cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4r34m7b
title: Data from: Individual- versus group-optimality in the production of secreted bacterial compounds

description: How unicellular organisms optimize the production of compounds is a
 fundamental biological question. While it is typically thought that
 production is optimized at the individual-cell level, secreted compounds
 could also allow for optimization at the group level, leading to a
 division of labor where a subset of cells produces and shares the compound
 with everyone. Using mathematical modelling, we show that the evolution of
 such division of labor depends on the cost function of compound
 production. Specifically, for any trait with saturating benefits, linear
 costs promote the evolution of uniform production levels across cells.
 Conversely, production costs that diminish with higher output levels favor
 the evolution of specialization – especially when compound shareability is
 high. When experimentally testing these predictions with pyoverdine, a
 secreted iron-scavenging compound produced by Pseudomonas aeruginosa, we
 found linear costs and, consistent with our model, detected uniform
 pyoverdine production levels across cells. We conclude that for shared
 compounds with saturating benefits, the evolution of division of labor is
 facilitated by a diminishing cost function. More generally, we note that
 shifts in the level of selection from individuals to groups do not solely
 require cooperation, but critically depend on mechanistic factors,
 including the distribution of compound synthesis costs.
description: Schiessl_etal_Evolution_dryadContains data for Figures 2, 4, 5 and S1Raw data for Figure 3Contains raw flow cytometry data for Figure 3. A description of this data can be found in the Excel sheet containing data for the remaining figures.Figure3.zip
DOI: 10.5061/dryad.158g44h
title: Data from: The potential for mass ratio and trait divergence effects to explain idiosyncratic impacts of nonnative invasive plants on carbon mineralization of decomposing leaf litter

description: 1. Invasive plant effects on litter decomposition tend to be idiosyncratic
 among species and ecosystems, which may arise from variation in the
 invader’s relative abundance (mass ratio effect), its relative functional
 difference to other species (trait divergence effect), and/or from
 species’ litter mixing that causes non-additive decomposition rates
 relative to single-species decomposition. 2. We use experimental
 microcosms to quantify the potential for mass ratio and trait divergence
 to explain effects of invasive litters on carbon mineralization rates of
 decomposing litter mixtures and to generate non-additive dynamics in two
 distinct forest litter types. 3. The relative strength and direction of
 the mass ratio and trait divergence effects on carbon mineralization
 values were moderated by interactions between each effect and the canopy
 litter mixture. In both maple-poplar and oak hickory litter mixtures, we
 found that the strength of the trait divergence effect increased with
 increasing proportions (mass ratio) of understory litter in the litter
 mixtures, suggesting that interactions between these two mechanisms are
 important for moderating the influence of understory invasions.
 Similarily, the addition of understory litter always caused synergistic,
 non-additive impacts on carbon mineralization, increasing carbon
 mineralization on average by 34%. For both litter mixtures, non-additivity
 increased with increasing trait divergence between understory and canopy
 litters. 4. Our findings show the potential for pronounced
 context-dependency in the impact of nonnative invasive species that arise
 via multiple mechansism and their interactions. As such, they suggest the
 necessity of accounting for frequently-theorized but infrequently-tested
 mechanisms relating to mass ratio and trait divergence. Accounting should
 improve understanding of when mass ratio and trait divergence affect
 ecosystem process rates, and hence build confidence in mechanistic
 projections of invader impacts.
description: Kuebbing and
 Bradford_Functional Ecology_Multi-species litter mixture CO2
 DataPlease see
 README.Kuebbing and
 Bradford_Functional Ecology_Single-species litter CO2
 DataPlease See
 READMEKuebbing and
 Bradford_Functional Ecology_Species TraitDataPlease See
 README
DOI: 10.5061/dryad.n8g55b6
title: Data from: Assortative interactions revealed in a fission-fusion society of Australian humpback dolphins

description: Understanding individual interactions within a community or population
 provides valuable insight into its social system, ecology and, ultimately,
 resilience against external stimuli. Here, we used photo-identification
 data, generalised affiliation indices and social network analyses to
 investigate dyadic relationships, assortative interactions and social
 clustering in the Australian humpback dolphin (Sousa sahulensis).
 Boat-based surveys were conducted between May 2013 and October 2015 around
 the North West Cape, Western Australia. Our results indicated a
 fission-fusion society, characterised by non-random dyadic relationships.
 Assortative interactions were identified both within and between sexes,
 and were higher amongst members of the same sex, indicating same-sex
 preferred affiliations and sexual segregation. Assortative interactions by
 geographic locations were also identified, but with no evidence of
 distinct social communities or clusters, or affiliations based on
 residency patterns. We noted high residency amongst females. Models of
 temporal patterns of association demonstrated variable levels of
 stability, including stable (preferred companionships) as well as fluid
 (casual acquaintances) associations. We also demonstrated some social
 avoidance. Our results point to greater social complexity than previously
 recognised for humpback dolphins and, along with knowledge of population
 size and habitat use, provide the necessary baseline upon which to assess
 the influence of increasing human activities on this endemic, Vulnerable
 species.
description: SOCPROGinputInput file for software SOCPROG to conduct association analyses. See 'README' text file for more detail.SOCPROG_SuppMaterialSupplementary Material file for import into SOCPROG software for association analyses. See 'README' text file for more detail.GAI_Home_range_overlap_Adehabitat_inputThis is the input file for the ‘AdehabitatHR’ package (Calenge 2006) in R v 3.3.1 (R Core Team 2015) to look at individual home range overlap in the study area for use in Generalised Affiliation Indices (GAI) analyses. See 'README' text file for more detail.GAI_Home_range overlap_UDOIh1000_SOCPROG_inputThis file is a matrix of individuals and displays a utilization distribution overlap index (UDOI) for use in the home range overlap as a predictor variable in GAI analyses. See 'README' text file for more detail.AdehabitatHR R codeR code to install the 'AdehabitatHR' package, then run the code on the 'GAI_Home_range_overlap_Adehabitat_input.xls'. See 'README' text file for more detail.Adehabitat.RGAI_Temp_overlap_SOCPROG_inputSOCPROG input file to create the matrix of co-occurrence, and assess temporal overlap of individuals in GAI analyses. See 'README' text file for more detail.
DOI: 10.5061/dryad.sq5c00n
title: Data from: Variation in non-invasive ventilation use in amyotrophic lateral sclerosis

description: Objective: We sought to examine prevalence and predictors of non-invasive
 ventilation (NIV) in a composite cohort of amyotrophic lateral sclerosis
 (ALS) patients followed in a clinical trials setting (PRO-ACT database).
 Methods: NIV initiation and status were ascertained from response to
 question 12 of the revised ALS functional rating scale (ALSFRS-R). Factors
 affecting NIV use in patients with forced vital capacity (FVC) ≤ 50% of
 predicted were examined. Predictors of NIV were evaluated by Cox
 proportional hazard models and generalized linear mixed models. Results:
 Among 1,784 patients with 8,417 simultaneous ALSFRS-R and FVC% measures,
 NIV was used by 604 (33.9%). Of 918 encounters when FVC% ≤ 50%, NIV was
 reported in 482 (52.5%). Independent predictors of NIV initiation were
 lower FVC% (hazard ratio HR 1.27, 95% CI: 1.17-1.37 for 10% drop), dyspnea
 (HR 2.62, 95% CI: 1.87-3.69), orthopnea (HR 4.09, 95% CI: 3.02-5.55),
 lower bulbar and gross motor subscores of ALSFRS-R (HRs 1.09 (95% CI:
 1.03-1.14) and 1.13 (95% CI: 1.07-1.20) respectively, per point), and male
 sex (HR 1.73, 95% CI: 1.31-2.28). Adjusted for other variables, bulbar
 onset did not significantly influence time to NIV (HR 0.72 (95% CI:
 0.47-1.08)). Considerable unexplained variability in NIV use was found.
 Conclusion: NIV use was lower than expected in this ALS cohort that was
 likely to be optimally managed. Absence of respiratory symptoms and female
 sex may be barriers to NIV use. Prospective exploration of factors
 affecting adoption of NIV may help bridge this gap and improve care in
 ALS.
description: Supplementary
 DataSupplementary figures
 and tablesDryad
 Supplementary_Data_Thakore_et_al_ALS_NIV_2019.pdf
DOI: 10.5061/dryad.ts718t2
title: Data from: Genomic prediction of pumpkin hybrid performance

description: Genomic prediction has become an increasingly popular tool for hybrid
 performance evaluation in plant breeding, mainly because that it can
 reduce cost and accelerate a breeding program. In this study, we propose a
 systematic procedure to predict hybrid performance using a genomic
 selection (GS) model that takes both additive and dominance marker effects
 into account. We first demonstrate the advantage of the additive-dominance
 effects model over the only additive effects model through a simulation
 study. Based on the additive-dominance model, we predict genomic estimated
 breeding values (GEBVs) for individual hybrid combinations and their
 parental lines. The GEBV based specific combining ability (SCA) for each
 hybrid, and general combining ability (GCAs) for its parental lines are
 then derived to quantify the degree of mid-parent heterosis (MPH) or
 better parent heterosis (BPH) of the hybrid. Finally, we estimate the
 variance components due to additive and dominance gene action effects, and
 heritability using a genomic BLUP model. These estimates are used to
 justify the results of the genomic prediction study. A pumpkin data set is
 given to illustrate the provided procedure. The data set consists of 320
 parental lines with collected 61,179 SNP markers; 119, 120, 120 phenotypic
 values of hybrids on three quantitative traits within C. maxima; and 89,
 111, 90 phenotypic values of hybrids on the same three quantitative traits
 within C. moshata.
description: C_maxima_hybrid_additive_genotypeThe additive genotype data of 10,011 hybrids within C. maxima.C_maxima_hybrid_dominance_genotypeThe dominance genotype data of 10,011 hybrids within C. maxima.C_maxima_parental_genotypeThe genotype data of 142 accessions (parental lines) within C. maxima.C_maxima_hybrid_phenotype_FWTThe phenotypic data for fruit weight (FWT) of C. maxima hybrids. There are only 119 phenotypic values available.C_maxima_hybrid_phenotype.txt
DOI: 10.5061/dryad.q293c9g
title: Data from: Host responses to foreign eggs across the avian visual color space

description: Despite extensive research on the sensory and cognitive processes of host
 rejection of avian brood parasites’ eggs, the underlying perceptual and
 cognitive mechanisms are not sufficiently understood. Historically, most
 studies of host egg discrimination assumed that hosts rejected a
 parasite’s egg from their nest based on the total perceived color
 differences between the parasite’s egg and their own. A recent study used
 a continuous range of parasitic egg colors and discovered that hosts were
 more likely to reject browner parasitic eggs than parasitic eggs that were
 more blue-green, even when their absolute perceived color differences from
 the hosts’ own egg colors were similar. However, the extent of these color
 biases within the avian perceivable color space remains unclear.
 Therefore, we built upon this previous study by testing European
 blackbirds’ (Turdus merula) responses to model eggs spanning an
 unprecedented volume of the avian color space. We found that host
 decisions depended on avian perceived hue, saturation, and luminance of
 the parasite’s egg; hosts generally accepted eggs that were bluer or more
 blue-green, and more often rejected eggs that were less saturated or
 darker. We suggest that future studies investigate the underlying
 mechanism of foreign egg discrimination in other host lineages to
 determine the prevalence and phylogenetic conservation of such perceptual
 biases among birds.
description: Hanley et al. Am Nat -
 DataData associated with
 "Host responses to foreign eggs across the avian visual color
 space". These data were collected in the field, see Methods and
 information key for further information.
DOI: 10.5281/zenodo.18390116
title: Data for "Quantitative millennial reconstructions of Indian Ocean oxygenation unravel dynamics of ocean carbon storage"

description: This file is the dataset for the manuscript entitled "Quantitative millennial reconstructions of Indian Ocean oxygenation unravel dynamics of ocean carbon storage" by Huang et al., including surface calibration and oxygen reconstruction since the Last Glacial Maximum in the northern Indian Ocean, oxygen reconstruction of multi-proxies, and benthic isotopes.
DOI: 10.5281/zenodo.18390115
title: Data for "Quantitative millennial reconstructions of Indian Ocean oxygenation unravel dynamics of ocean carbon storage"

description: This file is the dataset for the manuscript entitled "Quantitative millennial reconstructions of Indian Ocean oxygenation unravel dynamics of ocean carbon storage" by Huang et al., including surface calibration and oxygen reconstruction since the Last Glacial Maximum in the northern Indian Ocean, oxygen reconstruction of multi-proxies, and benthic isotopes.
DOI: 10.5061/dryad.9021d2v
title: Data from: Morphological and digestive adjustments buffer performance: how staging shorebirds cope with severe food declines

description: Organisms cope with environmental stressors by behavioral, morphological,
 and physiological adjustments. Documentation of such adjustments in the
 wild provides information on the response space in nature and the extent
 to which behavioral and bodily adjustments lead to appropriate performance
 effects. Here we studied the morphological and digestive adjustments in a
 staging population of migrating Great Knots Calidris tenuirostris in
 response to stark declines in food abundance and quality at the Yalu Jiang
 estuarine wetland (northern Yellow Sea, China). At Yalu Jiang, from 2011
 to 2017 the densities of intertidal mollusks, the food of Great Knots,
 declined 15‐fold. The staple prey of Great Knots shifted from the
 relatively soft‐shelled bivalve Potamocorbula laevis in 2011–2012 to
 harder‐shelled mollusks such as the gastropod Umbonium thomasi in
 2016–2017. The crushing of the mollusks in the gizzard would require a
 threefold to 11‐fold increase in break force. This was partially resolved
 by a 15% increase in gizzard mass which would yield a 32% increase in
 shell processing capacity. The consumption of harder‐shelled mollusks was
 also accompanied by reliance on regurgitates to excrete unbreakable parts
 of prey, rather than the usual intestinal voidance of shell fragments as
 feces. Despite the changes in digestive morphology and strategy, there was
 still an 85% reduction in intake rate in 2016–2017 compared with
 2011–2012. With these morphological and digestive adjustments, the Great
 Knots remaining faithful to the staging site to a certain extent buffered
 the disadvantageous effects of dramatic food declines. However,
 compensation was not complete. Locally, birds will have had to extend
 foraging time and use a greater daily foraging range. This study offers a
 perspective on how individual animals may mitigate the effects of
 environmental change by morphological and digestive strategies and the
 limits to the response space of long‐distance migrating shorebirds in the
 wild.
description: Data files for
 'Morphological and digestive adjustments buffer performance: how
 staging shorebirds cope with severe food declines'Data file include 5
 files: 1) break force & prey quality; 2) Food availability & food
 composition & diet selection; 3) function response; 4) gizzard; 5) The
 weight proportion (%) of columelladata
 files.rar
DOI: 10.5061/dryad.m7f92c3
title: Data from: Linking the foraging behavior of three bee species to pollen dispersal and gene flow

description: Foraging behaviors that impact gene flow can guide the design of
 pollinator strategies to mitigate gene flow. Reduced gene flow is expected
 to minimize the impact of genetically engineered (GE) crops on feral and
 natural populations and to facilitate the coexistence of different
 agricultural markets. The goal of this study is to link foraging behavior
 to gene flow and identify behaviors that can help predict gene flow for
 different bee species. To reach this goal, we first examined and compared
 the foraging behaviors of three distinct bee species, the European honey
 bee, Apis mellifera L., the common eastern bumble bee, Bombus impatiens
 Cr., and the alfalfa leafcutting bee, Megachile rotundata F., foraging on
 Medicago sativa flowers. Each foraging behavior investigated differed
 among bee species. Both social bees exhibited directionality of movement
 and had similar residence, in contrast to the random movement and shorter
 residence of the solitary bee. Tripping rate and net distance traveled
 differed among the three bee species. We ranked each behavior among bee
 species and used the relative ranking as gene flow predictor before
 testing the predictions against empirical gene flow data. Tripping rate
 and net distance traveled, but not residence, predicted relative gene
 dispersal among bee species. Linking specific behaviors to gene flow
 provides mechanisms to explain differences in gene flow among bee species
 and guides the development of management practices to reduce gene flow.
 Although developed in one system, the approach developed here can be
 generalized to different plant/pollinator systems.
description: Brunetetal-Distance-Direction-ForagingBehavior-PloSONEThis file summarizes the distance traveled and direction flown between two consecutive racemes (cm) by bumble bees, honey bees and leafcutting bees. These data were collected over two years in patches of Medicago sativa.Brunetetal-NetDistances-ForagingBehavior-PlosOneThis file describes the net distance traveled by bumble bees, honey bees and leafcutting bees during a foraging bout on Medicato sativa. The net distance is the distance between where a bee started foraging in a patch and where it ended its foraging bout.Brunetetal-Residence-ForagingBehavior-PLoSONEThis file indicates the total number of flowers (residence) visited by bumble bees and honey bees during a full foraging bout in patches of Medicago sativa. Residence indicates all flowers visited by a bee between the time it entered and left the patch.Brunetetal-Tripping-ForagingBehavior-PloSONEThese data summarize the tripping rate of bumble bees, honey bees and leafcutting bees when visiting patches of Medicago sativa over two years. It includes the number of flowers visited in a raceme by a bee and the number of flowers tripped by a bee. A bee does not typically trip all flowers visited.
DOI: 10.5061/dryad.fr045hv
title: Data from: Linking plant genes to insect communities: identifying the genetic bases of plant traits and community composition

description: Community genetics aims to understand the effects of intraspecific genetic
 variation on community composition and diversity, thereby connecting
 community ecology with evolutionary biology. Thus far, research has shown
 that plant genetics can underlie variation in the composition of
 associated communities (e.g., insects, lichen, endophytes), and those
 communities can therefore be considered as extended phenotypes. This work,
 however, has been conducted primarily at the plant genotype level and has
 not identified the key underlying genes. To address this gap, we used
 genome-wide association mapping (GWAS) with a population of 445 aspen
 (Populus tremuloides) genets to identify the genes governing variation in
 plant traits (defense chemistry, bud phenology, leaf morphology, growth)
 and insect community composition. We found 49 significant SNP associations
 in 13 Populus genes that are correlated with chemical defense compounds
 and insect community traits. Most notably, we identified an early-nodulin
 like protein (ENODL) that was associated with insect community diversity
 and the abundance of interacting foundation species (ants and aphids).
 These findings support the concept that particular plant traits are the
 mechanistic link between plant genes and the composition of associated
 insect communities. In putting the “genes” into “genes to ecosystems
 ecology”, this work enhances understanding of the molecular genetic
 mechanisms that underlie plant-insect associations and the consequences
 thereof for the structure of ecological communities.
description: Insect_Community_BLUPsRank-transformed BLUPs (best linear unbiased predictors) of insect community traits, formatted for GWAS analyses.Tree_Trait_BLUPsWisAsp rank-transformed BLUPs of tree trait phenotypes, formatted for GWAS analyses.WisAsp bed fileWisAsp bed file for PLINK analyses.WisAsp.bedWisAsp bim fileWisAsp bim file for PLINK analyses.WisAsp.bimWisAsp fam fileWisAsp fam file for PLINK analyses.WisAsp.famBarker_etal_MolEcol_2019_metadataMetadata for WisAsp data files.