cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g7m364t
title: Data and R code from: Pollination interactions reveal direct costs and indirect benefits of plant–plant facilitation for ecosystem engineers

description: Ecosystem engineers substantially modify the environment via their impact
 on abiotic conditions and the biota, resulting in facilitation of
 associated species that would not otherwise grow. Yet, reciprocal effects
 are poorly understood as studies of plant–plant interactions usually
 estimate only benefits for associated species while hardly considering how
 another trophic level may mediate direct and indirect effects for
 ecosystem engineers. We run a field experiment with ecosystem engineers
 blooming either alone or with associated plants to decompose net effects
 and to test the hypothesis that pollinator-mediated interactions provide
 benefits which balance costs of facilitation by ecosystem engineers. We
 found that net costs of facilitation are accompanied by
 pollinator-mediated benefits. Despite ecosystem engineers producing less
 flowers per plant, they were visited by more and more diverse pollinators
 per flower when blooming with associated plants than when blooming alone.
 However, fruit set was unaffected by the presence of associated plants and
 seed production per plant was higher when ecosystem engineers bloomed
 alone. Our findings suggest that besides experiencing direct costs,
 ecosystem engineers can also benefit from facilitating other species via
 increasing their own visibility to pollinators. This study illuminates how
 the outcome of direct plant–plant interactions might be mediated by
 indirect interactions including third players.
description: insect_recordRInsect sampling and specimensseeds_cbSeed anf fruit datalosapio_costben_prscbR code for the analyseslosapio_costben_prscbR data image
DOI: 10.5061/dryad.83533nh
title: Data from: Of 11 candidate steroids, corticosterone concentration standardized for mass is the most reliable steroid-biomarker of nutritional stress across different feather types

description: 1. Measuring corticosterone in feathers has become an informative tool in
 avian ecology, enabling researchers to investigate carry-over effects and
 responses to environmental variability. Few studies have, however,
 explored whether corticosterone is the only hormone expressed in feathers,
 and is the most indicative of environmental stress. Essential questions
 remain as to how to compare hormone concentrations across different types
 of feathers and whether preening adds steroids, applied after feather
 growth. 2. We used liquid chromatography coupled to tandem mass
 spectrometry to quantify a suite of 11 steroid hormones in back, breast,
 tail, and primary feathers naturally grown at overlapping time intervals
 by rhinoceros auklet Cerorhinca monocerata captive-reared fledglings and
 wild-caught juveniles. The captive-reared birds were raised on either a
 restricted or control diet. Measured steroids included intermediates in
 the adrenal steroidogenesis pathway to glucocorticoids and the sex
 steroids pathway to androgens and estrogens. 3. Corticosterone was
 detected in the majority of feathers of each type. We also detected
 cortisone in back feathers, androstenedione in breast feathers, and
 testosterone in primary feathers. Captive fledglings raised on a
 restricted diet had higher concentrations of corticosterone in all four
 feather types than captive fledglings raised on a control diet.
 Corticosterone concentrations were reliably repeatable across feather
 types when standardized for feather mass, but not for feather length. Of
 the seven hormones looked for in uropygial gland secretions, only
 corticosterone was detected in one out of 23 samples. 4. We conclude that
 corticosterone is the best feather-steroid biomarker for detection of
 developmental nutritional stress, as it was the only hormone to manifest a
 signal of nutritional stress, and that exposure to stress can be compared
 among different feather types when corticosterone concentrations are
 standardized by feather mass.
description: LC_MSMS Steroids in RHAU
 FeathersRaw concentrations of 11
 steroids in rhinoceros auklet feathers from LC-MS/MS and concentrations of
 feather corticosterone standardized for feather mass, feather length, and
 length detrended for feather mass. Also included are the length and mass
 of feathers analyzed. The ReadMe file contains the lower limit of
 quantitation for each analysis run.LC_MSMS RHAU Data for
 Dryad.xlsx
DOI: 10.5061/dryad.q1223rs
title: Data from: Parasite-induced plasticity in host social behaviour depends on sex and susceptibility

description: Understanding the effects of parasites on host behaviour, of host
 behaviour on parasite infection, and the reciprocal interactions between
 these processes is vital to improving our understanding of animal
 behaviour and disease dynamics. However, behaviour and parasite infection
 are both highly variable within and between individual hosts, and how this
 variation affects behaviour-parasite feedbacks is poorly understood. For
 example, it is unclear how an individual’s behaviour before infection
 might change once it becomes infected, or as the infection progresses, and
 how these changes depend on the host’s parasite susceptibility. Here,
 using the guppy, Poecilia reticulata, and a directly-transmitted
 ectoparasite, Gyrodactylus turnbulli, I show that parasite-induced
 behavioural plasticity depends on host sex and susceptibility. Among
 females, time spent shoaling (‘sociality’), a behaviour that increases
 parasite transmission, did not depend on infection status (infected/not)
 or susceptibility. By contrast, male sociality in the absence of infection
 was negatively correlated with susceptibility, suggesting the most
 susceptible males use behaviour to avoid infection. However, in late
 infection when parasite transmission is most likely, male sociality and
 susceptibility became positively correlated, suggesting susceptible males
 modify their behaviour upon infection potentially to increase transmission
 and mating opportunities. I discuss the implications of these patterns for
 disease dynamics.
description: StephensonDataAll variables are described in full in the README file. This file also contains the R code and output in R Markdown format.
DOI: 10.5061/dryad.7q6q3s0
title: Data from: The multispecies coalescent model outperforms concatenation across diverse phylogenomic

description: A statistical framework of model comparison and model validation is
 essential to resolving the debates over concatenation and coalescent
 models in phylogenomic data analysis. A set of statistical tests are here
 applied and developed to evaluate and compare the adequacy of
 substitution, concatenation, and multispecies coalescent (MSC) models
 across 47 phylogenomic data sets collected across tree of life. Tests for
 substitution models and the concatenation assumption of topologically
 concordant gene trees suggest that a poor fit of substitution models (44%
 of loci rejecting the substitution model) and concatenation models (38% of
 loci rejecting the hypothesis of topologically congruent gene trees) is
 widespread.  Logistic regression shows that the proportions of GC
 content and informative sites are both negatively correlated with the fit
 of substitution models across loci. Moreover, a substantial violation of
 the concatenation assumption of congruent gene trees is consistently
 observed across 6 major groups (birds, mammals, fish, insects, reptiles,
 and others, including other invertebrates). In contrast, Bayesian model
 validation and comparison analyses conducted even on data sets reduced for
 computational efficiency suggest that, among those loci adequately
 described by a given substitution model, the proportion of loci rejecting
 the MSC model is 11%, significantly lower than those rejecting the
 substitution and concatenation models, and Bayesian model comparison
 strongly favors the MSC over concatenation across all data sets. Species
 tree inference suggests that loci rejecting the MSC have little effect on
 species tree estimation.  Our analysis reveals the value of model
 validation and comparison in phylogenomic data analysis, as well as the
 need for further improvements of multilocus models and computational tools
 for phylogenetic inference.
description: model_validation_data
DOI: 10.5061/dryad.kc7186p
title: Data from: Functional diversity enhances, but exploitative traits reduce tree mixture effects on microbial biomass

description: 1. Soil microorganisms play key roles in terrestrial biodiversity and
 ecosystem functions. Despite recent progress in elucidating the
 association between plant diversity and soil microorganisms, it remains
 unclear whether the functional properties of plant mixtures might alter
 this association. 2. We examined whether the effects of tree species
 mixtures on soil microbial biomass were impacted by the functional
 diversity (FD) and community-weighted-mean (CWM) of tree mixtures, by
 conducting a global meta-analysis involving 123 paired observations of
 tree mixtures and the corresponding monocultures from 38 studies in
 forests. 3. We found that the tree mixture effect on microbial biomass
 increased with the FD of specific leaf area (SLA), leaf N and P content,
 as well as the FD based on all of these traits plus leaf dry matter
 content. Meanwhile, the responses of microbial biomass to tree mixtures
 decreased with the CWM of SLA, leaf N, and P content. The effects of FD
 and CWM remained consistent, despite variable tree species richness, stand
 age and climatic factors. 4. Our results provide a new insight that the
 functional properties of plants may alter the magnitude of the association
 between plant diversity and soil microorganisms.
description: Tree mixture and
 microbial biomass datasetFile containing the
 dataset for tree mixture effects on microbial biomass along with the
 information of climates, stand age, tree species richness as well as
 functional diversity and community-weighted-mean of different plant
 traitsFUE-Data-Final.csv
DOI: 10.5061/dryad.r1h8gm4
title: Data from: Metabolically similar cohorts of bacteria exhibit strong co-occurrence patterns with diet items and eukaryotic microbes in lizard guts

description: Gut microbiomes perform essential services for their hosts, including
 helping them to digest food and manage pathogens and parasites. Performing
 these services requires a diverse and constantly changing set of metabolic
 functions from the bacteria in the microbiome. The metabolic repertoire of
 the microbiome is ultimately dependent on the outcomes of the ecological
 interactions of its member microbes, as these interactions in part
 determine the taxonomic composition of the microbiome. The ecological
 processes that underpin the microbiome's ability to handle a variety
 of metabolic challenges might involve rapid turnover of the gut microbiome
 in response to new metabolic challenges, or it might entail maintaining
 sufficient diversity in the microbiome that any new metabolic demands can
 be met from an existing set of bacteria. To differentiate between these
 scenarios, we examine the gut bacteria and resident eukaryotes of two
 generalist-insectivore lizards, while simultaneously identifying the
 arthropod prey each lizard was digesting at the time of sampling. We find
 that the cohorts of bacteria that occur significantly more or less often
 than expected with arthropod diet items or eukaryotes include bacteria
 species that are highly similar to each other metabolically. This pattern
 in the bacteria microbiome could represent an early step in the taxonomic
 shifts in bacteria microbiome that occur when host lineages change their
 in diet niche over evolutionary timescales.
description: Table_S1host-by-microbiome taxon table, populated by the number of sequences of each microbe found in each hostTable_S2slope and regression coefficients of cooccurrence vs. functional similarity of bacteria in all possible pairs of the three most common bacteria phyla in our samples
DOI: 10.5061/dryad.2n3fd2p
title: Data from: Mite load predicts the quality of sexual color and locomotor performance in a sexually dichromatic lizard

description: Since Darwin, the maintenance of bright sexual colors has recurrently been
 linked to mate preference. However, the mechanisms underpinning such
 preferences for bright colors would not be resolved for another century.
 Likely, the idea of selection for colors that could decrease the chances
 of survival (e.g. flashy colors that can inadvertently attract predators)
 was perceived as counterintuitive. It is now widely-accepted that these
 extreme colors often communicate to mates the ability to survive despite a
 ‘handicap’ and act as honest signals of individual quality when they are
 correlated with the quality of other traits that are directly linked to
 individual fitness. Sexual colors in males are frequently perceived as
 indicators of infection resistance, in particular. Still, there remains
 considerable discord among studies attempting to parse the relationships
 between the variables associating sexual color and infection resistance,
 such as habitat type and body size. This discord may arise from complex
 interactions between these variables. Here, we ask if sexual color in male
 Florida scrub lizards (Sceloporus woodi) is an honest signal of resistance
 to chigger mite infection. To this end, we use linear modeling to explore
 relationships between mite load, different components of sexual color,
 ecological performance, body size, and habitat type. Our data show that
 that the brightness of sexual color in scrub lizards is negatively
 associated with the interaction between mite load and body size, and scrub
 lizards suffer decreased endurance capacity with increases in mite load.
 Our data also indicate that mite load, performance, and sexual color in
 male scrub lizards can vary between habitat types. Collectively these
 results suggest that sexual color in scrub lizards is an honest indicator
 of individual quality and further underscore the importance of considering
 multiple factors when testing hypotheses related to the maintenance of
 sexual color.
description: honest_signalsThis is the final data set for which all final (and published) analyses were completed.sex_colorThis is the R script used to run all final analyses.
DOI: 10.5061/dryad.k71rd89
title: Data from: A selfish genetic element linked to increased lifespan impacts metabolism in female house mice

description: Gene drive systems can lead to the evolution of traits that further
 enhance the transmission of the driving element. In gene drive, one allele
 is transmitted to offspring at a higher frequency than the homologous
 allele. This has a range of consequences, which generally include a
 reduction in fitness of the carrier of the driving allele, making such
 systems selfish. The t haplotype is one such driver, found in house mice.
 It is linked to a reduction in litter size in matings among heterozygous
 animals, but also to increased lifespan in wild females that carry it.
 Here, we tested whether carrying the t haplotype was associated with
 altered resting metabolic rate (RMR). We show that females carrying the t
 haplotype decrease RMR as they increase in size, compared to wildtype
 females or males of either genotype. Our study elucidates a plausible
 mechanism by which a selfish genetic element increases lifespan.
description: Resting metabolic rate
 dataThis file contains the
 respirometer results run in the laboratory. Box is the respirometer box;
 ID is the animal identity; sex is the animal sex; haplotype is the
 haplotype of the animal (w for wildtype and t for t-haplotype); VO2_abs is
 the resting VO2 value; pair indicates the sibling pair that was compared
 (from same litter and run at the same time in respirometer); mean_bm
 constitutes the average of the body mass measurements at the beginning and
 end of the respirometry quantification.LopesLindholmRMR.xlsx
DOI: 10.5061/dryad.d152444
title: Data from: A growth-defense trade-off is general across native and exotic grasses

description: High-resource environments typically favor quick-growing, poorly-defended
 plants, while resource-poor environments typically favor slow-growing,
 well-defended plants. The prevailing hypothesis explaining this pattern
 states that, as resource availability increases, well-defended,
 slow-growing species are replaced by poorly defended, fast-growing
 species. A second hypothesis states that greater resource availability
 increases allocation to growth at the expense of defense, within species.
 Regardless of mechanism, if exotic species are released from enemies
 relative to natives, shifts in allocation to growth and defense both
 within and among species could differ by geographic provenance. To test
 whether resource availability alters growth or defense, within and among
 species, and whether any such effects differ between natives and exotics,
 we manipulated soil nutrient supply and access of aboveground insect
 herbivores and fungal pathogens under field conditions to individuals of
 six native and six exotic grass species that co-occurred in a North
 Carolina old field. The prevailing hypothesis’ prediction—that
 species-level enemy impact increases with species’ nutrient
 responsiveness—was confirmed. Moreover, this relationship did not differ
 between native and exotic species. The second hypothesis’ prediction—that
 individual-level enemy impact increases with nutrient supply, after
 accounting for species-level variation in performance—was not supported.
 Together, these results support the idea, across native and exotic
 species, that plant species turnover is the primary mechanism underlying
 effects of nutrient enrichment on allocation to growth and defense in
 plant communities.
description: Growth-defense trade-off
 dataData file supporting the
 manuscript, "A growth-defense trade-off is general across native and
 exotic grasses". block is a spatial block; nutrients is a
 fertilization treatment with two levels (high NPK, low NPK); enemies is an
 enemy exclusion treatment with two levels (excluded: sprayed with
 fungicide and insecticide, present: unsprayed); replicate is the whole
 plot in which each experimental unit was located; id is a unique
 identifier for each experimental unit; species_full is the full species
 name required to match to phylogenetic tree; species is an abbreviated
 species name; pathway is photosynthetic pathway; provenance is native to
 North Carolina, USA or not (exotic); mass is aboveground biomass (g);
 leaf_n is % leaf N content; leaf_c is % leaf C content; lma is leaf mass
 per area; leaf_n_std, leaf_c_std, and lma_std are standardized such that
 mean = 0 and sd = 1; tot_damage_audps is total foliar damage (insect
 herbivory + fungal disease + mollusk herbivory) calculated using the area
 under the disease progress stairs.Heckman_et_al_growth_defense_data.csv
DOI: 10.5061/dryad.g01j27q
title: Data from: Food and habitat provisions jointly determine competitive and facilitative interactions among distantly related herbivores

description: 1. Interactions between distantly related herbivores exert powerful
 influences on ecosystems, but most studies to date have only considered
 unidirectional effects. Few have simultaneously examined the mutual
 effects that vertebrate herbivores and insect herbivores have on one
 another. 2. We conducted a set of manipulative experiments to evaluate the
 potential competition and facilitation between two pairs of distantly
 related herbivore taxa: an insect caterpillar (Gynaephora alpherakii) and
 two large vertebrate herbivores, yak (Bos grunniens) and Tibetan sheep
 (Ovis aries tibetica). 3. We found that these large herbivores
 consistently increased the density of caterpillars likely by improving the
 habitat for caterpillars. The caterpillars, in turn, decreased yak but
 increased Tibetan sheep foraging time and intake bites by differently
 changing available food resources of the two large herbivores. Diet
 preferences of herbivores modified the habitat and food resources, thereby
 causing a diet-mediated competition between yak and caterpillars, and
 facilitation between sheep and caterpillars. The vertebrate herbivores
 non-feeding upon Lamiophlomis rotata and Gentiana straminea, the
 caterpillars preferred habitat, increased densities of the two plant
 species, thus favoring the caterpillars. In turn, the caterpillar
 preference for Kobresia pygmaea, significantly reduced food resources for
 yak, while promoted food resources (multiple forbs) for sheep. 4.
 Synthesis. Our study indicates that two different mechanisms (the changes
 in habitat and food availability) induced by herbivore foraging jointly
 determine competitive and facilitative interactions between distantly
 related herbivore species. We also suggest that examining the
 bidirectional effects between herbivores offers a better understanding of
 competition and facilitation in terrestrial animal communities.
description: caterpillar treatment
 experimentPlant species biomass
 and livestock foraging behavior traits data by the experiment of
 caterpillar removal treatmentscaterpillar_treatment_exp.xlsxlivestock treatment experiment dataPlant species responses and caterpillar density dynamic by the large herbivores treatments (Yak, Sheep, Yak and sheep, Control)livestock_treatment_exp.xlsx
DOI: 10.5061/dryad.qr5s6b8
title: Data from: Expressed vomeronasal type-1 receptors (V1rs) in bats uncover conserved sequences underlying social chemical signaling

description: In mammals, social and reproductive behaviors are mediated by chemical
 cues encoded by hyperdiverse families of receptors expressed in the
 vomeronasal organ. Between species, the number of intact receptors can
 vary by orders of magnitude. However, the evolutionary processes behind
 variation in receptor number, and its link to fitness-related behaviors
 are not well understood. From vomeronasal transcriptomes, we discovered
 the first evidence of intact vomeronasal type-1 receptor (V1r) genes in
 bats, and we tested whether putatively functional bat receptors were
 orthologous to those of related taxa, or whether bats have evolved novel
 receptors. Instead of lineage-specific duplications, we found that bat
 V1rs in bats show high levels of orthology to those of their relatives,
 and receptors are under comparative levels of purifying selection compared
 to non-bats. Despite widespread vomeronasal organ loss in bats, V1r copies
 have been retained for &gt;65 million years. The highly conserved
 nature of bat V1rs challenges our current understanding of mammalian V1r
 function and suggest roles other than conspecific recognition or mating
 initiation in social behavior.
description: forDryadqual_reports: summary statistics of Oyster River Protocol transcriptome assemblies garli: alignment and output of bootstraps and replicates of garli analyses blast: output of Trpc2 hits for each species within the transcriptomes relax: input alignment and tree and output json file paml: null models and clade model C model; input trees and alignments uPho: input trees and resulting orthogroups, as well as PAML models for orthogroups