cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0d0k824
title: Data from: Seedling recruitment correlates with seed input across seed sizes: implications for coexistence

description: Understanding controls on recruitment is critical to predicting community
 assembly, diversity and coexistence. Theory posits that at mean fecundity,
 recruitment of highly fecund small-seeded plants should be primarily
 microsite limited, which is indicated by a saturating recruitment
 function. In contrast, species that produce fewer large seeds are more
 likely to be seed-limited, which is characterized by a linear recruitment
 function. If these patterns hold in nature, seed predation that
 disproportionately affects larger-seeded species can limit their
 establishment. We tested these predictions by comparing recruitment
 functions among 16 co-occurring perennial forb species that vary by over
 two orders of magnitude in seed size. We also assessed how post-dispersal
 seed predation by mice influenced recruitment. We added seeds at densities
 from zero to three times natural fecundity of each species to undisturbed
 plots and examined spatial variation in recruitment by conducting
 experiments across ten grassland sites that varied in productivity and
 resource availability. Consistent across two replicated years, most
 species had linear recruitment functions across the range of added seed
 densities, indicative of seed-limited recruitment. Depending on year, the
 recruitment functions of only 19-37% of target species saturated near
 their average fecundity, and this was not associated with seed size.
 Recruitment was strongly inhibited by rodent seed predation for
 large-seeded species but not for smaller-seeded species. Proportional
 recruitment was more sensitive to spatial variation in recruitment
 conditions across sites for some small-seeded species than for
 large-seeded species. These results contradict the common belief that
 highly fecund small-seeded species suffer from microsite-limited
 recruitment. Rather, they imply that, at least episodically, recruitment
 can be strongly correlated to plant fecundity. However, proportional
 recruitment of small-seeded species was inhibited at productive sites to a
 greater extent than large-seeded species. Results also show that in a
 system where the dominant granivore prefers larger seeds, low-fecundity
 large-seeded species can suffer from even greater seed-limited recruitment
 than would occur in the absence of predators.
description: Maron_etal_Ecology_DATA2019Data associated with the manuscript.Maron_etal_Ecology_RCode2019R code to conduct main analyses presented in the paper.
DOI: 10.5061/dryad.1vr6g3f
title: Data from: Temporal variation in spatial genetic structure during population outbreaks: distinguishing among different potential drivers of spatial synchrony

description: Spatial synchrony is a common characteristic of spatio-temporal population
 dynamics across many taxa. While it is known that both dispersal and
 spatially autocorrelated environmental variation (i.e., the Moran effect)
 can synchronize populations, the relative contributions of each, and how
 they interact, is generally unknown. Distinguishing these mechanisms and
 their effects on synchrony can help us to better understand spatial
 population dynamics, design conservation and management strategies, and
 predict climate change impacts. Population genetic data can be used to
 tease apart these two processes as the spatio-temporal genetic patterns
 they create are expected to be different. A challenge, however, is that
 genetic data are often collected at a single point in time, which may
 introduce context-specific bias. Spatio-temporal sampling strategies can
 be used to reduce bias and to improve our characterization of the drivers
 of spatial synchrony. Using spatio-temporal analyses of genotypic data,
 our objective was to identify the relative support for these two
 mechanisms to the spatial synchrony in population dynamics of the
 irruptive forest insect pest, the spruce budworm (Choristoneura
 fumiferana), in Quebec (Canada). AMOVA, cluster analysis, isolation by
 distance and sPCA were used to characterize spatio-temporal genomic
 variation using 1370 SBW larvae sampled over four years (2012-2015) and
 genotyped at 3,562 SNP loci. We found evidence of overall weak spatial
 genetic structure that decreased from 2012 to 2015 and a genetic diversity
 homogenization among the sites. We also found genetic evidence of a
 long-distance dispersal event over &gt; 140 km. These results indicate
 that dispersal is the key mechanism involved in driving population
 synchrony of the outbreak. Early intervention management strategies that
 aim to control source populations have the potential to be effective
 through limiting dispersal. However, the timing of such interventions
 relative to outbreak progression is likely to influence their probability
 of success.
description: SNP data for population
 genetics analyseslarroqueetal2019.rarlarroqueetal2019_README.rSpruce budworm bw6 genome assemblyThis file contains a draft assembly of the spruce budworm (Choristoneura fumiferana) genome. The core assembly was generated from Roche 454 WGS reads (derived from DNA extracted from a single male pupa) assembled using Newbler. Subsequently, DNA from multiple male insects was subjected to PacBio sequencing; the reads thus obtained were used to improve scaffolding.bw6_scaffolds_and_unmerged_paths_03Feb15.fas
DOI: 10.5061/dryad.sk7fj41
title: Data from: Game of webs: species and web structure influence contest outcome in black widow spiders

description: Population-level trait variation within species plays an often-overlooked
 role in interspecific interactions. In this study we compared
 among-individual variation in web phenotype and foraging behavior between
 native black widows (Latrodectus hesperus) and invasive brown widows (L.
 geometricus). We staged repeated contests whereby native widows defended
 their webs against intruders of both species to 1) investigate how trait
 variation mediates web contest outcome among native widows and 2) see
 whether widow behavior differs in response to an invasive spider. In only
 one trait, the average number of foraging lines, did black widows differ
 from brown widows. Black widow residents that built more structural lines
 were more likely to successfully defend their webs from conspecific
 intruders (i.e., be the sole spider remaining on the web post
 interaction). This association between web structure and contest outcome
 did not exist in trials between black widows and invasive brown widows;
 however, in interspecific interactions, these same residents were more
 likely to have intruders remain on the web rather than drive them away.
 Surprisingly, brown widows did not usurp black widows. Brown widows were
 never observed signaling, yet black widow residents signaled equally to
 intruders of both species. Our results suggest that among-individual
 variation among native species can influence the response towards invasive
 competitors and outcome of these interactions.
description: widow web
 competitionWidow web competition
 data collected in the lab and created using R. Each row is an observation
 of a widow contest. Columns signify the id of web owner (focalID) and
 intruder (contest_ID). Behavioral data from web-building assays for both
 focal and intruder are included (e.g., total gumfooted lines, attack
 score) as well as other individual attributes: contest_black refers to
 whether the intruder was a black widow, 1 or brown widow, 0) , mass,
 logical expression if mated or not. In addition, observations scored from
 videos are recorded: number of bodyshakes and abdomen pulses
 ('abdomenpulse', 'bs.binom',
 'contest_bs.binom', 'contest_abdomenpulse') produced,
 whether contact was made, a fight occurred, and outcome of contest (1 =
 focal defended web, 2 = usurped, 0 = tie). Weight difference is the
 difference in mass between focal and intruder.full_widow_comp.csv
DOI: 10.5061/dryad.9tv0342
title: Data from: Contemporary sexual selection does not explain variation in male display traits among populations

description: Sexual selection is widely hypothesized to facilitate the evolution of
 reproductive isolation through divergence in sexual traits and sexual
 trait preferences. However, direct evidence of divergent sexual selection
 causing intraspecific trait divergence remains limited. Using the wolf
 spider Schizocosa crassipes, we characterized patterns of female mate
 choice within and among geographic locations and related those patterns to
 geographic variation in male display traits to test whether divergent
 sexual selection caused by mate choice explains intraspecific trait
 variation. We found evidence of phenotypic selection on male behavior
 arising from female mate choice, but no evidence that selection varied
 among locations. Only those suites of morphological and behavioral traits
 that did not influence mate choice varied geographically. These results
 are inconsistent with ongoing divergent sexual selection underlying the
 observed intraspecific divergence in male display traits. These findings
 align with theory on the potentially restrictive conditions under which
 divergent sexual selection may persist, and suggest that long-term studies
 capable of detecting periodic or transient divergent sexual selection will
 be critical to rigorously assess the relative importance of divergent
 sexual selection in intraspecific trait divergence.
description: Measures of display form
 and copulation success for male S. crassipesThis data file includes
 11 measures of the courtship displays of male Schizocosa crassipes wolf
 spiders collected from 7 populations in the southeastern US in 2016 and
 2017. There are 4 morphological measures: "MaleMassGrams" is the
 male's mass in grams; "CephWidthMean" is the males
 cephalothorax width in mm; "TuftArea" is the size of the
 male's tibial brush in mm^2; and "MeanTibDark.DivBy.WtStd"
 is the gray value of the male's tibia divided by the gray value of a
 white standard. There are 7 behavioral measurements:
 "LogLatencyToSignalSec" and "LogLatencyToBounceSec"
 are the log-transformed latencies (in seconds) to the male's first
 courtship signal and first "body bounce", respectively;
 "BouncesPerMin" is the number of body bounces per minute of
 observation; "LogMeanBounceIntervalSec" is the log-transformed
 mean interval (in seconds) between consecutive body bounces;
 "LogWaveBoutNum" is the log-transformed number of bouts of
 sustained leg-waving behavior; "TotalWaveDurSec" is the total
 duration (in seconds) of the male's leg-waving, and
 "LogMeanWaveDurSec" is the log-transformed mean duration (in
 seconds) of individual leg-waving bouts.The file also includes the outcome
 of the laboratory mating trial ["Copulation", 0 (no) or 1 (yes)]
 in which each male's courtship behavior was assayed. Each row
 corresponds to a mating trial. The collection year, collection site, and
 maturation date/age for both the male and female in each trial is
 included.S_crassipes_2016_2017_FinalDat.csv
DOI: 10.5061/dryad.4b526hv
title: Data from: Nitrogen addition reduces soil respiration but increases the relative contribution of heterotrophic component in an alpine meadow

description: 1. Disentangling the relative response sensitivity of soil autotrophic
 (Ra) and heterotrophic respiration (Rh) to nitrogen (N) enrichment is
 pivotal for evaluating soil carbon (C) storage and stability in the
 scenario of intensified N deposition. However, the mechanisms underlying
 differential sensitivities of Ra and Rh and relative contribution of Rh to
 soil respiration (Rs) with increasing N deposition remains elusive. 2. A
 manipulative field experiment with multi‐level N addition rates was
 conducted over three years (2015–2017) in an alpine meadow to explore the
 relative impact of N enrichment on Ra and Rh and the response of Rh/Rs
 ratio to the gradient of N addition. 3. Soil respiration components had
 different sensitivities to N enrichment, with Ra decreasing more than Rh,
 leading to a higher Rh/Rs ratio as a function of increasing N addition
 rates. Ra and Rh decreased nonlinearly as N addition rates increased, with
 a critical load of 8 g N m−2 yr−1 above which N enrichment significantly
 inhibited them. Ra and Rh were controlled by different abiotic and biotic
 factors and the regulation of controlling factors on soil respiration
 components varied over time. N induced reduction in the relative abundance
 of forb significantly affected Ra and this effect was mainly evident in
 the second and third year. Nitrogen enrichment significantly changed Rh in
 the third year and the decreased Rh under high doses of N addition could
 be attributed to the changes in microbial biomass C, soil substrate
 quality, and microbial composition. 4. Our study highlights the leading
 role of Ra in regulating Rs responses to N enrichment and the enhancement
 of Rh/Rs ratio with increasing N addition. We also emphasize that N
 induced shifts in plant community composition play a vital role in
 regulating Ra instead of Rh. The changing drivers of Ra and Rh with time
 suggests that long‐term experiments with multiple levels of N addition are
 further needed to test the nonlinear responses and underlying mechanisms
 of soil respiration components in face to aggravating N deposition.
description: DataFE-2019-00777-Data.xlsx
DOI: 10.5061/dryad.50q9k64
title: Data from: Who determines the timing of inflorescence closure of a sexual dandelion?: Pollen donors vs. recipients

description: Male-male competition for mating or fertilization opportunities may in
 theory select for male manipulative adaptation that can harm males’ mates,
 leading to sexual conflict. Evolutionary theory predicts that selection
 will favor the manipulation by pollen of the duration of its recipients’
 receptivity. However, there is insufficient evidence to show that pollen
 can exert effects on the duration of receptivity, a prerequisite for the
 evolution of pollen manipulative adaptation. Using a sexual diploid
 dandelion, Taraxacum japonicum, we conducted hand pollination experiments
 within and between populations to examine the effects of pollen on the
 timing of inflorescence (flower head) closure. We also examined the
 potential fitness consequences to the pollen recipients by field
 observation of seed production in populations with different inflorescence
 closure timing. Within-population experiments showed that pollination
 induced inflorescence closure even when some of the florets in the
 inflorescence were not yet pollinated with compatible pollen. Furthermore,
 between-population crosses revealed that pollen donors, recipients, and
 their interaction all influenced the timing of inflorescence closure.
 Different populations differed in the timing of inflorescence closure,
 which could affect the availability to the recipients of pollen for
 fertilization and thereby seed production. However, there were no
 significant differences in the rates of natural seed production in these
 populations. Our results demonstrate that pollen donors, as well as
 recipients, contribute to the duration of floral receptivity, confirming
 that a prerequisite for sexually antagonistic adaptation is satisfied and
 suggesting manipulative adaptation of pollen or its donor. We discuss the
 implications of our findings to the evolutionary theory of plant
 reproduction.
description: Kyogoku,Kataoka,Kondoh.2019.Evol.EcolHand pollination experiment in the green house to observe the time from pollination to inflorescence closure, field hand pollination experiment to observe inflorescence closure induced by pollination, and the proportion of filled seeds in the field.
DOI: 10.5061/dryad.fm4707v
title: Data from: A functional trade-off between trophic adaptation and parental care predicts sexual dimorphism in cichlid fish

description: Although sexual dimorphism is widespread in nature, its evolutionary
 causes often remain elusive. Here we report a case where a sex-specific
 conflicting functional demand related to parental care but not to sexual
 selection explains sexual dimorphism in a primarily trophic structure, the
 gill rakers of cichlid fishes. More specifically, we examined gill raker
 length in a representative set of cichlid fish species from Lake
 Tanganyika featuring three different parental care strategies: (i)
 uni-parental mouthbrooding, whereby only one parental sex incubates the
 eggs in the buccal cavity; (ii) bi-parental mouthbrooding, whereby both
 parents participate in mouthbrooding; and (iii) nest guarding without any
 mouthbrooding involved. As predicted from these different parental care
 strategies, we find sexual dimorphism in gill raker length to be present
 only in uni-parental mouthbrooders, but neither in bi-parental
 mouthbrooders nor in nest guarders. Moreover, variation in the extent of
 sexual dimorphism among uni-parental mouthbrooders appears to be related
 to trophic ecology. Overall, we present a so far unrecognised scenario for
 the evolution of sexual dimorphism that is not related to sexual selection
 or initial niche divergence between sexes. Instead, sexual dimorphism in
 gill raker length in uni-parental mouthbrooding cichlid fish appears to be
 the consequence of a sex-specific functional trade-off between a trophic
 function present in both sexes, and a reproductive function present only
 in the brooding sex.
description: Gill raker length
 measurementsRonco_et_al_Supplementary_data1_gill_raker.txtStable isotope dataRonco_et_al_Supplementary_data2_stable_isotope.txt
DOI: 10.5061/dryad.1v92t8b
title: Data from: Laboratory contamination in airway microbiome studies

description: Background: The low bacterial load in samples acquired from the lungs,
 have made studies on the airway microbiome vulnerable to contamination
 from bacterial DNA introduced during sampling and laboratory processing.
 We have examined the impact of laboratory contamination on samples
 collected from the lower airways by protected (through a sterile catheter)
 bronchoscopy and explored various in silico approaches to dealing with the
 contamination post-sequencing. Our analyses included quantitative PCR and
 targeted amplicon sequencing of the bacterial 16S rRNA gene. Results: The
 mean bacterial load varied by sample type for the 23 study subjects (oral
 wash&gt;1st fraction of protected bronchoalveolar
 lavage&gt;protected specimen brush&gt;2nd fraction of protected
 bronchoalveolar lavage; p &lt; 0.001). By comparison to a dilution
 series of know bacterial composition and load, an estimated 10-50% of the
 bacterial community profiles for lower airway samples could be traced back
 to contaminating bacterial DNA introduced from the laboratory. We
 determined the main source of laboratory contaminants to be the DNA
 extraction kit (FastDNA Spin Kit). The removal of contaminants identified
 using tools within the Decontam R package appeared to provide a balance
 between keeping and removing taxa found in both negative controls and
 study samples. Conclusions: The influence of laboratory contamination will
 vary across airway microbiome studies. By reporting estimates of
 contaminant levels and taking use of contaminant identification tools
 (e.g. the Decontam R package) based on statistical models that limit the
 subjectivity of the researcher, the accuracy of inter-study comparisons
 can be improved.
description: Drengenes_LaboratoryContamination_DRYAD_fastqFastq files generated by Illumina MiSeq sequencing of the bacterial 16S rRNA gene region V3V4 (164 samples, paired-end reads).Drengenes_LaboratoryContamination_DRYAD_MetadataMetadata file needed to rerun the bioinformatics analyses performed in Laboratory Contamination in Airway Microbiome Studies.
DOI: 10.5061/dryad.k3t3432
title: Data from: Effects of hydroperiod on growth, development, survival, and immune defenses in a temperate amphibian

description: 1. The many and varied effects of human induced environmental change have
 the potential to threaten animal biodiversity and species abundance.
 Importantly, human land use and global climate change are predicted to
 reduce water availability, which might have negative consequences for
 freshwater organisms. 2. In this study, we tested for an effect of a
 shortened hydroperiod on larval growth and development, and
 post-metamorphic survival and immune function in a temperate frog, Rana
 pipiens. 3. Animals developing under pond drying conditions metamorphosed
 at a smaller size and had lower survival after metamorphosis. We found
 sex-specific differences in larval period in our fastest drying treatment,
 with males metamorphosing more quickly than females. Individuals that
 developed under drying conditions also showed reduced skin swelling after
 PHA injection, indicating a compromised immune response. We found support
 for trade-offs between growth, development, and post-metamorphic immune
 function across hydroperiod treatments. Whole blood from animals with
 shorter larval periods had lower bacterial killing ability, and
 small-bodied juveniles had lower antibody titers. 4. Overall, our results
 indicate that a shortened hydroperiod can affect the rate of larval
 amphibian growth and development, and might negatively impact the
 condition of species that rely on freshwater for development. Our work
 improves understanding of the complex impacts that environmental stressors
 might have on the health of animal populations.
description: Effects of hydroperiod
 on growth, development, survival, and immune defenses in a temperate
 amphibianRaw data for the
 manuscript entitled "Effects of hydroperiod on growth, development,
 survival, and immune defenses in a temperate
 amphibian"Brannelly_Data.xlsx
DOI: 10.5061/dryad.1j43g7r
title: Data from: Temporal stability in a male African elephant social network

description: Social animals live in complex and variable socio-ecological environments
 where individuals adapt their behaviour to local conditions. Recently,
 there have been calls for studies of animal social networks to take
 account of temporal dynamics in social relationships as these have
 implications for the spread of information and disease, group cohesion,
 and the drivers of sociality, and there is evidence that maintaining
 stable social relationships has fitness benefits. It has recently been
 recognised that male elephants form strong social bonds with other males.
 The nature of these relationships, and thus network structure, may vary
 over time in response to environmental conditions and as individuals age.
 Using social network analysis, we examine the stability of relationships
 and network centrality in a population of male African elephants. Our
 results suggest that males may maintain stable social relationships with
 others over time. Older males show greater stability in network centrality
 than younger males, suggesting younger males face uncertainty in
 transitioning to adult society. For elephants, where older individuals
 function as social repositories of knowledge, maintaining a social network
 underpinned by older males could be of particular importance.
description: eledata_supplementary_materialsData describing associations among non-musth male elephants observed in male-only groups (bull groups, or lone bulls). Elephants were assumed to be associating under the Gambit of the Group assumption, where each elephant observed in a group was assumed to be associating with each other elephant in the group. Column headers are: ID, Group_Type ("LB" = Lone Bull, "B" = "Bull group"), Datetime, sampperiod (sampling period/SP of observation), age (mean estimated age over the sampling period), and group (a numeric value indicating which group each individual was observed in).