cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6078/d1z70c
title: The effects of solar wind structure on nanodust dynamics in the inner heliosphere

description: Datasets supporting the manuscript, "The effects of solar wind
 structure on nanodust dynamics in the inner heliosphere", J. Geophys.
 Res.: Space Physics Datasets are output from a nanodust dynamics model
 that uses background MHD electromagnetic fields to trace 1-30 nm grains as
 they evolve from the inner solar system outwards under the influence of
 forces such as gravity, electromagnetism, and radiation pressure. Output
 variables include nanodust flux, velocity distributions, and both measured
 and predicted (relative) count rates at the positions of NASA's
 STEREO A and B spacecraft in 2007.
description: All files in plain ASCII format.
DOI: 10.5061/dryad.cvdncjt21
title: Data from: Disparate patterns of movements and visits to points of interest located in urban hotspots across U.S. metropolitan cities during COVID-19

description: We examined the effect of social distancing on changes in visits to urban
 hotspot points of interest. In a pandemic situation, urban hotspots could
 be potential superspreader areas as visits to urban hotspots can increase
 the risk of contact and transmission of a disease among a population. We
 mapped origin-destination networks from census block groups to points of
 interest (POIs), such as restaurants, museums, and schools, in sixteen
 cities in the United States. We adopted a coarse-grain approach to examine
 patterns of visits to POIs among hotspots and non-hotspots from January to
 May 2020. Also, we conducted chi-square tests to identify POIs with
 significant flux-in changes during the analysis period. The results showed
 disparate patterns across cities in terms of reduction in hotspot POI
 visits. Sixteen cities are divided into two categories. In one category,
 which includes the cities of, San Francisco, Seattle, and Chicago, we
 observe a considerable decrease in hotspot POI visits, while in another
 category, including the cites of, Austin, Houston, and San Diego, the
 visits to hotspots did not greatly decrease. While all the cities
 exhibited overall decreasing visits to POIs, one category maintained the
 proportion of visits to hotspot POIs. The proportion of visits to some
 POIs (e.g., Restaurants) remained stable during the social distancing
 period, while some POIs had an increased proportion of visits (e.g.,
 Grocery Stores). We also identified POIs with significant flux-in changes,
 showing that related businesses were greatly affected by social
 distancing.
description: SafeGraph provided the raw
 data: https://docs.safegraph.com/docs/weekly-patterns.
DOI: 10.5061/dryad.dz08kprvk
title: Data from: Virulence phenotypes result from interactions between pathogen ploidy and genetic background

description: Studying fungal virulence is often challenging and frequently depends on
 many contexts, including host immune status and pathogen genetic
 background. However, the role of ploidy has often been overlooked when
 studying virulence in eukaryotic pathogens. Since fungal pathogens,
 including the human opportunistic pathogen Candida albicans, can display
 extensive ploidy variation, assessing how ploidy impacts virulence has
 important clinical relevance. As an opportunistic pathogen, C. albicans
 causes non-lethal, superficial infections in healthy individuals, but
 life-threatening bloodstream infections in individuals with compromised
 immune function. Here, we determined how both ploidy and genetic
 background of C. albicans impacts virulence phenotypes in healthy and
 immunocompromised nematode hosts by characterizing virulence phenotypes in
 four near-isogenic diploid and tetraploid pairs of strains, which included
 both laboratory and clinical genetic backgrounds. We found that C.
 albicans infections decreased host survival and negatively impacted host
 reproduction, and we leveraged these two measures to survey both lethal
 and non-lethal virulence phenotypes across the multiple C. albicans
 strains. In this study, we found that regardless of pathogen ploidy or
 genetic background, immunocompromised hosts were susceptible to fungal
 infection compared to healthy hosts. Furthermore, for each host context,
 we found a significant interaction between C. albicans genetic background
 and ploidy on virulence phenotypes, but no global differences between
 diploid and tetraploid pathogens were observed.
DOI: 10.15139/s3/mc1eox
title: MAP-FGS Protocol Design

description: Documentation of the design, protocol, and training materials for the Multi-Country Assessment of Prevalence of Female Genital Schistosomiais (MAP-FGS) Study
DOI: 10.5061/dryad.mgqnk98x9
title: Genetic variation for upper thermal tolerance diminishes within and between populations with increasing acclimation temperature in Atlantic salmon

description: Populations may counteract lasting temperature changes or recurrent
 extremes through plasticity or adaptation. However, it remains
 underexplored how outbreeding, either naturally, unintentionally, or
 facilitated, may modify a local response potential and whether
 genotype-by-environment interactions or between-trait correlations can
 restrict this potential. We quantified population differences and
 outbreeding effects, within-population genetic variation, and plasticity
 of these, for thermal performance proxy traits using 32 pedigreed wild,
 domesticated, and wild-domesticated Atlantic salmon families reared under
 common-garden conditions. Following exposure to ambient cold (11.6°C) or
 ~4- and ~8-degree warmer summer temperatures, populations differed notably
 for body length and critical thermal maximum (CTmax) and for thermal
 plasticity of length, condition, and CTmax, but not for haematocrit.
 Line-cross analysis suggested mostly additive and some dominant
 outbreeding effects on means and solely additive outbreeding effects on
 plasticity. Heritability was detected for all traits. However, with
 increasing acclimation temperature, differences in CTmax between
 populations and CTmax heritability diminished, and CTmax breeding values
 re-ranked. Furthermore, CTmax and body size were negatively correlated at
 the genetic and phenotypic levels, and there was indirect evidence for a
 positive correlation between growth potential and thermal performance
 breadth for growth. Thus, population differences (including those between
 wild and domesticated populations) in thermal performance and plasticity
 may present a genetic resource in addition to the within-population
 genetic variance to facilitate, or impede, thermal adaptation. However,
 unfavourable genotype-by-environment interactions and negative
 between-trait correlations may generally hamper joint evolution in
 response to increase in average temperature and temporary extremes.
description: Described in manuscript
description: A read me file with column header descriptors is added.
DOI: 10.5061/dryad.n8pk0p2sm
title: Evolution of breeding plumages in birds: a multiple-step pathway to seasonal dichromatism in New World Warblers (Aves: Parulidae)

description: Many species of birds show distinctive seasonal breeding and nonbreeding
 plumages. A number of hypotheses have been proposed for the evolution of
 this seasonal dichromatism, specifically related to the idea that birds
 may experience variable levels of sexual selection relative to natural
 selection throughout the year. However, these hypotheses have not
 addressed the selective forces that have shaped molt, the underlying
 mechanism of plumage change. Here, we examined relationships between
 life-history variation, the evolution of a seasonal molt, and seasonal
 plumage dichromatism in the new world warblers (Aves: Parulidae), a family
 with a remarkable diversity of plumage, molt, and life history strategies.
 We used phylogenetic comparative methods and path analysis to understand
 how and why distinctive breeding and nonbreeding plumages evolve in this
 family. We found that color change alone poorly explains the evolution of
 patterns of biannual molt evolution in warblers. Instead, molt evolution
 is better explained by a combination of other life-history factors,
 especially migration distance and foraging stratum. We found that the
 evolution of biannual molt and seasonal dichromatism are decoupled, with a
 biannual molt appearing earlier on the tree, more dispersed across taxa
 and body regions, and correlating with separate life-history factors than
 seasonal dichromatism. This result helps explain the apparent paradox of
 birds that molt biannually but show breeding plumages that are identical
 to the nonbreeding plumage. We find support for a two-step process for the
 evolution of distinctive breeding and non-breeding plumages: that
 prealternate molt evolves primarily under selection for feather renewal,
 with seasonal color change sometimes following later. These results reveal
 how life history strategies and a birds’ environment act upon multiple and
 separate feather functions to drive the evolution of feather replacement
 patterns and bird coloration. 
description: See Manuscript.
DOI: 10.5061/dryad.xgxd254dm
title: A paraphyletic ‘Silesauridae’ as an alternative hypothesis for the initial radiation of ornithischian dinosaurs

description: Whereas ornithischian dinosaurs are well-known from Jurassic and
 Cretaceous deposits, deciphering the origin and early evolution of the
 group remains one of the hardest challenges for palaeontologists. So far,
 there are no unequivocal records of ornithischians from Triassic beds.
 Here, we present an alternative evolutionary hypothesis that suggests
 consideration of traditional ‘silesaurids’ as a group of low-diversity
 clades representing a stem group leading to core ornithischians (i.e.
 unambiguous ornithischians, such as Heterodontosaurus tucki). This is
 particularly interesting because it fills most of the ghost lineages that
 emerge from the Triassic. Following the present hypothesis, the lineage
 that encompasses the Jurassic ornithischians evolved from ‘silesaurids’
 during the Middle to early Late Triassic, while typical ‘silesaurids’
 shared the land ecosystems with their relatives until the Late Triassic,
 when the group completely vanished. Therefore, Ornithischia changes from
 an obscure to a well-documented clade in the Triassic, and is represented
 by records from Gondwana and Laurasia. Furthermore, according to the
 present hypothesis, Ornithischia was the first group of dinosaurs to adopt
 an omnivorous/herbivorous diet. However, this behavior was achieved as a
 secondary step instead of an ancestral condition for ornithischians, as
 the earliest member of the clade is a faunivorous taxon. This pattern was
 subsequently followed by sauropodomorph dinosaurs. Indeed, the present
 scenario favors the independent acquisition of an herbivorous diet for
 ornithischians and sauropodomorphs during the Triassic, whereas the
 previous hypotheses suggested the independent acquisition for
 sauropodomorphs, ornithischians, and ‘silesaurids’.
description: The "Müller_and_Garcia_(Biology_Letters).tnt" file is
 the morphological dataset in the format for TNT v1.1 software (http://www.lillo.org.ar/phylogeny/tnt/). It can be opened directly in the "File&gt;Open input file" option.
DOI: 10.5061/dryad.gqnk98sjx
title: Data from: Macroevolutionary integration of phenotypes within and across ant worker castes

description: Phenotypic traits are often integrated into evolutionary modules: sets of
 organismal parts that evolve together. In social insect colonies the
 concepts of integration and modularity apply to sets of traits both within
 and among functionally and phenotypically differentiated castes. On
 macroevolutionary timescales, patterns of integration and modularity
 within and across castes can be clues to the selective and ecological
 factors shaping their evolution and diversification. We develop a set of
 hypotheses describing contrasting patterns of worker integration and apply
 this framework in a broad (246 species) comparative analysis of major and
 minor worker evolution in the hyperdiverse ant genus Pheidole. Using
 geometric morphometrics in a phylogenetic framework, we inferred fast and
 tightly integrated evolution of mesosoma shape between major and minor
 workers, but slower and more independent evolution of head shape between
 the two worker castes. Thus, Pheidole workers are evolving as a mixture of
 intra- and inter-caste integration and rate heterogeneity. The decoupling
 of homologous traits across worker castes may represent an important
 process facilitating the rise of social complexity.
description: See text for details.
description: "Pheidole_Morphology_Data_03282019.csv" is the main
 data file in wide format, which connects specimen IDs to species identity
 and summarizes principal components. Aligned landmarks for the head based
 on semi-landmarks are included in "Aligned_Head_Major.TPS" and
 "Aligned_Head_Minor.TPS". Unaligned landmarks for the head and
 mesosoma based on only true landmarks are included in the other .tps
 files, and filenames indicate whether they are majors or minors, and the
 head or mesosoma. "Pheidole_Tree.phy" is the phylogeny used, in
 PHYLIP format.
DOI: 10.15468/dl.xq8gur
title: Occurrence Download

description: A dataset containing 568 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bobgunnia madagascariensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 568 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002445-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.prr4xgxjg
title: Learning agents in black-scholes financial markets

description: Black-Scholes (BS) is a remarkable quotation model for European option
 pricing in financial markets. Option prices are calculated using an
 analytical formula whose main inputs are strike (at which price to
 exercise) and volatility. The BS framework assumes that volatility remains
 constant across all strikes, however, in practice it varies. How do
 traders come to learn these parameters? We introduce natural agent-based
 models, in which traders update their beliefs about the true implied
 volatility based on the opinions of other traders. We prove exponentially
 fast convergence of these opinion dynamics using techniques from control
 theory and leader-follower models, thus providing a resolution between
 theory and market practices. We allow for two different models, one with
 feedback and one with an unknown leader.
description: No data were used. Only simulations were used.
DOI: 10.5061/dryad.rv15dv45m
title: Chromosome-level genome assembly of Chinese mitten crab (Eriocheir japonica sinensis)

description: The Chinese mitten crab (Eriocheir japonica sinensis) is one of the most
 popular breeding species of crab in China due to its high economic and
 nutritional value. However, earlier published genome assemblies of E. j.
 sinensis have been highly fragmented due to limited sequencing and
 assembly techniques. In this study, we performed high-coverage sequencing
 of the Chinese mitten crab using advanced high-through chromosome
 conformation capture (Hi-C) technology and anchored these Hi-C data to
 previously published contig-level genome assembly for chromosome
 construction. Thus, we successfully assembled the first chromosome-level
 reference genome of E. j. sinensis, which contained 72 chromosomes with a
 N50 length of 17.61 Mb. Evaluation results demonstrated a high degree of
 genomic connectivity and accuracy. Acquisition of the chromosome-level
 genome of E. j. sinensis not only provides a basis for the study of
 adaptive evolution in crabs by comparative genomics, but should also help
 in studies on the growth, development, and reproduction of the Chinese
 mitten crab.
DOI: 10.5061/dryad.fttdz08qf
title: Data from: Extremely widespread parthenogenesis and a trade-off between alternative forms of reproduction in mayflies (Ephemeroptera)

description: Studying alternative forms of reproduction in natural populations is of
 fundamental importance for understanding the costs and benefits of sex.
 Mayflies are one of the few animal groups where sexual reproduction
 co-occurs with different types of parthenogenesis, providing ideal
 conditions for identifying benefits of sex in natural populations. Here,
 we establish a catalogue of all known mayfly species capable of
 reproducing by parthenogenesis, as well as species unable to do so.
 Overall, 1.8% of the described species reproduce parthenogenetically,
 which is an order of magnitude higher than reported in other animal
 groups. This frequency even reaches 47.8% if estimates are based on the
 number of studied rather than described mayfly species, as reproductive
 modes have thus far been studied in only 17 out of 42 families. We find
 that sex is a more successful strategy than parthenogenesis (associated
 with a higher hatching success of eggs), with a trade-off between the
 hatching success of parthenogenetic and sexual eggs. This means that
 improving the capacity for parthenogenesis may come at a cost for sexual
 reproduction. Such a trade-off can help explain why facultative
 parthenogenesis is extremely rare among animals despite its potential to
 combine the benefits of sexual and parthenogenetic reproduction. We argue
 that parthenogenesis is frequently selected in mayflies in spite of this
 probable trade-off because their typically low dispersal ability and short
 and fragile adult life may frequently generate situations of mate
 limitation in females. Mayflies are currently clearly underappreciated for
 understanding the benefits of sex under natural conditions.
description: The species list was compiled by collecting information from a
 thorough search of the literature (review). Our survey combined with
 personal communications and observations generated a list of 136 mayfly
 species. When available for a given species, information on its
 geographical distribution, cytological mechanism of parthenogenesis and
 sex determination was included in the database (Appendix).
description: Acronyms and legends used in the database are define at the end
 of the File.
DOI: 10.5061/dryad.n2z34tmtn
title: Data from Effects of social experience, aggressiveness and comb size on contest success in male domestic fowl

description: The ability to dominate conspecifics and thereby gain access to resources
 depends on a number of traits and skills. Experience of dominance
 relationships during development is a potential source of learning such
 skills. We here study the importance of social experience, aggressiveness,
 and morphological traits for competitiveness in social interactions
 (winning duels) in male domestic fowl (Gallus gallus domesticus). We let
 males grow up either as a single (dominant) male or as an intermediately
 ranked male in a group of males, and measured their success in duels
 against different opponents. We found that single-raised males had lower
 competitive ability than group-raised males, and that aggression and comb
 size had positive effects on competitive ability. This indicates that
 experience of dominance interactions increases future success in duels. We
 similarly studied the consequences of growing up as a dominant or
 subordinate in a pair of males, finding no statistically significant
 effect of the dominance position on competitive ability. Finally, we found
 that males were consistent over time in competitive ability. We conclude
 that social experience increases competitive ability in male domestic
 fowl, but that certain behavioural and morphological characteristics have
 an equal or even stronger influence on duel outcomes.
DOI: 10.5061/dryad.cz8w9gj1d
title: Data from: Temporal dynamics of competitive fertilization in social groups of red junglefowl (Gallus gallus) shed new light on avian sperm competition

description: Studies of birds have made a fundamental contribution to elucidating sperm
 competition processes, experimentally demonstrating the role of individual
 mechanisms in competitive fertilisation. However, the relative importance
 of these mechanisms and the way in which they interact under natural
 conditions remain largely unexplored. Here, we conduct a detailed
 behavioural study of freely-mating replicate groups of red junglefowl,
 Gallus gallus, to predict the probability that competing males fertilise
 individual eggs over the course of 10-day trials. Remating frequently with
 a female and mating last increased a male’s probability of fertilisation,
 but only for eggs ovulated in the last days of a trial. Conversely, older
 males, and those mating with more polyandrous females, had consistently
 lower fertilisation success. Similarly, resistance to a male’s mating
 attempts, particularly by younger females, reduced fertilisation
 probability. After considering these factors, male social status, partner
 relatedness and the estimated state of a male extragonadal sperm reserves
 did not predict sperm competition outcomes. These results shed new light
 on sperm competition dynamics in taxa such as birds, with prolonged female
 sperm storage and staggered fertilisations.
description: Fully described in the paper.
description: This entry has three files:
 RSTB-2020-0081_dataset.csv - contains the necessary data to
 replicate all results in this study.
 RSTB-2020-0081_Rscript.R - contains the R code to reproduce
 results from the main body of the study, including Tables 1-2 and Figure
 1. RSTB-2020-0081_Rscript.html - an html file of the
 above-mentioned R code.
DOI: 10.5061/dryad.8kprr4xkj
title: Phosphate bound to calcareous sediments hamper skeletal development of juvenile coral

description: To test the hypothesis that terrestrial runoff affects the functions of
 calcareous sediments in coral reefs and hampers the development of corals,
 we analysed calcareous sediments with different levels of bound phosphate,
 collected from reef areas of Okinawajima, Japan. We confirmed that
 phosphate bound to calcareous sediments were readily released into ambient
 seawater, resulting in much higher concentrations of phosphorous in
 seawater from heavily polluted areas (4.3 to 19.0 µM as compared
 with &lt; 0.096 μM in natural ambient seawater). Additionally, we
 examined the effect of phosphate released from calcareous sediments on the
 development of Acropora digitifera coral juveniles. We
 found that high phosphate concentrations in seawater clearly inhibit
 skeletal formation of coral juveniles. Our results demonstrate that
 calcareous sediments in reef areas play a crucial role in mediating the
 impact of terrestrial runoff on corals by storing and releasing
 phosphate in seawater.