cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8fb46m5
title: Data from: Genome-wide association studies in apple reveal loci of large effect controlling apple polyphenols

description: Apples are a nutritious food source with significant amounts of
 polyphenols that contribute to human health and wellbeing, primarily as
 dietary antioxidants. Although numerous pre- and post-harvest factors can
 affect the composition of polyphenols in apples, genetics is presumed to
 play a major role because polyphenol concentration varies dramatically
 among apple cultivars. Here we investigated the genetic architecture of
 apple polyphenols by combining high performance liquid chromatography
 (HPLC) data with ~100,000 single nucleotide polymorphisms (SNPs) from two
 diverse apple populations. We found that polyphenols can vary in
 concentration by up to two orders of magnitude across cultivars, and that
 this dramatic variation was often predictable using genetic markers and
 frequently controlled by a small number of large effect genetic loci.
 Using GWAS, we identified candidate genes for the production of
 quercitrin, epicatechin, catechin, chlorogenic acid, 4-O-caffeoylquinic
 acid and procyanidins B1, B2, and C1. Our observation that a relatively
 simple genetic architecture underlies the dramatic variation of key
 polyphenols in apples suggests that breeders may be able to improve the
 nutritional value of apples through marker-assisted breeding or gene
 editing.
description: Apple genotype
 dataGenotype data in PLINK
 format. README file is included in zipped file.McClure_dryad_datapack.zip
DOI: 10.5061/dryad.179116t
title: Data from: Evaluating the performance of targeted sequence capture, RNA-Seq, and degenerate-primer PCR cloning for sequencing the largest mammalian multigene family

description: Multigene families evolve from single-copy ancestral genes via
 duplication, and typically encode proteins critical to key biological
 processes. Molecular analyses of these gene families require
 high-confidence sequences, but the high sequence similarity of the members
 can create challenges for sequencing and downstream analyses. Focusing on
 the common vampire bat, Desmodus rotundus, we evaluated how different
 sequencing approaches performed in recovering the largest mammalian
 protein-coding multigene family: olfactory receptors (OR). Using the
 genome as a reference, we determined the proportion of putatively
 protein-coding receptors recovered by: 1) amplicons from degenerate
 primers sequenced via Sanger technology, 2) RNA-Seq of the main olfactory
 epithelium, and 3) those genes “captured” with probes designed from
 transcriptomes of closely-related species. Our initial re-annotation of
 the high-quality vampire bat genome resulted in &gt;400 intact OR
 genes, more than doubling the original estimate. Sanger-sequenced
 amplicons performed the poorest among the three approaches, detecting 50%
 of the annotated genomic ORs, and targeted sequence capture recovered
 nearly 75% of annotated genes. Each sequencing approach assembled
 high-quality sequences, even if it did not recover all receptors in the
 genome. While some variation may be due to limitations of the study design
 (e.g. different individuals), variation among approaches was mostly caused
 by low coverage of some receptors rather than high rates of assembly
 error. Given this variability, we caution against using the counts of
 intact receptors per species to model the birth-death process of multigene
 families. Instead, our results support the use of orthologous sequences to
 explore and model the evolutionary processes shaping these genes.
description: Assembly and Mapping
 scripts and data for Desmodus rotundus olfactory
 receptorsBash commands to for
 transcriptome and targeted bait capture assemblies of Desmodus rotundus
 olfactory receptors. FASTA files include ORs detected for each sequencing
 method. Mapping bash commands for each assembly
 approach.Desmodus_rotundus_OR.zip
DOI: 10.5061/dryad.r14s582
title: Data from: Effects of soil type and light on height growth, biomass partitioning, and nitrogen dynamics on 22 species of tropical dry forest tree seedlings: comparisons between legumes and nonlegumes

description: PREMISE OF THE STUDY: The seedling stage is particularly vulnerable to
 resource limitation, with potential consequences for community
 composition. We investigated how light and soil variation affected early
 growth, biomass partitioning, morphology, and physiology of 22 tree
 species common in tropical dry forest, including eight legumes. Our
 hypothesis was that legume seedlings are better at taking advantage of
 increased resource availability, which contributes to their successful
 regeneration in tropical dry forests. METHODS: We grew seedlings in a
 full-factorial design under two light levels in two soil types that
 differed in nutrient concentrations and soil moisture. We measured height
 biweekly and, at final harvest, biomass partitioning, internode segments,
 leaf carbon, nitrogen, δ 13 C, and δ 15 N. KEY RESULTS: Legumes initially
 grew taller and maintained that height advantage over time under all
 experimental conditions. Legumes also had the highest final total biomass
 and water-use efficiency in the high-light and high-resource soil. For
 nitrogen-fixing legumes, the amount of nitrogen derived from fixation was
 highest in the richer soil. Although seed mass tended to be larger in
 legumes, seed size alone did not account for all the differences between
 legumes and nonlegumes. Both belowground and aboveground resources were
 limiting to early seedling growth and function. CONCLUSIONS: Legumes may
 have a different regeneration niche, in that they germinate rapidly and
 grow taller than other species immediately after germination, maximizing
 their performance when light and belowground resources are readily
 available, and potentially permitting them to take advantage of high
 light, nutrient, and water availability at the beginning of the wet
 season.
description: Tree seedling
 measurement data from shadehouse experimentTree sending height and
 biomass data from a shadehouse experiment with 22 dry forest tree species.
 Soil treatment abbreviations indicate the locations where the soil was
 collected SE=Santa Elena, PV=Palo Verde. Nutrient level abbreviations:
 LN=low nutrient soil, HN=high nutrient soil.shadehouse_data.csv
DOI: 10.5061/dryad.8mb0c27
title: Data from: Maladaptation beyond a geographic range limit driven by antagonistic and mutualistic biotic interactions across an abiotic gradient

description: Species’ geographic range limits often result from maladaptation to the
 novel environments beyond the range margin. However, we rarely know which
 aspects of the n-dimensional environment are driving this maladaptation.
 Especially of interest is the influence of abiotic versus biotic factors
 in delimiting species’ distributions. We conducted a two-year reciprocal
 transplant experiment involving manipulations of the biotic environment to
 explore how spatio-temporal gradients in precipitation, fatal mammalian
 herbivory, and pollination affected lifetime fitness within and beyond the
 range of the California annual plant, Clarkia xantiana ssp. xantiana. In
 the first, drier year of the experiment, fitness outside the range edge
 was limited mainly by low precipitation, and there was some evidence for
 local adaptation within the range. In the second, wetter year, we did not
 observe abiotic limitations to plant fitness outside the range; instead
 biotic interactions, especially herbivory, limited fitness outside the
 range. Together, protection from herbivory and supplementation of pollen
 resulted in 3-7 fold increases in lifetime fitness outside the range
 margin in the abiotically benign year. Overall, our work demonstrates the
 importance of biotic interactions, particularly as they interact with the
 abiotic environment, in determining fitness beyond geographic range
 boundaries.
description: Plant Phenotypic Data
 for Transplant Year 1These data were
 collected in the field in year 1 of the transplant experiment (2015-2016).
 Variable definitions are in the readme file.BenningEvol2019_Year1.csvPlant Phenotypic Data for Transplant Year 2These data were collected in the field in year 2 of the transplant experiment (2016-2017). Variable definitions are in the readme file.BenningEvol2019_Year2.csvPollinator visitation dataData from pollinator observations at the six transplant sites. Variable "Flowers" indicates the number of flowers observed during that 10 minute observation period. "Visits" indicates the total number of pollinator visits observed during that 10 minute observation period.BenningEvol2019_Visitation.csvPollen Supplementation DataData from pollen supplementation experiment in year 2 of the transplant experiment, arranged as "wide" data with control and supplemented fruits from the same plant on the same row. Variable "Grid" indicates the planting grid ID. "Cell" is the planting cell ID. "c" indicates the number of seeds in the control fruit; "s" indicates the number of seeds in the supplemented fruit. "pollLimit" is the calculated pollen limitation metric.BenningEvol2019_Pollination.csvR AnalysesR Markdown file containing analyses used in the manuscript.BenningEvol2019_Dryad.Rmd
DOI: 10.5061/dryad.g3dc83m
title: Data from: Females prefer the calls of better fathers in a Neotropical frog with biparental care

description: Male secondary sexual traits potentially function as indicators of direct
 or indirect fitness benefits to females. Direct benefits, such as paternal
 care, may be especially important to females in species with biparental
 care. In an experimental field study of the golden rocket frog
 (Anomaloglossus beebei), a Neotropical species with biparental care, we
 tested predictions from four hypotheses proposed to explain the
 evolutionary relationship between male secondary sexual traits and
 paternal care quality (the “good parent,” “differential-allocation,”
 “trade-off,” and “essential male care” hypotheses). We examined: (i) the
 influence of paternal care on offspring survival, (ii) the relationships
 between male calls and paternal care, maternal care, and opportunities for
 males to acquire multiple mates, and (iii) female preferences for three
 acoustic properties of male advertisement calls. Our results reveal that
 paternal care positively impacts offspring survival, that males producing
 longer calls also provide higher quality paternal care in the form of
 greater egg attendance and territory defense, and that females prefer
 longer calls. Females did not discriminate among potential mates based on
 differences in dominant frequency or call rate. These findings, which
 suggest male advertisement calls are indicators of potential direct
 benefits to females in the form of paternal care, are consistent with the
 good parent hypothesis and inconsistent with the trade-off,
 differential-allocation, and essential male care hypotheses.
description: READMEThis file explains all
 of the variables in each of the datasets that accompany: Pettitt BA,
 Bourne GR, Bee MA 2019ms. Females prefer the calls of better fathers in a
 Neotropical frog with biparental careOffspringFateData set associated with male removal experiment and used to run nonparametric Mann-Whitney U tests to compare the differences between the two treatments in the percent of clutch hatched and the causes of offspring mortality.SurvivalAnalysisData set associated with male removal experiment and used to generate Kaplan-Meier survival curves for the longest surviving offspring of clutches with and without attending males and to compare the functions between these treatments using a log-rank test.CorrelationsData set associated with quantifying paternal care, maternal care, and mating opportunities and used to run two-tailed Spearman's rank-order correlations to examine the relationships among call properties and paternal care, maternal care, and male mating effort.FemalePlaybacksData set associated with female two-alternative choice experiments and used to run two-tailed binomial tests to test the null hypothesis that the proportion of subjects choosing each paired stimulus did not differ from 0.5.
DOI: 10.5061/dryad.20rg064
title: Data from: Does city life reduce neophobia? A study on wild black-capped chickadees

description: As human populations increase and city borders grow, many animals have to
 modify foraging behaviours in order to exploit evolutionarily novel urban
 food sources that could aid their survival. Neophobia, the fear of
 novelty, can lead to missed opportunities in these cases. Here we studied
 the novelty response of wild animals in ecologically relevant conditions
 while controlling for individual characteristics and potential differences
 in foraging group size. We predicted that urban black-capped chickadees
 (Poecile atricapillus) would be more likely to initially contact novelty
 than rural chickadees, and that subordinates and juveniles would be more
 likely to first contact novelty than dominants and adults, respectively.
 We ran replicated experiments using three novelty types (object, colour,
 or food) on six sites, during which we registered feeder choice of 71
 tagged individuals. We found that urban chickadees showed less neophobia
 than their rural counterparts, the latter having a higher probability of
 initially contacting the familiar feeder before approaching the novel
 feeder. There was no significant effect of an individual’s dominance, age
 or sex on its first choice of feeder, nor was there an effect of novelty
 type. Overall, our results suggest that urban chickadees exhibit less
 neophobia than their rural counterparts, because they have generally
 learned to tolerate novelty in their habitat, they have adapted to live in
 an environment that rewards low neophobia, and/or they are less reluctant
 to use feeders at new locations.
description: ChickadeeNeophobiaDataData collected on neophobia of wild black-capped chickadees in both urban and rural environments.Data.csv
DOI: 10.5061/dryad.4152128
title: Data from: Integrated population model reveals that Kestrels breeding in nest boxes operate as a source population

description: The identification of the source-sink status of a population is critical
 for the establishment of conservation plans and enacting smart management
 decisions. We developed an integrated population model to formally assess
 the source status of a kestrel Falco tinnunculus population breeding in
 nest boxes in Switzerland. We estimated juvenile and adult survival,
 reproduction and net dispersal (emigration/immigration) by jointly
 analyzing capture-recapture, dead recovery, breeding monitoring and
 population survey data. We also investigated the role of nest boxes on
 kestrel demography and assessed the contributions of vital rates to
 realized population growth rates. The results indicate that the kestrel
 population breeding in nest boxes has acted as a source over the 15 years
 of the study duration. A quantitative approach suggests that a substantial
 number of individuals have emigrated annually from this population likely
 affecting the population dynamics outside the management area. Variation
 in fecundity explained 34% of the temporal variability of the population
 growth rate. Moreover, a literature review suggests that kestrel pairs
 produce on average 1.4 chicks more per breeding attempt in nest boxes
 compared to natural open nests. Together, these findings suggest that
 fecundity was an important driver for the dynamics of this population and
 that nest boxes have contributed to its raise. Nest boxes are regularly
 used as an efficient tool for conservation management. We suggest that
 such a conservation action can result in the establishment of a source
 population being beneficial for populations both inside and outside the
 managed area.
description: Kestrel
DOI: 10.5061/dryad.9tg3t75
title: Data from: Exploring the temporal variability of a food web using long-term biomonitoring data

description: Ecological communities are constantly being reshaped in the face of
 environmental change and anthropogenic pressures. Yet, how food webs
 change over time remains poorly understood. Food web science is
 characterized by a trade-off between complexity (in terms of the number of
 species and feeding links) and dynamics. Topological analysis can use
 complex, highly resolved empirical food web models to explore the
 architecture of feeding interactions but is limited to a static view,
 whereas ecosystem models can be dynamic but use highly aggregated food
 webs. Here, we explore the temporal dynamics of a highly resolved
 empirical food web over a time period of 18 years, using the German Bight
 fish and benthic epifauna community as our case study. We relied on
 long-term monitoring ecosystem surveys (from 1998 to 2015) to build a
 metaweb, i.e. the meta food web containing all species recorded over the
 time span of our study. We then combined time series of species abundances
 with topological network analysis to construct annual food web snapshots.
 We developed a new approach, “node-weighted” food web metrics by including
 species abundances to represent the temporal dynamics of food web
 structure, focusing on generality and vulnerability. Our results suggest
 that structural food web properties change through time; however, binary
 food web structural properties may not be as temporally variable as the
 underlying changes in species composition. Further, the node-weighted
 metrics enabled us to detect that food web structure was influenced by
 changes in species composition during the first half of the time series
 and more strongly by changes in species dominance during the second half.
 Our results demonstrate how ecosystem surveys can be used to monitor
 temporal changes in food web structure, which are important ecosystem
 indicators for building marine management and conservation plans.
description: Meta-food
 webThe dataset includes
 three tables that we described in the Supplementary associated to the
 publication–same as the readme file, (doi.org/10.1111/ecog.04461): (A)
 Species list: taxonomic information on the taxa included in our analysis;
 (B) Pairwise list: a pairwise list that reports all possible interactions
 between taxa included in our metaweb; (C) Reference list: a table
 containing the references for trophic interactions (i.e. same as the
 pairwise list but with duplicated trophic
 interactions).Olivier et al. 2019_Ecography -
 Meta-foodweb.zip
DOI: 10.5061/dryad.5br2q79
title: Data from: Variability in gut passage time of Asian hornbills

description: Seed gut passage time through animals influence germination and
 displacement distance of seeds from parent plants. Hornbills are the
 largest avian seed dispersers in Asian tropical forests. In this study, we
 compared gut passage times for five large seeded tree species across gut
 passage trials, for three hornbill species. This study was conducted on
 six captive birds in Nagaland, India. The gut passage time of seeds for
 the tree species varied from 5 to 536 minutes. There was no difference in
 gut passage times between trials, between male and female birds and
 different fruit tree species for the Oriental Pied Hornbill. For the
 Rufous-necked Hornbill, we found differences in gut passage times across
 trials for Beilschmiedia assamica and Polyalthia simiarum, between
 individuals for Livistona jenkinsiana and across tree species, especially
 for the female. For the Wreathed Hornbill, we found differences in gut
 passage times across trials for Aglaia spectabilis and Syzygium cumini,
 between individuals for Beilschmiedia assamica and Livistona jenkinsiana
 and across tree species only for the female bird. Mean gut passage times
 reported here are higher than those reported previously for Asian
 hornbills. Context-specific variability in gut passage times highlights
 the need to examine the causes that result in these inconsistent patterns.
description: SMJ_Shukla_etal_gpt_dataGut passage time data for five tree species (Aglaia spectabilis, Beilschmiedia assamica, Polyalthia simiarum, Livistona jenkinsiana, and Syzygium cumini) of Oriental Pied Hornbill, Rufous-necked Hornbill and Wreathed HornbillSMJ_Shukla_etal_data_descriptionData description of the gut passage data
DOI: 10.5061/dryad.kr06n63
title: Data from: Regulation of macrophage foam cell formation during nitrogen mustard (NM)-induced pulmonary fibrosis by lung lipids

description: Nitrogen mustard (NM) is a vesicant known to target the lung, causing
 acute injury which progresses to fibrosis. Evidence suggests that
 activated macrophages contribute to the pathologic response to NM. In
 these studies, we analyzed the role of lung lipids generated following NM
 exposure on macrophage activation and phenotype. Treatment of rats with NM
 (0.125 mg/kg, i.t.) resulted in a time-related increase in enlarged
 vacuolated macrophages in the lung. At 28 d post exposure, macrophages
 stained positively for Oil Red O, a marker of neutral lipids. This was
 correlated with an accumulation of oxidized phospholipids in lung
 macrophages and epithelial cells, and increases in bronchoalveolar lavage
 fluid (BAL) phospholipids and cholesterol. RNA-sequencing and
 immunohistochemical analysis revealed that lipid handling pathways under
 the control of the transcription factors LXR, FXR, PPAR-ɣ and SREBP were
 significantly altered following NM exposure. Whereas at 1-3 d post NM, FXR
 and the downstream oxidized low density lipoprotein receptor, Cd36, were
 increased, Lxr and the lipid efflux transporters, Abca1 and Abcg1, were
 reduced. Treatment of naïve lung macrophages with phospholipid and
 cholesterol enriched large aggregate fractions of BAL prepared 3 d after
 NM exposure resulted in upregulation of Nos2 and Ptgs2, markers of
 pro-inflammatory activation, while large aggregate fractions prepared 28 d
 post NM upregulated expression of the anti-inflammatory markers, Il10,
 Cd163, and Cx3cr1, and induced the formation of lipid-laden foamy
 macrophages. These data suggest that NM-induced alterations in lipid
 handling and metabolism drive macrophage foam cell formation, potentially
 contributing to the development of pulmonary fibrosis.
description: fpkm isoform
 matrixNM28d vs PBS sig
 isoformsDifferentially expressed
 genes (Fold change &gt; +/- 1.5; q-value &lt; 0.05) in alveolar
 macrophages 28d post Nitrogen mustard exposureNM1d vs PBS sig
 isoformsDifferentially expressed
 genes (Fold change &gt; +/- 1.5; q-value &lt; 0.05) in alveolar
 macrophages 1d post Nitrogen mustard exposureIPA Enrichment
 dataIPA Core Analysis
 performed on differentially expressed genes (Fold change &gt; +/- 1.5;
 q-value &lt; 0.05).IPA
 data.xlsx