proliferated because of this parameter’s
 relationship to the short-term impacts of genetic stochasticity and
 long-term population viability. Thus, having a sound understanding of both
 Nc and Ne, including population connectivity, provides valuable insights
 into both the demographic and genetic risks to extinction. Here, we
 assessed microsatellite DNA variation in four (of five known) anadromous
 northern Dolly Varden (NDV, Salvelinus malma malma) populations from
 Canada’s western Arctic region, to estimate Ne using both temporal-based
 and single-sample estimators and to test for associations between Ne and
 Nc. We also employed approximate Bayesian computation (ABC) to evaluate
 several evolutionary scenarios that have potentially shaped contemporary
 population structure in this species, focusing particularly on population
 size and connectivity. We found evidence for moderate to large
 contemporary and historical Ne, suggesting that short- and long-term
 extinction risks are low for these populations. Estimates of contemporary
 and long-term Ne were variable within and among populations and overall
 estimates could not be reliably linked with Nc or available spawning
 habitat. The overall estimate of Ne/Nc, was 0.152 and ranged from 0.024 to
 0.442 when including errors around the estimate of Ne and Nc. Finally, ABC
 analyses suggest that NDV had a common origin followed by divergence in
 isolation while maintaining large effective sizes, but also that these
 populations were bottlenecked in the past, likely the result of
 post-glacial colonization processes. These results corroborate indications
 of limited gene flow at present, indicating independent demographic and
 evolutionary trajectories that imply NDV is best managed on a
 per-river-population basis. Overall, the results of this study further our
 general understanding of Ne, Ne/Nc and demographic independence in NDV,
 and provide a comprehensive and quantitative assessment of the potential
 genetic and demographic risk status of Arctic anadromous salmonids,
 including baselines for future monitoring.
description: 3D Genepop
 FileGenepop file (3 digit)
 containing raw microsatellite data used for all
 analyses.Genepop 3
 Digit
DOI: 10.5061/dryad.f8n8p13
title: Data from: Family Naticidae (Gastropoda) from the Upper Jurassic of Kutch, India and a critical reappraisal of taxonomy and time of origination of the family

description: Because of mostly nondescript shells and frequent convergence, naticid
 taxonomy is in a state of flux. Inadequate preservation of naticid body
 fossils has further complicated the matter in determining the true
 affinity and the exact time of origination of the clade. As a result, a
 plethora of classificatory schemes of naticid phylogeny and times of
 origin has been proposed. In many previous studies, true naticid
 affinities of fossils have been sought based on single or a few
 morphological characters, which are susceptible to poor preservation. In
 the present paper, we have attempted a holistic reappraisal of naticid
 taxonomy based on an extensive database of shell morphological characters
 and identified many distinct family- and subfamily-specific characters
 which survive fossilization. This approach has enabled us to identify
 three new naticid species from the Late Jurassic horizons of Kutch, India,
 thus extending back the time of origin of the family Naticidae by 30 Ma.
 Analysis of character matrix data reveals that the present species belong
 to two subfamilies, Gyrodinae and Polinicinae. The species are Gyrodes
 mahalanobisi new species, Euspira jhuraensis new species, and Euspira
 lakhaparensis new species. The occurrence of typical naticid drill holes
 on various coeval gastropod and bivalve taxa along with these body fossils
 provides strong supporting evidence for the naticid affinity of these
 forms.
description: Supplementary Table
 1Character matrix data of
 several naticid genera and species to distinguish subfamilies within
 Naticidae and the out group Ampullospirinae. Major sources are Popenoe et
 al., 1987 (1); Aronowsky, 2003 (2), Marincovich, 1977(3), Majima, 1989
 (4), Kilburn, 1976 (5).Supplementary Table
 2List
 of all Jurassic naticid genera reported in the Paleobiology Database
 (PBDB; www.paleobiodb.org) from different parts of the world. Only
 genus-level information has been listed. ‘Indet.’ forms are excluded from
 the list.
DOI: 10.5061/dryad.83np7
title: Data from: Systemic enrichment of antifungal traits in the rhizosphere microbiome after pathogen attack

description: 1. Plant-associated microbial communities are crucial for plant growth and
 play an important role in disease suppression. Community composition and
 function change upon pathogen attack, yet to date we do not know if these
 changes are a side effect of the infection or actively driven by the
 plant. 2. Here we used a split-root approach to test whether barley plants
 recruit bacteria carrying antifungal traits upon infestation with Fusarium
 graminearum. Split-root systems allow disentangling local infection
 effects, such as root damage, from systemic, plant-driven effects on
 microbiome functionality. We assessed the recruitment of fluorescent
 pseudomonads, a taxon correlated with disease suppression, and of two
 well-described antifungal genes (phlD coding for 2,4-DAPG and hcnAB coding
 for HCN). 3. We show an enrichment of fluorescent pseudomonads, phlD and
 hcnAB upon pathogen infection. This effect was only measurable in the
 uninfected root compartment. We link these effects to an increased
 chemotaxis of pseudomonads towards exudates of infected plants. 4.
 Synthesis. We conclude that barley plants selectively recruited bacteria
 carrying antifungal traits upon pathogen attack and that the pathogen
 application locally interfered with this process. By disentangling these
 two effects we set the base for enhancing strategies unravelling how
 pathogens and plant hosts jointly shape microbiome functionality.
description: data of the soil and
 chemotaxis experiment.xls file with four
 sheets including the data and meta-data of the soil experiment and the
 chemotaxis experimentdata_systemic_enrichment_of_antifungal_traits_in_the_rhizosphere_microbiome_after_pathogen_attack.xls
DOI: 10.5061/dryad.cs31j
title: Data from: An experimental study of strong reciprocity in bacteria

description: Strong reciprocity, whereby cooperators punish non-cooperators, may help
 to explain the evolutionary success of cooperative behaviours. However,
 theory suggests that selection for strong reciprocity can depend upon
 tight genetic linkage between cooperation and punishment, to avoid the
 strategy being outcompeted by non-punishing cooperators. We tested this
 hypothesis using experimental populations of the bacterium Pseudomonas
 aeruginosa, which cooperate by producing iron-scavenging siderophores and,
 in this context, punish non-cooperators with toxins. Consistent with
 theory, we show that cooperative punishers can indeed invade cheats, but
 only when the traits are tightly linked. These results emphasize that
 punishment is only likely to be favoured when the punishment itself leads
 to a direct or indirect fitness benefit to the actor.
description: An experimental study of
 strong reciprocity in bacteriaIncluded in this file
 are the colony forming unit (CFU) counts for each competition between
 strains over time. Proportions of each strain are calculated and can be
 seen in figure 1 in the associated publication.An experimental sutdy of strong
 reciprocity in bacteria.xls
DOI: 10.5061/dryad.p2kf0
title: Data from: Do seaducks minimise the flightless period?: inter- and intra-specific comparisons of remigial moult

description: Remigial moult is one of the crucial events in the annual life cycle of
 waterfowl as it is energetically costly, lasts several weeks, and is a
 period of high vulnerability due to flightlessness. In waterfowl, remigial
 moult can be considered as an energy-predation trade-off, meaning that
 heavier individuals would minimise the flightless period by increasing
 feather growth rate and energy expenditure. Alternatively, they could
 reduce body mass at the end of this period, thereby reducing wing-loading
 to increase flight capability. We studied timing of remigial moult,
 primary growth rates, flightlessness duration, and the pattern of body
 mass variation in 5 species of captive seaducks (Melanitta fusca, M.
 perspicillata, Clangula hyemalis, Histrionicus histrionicus, and Somateria
 mollissima) ranging in size from 0.5 to 2.0 kg. Their feather growth rates
 weakly increased with body mass (M0.059) and no correlation was found at
 the intra-specific level. Consequently, heavier seaduck species and
 especially heavier individuals had a longer flightless period. Although
 birds had access to food ad libidum, body mass first increased then
 decreased, the latter coinciding with maximum feather growth rate. Level
 of body mass when birds regained flight ability was similar to level
 observed at the beginning of remigial moult, suggesting they were not
 using a strategic reduction of body mass to reduce the flightlessness
 duration. We suggest that the moulting strategy of seaducks may be the
 result of a compromise between using an intense moult strategy
 (simultaneous moult) and a low feather growth rate without prejudice to
 feather quality. Despite the controlled captive status of the studied
 seaducks, all five species as well as both sexes within each species
 showed timing of moult reflecting that of wild birds, suggesting there is
 a genetic component acting to shape moult timing within wild birds.
description: Seaducks_Data_Viain_et_al
DOI: 10.5061/dryad.r0h7s
title: Data from: Cichlid fish use coloration as a cue to assess the threat status of heterospecific intruders

description: The ability to assess the threat posed by competitors, and to respond
 appropriately, is important for reducing the costs of aggression. In this
 respect, aggression directed toward heterospecifics is often just as
 significant as aggression among conspecifics. This is especially true for
 cichlid fish that share breeding grounds with heterospecifics. Indeed,
 cichlids are known to differentiate not only between conspecifics that
 pose different levels of threat but also between heterospecific
 territorial intruders by directing more aggression toward nonbreeding
 individuals. To assess whether the ability to make such distinctions could
 be based on color cues alone, we carried out a field study in which we
 experimentally presented Amphilophus sagittae cichlid pairs with model
 intruders of a sympatric congener, Amphilophus xiloaensis, in breeding
 versus nonbreeding coloration. Consistent with our prediction, we found
 that A. sagittae exhibited more aggression toward A. xiloaensis models of
 the latter color type. The results are, to our knowledge, the first to
 show that territory holders can, based on coloration alone, assess
 variation among individuals of a species other than their own in the
 threat posed to offspring survival.
description: Aggression
 dataField data: aggression
 by territory holding fish towards model intruders. Sex and length of the
 territory holders, water depth at the territory, and model intruder type
 are also listed.Color
 scoresR + G + B color scores
 for the model ("dummy") intruders used in the
 experiment.
DOI: 10.5061/dryad.1d0m9
title: Data from: Oxidative status and fitness components in the Seychelles warbler

description: Oxidative damage, caused by reactive oxygen species during aerobic
 respiration, is thought to be an important mediator of life-history
 trade-offs. To mitigate oxidative damage, antioxidant defence mechanisms
 are deployed, often at the cost of resource allocation to other body
 functions. Both reduced resource allocation to body functions and direct
 oxidative damage may decrease individual fitness, through reducing
 survival and/or reproductive output. The oxidative costs of reproduction
 have gained much attention recently, but few studies have investigated the
 long-term consequences of oxidative damage on survival and (future)
 reproductive output under natural conditions. Using a wild population of
 the cooperatively breeding Seychelles warbler (Acrocephalus sechellensis),
 we tested the prediction that high levels of reactive oxygen species, or
 high antioxidant investments to avoid oxidative damage, have fitness
 consequences because they reduce survival and/or reproductive output. We
 found that individuals with higher circulating non-enzymatic antioxidant
 capacity had a lower probability of surviving until the next year.
 However, neither current reproductive output, nor future reproductive
 output in the surviving individuals, was associated with circulating
 non-enzymatic antioxidant capacity or oxidative damage. The negative
 relationship between antioxidant capacity and survival that we observed
 concurs with the findings of an extensive comparative study on birds,
 however the mechanisms underlying this association remain to be resolved.
description: Oxidative status and
 fitness components in the Seychelles warblerData on oxidative status
 (dROMs=oxidative damage, OXY=plasma antioxidant capacity) and fitness
 components (reproductive output, survival) in the Seychelles
 warbler.Data_VanDeCrommenacker_2017_FuncEcol.xlsx
DOI: 10.5061/dryad.t6j7p
title: Data from: Keystone individuals alter ecological and evolutionary consumer-resource dynamics

description: Intraspecific variation is central to our understanding of evolution and
 ecology, but these fields generally consider either the mean trait value
 or its variance. Alternatively, the keystone individual concept from
 behavioral ecology posits that a single individual with an extreme
 phenotype can have disproportionate and irreplaceable effects on group
 dynamics. Here, I generalize this concept to include non-behavioral traits
 and broader ecological and evolutionary dynamics. I test for the effects
 of individuals with extreme phenotypes on the ecology and evolution or a
 gall-forming fly and its natural enemies that select for opposite gall
 sizes. Specifically I introduce a putatively keystone predator-attracting
 individual gall-maker, hypothesizing that the presence of such an
 individual should (i) increase gall-maker population-level mortality, (ii)
 cause consumer communities to be dominated by species that are most
 attracted to the keystone individual, (iii) increase selection for traits
 conferring defense against the most common consumer, and (iv) weaken
 patterns of stabilizing selection. I find support for both the ecological
 and evolutionary consequences of single individuals with extreme
 phenotypes, suggesting that they can be considered keystone individuals. I
 discuss the generality of the keystone individual concept, suggesting
 likely consequences for ecology and evolution.
description: focal_gall_DRYAD_DATA_AMNATMortality and attack rate data for Eurosta.
DOI: 10.15468/dl.ydjuvu
title: Occurrence Download

description: A dataset containing 1299 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Aonidiella aurantii)"
 ]
}

 The dataset includes 1299 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000983-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.m27k7
title: Data from: Cultural isolation is greater than genetic isolation across an avian hybrid zone

description: Elucidating the relationship between genetic and cultural evolution is
 important in understanding speciation, as learned premating barriers might
 be involved in maintaining species differences. Here we test this
 relationship by examining a widely recognized premating barrier, bird
 song, in a hybrid zone between black-throated green (Setophaga virens) and
 Townsend's warblers (S. townsendi). We use song analysis, genomic
 techniques and playback experiments to characterize the cultural and
 genetic backgrounds of individuals in this region, expecting that if song
 is an important reproductive barrier between these species, there should
 be a strong relationship between song and genotype. We show that songs in
 the hybrid zone correspond to the distinctly different songs found in
 allopatry but that song and genotype are not tightly coupled in sympatry.
 Allopatric individuals responded only to local songs, indicating that
 individuals may have learned to respond to songs they commonly hear. We
 observed discordance between song and genotype clines; a narrower cline
 suggests that cultural selection on song is stronger than natural
 selection on genotype. These findings indicate that song is unlikely to
 play a role in reproductive isolation between these species, and we
 suggest that spatial variation in song may nonetheless be maintained by
 frequency-dependent cultural selection. This decoupling of genes and
 culture may contribute to hybridization in this region.
description: Kenyon et al_main data
 setKenyon et al_playback
 data set
DOI: 10.5061/dryad.ng017rc
title: Data from: Patent foramen ovale closure, antiplatelet therapy or anticoagulation in patients with patent foramen ovale and cryptogenic stroke: a systematic review and network meta-analysis incorporating complementary external evidence

description: Objective: To examine the relative impact of three management options in
 patients less than 60 years old with cryptogenic stroke and a patent
 foramen ovale (PFO): PFO closure plus antiplatelet therapy, antiplatelet
 therapy alone, and anticoagulation alone. Design: Systematic review and
 network meta-analysis (NMA) supported by complementary external evidence
 Data sources: Medline, EMBASE, and Cochrane CENTRAL. Study selection:
 Randomised controlled trials (RCTs) addressing PFO closure and/or medical
 therapies in patients with PFO and cryptogenic stroke. Review methods: We
 conducted an NMA complemented with external evidence and rated certainty
 of evidence using the GRADE system. Results: Ten RCTs in eight studies
 proved eligible (n=4416). PFO closure versus antiplatelet therapy probably
 results in substantial reduction in ischaemic stroke recurrence (risk
 difference per 1000 patients over 5 years [RD]: -87, 95% credible interval
 [CrI] -100 to -33; moderate certainty). Compared with anticoagulation, PFO
 closure may confer little or no difference in ischaemic stroke recurrence
 (low certainty) but probably has a lower risk of major bleeding (RD -20,
 95% Crl -27 to -2, moderate certainty). Relative to either medical
 therapy, PFO closure probably increases the risk of persistent atrial
 fibrillation (RD 18, CI +5 to +56, moderate certainty) and device-related
 adverse events (RD +36, 95% CI +23 to +50, high certainty).
 Anticoagulation, compared to antiplatelet therapy, may reduce the risk of
 ischaemic stroke recurrence (RD -71, 95% CrI -100 to +17, low certainty),
 but probably increases the risk of major bleeding (RD +12, CrI -5 to +65,
 moderate certainty). Conclusions: In patients less than 60 years old, PFO
 closure probably confers an important reduction in ischaemic stroke
 recurrence compared to antiplatelet therapy alone but may make no
 difference compared to anticoagulation. PFO closure incurs a risk of
 persistent atrial fibrillation and device-related adverse events. Compared
 to alternatives, anticoagulation probably increases major bleeding.
description: PFO and Cryptogenic
 Stroke Data FileThis file contains 4
 sheet. PFO vs Medical Therapy, PFO vs Antiplatelet, PFO vs
 Anticoagulation, and Anticoagulation vs Antiplatelet