cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7pvmcvdtp
title: Phylogenomics, introgression, and demographic history of South American true toads (Rhinella)

description: The effects of genetic introgression on species boundaries and how they
 affect species’ integrity and persistence over evolutionary time have
 received increased attention. The increasing availability of genomic data
 has revealed contrasting patterns of gene flow across genomic regions,
 which impose challenges to inferences of evolutionary relationships and of
 patterns of genetic admixture across lineages. By characterizing patterns
 of variation across thousands of genomic loci in a widespread complex of
 true toads (Rhinella), we assess the true extent of genetic introgression
 across species thought to hybridize to extreme degrees based on natural
 history observations and multi-locus analyses. Comprehensive geographic
 sampling of five large-ranged Neotropical taxa revealed multiple distinct
 evolutionary lineages that span large geographic areas and, at times,
 distinct biomes. The inferred major clades and genetic clusters largely
 correspond to currently recognized taxa; however, we also found evidence
 of cryptic diversity within taxa. While previous phylogenetic studies
 revealed extensive mito-nuclear discordance, our genetic clustering
 analyses uncovered several admixed individuals within major genetic
 groups. Accordingly, historical demographic analyses supported that the
 evolutionary history of these toads involved cross-taxon gene flow both at
 ancient and recent times. Lastly, ABBA-BABA tests revealed widespread
 allele sharing across species boundaries, a pattern that can be
 confidently attributed to genetic introgression as opposed to incomplete
 lineage sorting. These results confirm previous assertions that the
 evolutionary history of Rhinella was characterized by various levels of
 hybridization even across environmentally heterogeneous regions, posing
 exciting questions about what factors prevent complete fusion of diverging
 yet highly interdependent evolutionary lineages.
description: Genomic DNA was extracted, amphified, and sequenced using
 16S-specific primers, and used to generate an .xml file to run a
 time-calibrated phylogeny in BEAST. All other data files were generated
 with double-digest restriction site-associated DNA sequence (ddRADseq)
 data. Briefly, ddRADseq libraries were generated using SbfI and MspI
 restriction enzymes, tagging fragments with individual barcodes at the
 University of Texas at Arlington. Libraries were then sequenced on a
 single lane on an Illumina HiSeq 2500 platform. The resulting data was
 demultiplexed using ipyrad, which generated input files for the programs
 used in this analysis.
description: To read tree files: Figtree
 <pre>For analyses:<br> - Beast<br> - Admixture<br>
 - dadi <br> - R<br> - Dsuite</pre>
DOI: 10.5061/dryad.r4xgxd2df
title: Genetic basis of growth, spring phenology and susceptibility to biotic stressors in maritime pine

description: Forest ecosystems are increasingly challenged by extreme events, e.g.
 drought, storms, pest and pathogenic fungi outbreaks, causing severe
 ecological and economical losses. Understanding the genetic basis of
 adaptive traits in tree species is of key importance to preserve forest
 ecosystems, as genetic variation in a trait (i.e. heritability) determines
 its potential for human-mediated or evolutionary change. Maritime pine
 (Pinus pinaster Aiton), a conifer widely distributed in southwestern
 Europe and northwestern Africa, grows under contrasted environmental
 conditions promoting local adaptation. Genetic variation at adaptive
 phenotypes, including height, growth phenology and susceptibility to two
 fungal pathogens (Diplodia sapinea and Armillaria ostoyae) and an insect
 pest (Thaumetopoea pityocampa), were assessed in a range-wide clonal
 common garden of maritime pine. Broad-sense heritability was significant
 for height (0.219), growth phenology (0.165-0.310) and pathogen
 susceptibility (necrosis length caused by D. sapinea, 0.152; and by A.
 ostoyae, 0.021) measured after inoculation under controlled conditions,
 but not for pine processionary moth incidence in the common garden. The
 correlations of trait variation among populations revealed contrasting
 trends for pathogen susceptibility to D. sapinea and A. ostoyae with
 respect to height. Taller trees showed longer necrosis length caused by D.
 sapinea while shorter trees were more affected by A. ostoyae. Moreover,
 maritime pine populations from areas with high summer temperatures and
 frequent droughts were less susceptible to D. sapinea but more susceptible
 to A. ostoyae. Finally, an association study using 4,227 genome-wide SNPs
 revealed several loci significantly associated to each trait (range of
 3-26), including a possibly disease-induced translation initiation factor,
 eIF-5. This study provides important insights to develop genetic
 conservation and breeding strategies integrating species responses to
 biotic stressors.
DOI: 10.5061/dryad.k3j9kd58c
title: Early life growth and telomere length in wild boar piglets 2018

description: Life history theory predicts a trade-off between growth rates and
 lifespan, which is reflected by telomere length, a biomarker of somatic
 state. We investigated the correlation between telomere length and early
 life growth of wild boar piglets, Sus scrofa, kept under semi-natural
 conditions with high food availability to examine our hypothesis that
 increased pre-and post-natal growth will lead to telomere length attrition
 but that a high supply of nutrient may provide the possibility to
 compensate telomere loss via telomere repair mechanisms. As predicted, our
 data showed a clear negative correlation between birth body mass and
 initial telomere length: heavier neonates had shorter telomeres at birth,
 and we did not find an influence of the mother on initial telomere length.
 Body mass at birth correlated with body mass later in life and post-natal
 growth rate did not affect telomere length. We observed an increase in
 telomere length during postnatal development, suggesting that high food
 availability allowed piglets to invest into both, growth and telomere
 restoration. The increase in telomere length over the duration of the
 study was not accompanied by telomerase activity, thus telomere elongation
 was either caused by alternative mechanisms or by short pulses of
 telomerase activity, that we missed. Taken together, this study suggests a
 trade-off between investment into growth and telomere maintenance even
 before birth and the possibility to compensate telomere attrition during
 growth under high amounts of available energy.
description: Data on body mass, body length and relative telomere length was
 sampled from 26 wild boar piglets (Sus scrofa) of four different litters
 during their first four months of life. Animals were kept in semi-natural
 conditions with high food availability and data were collected from March
 to July 2018. DNA was extracted from buccal mucosa and relative telomere
 length (RTL) was assessed using the real-time quantitative polymerase
 chain reaction method (qPCR).
description: The readme file contains an explanation of each of the variables
 in the dataset, its measurement units, and the way it was calculated. N/A
 =  values not available. Information on how the measurements were done can
 be found in the associated manuscript referenced above.
DOI: 10.5061/dryad.ttdz08m0c
title: Convergent evolution of elaborate nests as structural defences in birds

description: The pendent nests of some weaverbird and icterid species are among the
 most complex structures built by any animal, but why they have evolved
 remains to be explained. The precarious attachments and extended entrance
 tunnels characteristic of these nests are widely speculated to act as
 structural defences against invasion by nest predators, particularly
 tree-climbing snakes, but this hypothesis has yet to be systematically
 tested. We use phylogenetic comparative methods to investigate the
 relationship between nest structure and developmental period length, a
 proxy for offspring mortality, in weaverbirds (Ploceidae) and icterids
 (Icteridae), two bird families in which highly elaborate pendent nests
 have independently evolved. We find that more elaborate nests,
 particularly those with entrance tunnels, are associated with longer
 developmental periods in both families. This finding is robust to
 potentially confounding effects of body mass, phylogenetic relationships,
 nest location and latitude. Our results are consistent with the hypothesis
 that elaborate nest structures in birds can function as structural
 defences, resulting in lower offspring mortality and slower development.
 More generally, our findings suggest that constructing complex, protective
 structures may buffer against environmental hazards, reducing extrinsic
 mortality and contributing to the evolution of slower life histories in
 diverse animal lineages, even humans.
description: Please see Methods section of associated manuscript. 
description: Please see README file.
DOI: 10.5061/dryad.wh70rxwpf
title: Genome annotation of Apeltes quadracus

description: Chromosomal fusions have been hypothesized to facilitate adaptation to
 divergent environments, both by bringing together previously unlinked
 adaptive alleles and by creating regions of low recombination that
 facilitate the linkage of adaptive alleles. But, there is little empirical
 evidence to support this hypothesis. Here, we address this knowledge gap
 by studying threespine stickleback (Gasterosteus aculeatus), in which
 ancestral marine fish have repeatedly adapted to freshwater across the
 northern hemisphere. By comparing the threespine stickleback genome to a
 de novo assembly of the fourspine stickleback (Apeltes quadracus) and an
 outgroup species, we find two chromosomal fusion events have occurred in
 the threespine stickleback lineage. On these fused chromosomes, we find an
 enrichment of quantitative trait loci (QTL) underlying traits that
 contribute to marine versus freshwater adaptation. By comparing whole
 genome sequences of freshwater and marine threespine stickleback
 populations, we also find an enrichment of regions under divergent
 selection on these two fused chromosomes. Surprisingly, we find elevated
 genetic diversity within regions under selection in the freshwater
 population. However, these results are consistent with a recent simulation
 study showing that gene flow can increase diversity in genomic regions
 associated with local adaptation. Our demographic models provide evidence
 for gene flow between the marine and freshwater populations. By combining
 our results with those of previous studies, we propose that these fusions
 created regions of low recombination that enabled the formation of
 adaptative clusters, thereby facilitating freshwater adaptation in the
 face of recurrent gene flow between marine and freshwater threespine
 sticklebacks.
description: Gene structures of fourpine
 stickleback were predicted by Maker2 and functional annotation was
 conducted by eggnog-mapper2.
DOI: 10.5281/zenodo.18391992
title: Filtering out euroskepticism: Media influence and interpersonal communication in an agent-based model of Brexit opinion dynamics

description: Data generated by the agent-based model described in “Filtering out Euroskepticism: Media Influence and Interpersonal Communication in an Agent-Based Model of Brexit Opinion Dynamics.”The datasets can be used to replicate the figures and results reported in the paper.
DOI: 10.5281/zenodo.18391994
title: Filtering out euroskepticism: Media influence and interpersonal communication in an agent-based model of Brexit opinion dynamics

description: Data generated by the agent-based model described in “Filtering out Euroskepticism: Media Influence and Interpersonal Communication in an Agent-Based Model of Brexit Opinion Dynamics.”The datasets can be used to replicate the figures and results reported in the paper.
DOI: 10.5061/dryad.t4b8gtj3d
title: Isolating human monoclonal antibodies against adeno-associated virus from donors with pre-existing immunity

description: With the advent of single B-cell cloning technology, we can isolate
 antibodies against virtually any antigen to study the interaction of a
 given pathogen with the immune system and develop novel therapeutic
 strategies. Antibodies directed against the capsid of adeno-associated
 viruses (AAV) are a significant obstacle to effectively leveraging AAV as
 a gene-delivery vector in seropositive individuals. In order to design
 next-generation vectors that can evade neutralization by these antibodies,
 studies have mapped the epitopes of mousemonoclonal antibodies generated
 by immunization with AAV. Although these studies provide critical
 information regarding capsid immunogenicity, they cannot address (1)
 differences in the antibody repertoire generated in humans following AAV
 natural infection; or (2) how reactions can vary when generated in
 response to vector administration. Here, we isolated and evaluated a panel
 of novel, fully human anti-AAV antibodies by cloning single memory B cells
 from a seropositive normal donor. We have validated the utility of this
 approach to study AAV immunology. Our goal is to leverage this knowledge
 to design novel AAV variants that can effectively transduce target tissues
 in individuals with AAV-neutralizing antibodies.
DOI: 10.15468/dl.427t97
title: Occurrence Download

description: A dataset containing 221 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Diospyros dumetorum"
 ]
}

 The dataset includes 221 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002964-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9cnp5hqk2
title: Northern Bobwhite juvenile survival southwest Missouri 2016-2018

description: These data and code are associated with the publication in Ornithological
 Applications entitled "Northern Bobwhite juvenile survival is greater
 on native grasslands managed with fire and grazing, and lower in
 non-native field borders and strip crop fields." We evaluated the
 influence of brood age, vegetation cover type, woody vegetation structure,
 habitat management, and landscape cover on juvenile survival in southwest
 Missouri 2016-2018.
description: Survival data were collected using brood capture and radio-telemetry field
 methods. Vegetation and habitat management covariates from locations of
 juvenile survival observations were calculated from maps derived from
 field observations, management histories, LiDAR data, and remotely sensed
 land cover data.
description: Please review the associated publication and electronic
 supplementary material for detailed descriptions of vegetation and habitat
 management covariates. We have provided a ReadMe.txt
 file defining columns in the dataset as well as code used to estimate
 juvenile survival using the logistic exposure method.
DOI: 10.5061/dryad.76hdr7sxz
title: Siderophores drive invasion dynamics in bacterial communities through their dual role as public good versus public bad

description: Microbial invasions can compromise ecosystem services and spur dysbiosis
 and disease in hosts. Nevertheless, the mechanisms determining invasion
 outcomes often remain unclear. Here, we examine the role of
 iron-scavenging siderophores in driving invasions of Pseudomonas
 aeruginosa into resident communities of environmental pseudomonads.
 Siderophores can be “public goods” by delivering iron to individuals
 possessing matching receptors; but they can also be “public bads” by
 withholding iron from competitors lacking these receptors. Accordingly,
 siderophores should either promote or impede invasion, depending on their
 effects on invader and resident growth. Using supernatant feeding and
 invasion assays, we show that invasion success indeed increased when the
 invader could use its siderophores to inhibit (public bad) rather than
 stimulate (public good) resident growth. Conversely, invasion success
 decreased the more the invader was inhibited by the residents’
 siderophores. Our findings identify siderophores as a major driver of
 invasion dynamics in bacterial communities under iron-limited conditions.
DOI: 10.5061/dryad.3ffbg79js
title: Optimising flower fields as an effective farmland eco-scheme also during non-breeding

description: 1. The Common Agricultural Policy (CAP) of the European Union implements
 several farmland eco-schemes, but most are considered ineffective in
 halting the population declines of farmland birds. Sown flower fields are
 among the few eco-scheme types that rate as clearly beneficial. Yet,
 current CAP regulations lack minimum criteria for flower fields to qualify
 as eco-scheme, and thus only partially exploit their potential
 biodiversity benefits. 2. Earlier research on the attraction of farmland
 birds to different types of sown flower fields has focused on the breeding
 season. We know far less about relative use of these fields during the
 non-breeding season, when food limitation can become severe. We therefore
 compared the attractiveness of four flower field types in SW Germany to 17
 bird species during autumn and winter. Based on replicate surveys on
 75–168 fields, we analysed bird incidences across these four types, and in
 relation to vegetation structure and landscape features. 3. Flower field
 types showed little variation in species richness, but striking
 differences in selection by particular species. Finches and tits were
 disproportionally abundant on fields in their first year since sowing,
 buntings and whinchat on fields in later successional stages. Most flower
 fields established under CAP greening regulations were ploughed between
 September and November of their first year. Therefore, such fields cannot
 support farmland birds and other wildlife during a critical phase in their
 annual cycle. 4. Birds were consistently more abundant on larger fields
 with a differentiated vegetation structure. Flower fields along hedgerows
 and groves primarily attracted inhabitants of woodland ecotones, while
 farmland birds had higher incidences on fields embedded in open
 landscapes. 5. 'Policy implications'. EU member states currently
 revise their farmland eco-schemes. We propose to formulate minimum quality
 standards to assure that flower fields effectively support farmland birds
 also during the non-breeding season. These include an at least biennial
 cycle, more diversified seed mixtures, field sizes exceeding 12 m width or
 0.18 ha area, and local diversity in their placement relative to other
 landscape elements such as hedgerows.
DOI: 10.5061/dryad.8931zcrrs
title: Football is becoming more predictable: Network analysis of 88 thousand matches in 11 major leagues

description: In recent years excessive monetization of football and professionalism
 among the players has been argued to have affected the quality of the
 match in different ways. On the one hand, playing football has become a
 high-income profession and the players are highly motivated; on the other
 hand, stronger teams have higher incomes and therefore afford better
 players leading to an even stronger appearance in tournaments that can
 make the game more imbalanced and hence predictable. To quantify and
 document this observation, in this work we take a minimalist network
 science approach to measure the predictability of football over 26 years
 in major European leagues. We show that over time, the games in major
 leagues have indeed become more predictable. We provide further support
 for this observation by showing that inequality between teams has
 increased and the home-field advantage has been vanishing ubiquitously. We
 do not include any direct analysis on the effects of monetization on
 football’s predictability or therefore, lack of excitement, however, we
 propose several hypotheses which could be tested in future analyses.
DOI: 10.5061/dryad.b2rbnzsgk
title: Energy expenditure does not explain step length-width choices during walking

description: Healthy young adults have a most preferred walking speed, step length, and
 step width that are close to energetically optimal. However, people can
 choose to walk with a multitude of different step lengths and widths,
 which can vary in both energy expenditure and preference. Here we further
 investigate step length-width preferences and their relationship to energy
 expenditure. In line with a growing body of research, we hypothesized that
 people's preferred stepping patterns would not be fully explained by
 metabolic energy expenditure. To test this hypothesis we used a
 two-alternative forced-choice paradigm. Fifteen participants walked on an
 oversized treadmill. Each trial participants experienced two stepping
 patterns and then chose the pattern they preferred. Over time, we adapted
 the choices such that there was 50% chance of choosing one pattern over
 another (equally preferred). If people's preferences are based solely
 on metabolic energy expenditure, then these equally preferred stepping
 patterns should have equal energy expenditure. We found that energy
 expenditure differed across equally preferred step length-width patterns
 (p &lt; 0.001). On average, longer steps with higher energy
 expenditures were preferred over shorter and wider steps with lower energy
 expenditures (p &lt; 0.001). We also asked participants to rank a set
 of shorter, wider, and longer steps from most preferred to least
 preferred, and from most energy expended to least energy expended. Only
 7/15 participants had the same rankings for their preferences and
 perceived energy expenditure. Our results suggest that energy expenditure
 is not the only factor influencing a person's conscious gait choices.
 --