cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7h44j0zt5
title: Benefits and costs of hosting facultative symbionts in plant-sucking insects: a meta-analysis

description: This dataset contains data from a meta-analysis on the benefits and costs
 of hosting secondar symbionts in plant-sucking insects, as described in
 the paper: "Zytynska, S.E., Tighiouart, K. & Frago, E. (2021)
 Benefits and costs of hosting facultative symbionts in plant-sucking
 insects: A meta-analysis. Molecular
 Ecology https://doi.org/10.1111/mec.15897 " Many
 animals have evolved associations with symbiotic microbes that benefit the
 host through increased growth, lifespan, and survival. Some interactions
 are obligate (essential for survival) while others are facultative
 (beneficial but not essential). Not all individuals host all facultative
 symbionts in a population, and thus there is likely a trade-off between
 the cost of hosting these symbionts and the benefits they confer to the
 host. Plant-sucking insects have been one of the most important models to
 test these costs and benefits experimentally. This research is now moving
 beyond the description of symbiont effects towards understanding the
 mechanisms of action, and their role in the wider ecological community. We
 present a quantitative and systematic analysis of the published evidence
 exploring this question. We found that whitefly and true bugs experience
 benefits through increased growth and fecundity, whereas aphids experience
 costs to their fecundity but benefits through increased resistance to
 natural enemies. We also report the lack of data in some plant-sucking
 groups, and explore variation in effect strengths and directions across
 aphid host, symbiont and plant species thus highlighting the importance of
 considering the context dependency of these interactions.
description: Meta-analysis: The main
 inclusion criteria across the groups were: (1) data on at least one insect
 species; (2) an experimental test of facultative symbiont effects on
 insects, either experimentally cured of a symbiont, or inoculated with one
 (Experimental), or a comparison of field-collected infected and uninfected
 aphids (Natural); (3) any of the following types of variables tested: any
 behaviour, growth, fecundity, survival, or parasitism-resistance related
 variable; and (4) data on means, an estimation of variation, and sample
 size. In addition, we only included studies that used artificial curing
 methods (e.g. antibiotics) with demonstrated negative effects on
 symbionts, but not their insect hosts. If novel methods to remove
 symbionts were used, we only included studies that demonstrated that the
 technique used had no direct negative effects on insect fitness.
 Analysis: data were
 analysed in R using metafor package.
description: The ReadMe file contains an explanation of each of the variables
 in the dataset, the extracted data, the assigned group and the associated
 values of Hedges' g used in the meta-analysis (also see the R code
 file).  Three datasets (1) main
 dataset for Heteroptera, whitefly and aphids (2) aphid
 dataset for host-plant effects (3) aphid dataset for
 multiple hosting of symbionts
DOI: 10.5061/dryad.x0k6djhhw
title: Datasets for phylogenetic analyses of Pavlomulina ranunculiformis

description: Rapidly accumulating genetic data from environmental sequencing approaches
 have revealed an extraordinary level of unsuspected diversity within
 marine phytoplankton, which is responsible for around 50% of global net
 primary production. However, the phenotypic identity of many of the
 organisms distinguished by environmental DNA sequences remains unclear.
 The rappemonads are a plastid-bearing protistan lineage that to date has
 only been identified by environmental plastid 16S rRNA sequences. The
 phenotypic identity of this group, which does not confidently cluster in
 any known algal clades in 16S rRNA phylogenetic reconstructions, has
 remained unknown since the first report of environmental sequences over
 two decades ago. We show that rappemonads are closely related to a
 haptophyte microalga, Pavlomulina ranunculiformis gen. nov. sp. nov., and
 belong to a new haptophyte class, the Rappephyceae. Organellar
 phylogenomic analyses provide strong evidence for the inclusion of this
 lineage within the Haptophyta as a sister group to the Prymnesiophyceae.
 Members of this new class have a cosmopolitan distribution in coastal and
 oceanic regions. The relative read abundance of Rappephyceae in a large
 environmental barcoding dataset was comparable to, or greater than, that
 of major haptophyte species, such as the bloom-forming Gephyrocapsa
 huxleyi and Prymnesium parvum, indicating that they likely have a
 significant impact as primary producers. Detailed characterization of
 Pavlomulina allowed for reconstruction of the ancient evolutionary history
 of the Haptophyta, a group that is one of most important components of
 extant marine phytoplankton communities.
description: The original alignment data for organellar phylogenomics are
 kindly provided from Dr. Sergio A. Munoz-Gomez and Dr. Christopher J.
 Jackson, published in https://doi.org/10.1016/j.cub.2017.04.054 and
 https://doi.org/10.1093/gbe/evu218, respectively. Plastid 16S and nuclear
 18S rRNA genes were retrieved as described in
 https://doi.org/10.1016/j.cub.2021.03.012. The original dataset of plastid
 Rpl36 was obtained from https://doi.org/10.1186/1471-2164-15-604. The
 corresponding gene/protein sequences of Pavlomulina ranunculiformis were
 added to the datasets. Alignment was performed by MAFFT
 L-INS-i.<br> Ambiguously aligned sites were selected and trimmed by
 Gblocks (-t=d and -b5=h for nucleotides and -t=p and -b5=h for amino
 acids).<br> Single protein datasets were then concatenated for
 phylogenomics.
DOI: 10.5061/dryad.hhmgqnkg5
title: Standardized nuclear markers improve and homogenize species delimitation in Metazoa

description: Species are the fundamental units of life and evolution. Their recognition
 is essential for science and society. Molecular methods have been
 increasingly employed for the identification of animal species, despite
 several challenges.  Here, we explore with genomic data from nine
 animal lineages a set of nuclear markers, namely metazoan-level
 universal single-copy orthologs (metazoan USCOs), for their use in species
 delimitation. Our data sets include arthropods and vertebrates. We use
 various data assembly strategies and employ coalescent-based species
 inference as well as population admixture analyses and phenetic methods.
 We demonstrate that metazoan USCOs well distinguish closely related
 morphospecies and consistently outperform classical mitochondrial DNA
 barcoding in discriminating closely related species in different animal
 taxa. USCOs overcome the general shortcomings of mitochondrial DNA
 barcodes, and due to standardization across Metazoa, also those of other
 approaches. They accurately assign samples not only to lower but also to
 higher taxonomic levels.  Metazoan USCOs provide a powerful and
 unifying framework for DNA-based species delimitation and taxonomy in
 animals and their employment could result in a more efficient use of
 research data and resources.
description: Sequences were obtained from targeted enrichment of universal
 single-copy orthologous loci (USCOs) from nine different animal genera.
 Reads were ssembled and aligned with seven different approaches (see
 Supplementary Information of paper for details). In each dataset,
 alignment positions present in less than three individuals were excluded,
 additionally reduced datasets were generated that include only positions
 present in all individuals. Phylogenetic trees were created with IQ-TREE
 both for concatenated alignments and for individual genes, and
 coalescent-based analyses were done with ASTRAL based on the individual
 gene trees. Species delimitation analyses were conducted with BPP based on
 the ASTRAL trees. SNPs were extracted from the alignments with
 snp-sites. CO1 sequences were obtained by Sanger sequencing (arthropods)
 or extracted from USCO reads (frogs) and phylogenetic trees based on them
 calculated with PhyML.
description: All alignments, including SNP datasets, are in FASTA format and
 can be opened with standard alignment viewers. In alignments for
 approaches A1 and A2, ambiguity codes (R, Y, W, S, M, K) stand for
 positions inferred to be heterozygous. Phylogenetic
 trees are in NEWICK format, files including multiple named trees are in
 NEXUS format. Both can be opened in a standard phylogenetic tree viewer
 such as FigTree. Individual gene trees are unrooted, trees based on whole
 USCO datasets are rooted.  SNP datasets recoded for
 NMDS analysis are tab-delimited text and numbers have the following
 meaning: 0: homozygous for more common allele, 1: heterozygous, 2:
 homozygous for less common allele. Unknown positions are represented by
 empty cells.
DOI: 10.25338/b8p35m
title: Linked networks reveal dual roles of insect dispersal and species sorting for bacterial communities in flowers

description: Due to the difficulty of tracking microbial dispersal, it is rarely
 possible to disentangle the relative importance of dispersal and species
 sorting for microbial community assembly. Here, we leverage a detailed
 multilevel network to examine drivers of bacterial community assembly
 within flowers. We observed flower visitors to 20 focal plant species in a
 coflowering community in the Sierra Nevada, revealing 289 species of
 arthropods. We also analyzed bacterial communities on flowers of each
 species. We found that plant species with similar visitor communities tend
 to have similar bacterial communities, and visitor identity to be more
 important than plant relatedness in structuring floral bacterial
 communities. However, plant species that were hubs of arthropod visitation
 were not necessarily hubs of floral bacteria, suggesting an important role
 for species sorting. Across plant species, the composition of
 flower-visiting Diptera (flies), bees and non-bee Hymenoptera best
 predicted bacterial species composition on flowers. Taken together, our
 analyses suggest dispersal is important in determining similarity in
 microbial communities across plant species, but not as important in
 determining the overall macrostructure (nestedness, modularity) and
 microstructure (connectedness based on shared interactors) of the floral
 bacterial network. A multilevel network approach thus allows us to address
 features of community assembly that cannot be considered when viewing
 networks as separate entities.
DOI: 10.5061/dryad.8931zcrq5
title: A masculinizing supergene underlies an exaggerated male reproductive morph in a spider

description: In many species, individuals can develop into strikingly different morphs,
 which are determined by a simple Mendelian locus. How selection shapes
 loci that control complex p henotypic differences remains poorly
 understood. In the spider gibbosus, males either develop into a
 ‘hunched’morph with conspicuous head structures or as a fast developing
 ‘flat’morph with a female- like appearance. We show that the hunched
 differs from the f lat-determinin g allele by a hunch-specific genomic
 fragment of approximately 3 megabases. This fragment comprises dozens of
 genes that duplicated from genes found at different chromosomes. All
 functional duplicates, including doublesex- a key sexual differentiation
 regulatory gene, show male-specific expression, which il lustrates their
 combined role as a masculinizing supergene. Our findings demonstrate how
 extensive indel polymorphisms and duplications of regulatory genes may
 contribute to t he evolution of co-adapted gene clusters, sex-limi ted
 reproductive morphs, and the enigmatic evolution of exaggerated sexual
 traits in general.
DOI: 10.5061/dryad.m37pvmd1n
title: Adherence to wearing facemasks during the COVID-19 pandemic

description: This study reports a comprehensive empirical investigation of the nature
 and correlates of anti-mask attitudes during the COVID-19 pandemic.
 Accumulating evidence underscores the importance of facemasks, as worn by
 the general public, in limiting the spread of infection. Accordingly, mask
 wearing has become increasingly mandatory in public places such as stores
 and on public transit. Although the public has been generally adherent to
 mask wearing, a small but vocal group of individuals refuse to wear masks.
 Anti-mask protest rallies have occurred in many places throughout the
 world, sometimes erupting violently. Few empirical studies have examined
 the relationship between anti-mask attitudes and mask non-adherence and
 little is known about how such attitudes relate to one another or other
 factors (e.g., non-adherence to social distancing, anti-vaccination
 attitudes). To investigate these issues, the present study surveyed 2,078
 adults from the US and Canada. Consistent with other surveys, we found
 that most (84%) people wore masks because of COVID-19. The 16% who did not
 wear masks scored higher on most measures of negative attitudes towards
 masks. Network analyses indicated that negative attitudes about masks
 formed an intercorrelated network, with the central nodes in the network
 being (a) beliefs that masks are ineffective in preventing COVID-19, and
 (b) psychological reactance (PR; i.e., an aversion to being forced to wear
 masks). These central nodes served as links, connecting the network of
 anti-masks attitudes to negative attitudes toward SARSCoV2 vaccination,
 beliefs that the threat of COVID-19 has been exaggerated, disregard for
 social distancing, and political conservatism. Findings regarding PR are
 important because, theoretically, PR is likely to strengthen other
 anti-masks attitudes (e.g., beliefs that masks are ineffective) because
 people with strong PR react with anger and counter-arguments when their
 beliefs are challenged, thereby leading to a strengthening of their
 anti-mask beliefs. Implications for improving mask adherence are
 discussed.
description: SPSS file.
DOI: 10.5061/dryad.3xsj3txfv
title: Detection histories for Lycalopex griseus, Lycalopex culpaeus, Leopardus guigna, and Canis familiaris and habitat destruction covariate data for Los Lagos Chile (2019)

description: In an increasingly anthropogenic world, species face multiple interacting
 threats. Habitat fragmentation and domestic dogs are two perturbations
 threatening terrestrial mammals globally. Our aim was to determine if (1)
 the spatial use of domestic dogs increases with habitat destruction and
 (2) whether domestic dogs and habitat destruction drive the spatial use of
 native carnivores in a heavily degraded agricultural landscape in the
 central valley/Andean foothills transition of Los Lagos, Chile. We
 implemented a camera trap survey in a fragmented landscape comprised of
 native forest patches amidst a matrix of pastureland. We used
 single-species occupancy models to assess the impact of domestic dogs and
 habitat destruction on three mesocarnivores – the foxes, culpeo (Lycalopex
 culpaeus) and chilla (Lycalopex griseus) and the wild cat güiña (Leopardus
 guigna). Additionally, we compared temporal overlap of all study species
 (including domestic dogs). Detection rates for both the foxes increased
 with domestic dog occupancy, while factors driving occupancy differed for
 each of the native species. We found that a 12% projected increase in
 domestic dog occupancy negatively impacted the spatial use of the culpeo.
 Habitat loss and fragmentation were positive drivers for chilla and
 domestic dog occupancy. The güiña did not respond to fragmentation and
 other habitat covariates or domestic dog occupancy. All native carnivore
 species were primarily nocturnal, while the domestic dog was almost
 entirely diurnal.
description: Detection histories were generated from species occurrence data
 gathered from a camera trap survey in the Los Lagos region of Chile in
 2019. A 30-minute quite period was introduced for conspecifics. Covariate
 data was collected through field measurements (understory), from the
 camera traps (small mammal and dog trap success), and through digitization
 of satellite imagery. The 'camtrapR' package
 was implemented in R to organize the camera data and generate the
 detection histories.
description: Dryad_README.txt details the contents of each file, including how
 each covariate was obtained. CHILLA.csv – Detection history for the
 chilla fox (Lycalopex griseus). CULPEO.csv – Detection history for the
 culpeo fox (Lycalopex culpaeus). DOG.csv – Detection history for the
 domestic dog (Canis familiaris). GUIGNA.csv – Detection history for the
 guigna (Leopardus guigna). chile_covars_dryad.csv -  contains the
 site level covariate values that were used for occupancy modeling. The
 site order for this file and the detection history files is
 identical.
DOI: 10.5061/dryad.x95x69phc
title: Estuarine fishes associated with intertidal oyster reefs characterised using environmental DNA and baited remote underwater video

description: It has been widely shown that oyster reefs enhance local biodiversity and
 fisheries production. Therefore, in this study fish assemblages from
 oyster reefs were compared to sandy habitats using environmental DNA
 (eDNA) metabarcoding and baited remote underwater video. Fish
 diversity from eDNA was characterised using three metabarcoding assays -
 two that target the mitochondrial 16S region and one that targets the 12S
 region. Fish assemblages differed with each assay, as well as to
 that detected by BRUVs. Overall, 112 fish genera were identified, with 78
 more genera detected using eDNA metabarcoding than those observed with
 BRUVs. Both eDNA and BRUVs resolved a higher number of fish genera
 associated with oyster reefs than with sand sites, and a different fish
 composition between habitats was also resolved using each method.
 Furthermore, eDNA was shown to be useful towards characterising the gamma
 diversity of the estuary, due to the intertidal nature and hydrodynamics
 of the system, as well as the alpha diversity associated with oyster reefs
 and sand sites.
description: DNA was extracted from seawater samples collected from Port
 Stephens, NSW Australia. The DNA was used in PCR using
 three independent metabarcoding assays (16SNest, Fish16S and MiFishU) to
 generate amplicon libraries.  Sequence data files were
 generated from the amplicon libraries on an Illumina MiSeq using a 300
 cycle kit V2. At the same sites as for eDNA, baited
 mini-BRUVs were deployed for 30 minutes.
description: Fastq files (i.e. list of DNA barcode sequences) for each sample
 and metabarcoding assay are provided. Files names
 indicate the habitat (e.g. osyter) where the sample was collected from,
 followed by the site number (e.g. 1), metabarcoding assay (e.g. 16SFish),
 the date of collection (e.g. Mar19), and finally the unique sample
 identifier (e.g. 89).  For example:
 Oyster1_16SFish_Mar19_89. Additional controls
 (negative, extraction, filtration) are also indicated in sample
 names. In the excel datasheet, MaxN data of fish
 detections using BRUVs were generated with Event Measure. Habitat and site
 names for BRUV samples are consistent with the eDNA file
 names.
DOI: 10.5068/d1h67f
title: Do early life experiences predict variation in the general factor of personality (GFP)?

description: Evolutionary approaches to examine human personality variation have used
 the Big Five as given, tested higher order latent structures like the Big
 Two or the General Factor of Personality (GFP), or applied domain-specific
 psychological adaptations. Yet, debates regarding the adaptive
 significance of personality variation are ongoing. We focus on latent
 factor models and test adaptationist hypotheses linking facultative
 responses of the GFP, its subparts (i.e., metatrait alpha), and
 extraversion to early life experiences in 366 U.S. undergraduates. To
 address the problem of shared method variance, we assessed Big Five
 personality traits using both self-report and stranger-rating from brief
 videotaped interviews. Structural equation modeling, from the
 self-reported Big Five dimensions only, revealed a well-fitting GFP, which
 was related to father-closeness. A GFP comprised of the other-rated Big
 Five dimensions could not be extracted. Results from metatrait alpha were
 also unsupported. Lastly, we found some support for an alternative
 hypothesis that extraversion (men only) is ontogenetically calibrated to
 physical phenotypic traits that affect individuals’ bargaining power. Our
 findings cast doubt on the value of the GFP as a valid construct. We
 discuss how the field of personality science may benefit from adopting a
 bottom-up as opposed to a top-down approach.
description: See GFPdataReadMe.txt file.
DOI: 10.5061/dryad.9cnp5hqh6
title: Data and R code from: Fire-induced loss of the world’s most biodiverse forests in Latin America

description: Fire plays a dominant role in deforestation, particularly in the tropics,
 but the relative extent of transformations and influence of fire frequency
 on eventual forest loss remain unclear. Here we analyze the frequency of
 fire and its influence on post-fire forest trajectories between 2001-2018.
 We account for ~1.1% of Latin American forests burnt in 2002-2003
 (8,465,850 ha). Although 40.1% of forests (3,393,250 ha) burned only once,
 by 2018~48% of the evergreen forests converted to other, primarily
 grass-dominated uses. While greater fire frequency yielded more
 transformation, our results reveal the staggering impact of even a single
 fire. Increasing fire frequency imposes greater risks of irreversible
 forest loss, transforming forests into ecosystems increasingly vulnerable
 to disturbance and degradation. Reversing this trend is indispensable to
 both mitigate and adapt to climate change globally. As climate change
 transforms fire regimes across the region, key actions are needed to
 conserve Latin American forests.
description: Data and R code for alluvial plots and Bayesian analyses for
 Fire-induced loss of the world’s most biodiverse forests in Latin
 America Address data queries to
 darmenterasp@unal.edu.co and Bayesian R code related queries to
 liliana.davalos@stonybrook.edu 1) Place all files in a
 single folder, 2) alluvial_2step.R makes two-step
 alluvial plots that require further editing to look as in the
 paper, 3) alluvial_countries.R makes single step
 alluvial plots for each country, 4)
 poisson_overdisperse.R runs MCMCglmm models on the overdispersed
 Poisson-distributed data and saves them to an RData file needed for
 plotting coefficients, 5) poisson_plot.R plots the
 coefficients for the best fit model, requires RData output from step
 4.
DOI: 10.5061/dryad.v41ns1rv9
title: Superoxide is promoted by sucrose and affects amplitude of circadian rhythms in the evening

description: Plants must coordinate photosynthetic metabolism with the daily
 environment and adapt rhythmic physiology and development to match carbon
 availability. Circadian clocks drive biological rhythms which adjust to
 environmental cues. Products of photosynthetic metabolism, including
 sugars and reactive oxygen species (ROS), are closely associated with the
 plant circadian clock and sugars have been shown to provide metabolic
 feedback to the circadian oscillator. Here, we report a comprehensive
 sugar-regulated transcriptome of Arabidopsis and identify genes associated
 with redox and ROS processes as a prominent feature of the transcriptional
 response. We show that sucrose increases levels of superoxide (O2–) which
 is required for transcriptional and growth responses to sugar. We identify
 circadian rhythms of O2–-regulated transcripts which are phased around
 dusk and find that O2– is required for sucrose to promote
 expression of TIMING OF CAB1 (TOC1) in the evening. Our
 data reveal a role for O2– as a metabolic signal affecting
 transcriptional control of the circadian oscillator in Arabidopsis.