cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tx95x69vr
title: Shifts in sexual dimorphism across a mass extinction in ostracods: implications for sexual selection as a factor in extinction risk

description: Sexual selection often favors investment in expensive sexual traits that
 help individuals compete for mates. In a rapidly changing environment,
 however, allocation of resources to traits related to reproduction at the
 expense of those related to survival may elevate extinction risk.
 Empirical testing of this hypothesis in the fossil record, where
 extinction can be directly documented, is largely lacking. The
 rich fossil record of cytheroid ostracods offers a unique study system in
 this context: the male shell is systematically more elongate than that of
 females, and thus the sexes can be distinguished, even in
 fossils. Using mixture models to identify sex clusters from size
 and shape variables derived from the digitized valve outlines of adult
 ostracods, we estimated sexual dimorphism in ostracod species before and
 after the Cretaceous/Paleogene mass extinction in the United States
 Coastal Plain. Across this boundary, we document a substantial shift in
 sexual dimorphism, driven largely by a pronounced decline in the taxa with
 dimorphism indicating both very high and very low male investment. The
 shift away from high male investment, which arises largely from
 evolutionary changes within genera that persist through the extinction,
 parallels extinction selectivity previously documented during the Late
 Cretaceous under a background extinction regime. Our results suggest that
 sexual selection and the allocation of resources towards survival versus
 reproduction may be an important factor for species extinction during both
 background and mass extinctions. 
description: Ostracode specimens were imaged and their outlines digitized.
  Size was measured as the area enclosed by the valve outline and shape as
 the ratio of major tominor axis of the best-fit ellipse to the outline.
  Mixture models were used to find male and female clusters, and sexual
 dimorphism was computed as the difference between male and female means in
 size and shape.
DOI: 10.5061/dryad.zpc866t6n
title: Divergence, gene flow, and speciation in eight lineages of trans-Beringian birds

description: Determining how genetic diversity is structured between populations that
 span the divergence continuum from populations to biological species is
 key to understanding the generation and maintenance of biodiversity. We
 investigated genetic divergence and gene flow in eight lineages of birds
 with a trans-Beringian distribution, where Asian and North American
 populations have likely been split and reunited through multiple
 Pleistocene glacial cycles. Our study transects the speciation process,
 including eight pairwise comparisons in three orders (ducks, shorebirds,
 and passerines) at population, subspecies, and species levels. Using
 ultraconserved elements (UCEs), we found that these lineages represent
 conditions from slightly differentiated populations to full biological
 species. Although allopatric speciation is considered the predominant mode
 of divergence in birds, all of our best divergence models included gene
 flow, supporting speciation with gene flow as the predominant mode in
 Beringia. In our eight lineages, three were best described by a
 split-migration model (divergence with gene flow), three best fit a
 secondary-contact scenario (isolation followed by gene flow), and two
 showed support for both models. The lineages were not evenly distributed
 across a divergence space defined by gene flow (M) and differentiation
 (FST), instead forming two discontinuous groups: one with relatively
 shallow divergence, no fixed SNPs, and high rates of gene flow between
 populations; and the second with relatively deeply divergent lineages,
 multiple fixed SNPs, and low gene flow. Our results highlight the
 important role that gene flow plays in avian divergence in Beringia.
description: Details on data production and bioinformatics pipeline are givien
 in the cited paper.
description: Reference sequences combine multiple individuals, as detailed in
 the paper. SNP datasets labeled "*_allSNPs.vcf" files are
 complete for all individuals (100% coverage with both alleles called). SNP
 datasets labeled "*_thinnedSNPs.vcf" files are thinned to one
 SNP per locus and Z-linked loci have been removed.
DOI: 10.5061/dryad.nzs7h44pk
title: Video recordings of strepsipterans-parasitized and non-strepsipteran-parasitized bees flower-visiting behaviour

description: Data consists mostly of strepsipterans-parasitized and
 non-strepsipteran-parasitized bees flower-visiting behaviour
 on Hydrangea serrata inflorescences.  We
 analysed the recorded video by comparing time spent on an inflorescence
 between parasitized and unparasitized bees, Lasioglossum apristum
 and by comparing each bee's behaviour on the flower. We defined four
 flower-visiting behavioural units: (1) walking on flowers, (2) touching
 antennae and mouth to the flower, (3) collecting pollen, and (4) bending
 the abdomen downward and pressing the dorsal abdomen against the flower.
 We also observed whether the mouth of the bee touched a pistil or its
 base, where nectar might be found. Among these four behavioural units,
 unit 1 is incompatible with the other behavioural units, whereas units 2
 and 3 and units 2 and 4 are compatible pairs and often occurred
 simultaneously. Units 3 and 4 never occur in the same bee. The behavioural
 repertoires of parasitized and unparasitized bees and the time spent on
 each behavioural unit were determined from video frames. We measured the
 cumulative time spent on each behavioural unit by each flower-visiting bee
 and then compared how parasitized and unparasitized bees allocated their
 flower-visiting time to the behaviour units.
DOI: 10.5061/dryad.95x69p8h7
title: Predictive ability of perennial ryegrass spaced-plant nurseries for turfgrass and seed production swards in Minnesota

description: Turf-type perennial ryegrass (Lolium perenne L.) success depends both on
 adequate turfgrass quality and economic seed yield. In most breeding
 programs, spaced plants are the initial unit of selection in which
 observations of related individuals dictate selections of superior
 germplasm for further testing. As such, spaced plants must be predictive
 of both seed production and turfgrass growing environments. This study
 investigated the effectiveness of both standard (3 plants m-2) and
 competitive (23 plants m-2) spaced-plant nurseries as selection
 environments with respect to two sward environments as well as employed a
 novel image analysis technique for several key traits. Seed production,
 turfgrass, and the two spaced-plant growing environments were tested at
 two locations in Minnesota. Turfgrass quality traits were measured in 2017
 and 2018 and seed production traits were measured in 2018. Automated image
 analysis was able to predict the traditional visual scoring values at both
 locations for crown rust severity (rp &gt; 0.79, P &lt; 0.001),
 winter injury (rp &gt; 0.89, P &lt; 0.001), and texture (rp
 &gt; 0.88, P &lt; 0.001). Increasing competition in between spaced
 plants altered plant phenotype and improved accuracy for vegetative
 biomass, crown rust severity, seed yield, and at one location, turfgrass
 quality. There was no benefit of increasing competition for several traits
 such as genetic color, fertile tillers, and spikelet number. While the
 competitive design was not useful for all traits, from a feasibility
 standpoint the competitive design took up less space and often made
 measurements and observations much easier for bunch-type grasses.
description: The attached file contains the metadata explaining haw data is
 organized and was collected.
DOI: 10.5061/dryad.cnp5hqc2s
title: Data from: The evolution of sexually dimorphic cuticular hydrocarbons in blowflies (Diptera: Calliphoridae)Cuticular hydrocarbons of Australian Chrysomya (Diptera: Calliphoridae)

description: Cuticular hydrocarbons (CHCs) are organic compounds found on the cuticles
 of all insects which can act as close-contact pheromones, while also
 providing a hydrophobic barrier to water loss. Given their widespread
 importance in sexual behaviour and survival, CHCs have likely contributed
 heavily to the adaptation and speciation of insects. Despite this, the
 patterns and mechanisms of their diversification have been studied in very
 few taxa. This dataset constitutes the first of CHCs in
 Australian Chrysomya blowflies. The data
 demonstrate that blowflies express an exceptional diversity of CHCs, which
 have diversified in a non-phylogenetic and punctuated manner, are
 species-specific, and sexually dimorphic.
DOI: 10.5061/dryad.rjdfn2z82
title: Competitive advantage of rare behaviors induces adaptive diversity rather than social conformity in skill learning

description: Recent studies have emphasized the role of social learning and cultural
 transmission in promoting conformity and uniformity in animal groups, but
 little attention has been given to the role of negative
 frequency-dependent learning in impeding conformity and promoting
 diversity instead. Here we show experimentally that under competitive
 conditions, that are common in nature, social foragers (although capable
 of social learning) are likely to develop diversity in foraging
 specialization rather than uniformity. Naïve house sparrows that were
 introduced into groups of foraging specialists did not conform to the
 behaviour of the specialists but, rather, learned to use the alternative
 food-related cues, thus forming groups of complementary specialists. We
 further show that individuals in such groups may forage more effectively
 in diverse environments. Our results suggest that when the benefit from
 socially acquired skills diminishes through competition in a negative
 frequency-dependent manner, animal societies will become behaviourally
 diverse rather than uniform.
DOI: 10.15468/dl.fgrg6a
title: Occurrence Download

description: A dataset containing 289 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((159.00094 -48.95058,200.03306 -48.95058,200.03306 -32.54476,159.00094 -32.54476,159.00094 -48.95058))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Eurhynchium praelongum"
 ]
}

 The dataset includes 289 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002470-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.r2280gbb7
title: The Alginate Immobilization of Metabolic Enzymes (AIME) platform retrofits an estrogen receptor transactivation assay with metabolic competence

description: The U.S. EPA Endocrine Disruptor Screening Program utilizes data across
 the ToxCast/Tox21 high-throughput screening (HTS) programs to evaluate the
 biological effects of potential endocrine active substances (EAS). A
 potential limitation to the use of in vitro assay data in regulatory
 decision-making is the lack of coverage for xenobiotic metabolic
 processes. Both hepatic- and peripheral-tissue metabolism can yield
 metabolites that exhibit greater activity than the parent compound
 (bioactivation) or are inactive (bioinactivation) for a given biological
 target. Interpretation of biological effect data for both putative EAS, as
 well as other chemicals, screened in HTS assays may benefit from the
 addition of xenobiotic metabolic capabilities to decrease the uncertainty
 in predicting potential hazards to human health. The objective of this
 study was to develop an approach to retrofit existing HTS assays with
 hepatic metabolism. The Alginate Immobilization of Metabolic Enzymes
 (AIME) platform encapsulates hepatic S9 fractions in alginate microspheres
 attached to 96-well peg lids. Functional characterization across a panel
 of reference substrates for phase I cytochrome P450 enzymes revealed
 substrate depletion with expected metabolite accumulation. Performance of
 the AIME method in the VM7Luc estrogen receptor (ER) transactivation assay
 was evaluated across 15 reference chemicals and 48 test chemicals that
 yield metabolites previously identified as ER active or inactive. The
 results demonstrate the utility of applying the AIME method for
 identification of false positive and false negative target assay effects,
 reprioritization of hazard based on metabolism-dependent bioactivity, and
 enhanced in vivo concordance with the rodent uterotrophic bioassay.
 Integration of the AIME metabolism method may prove useful for future
 biochemical and cell-based HTS applications.
DOI: 10.5061/dryad.t4b8gtj04
title: Source data for: Presynaptic NMDARs cooperate with local spikes toward GABA release from the reciprocal olfactory bulb granule cell spine

description: In the rodent olfactory bulb the smooth dendrites of the principal
 glutamatergic mitral cells (MCs) form reciprocal dendrodendritic synapses
 with large spines on GABAergic granule cells (GC), where unitary release
 of glutamate can trigger postsynaptic local activation of voltage-gated
 Na+-channels (Navs), i.e. a spine spike. Can such single MC input evoke
 reciprocal release? We find that unitary-like activation via two-photon
 uncaging of glutamate causes GC spines to release GABA both synchronously
 and asynchronously onto MC dendrites. This release indeed requires
 activation of Navs and high-voltage-activated Ca2+-channels (HVACCs), but
 also of NMDA receptors (NMDAR). Simulations show temporally overlapping
 HVACC- and NMDAR-mediated Ca2+-currents during the spine spike, and
 ultrastructural data prove NMDAR presence within the GABAergic presynapse.
 The cooperative action of presynaptic NMDARs allows to implement
 synapse-specific, activity-dependent lateral inhibition and thus could
 provide an efficient solution to combinatorial percept synthesis in a
 sensory system with many receptor channels.
description: electrophysiology: whole cell recording of evoked inhibitory
 currents in voltage clamp from mitral cells in acute brain slices of
 juvenile rats stimulation: two-photon uncaging of
 glutamate onto the reciprocal granule cell spines, guided by two-color
 two-photon imaging of mitral cell dendrites and granule cell spines (in
 VGAT-Venus rats) processing: IGOR, Excel; the provided
 data contain all that is shown in the figures (example traces, cumulative
 data sets) but not every single experiment simulations:
 NEURON/Python code for model and robustness testing; all files without
 prefix "Fig" are part of the simulation code
 ultrastructure: analyses were made on pre-existing sections with
 immunogold labelling of NMDA receptors; cumulative data are
 provided
description: There is a Readme file enclosed with the simulation source
 code.
DOI: 10.5061/dryad.wwpzgmsgx
title: The phantom chorus: birdsong boosts human well-being in protected areas

description: Spending time in nature is known to benefit human health and well-being,
 but evidence is mixed as to whether biodiversity or perceptions of
 biodiversity contribute to these benefits. Perhaps more importantly,
 little is known about the sensory modalities by which humans perceive
 biodiversity and obtain benefits from their interactions with nature.
 Here, we used a “phantom bird song chorus” consisting of hidden speakers
 to experimentally increase audible birdsong biodiversity during “on” and
 “off” (i.e., ambient conditions) blocks on two trails to study the role of
 audition in biodiversity perception and self-reported well-being among
 hikers. Hikers exposed to the phantom chorus reported higher
 levels of restorative effects compared to those that experienced ambient
 conditions on both trails; however, increased restorative effects were
 directly linked to the phantom chorus on one trail and indirectly linked
 to the phantom chorus on the other trail through perceptions of avian
 biodiversity. Our findings add to a growing body of evidence linking
 mental health to nature experiences and suggest that audition is an
 important modality by which natural environments confer restorative
 effects. Finally, our results suggest that maintaining or improving
 natural soundscapes within protected areas may be an important component
 to maximizing human experiences.
description: This study took place in Boulder Open-Space and Mountain Parks,
 Boulder, Colorado. Data collection included: visitor surveys, point counts
 of birds and acoustic recordings to capture ambient sound
 levels.
description: Three datasets and associated ReadMe files are included in this
 submission: 1) Survey responses from hikers.
 2) Data reflecting bird species richness without the phantom
 chorus, plus bird species richness with the inclusion of those used in the
 phantom chorus. 3) Hourly sound level data (L50,
 A-weighted dB). Ninty-two hourly sound level values from Gregory Canyon
 were removed from the original dataset because recording units had
 different settings, and thus were not directly comparable to the
 others.
DOI: 10.5061/dryad.vx0k6djpg
title: Generalized hidden Markov models for phylogenetic comparative datasets

description: Hidden Markov models (HMM) have emerged as an important tool for
 understanding the evolution of characters that take on discrete states.
 Their flexibility and biological sensibility make them appealing for many
 phylogenetic comparative applications. Previously available packages
 placed unnecessary limits on the number of observed and hidden states that
 can be considered when estimating transition rates and inferring ancestral
 states on a phylogeny. To address these issues, we expanded the
 capabilities of the R package corHMM to handle n-state and n-character
 problems and provide users with a streamlined set of functions to create
 custom HMMs for any biological question of arbitrary complexity. We show
 that increasing the number of observed states increases the accuracy of
 ancestral state reconstruction. We also explore the conditions for when an
 HMM is most effective, finding that an HMM is an appropriate model when
 the degree of rate heterogeneity is moderate to high. Finally, we
 demonstrate the importance of these generalizations by reconstructing the
 phyllotaxy of the ancestral angiosperm flower. Partially contradicting
 previous results, we find the most likely state to be a whorled perianth,
 whorled androecium, whorled gynoecium. The difference between our analysis
 and previous studies was that our modeling explicitly allowed for the
 correlated evolution of several flower characters.
description: CorHMMSimsData: includes std_rates (which compares 2,3,4 state
 models), state-process-diff (results of the state-dependent model fits),
 param-process-bias (results of the parameter-process bias model
 fits) CorHMMCaseStudyDataAndResults: includes the data
 necessary and model fits from the case study
 CorHMMScripts: the scripts needed to recreate our simulations,
 figures, and analysis
DOI: 10.15468/dl.595htu
title: Occurrence Download

description: A dataset containing 90 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Brownea multijuga",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 90 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002472-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.g1jwstqp3
title: Variation in frequency of plastid RNA editing within Adiantum (Pteridaceae) implies rapid evolution in fern plastomes

description: Premise Recent advances in studies of plant RNA editing have demonstrated
 that the number of editing sites can vary widely among large taxonomic
 groups (orders, families). Yet, very little is known about intrageneric
 variation in frequency of plant RNA editing, and no study has been
 conducted in ferns. Methods We determined plastid RNA editing counts for
 two species of Adiantum (Pteridaceae), A. shastense and A. aleuticum, by
 implementing a pipeline that integrated read mapping and SNP calling
 software to identify RNA editing sites. We then compared the edits found
 in A. aleuticum and A. shastense with previously published edits from A.
 capillus-veneris by generating alignments for each plastid gene. Results
 We found direct evidence for 505 and 509 plastid RNA editing sites in A.
 aleuticum and A. shastense, respectively, compared with 350 sites in A.
 capillus-veneris. We observed striking variation in the number and
 location of the RNA editing sites among the three species, with reverse
 (U-to-C) editing sites showing a higher degree of conservation than
 forward (C-to-U) sites. Additionally, sites involving start and stop
 codons were highly conserved. Conclusions Variation in RNA editing
 frequency observed within Adiantum implies that RNA editing sites can be
 rapidly gained or lost throughout evolution. However, varying degrees of
 conservation between both C-to-U and U-to-C sites and sites in start or
 stop codons, versus other codons, hints at the likely independent origin
 of both types of edits and a potential selective advantage conferred by
 RNA editing.
description: Adiantum shastense and Adiautum aleuticum editing sites were
 identified as described in Fauskee et al., 2020. For methods involving the
 identification of RNA editing sites in Adiantum capillus-verneris see Wolf
 et al., 2003.
DOI: 10.5061/dryad.4qrfj6q7z
title: Data from: Between predators and parasitoids: complex interactions among shelter traits, predation, and parasitism in a shelter-building caterpillar community

description: Shelter building is widespread in the animal world and such shelters often
 influence the success of their builders. Shelters built by caterpillars
 influence the likelihood of attacks by natural enemies, but how particular
 shelter traits influence caterpillar survival is not known. Furthermore,
 the differential effects of certain shelter traits on some natural
 enemies, such as predators, may lead to “enemy-free space” for other
 natural enemies (parasitoids). The parasitoid enemy-free space hypothesis
 has not been directly tested for shelter-building caterpillars. To
 understand how shelter traits influence caterpillar survival, shelter
 traits, predation, and parasitism were measured simultaneously for 24
 caterpillar morphospecies (1465 caterpillars) in a tropical dry forest and
 analyzed in a phylogenetic context. Shelter type, shelter openness, and
 whether shelters accumulated frass had different amounts of phylogenetic
 signal, with frass accumulation displaying the most and shelter openness
 the least. All three traits affected the frequency with which caterpillar
 species experienced predation. Predation was elevated in two shelter types
 (leaf folds and leaf rolls) compared to cut-and-fold shelters.
 Combinations of shelter openness and frass accumulation also affected
 predation, with closed frass-free shelters having the lowest predation and
 closed frass-filled shelters having the highest. Parasitism was not
 affected by shelter traits but was strongly correlated with evolutionary
 history and negatively correlated with predation. These results confirm a
 trade-off between predation and parasitism and demonstrate that predation
 can be more frequent than parasitism. Different shelter types result in
 different amounts of predation. These defensive shelter traits and their
 effectiveness also vary phylogenetically. Together, our results suggest
 that predation and parasitism determine the success of shelter-building
 caterpillars, and that success is a function of the specific shelter they
 construct. More generally, our results demonstrate the importance of
 considering the effects of defensive traits on both predators and
 parasitoids when investigating interactions between herbivores and natural
 enemies.