cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.21104
title: Data from: Biodiversity as insurance for sapling survival in experimental tree plantations

description: Biodiversity can insure ecosystems against declines in their functioning
 by increasing the mean level of ecosystem processes and decreasing the
 spatial or temporal variance of these processes. On this basis, mixing
 tree species is expected to be an effective management strategy to reduce
 the risk of planting failure in young plantations. We examined the effects
 of biodiversity insurance on sapling survival in three tree diversity
 experiments across Belgium. Based on the survival scoring of 89 254
 saplings, planted in 126 plots with up to four-species mixtures, we tested
 two hypotheses: (i) variability in plot-level survival is lower for
 mixtures compared to monocultures due to compensation among the species
 (i.e. buffering effect) and (ii) mean survival is higher due to
 facilitation (i.e. performance-enhancing effect). Variation in plot-level
 survival decreased strongly with diversity, indicating a buffering effect.
 The risk of severe planting failure was reduced in mixtures because
 species exhibit different survival rates; therefore, mixing ensures that
 not all trees in the plantation are equally susceptible to environmental
 stressors. In contrast, the mean plot-level survival did not increase with
 diversity, and thus, an overall performance-enhancing effect was lacking.
 However, species-level analyses did show performance-enhancing effects,
 where some species profited from mixing while others did not. Synthesis
 and applications. We conclude that biodiversity through mixing tree
 species insures young experimental plantations against planting failure
 and is therefore highly recommended as a planting management strategy. The
 risk of large mortality gaps is reduced if tree plantation saplings are
 mixed at the scale of individual trees or small cells of trees.
description: Sapling survival
 dataSurvival data collected
 in the experimental fields of FORBIO
 (http://www.treedivbelgium.ugent.be/). This includes data at the plot
 level for the sites Hechtel-Eksel, Zedelgem and Gedinne combined (Sheet:
 "data plot level") and data at tree level for the sites
 Hechtel-Eksel, Zedelgem and Gedinne seperately (Sheets: "data tree
 level Hechtel-Eksel", "data tree level Zedelgem" and
 "data tree level Gedinne"). Column headers are explained in the
 sheet "variables explained".Data Biodiversity for sapling
 survival.xlsx
DOI: 10.5061/dryad.9t0n8
title: Data from: Community functional trait composition at the continental scale: the effects of non-ecological processes

description: Ecological communities and their response to environmental gradients are
 increasingly being described by measures of trait composition at the
 community level – the trait-based approach. Whether ecological or
 non-ecological processes influence trait composition between communities
 has been debated. Understanding the processes that influence trait
 composition is important for reconstructing paleoenvironmental conditions
 from fossil deposits and for understanding changes in community
 functionality through time. Here, we assess the influence of ecological
 and non-ecological processes on the distribution of traits within North
 American mammals. We found that non-ecological processes including
 historical contingency, spatial autocorrelation, and evolutionary history
 do not influence trait composition; however, the variance in trait
 composition is highly explained by climate gradients. Our results suggest
 that habitat breadth, terrestriality, diet breadth, and reproductive
 traits are strong candidates as proxies for measuring functional aspects
 of environments in the past and present.
description: Derived data for
 ecometric analysisThis zip folder includes
 csv files of derived trait data, climate data, and geographic presence and
 absence data for North American mammals, excluding bats. All of the
 geographic occurrences are sampled at 50 km, 100 km, and 250 km
 equidistant points across North America.DryadArchive.zip
DOI: 10.5061/dryad.pf67c
title: Data from: Camp stability predicts patterns of hunter–gatherer cooperation

description: Humans regularly cooperate with non-kin, which has been theorized to
 require reciprocity between repeatedly interacting and trusting
 individuals. However, the role of repeated interactions has not previously
 been demonstrated in explaining real-world patterns of hunter–gatherer
 cooperation. Here we explore cooperation among the Agta, a population of
 Filipino hunter–gatherers, using data from both actual resource transfers
 and two experimental games across multiple camps. Patterns of cooperation
 vary greatly between camps and depend on socio-ecological context. Stable
 camps (with fewer changes in membership over time) were associated with
 greater reciprocal sharing, indicating that an increased likelihood of
 future interactions facilitates reciprocity. This is the first study
 reporting an association between reciprocal cooperation and
 hunter–gatherer band stability. Under conditions of low camp stability
 individuals still acquire resources from others, but do so via demand
 sharing (taking from others), rather than based on reciprocal
 considerations. Hunter–gatherer cooperation may either be characterized as
 reciprocity or demand sharing depending on socio-ecological conditions.
description: Smith et al.
 dataData used in analysis
 of: Camp Stability Predicts Patterns of Hunter-Gatherer Cooperation (Smith
 et al. 2016)Smith_Data.xlsx
DOI: 10.5061/dryad.11cd0
title: Data from: Secondary contact and asymmetrical gene flow in a cosmopolitan marine fish across the Benguela upwelling zone

description: The combination of oceanographic barriers and habitat heterogeneity are
 known to reduce connectivity and leave specific genetic signatures in the
 demographic history of marine species. However, barriers to gene flow in
 the marine environment are almost never impermeable which inevitably
 allows secondary contact to occur. In this study eight sampling sites
 (five along the South African coastline, one each in Angola, Senegal and
 Portugal) were chosen to examine the population genetic structure and
 phylogeographic history of the cosmopolitan bluefish (Pomatomus
 saltatrix), distributed across a large South-east Atlantic upwelling zone.
 Bayesian clustering and FST analyses were applied to mtDNA cytochrome b,
 intron AM2B1 and 15 microsatellite loci. We detected uncharacteristically
 high genetic differentiation (FST 0.15-0.20; p&lt;0.001) between the
 fish sampled from South Africa and the other sites, strongly influenced by
 five outlier microsatellite loci located in conserved intergenic regions.
 In addition, differentiation among the remaining East Atlantic sites was
 detected, although mtDNA indicated past isolation with subsequent
 secondary contact between these East Atlantic populations. We further
 identified secondary contact, with unidirectional gene flow from South
 Africa to Angola. The directional contact is likely explained by a
 combination of the northward flowing offshore current and endogenous
 incompatibilities restricting integration of certain regions of the genome
 and limiting gene flow to the south. The results confirm that the dynamic
 system associated with the Benguela Current upwelling zone influences
 species distributions and population processes in the South-east Atlantic.
description: EastAltantic_genotypic
 data_PsaltatrixMicrosatellite genotypic
 data for Pomatomus saltatrixIMa_combined_elf_15loci_1IMa input file, 15 loci (cytochrome b, AM2B1 intron and 13 microsatellite loci)IMa_elf_com_out_mu1_22IMa output file 15 loci (cytochrome b, AM2B1 intron and 15 microsatellite loci)
DOI: 10.5061/dryad.jg33m
title: Data from: Effects of host genetics and environment on egg-associated microbiotas in brown trout (Salmo trutta)

description: Recent studies found fish egg-specific bacterial communities that changed
 over the course of embryogenesis, suggesting an interaction between the
 developing host and its microbiota. Indeed, single-strain infections
 demonstrated that the virulence of opportunistic bacteria is influenced by
 environmental factors and host immune genes. However, the interplay
 between a fish embryo host and its microbiota has not been studied yet at
 the community level. To test whether host genetics affects the assemblage
 of egg-associated bacteria, adult brown trout (Salmo trutta) were sampled
 from a natural population. Their gametes were used for full-factorial in
 vitro fertilizations to separate sire from dam effects. In total, 2520
 embryos were singly raised under experimental conditions that differently
 support microbial growth. High-throughput 16S rRNA amplicon sequencing was
 applied to characterize bacterial communities on milt and fertilized eggs
 across treatments. Dam and sire identity influenced embryo mortality, time
 until hatching and composition of egg-associated microbiotas, but no link
 between bacterial communities on milt and on fertilized eggs could be
 found. Elevated resources increased embryo mortality and modified
 bacterial communities with a shift in their putative functional potential.
 Resource availability did not significantly affect any parental effects on
 embryo performance. Sire identity affected bacterial diversity that turned
 out to be a significant predictor of hatching time: embryos associated
 with high bacterial diversity hatched later. We conclude that both host
 genetics and the availability of resources define diversity and
 composition of egg-associated bacterial communities that then affect the
 life history of their hosts.
description: OTU
 fileThis file contains all
 the bacterial taxa (OTU = operational taxonomic unit of bacteria) that we
 could sequence on brown trout egg samples in our study. This file is used
 to work with QIIME. There is a parallel file to this one that contains all
 the metadata (map file).otu_table_text.txtMap file for QIIME analysisThis file contains all metadata to the OTU file, used with QIIME. it explains what the brown trout egg samples are and how they related to the OTU file.map_file_submission.txtEmbryo performance across treatments and familiesThis file contains all the data on embryo performance. This includes survival, time until hatching, bacterial diversities on the eggs, and origin of the embryo (mother and father).embryo_performance_submission.txtR script for analysis of embryo performanceThis is an R script that was used to analyze embryo performance (input file is called "embryo_performance_submission.txt" and also provided here). Data was analyzed with the R-package "lme4".embryo_performance.R
DOI: 10.15468/dl.m8nb49
title: Occurrence Download

description: A dataset containing 73204 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Culex pipiens",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2000"
 ]
}

 The dataset includes 73204 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001422-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.528tv
title: Data from: Ultra structural changes occurring in duct ectasia and periductal mastitits and their significance in etiopathogenesis

description: Introduction: Duct Ectasia (DE) and Periductal Mastitis (PDM) are the most
 common benign breast conditions seen in women. The etiopathogenesis of
 these entities is still not clear and most of the theories regarding the
 causation are based on the histological features as seen on light
 microscopy. The ultramicroscopic features associated with these conditions
 that may give more insight to the etiopathogenesis are unknown. Aim: To
 study the ultrastructural changes occurring in mammary duct cones in
 patients with DE and PDM using Transmission Electron Microscopic (TEM).
 Method: Major ducts removed by radical duct excision from 21 patients with
 final histopathological diagnosis of DE and PDM were subjected to TEM
 study with 2 normal duct samples as controls Results: The TEM features of
 DE were denudation of the epithelial cells with focal loss of microvilli,
 widening of the inter-epithelial junctions with focal disruption of the T
 bars, periductal collagenisation without inflammation; and features
 suggestive of Epithelial Mesenchymal Transition (EMT). PDM features are
 intact epithelial lining with proliferative epithelium and periductal
 collagenisation with inflammation. Conclusions: Based on the TEM findings,
 we suggest that DE and PDM are two different entities. EMT is a novel
 finding observed in DE in this study.
description: plos 1 supplementary
 dataincludes the following,
 1. electron microscopy procedure 2. photomicrographs and
 electromicrographs with descriptions related to the study 3. surgical
 procedure of duct excisionPLOS 1 Supplementary
 data.docx
DOI: 10.5061/dryad.r08vm
title: Data from: Effects of complex life cycles on genetic diversity: cyclical parthenogenesis

description: Neutral patterns of population genetic diversity in species with complex
 life cycles are difficult to anticipate. Cyclical parthenogenesis (CP), in
 which organisms undergo several rounds of clonal reproduction followed by
 a sexual event, is one such life cycle. Many species, including crop pests
 (aphids), human parasites (trematodes) or models used in evolutionary
 science (Daphnia), are cyclical parthenogens. It is therefore crucial to
 understand the impact of such a life cycle on neutral genetic diversity.
 In this paper, we describe distributions of genetic diversity under
 conditions of CP with various clonal phase lengths. Using a Markov chain
 model of CP for a single locus and individual-based simulations for two
 loci, our analysis first demonstrates that strong departures from full
 sexuality are observed after only a few generations of clonality. The
 convergence towards predictions made under conditions of full clonality
 during the clonal phase depends on the balance between mutations and
 genetic drift. Second, the sexual event of CP usually resets the genetic
 diversity at a single locus towards predictions made under full sexuality.
 However, this single recombination event is insufficient to reshuffle
 gametic phases towards full-sexuality predictions. Finally, for similar
 levels of clonality, CP and acyclic partial clonality (wherein a fixed
 proportion of individuals are clonally produced within each generation)
 differentially affect the distribution of genetic diversity. Overall, this
 work provides solid predictions of neutral genetic diversity that may
 serve as a null model in detecting the action of common evolutionary or
 demographic processes in cyclical parthenogens (for example, selection or
 bottlenecks).
description: Python code for Markov
 chain modelPython code used to
 compute exact stationary probability distribution of genotypic
 states.Python code for
 simulator of gametic phase disequilibriumPython code used to
 simulate gametic phase disequilibrium between two independent loci for
 different levels of clonality.Single locus
 analysisDatasets obtained from
 the single locus markov chain model + R scripts for producing the figures
 presented within the article.Two loci
 analysisDatasets obtained from
 the simulator of gametic phase disequilibrium between two loci + R script
 for producing the figures presented in the paper
DOI: 10.5061/dryad.nj938
title: Data from: Impact of lexical and sentiment factors on the popularity of scientific papers

description: We investigate how textual properties of scientific papers relate to the
 number of citations they receive. Our main finding is that correlations
 are nonlinear and affect differently the most cited and typical papers.
 For instance, we find that, in most journals, short titles correlate
 positively with citations only for the most cited papers, whereas for
 typical papers, the correlation is usually negative. Our analysis of six
 different factors, calculated both at the title and abstract level of 4.3
 million papers in over 1500 journals, reveals the number of authors, and
 the length and complexity of the abstract, as having the strongest
 (positive) influence on the number of citations.
description: science_title_charsExemplary information enabling to recover quantile dependence for number of characters in Science journal in years 1995-2004.aggregatedAggregated information about quantile regression slope coefficients beta(low), beta(half) and beta(top) as well as their uncertainties for all examined journals and factors
DOI: 10.5061/dryad.4v5r8
title: Data from: Foraging at the edge of the world: low‐altitude, high‐speed maneuvering in barn swallows

description: While prior studies of swallow manoeuvering have focused on slow-speed
 flight and obstacle avoidance in still air, swallows survive by foraging
 at high speeds in windy environments. Recent advances in field-portable,
 high-speed video systems, coupled with precise anemometry, permit measures
 of high-speed aerial performance of birds in a natural state. We undertook
 the present study to test: (i) the manner in which barn swallows (Hirundo
 rustica) may exploit wind dynamics and ground effect while foraging and
 (ii) the relative importance of flapping versus gliding for accomplishing
 high-speed manoeuvers. Using multi-camera videography synchronized with
 wind-velocity measurements, we tracked coursing manoeuvers in pursuit of
 prey. Wind speed averaged 1.3–2.0 m s−1 across the atmospheric boundary
 layer, exhibiting a shear gradient greater than expected, with
 instantaneous speeds of 0.02–6.1 m s−1. While barn swallows tended to flap
 throughout turns, they exhibited reduced wingbeat frequency, relying on
 glides and partial bounds during maximal manoeuvers. Further, the birds
 capitalized on the near-earth wind speed gradient to gain kinetic and
 potential energy during both flapping and gliding turns; providing
 evidence that such behaviour is not limited to large, fixed-wing soaring
 seabirds and that exploitation of wind gradients by small aerial
 insectivores may be a significant aspect of their aeroecology.
description: Barn Swallow free-flight
 trajectoriesZip archive containing
 the trajectory kinematics and wind conditions for Barn Swallows engaged in
 foraging near the Oregon Institute of Marine Biology station in Coos Bay,
 Oregon.OIMB_barn_swallow_kinematics_aeroecology.zip
DOI: 10.5061/dryad.t92g5
title: Data from: Altered expression of pectoral myosin heavy chain isoforms corresponds to migration status in the white-crowned sparrow (Zonotrichia leucophrys gambelii)

description: Birds undergo numerous changes as they progress through life-history
 stages, yet relatively few studies have examined how birds adapt to both
 the dynamic energetic and mechanical demands associated with such
 transitions. Myosin heavy chain (MyHC) expression, often linked with
 muscle fibre type, is strongly correlated with a muscle's mechanical
 power-generating capability, thus we examined several morphological
 properties, including MyHC expression of the pectoralis, in a
 long-distance migrant, the white-crowned sparrow (Zonotrichia leucophrys
 gambelii) throughout the progression from winter, spring departure and
 arrival on breeding grounds. White-crowned sparrows demonstrated
 significant phenotypic flexibility throughout the seasonal transition,
 including changes in prealternate moult status, lipid fuelling, body
 condition and flight muscle morphology. Pectoral MyHC expression also
 varied significantly over the course of the study. Wintering birds
 expressed a single, newly classified adult fast 2 isoform. At spring
 departure, pectoral isoform expression included two MyHC isoforms: the
 adult fast 2 isoform along with a smaller proportion of a newly present
 adult fast 1 isoform. By spring arrival, both adult fast isoforms present
 at departure remained, yet expression had shifted to a greater relative
 proportion of the adult fast 1 isoform. Altering pectoral MyHC isoform
 expression in preparation for and during spring migration may represent an
 adaptation to modulate muscle mechanical output to support long-distance
 flight.
description: MHC
 ExpressionData on the myosin heavy
 chain expression of white-crowned sparrow during spring
 migration.RSOS-Velten et
 al-Data.xlsx
DOI: 10.5061/dryad.tf0f5
title: Data from: A pleiotropic interaction between vision loss and hypermelanism in Astyanax mexicanus cave x surface hybrids

description: Background Cave-dwelling animals evolve various traits as a consequence of
 life in darkness. Constructive traits (e.g., enhanced non-visual sensory
 systems) presumably arise under strong selective pressures. The
 mechanism(s) driving regression of features, however, are not well
 understood. Quantitative trait locus (QTL) analyses in Astyanax mexicanus
 Pachón cave x surface hybrids revealed phenotypic effects associated with
 vision and pigmentation loss. Vision QTL were uniformly associated with
 reductions in the homozygous cave condition, however pigmentation QTL
 demonstrated mixed phenotypic effects. This implied pigmentation might be
 lost through both selective and neutral forces. Alternatively, in this
 report, we examined if a pleiotropic interaction may exist between vision
 and pigmentation since vision loss has been shown to result in darker skin
 in other fish and amphibian model systems. Results We discovered that
 certain members of Pachón x surface pedigrees are significantly darker
 than surface-dwelling fish. All of these “hypermelanic” individuals
 demonstrated severe visual system malformations suggesting they may be
 blind. A vision-mediated behavioral assay revealed that these fish, in
 stark contrast to surface fish, behaved the same as blind cavefish.
 Further, hypermelanic melanophores were larger and more dendritic in
 morphology compared to surface fish melanophores. However, hypermelanic
 melanophores responded normally to melanin-concentrating hormone
 suggesting darkening stemmed from vision loss, rather than a defect in
 pigment cell function. Finally, a number of genomic regions were
 coordinately associated with both reduced vision and increased
 pigmentation. Conclusions This work suggests hypermelanism in hybrid
 Astyanax results from blindness. This finding provides an alternative
 explanation for phenotypic effect studies of pigmentation QTL as stemming
 (at least in part) from environmental, rather than exclusively genetic,
 interactions between two regressive phenotypes. Further, this analysis
 reveals persistence of background adaptation in Astyanax. As the eye was
 lost in cave-dwelling forms, enhanced pigmentation resulted. Given the
 extreme cave environment, which is often devoid of nutrition, enhanced
 pigmentation may impose an energetic cost. Such an energetic cost would be
 selected against, as a means of energy conservation. Thus, the pleiotropic
 interaction between vision loss and pigmentation may reveal an additional
 selective pressure favoring the loss of pigmentation in cave-dwelling
 animals.
description: Allele and Trait
 ReanalysisThis spreadsheet
 includes a number of individual sheets including reanalyses and rankings
 of the original measures provided as supplementary information provided in
 Protas et al. (2007).