cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tc365
title: Data from: Cultural influence of social information use in pedestrian road-crossing behaviours

description: Social information use is common in a wide range of group-living animals,
 notably in humans. The role it plays in decision-making could be a key to
 understanding how social groups make collective decisions. The observation
 of road-crossing behaviours in the presence of other individuals is an
 ideal means to study the influence of social information on
 decision-making. This study investigated the influence of culture on
 social information used by pedestrians in a potentially dangerous
 scenario, namely road crossing. We scored the collective crossing of
 pedestrians at four locations in Nagoya (Japan) and three locations in
 Strasbourg (France). French pedestrians cross against the lights much more
 often (41.9%) than Japanese ones (2.1%). Individuals deciding to cross the
 road were strongly influenced by the behaviour and the presence of other
 pedestrians, especially in Japan, where a stronger conformism was noted.
 However, Japanese pedestrians were half as likely to be influenced by
 social information as their French counterparts when crossing at the red
 light, as they were more respectful of rules. Men show riskier behaviour
 than women (40.6% versus 25.7% of rule-breaking, respectively), deciding
 quickly and setting off earlier than women. Further related studies could
 help target specific preventive, culture-specific solutions for pedestrian
 safety.
description: Data for 1. Crossing
 against the red light at road crossingsInfraction_Japon_France.xlsxData for 3. Crossing collectively against the red lighttraverse_TOTAL_japon_france.csv
DOI: 10.5061/dryad.g23n4
title: Data from: Identification and characterization of Rubisco activase genes in Oryza punctata

description: Rubisco activase (Rca), a specific chaperone, catalyzes the in vivo
 activation of Rubisco, and thus plays a major role in plant
 photosynthesis. Although the genes encoding Rubisco activase have been
 studied in many model or economic plants, few studies have analyzed their
 homologs in the plants that closely related to crop species. In this
 study, an Rca gene was identified and characterized in a wild relative of
 rice, O. punctata Kotschy ex Steud. The gene was 2747 bp long and
 possessed six exons and five introns with 47% GC content. Further, cDNA
 sequencing produced two transcripts RcaL and RcaS that differed in the
 sequence by an inclusion of 99 bp at the carboxy terminus of RcaL.
 Sequence comparison between the two transcripts and the genomic DNA showed
 that there was a 20-bp alternative splicing event that occurred at the
 fifth intron of the gene leading to the synthesis of a short polypeptide.
 The leaf transcriptome analysis showed that RcaS had a higher expression
 level than that of RcaL in a normal growth environment. In addition, the
 yeast two-hybrid assays displayed the small isoform of Rubisco activase in
 close contact with the large subunit of the Rubisco in this species,
 supporting the side-on binding model of interaction between two proteins.
 This study broadens our understanding of the molecular characteristics of
 some essential genes in photosynthesis.
description: Supplement
 data
DOI: 10.5061/dryad.5mh88
title: Data from: Reduction of leaf area and symptom severity as proxies of disease-induced plant mortality: the example of the Cauliflower mosaic virus infecting two Brassicaceae hosts

description: Disease induced effects on host survival are important to understand the
 evolution of parasitic virulence and host resistance/tolerance.
 Unfortunately, experiments evaluating such effects are in most cases
 logistically demanding justifying the measurement of survival proxies. For
 plant hosts commonly used proxies are leaf area and the nature and
 severity of visual qualitative disease symptoms. In this study we tested
 whether these traits are indeed correlated to the host mortality rate
 induced by viral infection. We infected Brassica rapa and Arabidopsis
 thaliana plants with different natural isolates of Cauliflower mosaic
 virus (CaMV) and estimated over time the development of symptoms and the
 relative reduction of leaf area compared to healthy plants and followed
 plant mortality. We observed that the mortality of infected plants was
 correlated with the relative reduction of leaf area of both B. rapa and A.
 thaliana. Measures of mortality were also correlated with the severity of
 visual qualitative symptoms but the magnitude of the correlations and the
 time frame at which they were significant depended on the host plant:
 stronger and earlier correlations were observed on A. thaliana.
description: Doumayrou et
 al_Brassica_rapa_dataThis data file contains
 mortality measures and proxy data (i.e. mortality rate, reduction of leaf
 area and visual qualitative symptoms) of twenty natural isolates of
 Cauliflower mosaic virus infecting Brassica rapa to study the effect of
 CaMV infection on B. rapa and the relationship between the mortality rate
 and different proxies discussed in the manuscript.Doumayrou et
 al_Arabidopsis_thaliana_dataThis data file contains
 mortality measures and proxy data (i.e. mortality rate, reduction of leaf
 area and visual qualitative symptoms) of nine natural isolates of
 Cauliflower mosaic virus infecting Arabidopsis thaliana to study the
 effect of CaMV infection on A. thaliana and the relationship between the
 mortality rate and different proxies discussed in the
 manuscript.
DOI: 10.5061/dryad.6824131
title: Data from: Fungal endophyte‐infected leaf litter alters in‐stream microbial communities and negatively influences aquatic fungal sporulation

description: Endophytes are ubiquitous plant‐associated microbes and although they have
 the potential to alter the decomposition of infected leaf litter, this has
 not been well‐studied. The endophyte Rhytisma punctatum infects the leaves
 of Acer macrophyllum (bigleaf maple), causing the appearance of black ‘tar
 spots’ that persist in senesced leaves. Other foliar fungi also cause
 visible damage in healthy tissues of this host plant system including an
 unidentified bullseye‐shaped lesion, common in western Washington. Using
 three treatments of endophyte infection status in leaf tissue (R.
 punctatum‐infected, bullseye‐infected, lesion‐free), leaf litter discs
 were submerged in a third‐order temperate stream using mesh litter bags
 and harvested periodically over two months to determine the effects of
 litter treatment and incubation time on litter mass loss, fungal
 sporulation, and microbial community colonization. Litter containing
 symptomatic endophyte infections (Rhytisma or bullseye) had reduced
 sporulation of aquatic hyphomycetes, but decomposed significantly faster
 than lesion‐free or bullseye‐infected litter. Using amplicon‐based
 sequencing, we found a significant difference in bacterial communities
 colonizing Rhytisma‐infected and bullseye‐infected leaf litter, a
 significant difference in fungal communities colonizing Rhytisma‐infected
 leaf litter compared to the two other treatments, and a change in both
 community structure and relative abundances of bacterial and fungal taxa
 throughout the study period. Indicator Species Analysis clarified the
 drivers of these community shifts at the genus level. Our results show
 that endophyte‐associated, in‐stream sporulation and microbial community
 effects are observable within one species of leaf litter.
description: Wolfe_et_al_2018_bioinformaticsContains mapping files, OTU tables, bioinformatics processing script, and notesWolfe_et_al_2018_data_filesContains data and community matrix filesrhytisma_R_scriptR script for analyses and figures
DOI: 10.5061/dryad.q85s3
title: Data from: Patterns of size variation in bees at a continental scale: does Bergmann’s rule apply?

description: Body size latitudinal clines have been widley explained by the Bergmann’s
 rule in homeothermic vertebrates. However, there is no general consensus
 in poikilotherms organisms in particular in insects that represent the
 large majority of wildlife. Among them, bees are a highly diverse
 pollinators group with high economic and ecological value. Nevertheless,
 no comprehensive studies of species assemblages at a phylogenetically
 larger scale have been carried out even if they could identify the traits
 and the ecological conditions that generate different patterns of
 latitudinal size variation. We aimed to test Bergmann’s rule for wild bees
 by assessing relationships between body size and latitude at continental
 and community levels. We tested our hypotheses for bees showing different
 life history traits (i.e. sociality and nesting behaviour). We used
 142,008 distribution records of 615 bee species at 50 km x 50 km (CGRS)
 grids across the West Palearctic. We then applied Generalized Least
 Squares fitted linear model (GLS) to assess the relationship between
 latitude and mean body size of bees, taking into account spatial
 autocorrelation. For all bee species grouped, mean body size increased
 with higher latitudes, and so followed Bergmann’s rule. However,
 considering bee genera separately, four genera were consistent with
 Bergmann’s rule, while three showed a converse trend, and three showed no
 significant cline. All life history traits used here (i.e. solitary,
 social and parasitic behaviour; ground and stem nesting behaviour)
 displayed a Bergmann’s cline. In general there is a main trend for larger
 bees in colder habitats, which is likely to be related to their
 thermoregulatory abilities and partial endothermy, even if a “season
 length effect” (i.e. shorter foraging season) is a potential driver of the
 converse Bergmann’s cline particularly in bumblebees.
description: ITDmean_AndrenaITDmean_BombusITDmean_CamptopoeumITDmean_CeratinaITDmean_ClavipanurgusITDmean_ColletesITDmean_DasypodaITDmean_HabropodaITDmean_HalictusITDmean_LasioglossumITDmean_MacropisITDmean_DufoureaITDmean_MelittaITDmean_MelitturgaITDmean_NomiapisITDmean_NomioidesITDmean_PanurginusITDmean_PanurgusITDmean_RophitesITDmean_SystrophaITDmean_TetraloniellaITDmean_ThyreusITDmean_Xylocopa
DOI: 10.5061/dryad.5ht0853
title: Data from: Transgenerational effects of ungulates and pre-dispersal seed predators on offspring success and resistance to herbivory

description: Herbivorous mammals and insect pre-dispersal seed predators are two types
 of herbivores that, despite their functional and morphological
 differences, tend to severely impact many plant species, highly decreasing
 their seed production and even imperiling the performance of their
 offspring through transgenerational effects. However, how they influence
 offspring resistance to herbivory remains largely unknown. In this study
 we experimentally examined the effects of ungulates and pre-dispersal seed
 predators on seed quality as well as on the emergence, survival and
 resistance to herbivory of the seedlings of a semiarid herb. We found that
 ungulates reduced seedling recruitment but increased seedling resistance
 to leaf miners. These effects were probably a consequence of insufficient
 carbon provisioning in seeds that reduced seed viability and provoked
 carbon limitation in seedlings. Pre-dispersal seed predators did not
 influence seedling recruitment, but seedlings from mothers damaged by
 ungulates and by pre-dispersal seed predators suffered less herbivory by
 grasshoppers. Remarkably, intra-individual differences in damage by
 pre-dispersal seed predators affected the rate of damage underwent by
 seedlings. That is, seedlings derived from fruits attacked by seed
 predators were more resistant to herbivores than siblings derived from
 un-attacked fruits in plant populations exposed to ungulates. To our
 knowledge, this is the first study reporting variation in
 transgenerational-induced resistance of seedlings from the same maternal
 plant. This study is a valuable contribution to the understanding of
 transgenerational effects of multiple herbivores and their implications
 for a deeper comprehension of the natural systems in which they co-occur.
description: Transgenerational
 effects of ungulates and pre-dispersal seed predators on Moricandia
 moricandioidesTransgenerational
 effects of ungulates and seed predators on Moricandia moricandioides'
 seed quality and seedling emergence, performance and
 resistance.Moricandia moricandioides -
 transgenerational effects of ungulates and pre-dispersal seed
 predators.xlsx
DOI: 10.5061/dryad.sf375
title: Data from: Deep phylogeographic structuring of populations of the trapdoor spider Moggridgea tingle (Migidae) from southwestern Australia: evidence for long-term refugia within refugia

description: Southwestern Australia has been recognized as a biodiversity hotspot of
 global significance, and it is particularly well known for its
 considerable diversity of flowering plant species. Questions of interest
 are how this region became so diverse and whether its fauna show similarly
 diverse patterns of speciation. Here we have carried out a phylogeographic
 study of trapdoor spiders (Migidae: Moggridgea), a presumed Gondwanan
 lineage found in wet forest localities across southwestern Australia.
 Phylogenetic, molecular clock and population genetic analyses of
 mitochondrial (mtDNA) COI gene and ITS rRNA (internal transcribed spacer)
 data revealed considerable phylogeographic structuring of Moggridgea
 populations, with evidence for long-term (&gt; 3 million years)
 isolation of at least nine populations in different geographic locations,
 including upland regions of the Stirling and Porongurup Ranges. High
 levels of mtDNA divergence and no evidence of recent mitochondrial gene
 flow among valley populations of the Stirling Range suggest that
 individual valleys have acted as refugia for the spiders throughout the
 Pleistocene. Our findings support the hypothesis that climate change,
 particularly the aridification of Australia after the late Miocene, and
 the topography of the landscape, which allowed persistence of moist
 habitats, have been major drivers of speciation in southwestern Australia.
description: Moggridgea_COI_nexA text file containing the nexus input file of COI sequences from 103 Moggridgea spiders, including 95 Moggridgea tingle from south-western Australia (T numbers), 5 Moggridgea species from Africa and 3 Moggridgea australis from Kangaroo Island, South Australia. This nexus file was used to produce COI phylogenetic trees presented in the Cooper et al. (2011) Molecular Ecology paper.Moggridgea_COI_reduced_nexA text file containing the nexus input file of COI sequences from 47 Moggridgea spiders, including 46 Moggridgea tingle from south-western Australia (T numbers), and one Moggridgea australis from Kangaroo Island, South Australia. This nexus file contains a reduced COI dataset after removal of identical haplotype sequences and was used to produce COI phylogenetic trees presented in the Cooper et al. (2011) Molecular Ecology paper.Moggridgea_ITS_nexThis file is a text file containing 53 ITS rRNA sequences from Moggridgea tingle (T numbers), 3 from Moggridgea australis (Mog1-3) and 3 African Moggridgea (MY numbers). It was used to produce phylogenetic trees given in the Cooper et al. (2011) Molecular Ecology paper.
DOI: 10.5061/dryad.1369
title: Data from: Inter-specific gene flow dynamics during the Pleistocene-dated speciation of forest-dependent mosquitoes in Southeast Asia

description: Tropical forests have undergone repeated fragmentation and expansion
 during Pleistocene glacial and interglacial periods, respectively. The
 effects of this repeated forest fragmentation in driving vicariance in
 tropical taxa have been well studied. However, relatively little is known
 about how often this process results in allopatric speciation, since it
 may be inhibited by recurrent gene flow during repeated secondary contact,
 or to what extent Pleistocene-dated speciation results from ecological
 specialisation in the face of gene flow. Here, divergence times and gene
 flow between three closely-related mosquito species of the Anopheles dirus
 species complex endemic to the forests of Southeast Asia, are inferred
 using coalescent based Bayesian analysis. An Isolation with Migration
 model is applied to sequences of two mitochondrial and three nuclear
 genes, and 11 microsatellites. The divergence of An. scanloni has occurred
 despite unidirectional nuclear gene flow from this species into An. dirus.
 The inferred asymmetric gene flow may result from the unique evolutionary
 adaptation of An. scanloni to limestone karst habitat, and therefore the
 fitness advantage of this species over An. dirus in regions of sympatry.
 Mitochondrial introgression has led to the complete replacement of An.
 dirus haplotypes with those of An. baimaii through a recent (~62 kya)
 selective sweep. Speciation of An. baimaii and An. dirus is inferred to
 have involved allopatric divergence throughout much of the Pleistocene.
 Secondary contact and bidirectional gene flow has occurred only within the
 last 100,000 years, by which time the process of allopatric speciation
 seems to have been largely completed.
description: Sequenced fragments of
 the Hsp82 gene for Anopheles baimaii mosquitoesbaimaii_hsp_forgenbank.txtSequenced fragments of the Hsp82 gene for Anopheles dirus mosquitoesdirus_hsp_forgenbank.txtSequenced fragments of the Hsp82 gene for Anopheles scanloni mosquitoesscanloni_hsp_forgenbank.txtSequenced fragments of the Est6 gene for Anopheles baimaii mosquitoesest6_baimaii_unphased.txtSequenced fragments of the Est6 gene for Anopheles dirus mosquitoesdirus_est6_unphased.txtSequenced fragments of the Est6 gene for Anopheles scanloni mosquitoesest6_scanloni_unphased.txtSequenced fragments of the NinaE gene for Anopheles baimaii mosquitoesbaimaii_nina_unphased.txtSequenced fragments of the NinaE gene for Anopheles dirus mosquitoesdirus_nina_forgenbank.txtSequenced fragments of the NinaE gene for Anopheles scanloni mosquitoesscanloni_nina_unphased.txt
DOI: 10.5061/dryad.8v1f4
title: Data from: Genetic variation, simplicity and evolutionary constraints for function-valued traits

description: Understanding the patterns of genetic variation and constraint for
 continuous reaction norms, growth trajectories, and other function-valued
 traits is challenging. We describe and illustrate a recent analytical
 method, simple basis analysis (SBA), that uses the genetic
 variance-covariance (G) matrix to identify “simple” directions of genetic
 variation and genetic constraints that have straightforward biological
 interpretations. We discuss the parallels between the eigenvectors
 (principal components) identified by principal components analysis (PCA)
 and the simple basis (SB) vectors identified by SBA. We apply these
 methods to estimated G matrices obtained from 10 studies of thermal
 performance curves and growth curves. Our results suggest that variation
 in overall size across all ages represented most of the genetic variance
 in growth curves. In contrast, variation in overall performance across all
 temperatures represented less than one-third of the genetic variance in
 thermal performance curves in all cases, and genetic trade-offs between
 performance at higher versus lower temperatures were often important. The
 analyses also identify potential genetic constraints on patterns of early
 and later growth in growth curves. We suggest that SBA can be a useful
 complement or alternative to PCA for identifying biologically
 interpretable directions of genetic variation and constraint in
 function-valued traits.
description: RCodeZIP archive with R code,
 examples, and information on how to assess variability in an estimate that
 depends on an estimated covariance matrix.GmatricesG Matrices analyzed in the paper
DOI: 10.5061/dryad.j697v
title: Data from: Hierarchical population structure and habitat differences in a highly mobile marine species: the Atlantic spotted dolphin

description: Recent molecular studies have shown that highly mobile species with
 continuous distributions can exhibit fine-scale population structure. In
 this context, we assessed genetic structure within a marine species with
 high dispersal potential, the Atlantic spotted dolphin (Stenella
 frontalis). Using 19 microsatellite loci and mitochondrial control region
 sequences, population structure was investigated in the western North
 Atlantic, the Gulf of Mexico and the Azores Islands. Analyses of the
 microsatellite data identified four distinct genetic clusters, which were
 supported by the control region sequences. The highest level of divergence
 was seen between two clusters corresponding to previously-described
 morphotypes that inhabit oceanic and shelf waters. The combined
 morphological and genetic evidence suggests these two lineages are on
 distinct evolutionary trajectories and could be considered distinct
 subspecies despite their parapatry. Further analysis of the continental
 shelf cluster resulted in three groups: animals inhabiting shelf waters in
 the western North Atlantic, the eastern Gulf of Mexico, and the western
 Gulf of Mexico. Analyses of environmental data indicate the four genetic
 clusters inhabit distinct habitats in terms of depth and sea surface
 temperature. Contemporary dispersal rate estimates suggest all of these
 populations should be considered as distinct management units. Conversely,
 no significant genetic differentiation was observed between S. frontalis
 from offshore waters of the western North Atlantic and the Azores, which
 are separated by approximately 4500 km. Overall, the hierarchical
 structure observed within the Atlantic spotted dolphin shows that the
 biogeography of the species is complex because it is not shaped solely by
 geographic distance.
description: GSI
 files-"GSI_assignments_labels" = cluster assignment for each individual included in this analysis - "sfro_GSI_tree.phy" = phylip file containing sequences for all individuals included in this analysis -"100rooted.tre" = 100 bootstrap trees generated using PhyML and used to calculate the gsiTGSI.zipIM filesIM input file and command line: "Sfro_2POPs_MtCR_IM" = IM input file "IM_command_line" = IM command lineIM.zipR script: R_Get_sample_Depth"R_Get_sample_Depth.R" = This script was used to retrieve the depth of each sampling location.R_Get_sample_Depth.RR script: R_Get_sample_Value"R_Get_sample_Value.R" = This script was used to retrieve values of environmental data (present code: example for the turbidity data) for each sampling location.R_Get_sample_Value.RSample_location_micros"Sample_location_Micros.xls" = file containing each sample information (sex, collection date, region of collection) and microsatellite dataViricel_mtDNA_alignment"Viricel_mtDNA_alignment.fasta" = alignment of all mitochondrial DNA haplotypes (including heteroplasmic sequences)
DOI: 10.5061/dryad.29tm1d3
title: Data from: Morphological and anatomical observation during the formation of bulbils in Lilium lancifolium

description: Aerial bulbil, other than axillary branch and tendril, is a special
 propagative organ in Lilium lancifolium, but the development events
 occurring during bulbil formation of L. lancifolium have not been
 reported. In this study, we observed the changes of morphology and
 anatomical structure during the process of bulbil formation in L.
 lancifolium. The results indicated that bulbils of L. lancifolium formed
 in the joint region of leaf and stem and were derived from the division
 and diferentiation of axillary meristem cells. Bulbils frst generated on a
 certain leaf axil in the upper portion of stem, and then formed upward
 along the upper stem. The present study provides histological information
 for further studying the mechanism of bulbil formation.
description: Supplemental
 data