cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.95x69p8nt
title: Data for: Negative but antagonistic effects of neonicotinoid insecticides and ectoparasitic mites Varroa destructor on Apis mellifera honey bee food glands

description: Collaborative brood care by workers is essential for the functionality of
 eusocial honey bee, Apis mellifera, colonies. The hypopharyngeal
 food glands of workers play a crucial role in this context. Even though
 there is consensus that ubiquitous ectoparasitic mites Varroa destructor
 and widespread insecticides, such as neonicotinoids, are major stressors
 for honey bee health, their impact alone and in combination on the feeding
 glands of workers is poorly understood. Here, we show that both V.
 destructor and neonicotinoids reduce hypopharyngeal gland size, thereby
 potentially compromising collaborative brood care in colonies. In a
 fully-crossed laboratory experiment, the impact of mites and the
 neonicotinoids thiamethoxam and clothianidin alone and in combination on
 workers were evaluated. While the neonicotinoids did not impact survival
 and emergence body mass, the data confirm that V. destructor
 reduces both. Even though the interactions between both stressors were
 antagonistic and neutral, the clear detrimental effects of both stressors
 alone and in combination on worker longevity and food glands are
 remarkable. Besides reduced worker longevity, impaired brood care provided
 by workers exposed to V. destructor and neonicotinoids could be
 detrimental for honey bee colony functionality. Our findings highlight a
 mechanism to explain honey bee colonies losses globally.
description: This data set was collected during a semi-field experiment. The
 data were noted down on paper before being scanned and entered in
 Excel. 
description: Excel
DOI: 10.15468/dl.xk8quq
title: Occurrence Download

description: A dataset containing 597 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "TaxonKey is Ephemera glaucops"
 ]
}

 The dataset includes 597 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003200-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.xpnvx0kjk
title: Stability of patch-turnover relationships under equilibrium and nonequilibrium metapopulation dynamics driven by biogeography

description: Two controversial tenets of metapopulation biology are whether patch
 quality and the surrounding matrix are more important to turnover
 (colonization and extinction) than biogeography (patch area and isolation)
 and whether factors governing turnover during equilibrium also dominate
 nonequilibrium dynamics. We tested both tenets using 18 years of surveys
 for two secretive wetland birds, black and Virginia rails, during (1) a
 period of equilibrium with stable occupancy and (2) after drought and
 arrival of West Nile Virus (WNV), which resulted in WNV infections in
 rails, increased extinction and decreased colonization probabilities
 modified by WNV, nonequilibrium dynamics for both species, and occupancy
 decline for black rails. Area (primarily) and isolation (secondarily)
 drove turnover during both stable and unstable metapopulation dynamics,
 greatly exceeding the effects of patch quality and matrix conditions.
 Moreover, slopes between turnover and patch characteristics changed little
 between equilibrium and nonequilibrium, confirming the overriding
 influences of biogeographic factors on turnover.
description: These data comprise annual surveys
 for the occurrence of black and Virginia Rails at 307 wetland patches from
 2002–2019, characteristics of the patches and the matrix surrounding the
 patches, the number of rails captured and the proportion that tested
 seropositive for West Nile Virus from 2008–2013, and annual climatic
 conditions and West Nile Virus index measures for each year of
 study.
description: Program R (open source): All R files have been placed on
 Zenodo Program Presence (freeware)
DOI: 10.6078/d1zx4s
title: Data and code for: Plumage balances camouflage and thermoregulation in Horned Larks (Eremophila alpestris)

description: Animal coloration serves many biological functions and must therefore
 balance potentially competing selective pressures. For example, many
 animals have camouflage in which coloration matches the visual background
 that predators scan for prey. However, different colors reflect different
 amounts of solar radiation and may therefore have thermoregulatory
 implications as well. In this study, we examined geographic variation in
 dorsal patterning, coloration, and solar reflectance among Horned Larks
 (Eremophila alpestris) of the western United States. We found that plumage
 brightness was positively associated with soil granularity, aridity, and
 temperature. Plumage redness—both in terms of saturation (i.e., chroma)
 and hue—was positively associated with soil redness and temperature, while
 plumage patterning was positively associated with soil granularity.
 Together, these plumage-environment associations support both background
 matching and Gloger’s Rule, a widespread ecogeographic pattern in animal
 coloration. We also constructed thermoregulatory models that estimated
 cooling benefits provided by solar reflectance profiles of the dorsal
 plumage of each specimen based on the collection site. We found increased
 cooling benefits in hotter, more arid environments. Finally, cooling
 benefits were positively associated with residual brightness, such that
 individuals that were brighter than expected based on environmental
 conditions also had higher cooling benefits, suggesting a tradeoff between
 camouflage and thermoregulation. Together, these data suggest that natural
 selection has balanced camouflage and thermoregulation in Horned Larks and
 illustrate how multiple competing evolutionary pressures may interact to
 shape geographic variation in adaptive phenotypes.
description: This Dryad repository includes various data types and code to
 execute analyses associated with the manuscript titled "Plumage
 balances camouflage and thermoregulation in Horned Larks (Eremophila
 alpestris)."
description: The scripts included in this Dryad repository are to be run with
 R and Python.
DOI: 10.5061/dryad.mkkwh7137
title: Data for: Open COVID Trials (OCT) Project

description: The COVID-19 pandemic has brought substantial attention to the systems
 used to communicate biomedical research. In particular, the need to
 rapidly and credibly communicate research findings has led many
 stakeholders to encourage researchers to adopt open science practices such
 as posting preprints and sharing data. To examine the degree to which this
 has led to the actual adoption of such practices, we examined the
 “openness” of a sample of 539 published papers describing the results of
 randomized controlled trials testing interventions to prevent or treat
 COVID-19. The majority (56%) of the papers in this sample were free to
 read at the time of our investigation and 23.56% were preceded by
 preprints. However, there is no guarantee that the papers without an open
 license will be available without a subscription in the future, and only
 49.61% of the preprints we identified were linked to the subsequent
 peer-reviewed version. Of the 331 papers in our sample with statements
 identifying if (and how) related datasets were available, only a paucity
 indicated that data was available in a repository that facilitates rapid
 verification and reuse. Our results demonstrate that, while progress has
 been made, there is still a significant mismatch between aspiration and
 actual practice in the adoption of open science in an important area of
 the COVID-19 literature.
description: Data was pulled from publicly available sources (e.g. Unpaywall)
 and from manual inspection of the papers themselves. Instructions for
 members of the research team have been uploaded to Protocols.io - https://doi.org/10.17504/protocols.io.x54v9jx7zg3e
description: The data files are stored in an open file format and should be
 readable by most data analysis/visualization tools.
DOI: 10.5061/dryad.qfttdz0kv
title: Large flowers can be short-lived: Insights from a high Andean cactus

description: Long-lived and large flowers signify high floral maintenance costs.
 Species of arid/semiarid climates with large flowers are expected to have
 short flower lifespans and pollination-induced flower longevity in order
 to curb high floral water and other maintenance costs. We explored the
 context-dependent large flower/short flower longevity hypothesis in
 Eriosyce curvispina (Cactaceae), a large-flowered species of the semi-arid
 central Chilean Andes. We determined breeding system, flower visitation
 rates, and open-pollination fruit set and quantified floral water content.
 In a temperature-controlled field manipulative experiment, we measured
 potential flower longevity and tested for the presence of
 pollination-induced floral senescence. We measured the timespan of the
 complete flower cycle defined as from when the flowers began to open to
 when they were totally closed, and the timespan of fully open flowers
 defined as from when they were totally open until they began to close. The
 potential flower lifespan averaged 2.8 days (complete flower cycle) to 2.3
 days (fully open flower). The complete flower cycle lasted 21.5 hrs, but
 flowers were fully open for only 10.1 hrs across days. Flower longevity in
 days was far shorter than reported for a large sample of species in the
 area. No evidence was found for pollination-induced flower senescence as a
 complementary means for reducing floral maintenance costs. Eriosyce
 curvispina is self-incompatible and abundantly pollinated by two
 megachilid bees. The level of pollen limitation (L=0.36) was lower than
 the average reported for self-incompatible angiosperms. Thus, the short
 flower lifespan in E. curvispina is not an impediment to high fruit set.
 Flowers contain &gt;5 g of water of which &gt;2 g resides in
 &gt;40 petaloid tepals. The amount of water is far higher than in
 another large-flowered, non-cactus species in the area, but only about 15%
 of that reported in the giant sahuaro cactus, which has larger flowers
 than E. curvispina.
description: We determined breeding system, flower visitation rates, and
 open-pollination fruit set and quantified floral water content. In a
 temperature-controlled field manipulative experiment, we measured
 potential flower longevity and tested for the presence of
 pollination-induced floral senescence. We measured the timespan of the
 complete flower cycle defined as from when the flowers began to open to
 when they were totally closed, and the timespan of fully open flowers
 defined as from when they were totally open until they began to close. For
 details see the Methods section in the main text.
DOI: 10.15468/dl.svqub8
title: Occurrence Download

description: A dataset containing 918 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((31.83132 34.34103,34.56387 34.48404,34.75828 35.73986,32.10133 35.52918,31.83132 34.34103))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Araneae"
 ]
}

 The dataset includes 918 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003199-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.rv15dv49q
title: Variant Call File (VCF) for Genome-wide polymorphism and genic selection in feral and domesticated lineages of Cannabis sativa

description: A comprehensive understanding of the degree to which genomic variation is
 maintained by selection versus drift and gene flow is lacking in many
 important species such as Cannabis sativa (C.
 sativa), one of the oldest known crops to be cultivated by humans
 worldwide. We generated whole genome resequencing data across diverse
 samples of feralized (escaped domesticated lineages) and domesticated
 lineages of C. sativa. We performed analyses to examine
 population structure, and genome wide scans for FST, balancing selection,
 and positive selection. Our analyses identified evidence for
 sub-population structure and further support the Asian origin hypothesis
 of this species. Feral plants sourced from the U.S. exhibited broad
 regions on chromosomes 4 and 10 with high ?̅ST which may
 indicate chromosomal inversions maintained at high frequency in this
 sub-population. Both our balancing and positive selection analyses
 identified loci that may reflect differential selection for traits favored
 by natural selection and artificial selection in feral versus domesticated
 sub-populations. In the U.S. feral sub-population, we found six loci
 related to stress response under balancing selection and one gene involved
 in disease resistance under positive selection, suggesting local
 adaptation to new climates and biotic interactions. In the marijuana
 sub-population, we identified the gene SMALLER
 TRICHOMES WITH VARIABLE BRANCHES 2 to be under positive
 selection which suggests artificial selection for increased
 tetrahydrocannabinol yield. Overall the data generated, and results
 obtained from our study help to form a better understanding of the
 evolutionary history in C. sativa.
DOI: 10.6078/d1v41s
title: Environment and geography drive diversification within the Amazon tree, Protium subserratum

description: The lowland Amazon rainforest houses some of the greatest tree diversity
 on earth. While the vast majority of these species are rare, a small
 number are common and widespread. Several recent studies have found that
 some dominant species are actually composed of multiple independently
 evolving lineages. However, the extent to which widespread and common
 Amazonian tree species actually include multiple clades, each on their own
 unique evolutionary trajectory, is unknown. Here we investigate
 the extent to which lineage divergence may be occurring
 within Protium subserratum (Burseraceae), a common and widespread
 tree species that is monophyletic with populations exhibiting genotypic
 and phenotypic differences associated with environment and geography.
 Utilizing a combination of phylogenomic and population genomic methods
 with sampling from across the range using herbarium specimens, we found
 that P. subserratum contains at least eight distinct
 clades defined by geography and environment. Specialization onto
 white-sand soils has evolved independently at least two times within the
 species; however, phenotype is not correlated with soil type. Finally,
 cryptic diversity at the base of the Andes is associated with elevational
 shifts. Together these results lend support to the hypothesis that common
 and widespread Amazonian species may contain multiple, independently
 evolving lineages.
DOI: 10.5061/dryad.xpnvx0kjm
title: Dataset for: The redlegged earth mite draft genome provides new insights into pesticide resistance evolution and demography in its invasive Australian range

description: Data and analyses for Thia et al. "The redlegged earth mite draft
 genome provides new insights into pesticide resistance evolution and
 demography in its invasive Australian range" submitted
 to Journal of Evolutionary Biology. This repository comprises
 data and scripts used to replicate the analyses in this paper. The goals
 of this study were to: (1) assemble a draft reference genome
 for Halotydeus destructor; (2) perform a comparative analysis of
 acetylcholinesterase genes among different agricultural arthropod pests;
 (3) characterise the population genetic patterns among
 Australian H. destructor populations; and (4) perform demographic
 modelling to understand the evolutionary relationships between eastern and
 western populations of H. destructor in Australia.
description: Genome assembly for <em>Halotydeus destructor
 </em>was perform using a combination of PacBio long-reads and
 Illumina short-reads from a single population sourced from Wantirna South,
 Victoria, Australia. Annotation was performed using RNAseq Illumina
 short-reads from populations sourced in Western Australia. The genome has
 been submitted to GenBank: Assembly, ASM2275052v1; Genome,
 GCA_022750525.1<strong>.</strong>
 Comparative analyses used a variety of arthropod pest genomes
 sourced from GenBank. Acetylcholinesterase genes
 (<em>ace</em>) were extracted and these compared to those
 of <em>H. destructor</em>. Population
 genomics of Australian <em>H. destructor</em> used pool-seq
 Illumina short-reads from populations sampled in Western Australian
 (western populations) and Victoria (eastern populations). Population
 structure among these populations, and diversity within these populations,
 was estimated. Demographic analyses were performed
 using the forward-in-time simulator, <em>dadi</em>. We
 modelled the invasion of <em>H. destructor </em>into Australia
 and the split between eastern and western populations.
description: All data/script descriptions, and details for executing the
 analyses, are outlined in the README file,
 "README_Thia_2022_JEB.pdf".
DOI: 10.5061/dryad.wstqjq2q5
title: Evolutionary models demonstrate rapid and adaptive diversification of Australo-Papuan pythons

description: Lineages may diversify when they encounter available ecological niches.
 Adaptive divergence by ecological opportunity often appears to follow the
 invasion of a new environment with open ecological space. This
 evolutionary process is hypothesized to explain the explosive
 diversification of numerous Australian vertebrate groups following the
 collision of the Eurasian and Australian plates 25 million years ago. One
 of these groups is the pythons, which demonstrate their greatest
 phenotypic and ecological diversity in Australo-Papua (Australia and New
 Guinea). Here, using an updated and near complete time-calibrated
 phylogenomic hypothesis of the group, we show that following invasion of
 this region, pythons experienced a sudden burst of speciation rates
 coupled with multiple instances of accelerated phenotypic evolution in
 head and body shape and body size. These results are consistent with
 adaptive radiation theory with an initial rapid niche filling phase and
 later slow-down approaching niche saturation. We discuss these findings in
 the context of other Australo-Papuan adaptive radiations and the
 importance of incorporating adaptive diversification systems that are not
 extraordinarily species-rich but ecomorphologically diverse to understand
 how biodiversity is generated.
DOI: 10.5061/dryad.vmcvdncwt
title: Doublecortin and JIP3 are neural-specific counteracting regulators of dynein-mediated retrograde trafficking

description: Mutations in the microtubule (MT)-binding protein doublecortin (DCX) or in
 the MT-based molecular motor dynein result in lissencephaly. However, a
 functional link between DCX and dynein has not been defined. Here, we
 demonstrate that DCX negatively regulates dynein-mediated retrograde
 transport by reducing dynein’s association with MTs and by disrupting the
 composition of the dynein motor complex. Previous work showed an increased
 binding of the adaptor protein C-Jun-amino-terminal kinase-interacting
 protein 3 (JIP3) to dynein in the absence of DCX. Using purified
 components, we demonstrate that JIP3 forms an active motor complex with
 dynein and its cofactor dynactin with two dyneins per complex. DCX
 competes with the binding of the second dynein, resulting in a velocity
 reduction of the complex. We conclude that DCX negatively regulates
 dynein-mediated retrograde transport through two critical interactions by
 regulating dynein binding to MTs and by regulating the association of JIP3
 to the dynein motor complex.
description: Excel can be used to open the file
DOI: 10.5061/dryad.4qrfj6qd3
title: Foraging on anthropogenic food predicts problem-solving skills in a seabird

description: Species and populations with greater cognitive performance are more
 successful at adapting to changing habitats. Accordingly, urban species
 and populations often outperform their rural counterparts on
 problem-solving tests. Paradoxically, urban foraging also might be
 detrimental to the development and integrity of animals’ brains because
 anthropogenic foods often lack essential nutrients such as the long-chain
 omega-3 fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid
 (DHA), which are important for cognitive performance in mammals and
 possibly birds. We tested whether urbanization or consumption of EPA and
 DHA are associated with problem-solving abilities in ring-billed gulls, a
 seabird that historically exploited marine environments rich in omega-3
 fatty acids but now also thrives in urban centres. Using incubating adults
 nesting across a range of rural to urban colonies with equal access to the
 ocean, we tested whether urban gulls preferentially consumed anthropogenic
 food while rural nesters relied on marine organisms. As we expected
 individual variation in foraging habits within nesting location, we
 characterized each captured gulls’ diet using stable isotope and fatty
 acid analyses of their red blood cells. To test their problem-solving
 abilities, we presented the sampled birds with a horizontal rendition of
 the string-pull test, a foraging puzzle often used in animal cognitive
 studies. The isotopic and fatty acid profiles of urban nesters indicated a
 diet comprising primarily anthropogenic food, whereas the profiles of
 rural nesters indicated a high reliance on marine organisms. Despite the
 gulls’ degree of access to urban foraging habitat not predicting solving
 success, birds with biochemical profiles reflecting anthropogenic food
 (less DHA and a higher carbon-13 ratio in their red blood cells) had a
 greater probability of solving the string-pull test. These results suggest
 that experience foraging on anthropogenic food is the main explanatory
 factor leading to successful problem-solving, while regular consumption of
 omega-3s during incubation appears inconsequential.
DOI: 10.5061/dryad.3xsj3txk4
title: Data from: Navigating the scales of diversity in subtropical and coastal fish assemblages ascertained by eDNA and visual surveys

description: Environmental DNA (eDNA) metabarcoding emerges as a powerful method,
 allowing a more exhaustive investigation of fish fauna than any other
 methods. Yet, the general use of eDNA as a replacement of traditional
 methods such as visual surveys or physical sampling remains debatable.
 Therefore, a prior understanding of eDNA’s spatial resolution is
 necessary. This study aimed to compare the assessments of fish diversity
 at three spatial scales by eDNA, underwater visual census (UVC), and
 diver-operated video (DOV) surveys across 21 reef sites in northern
 Taiwan. The specific objectives were to explore the regional species pool
 (γ-diversity), reveal spatial patterns of fish assemblages (β-diversity),
 and disentangle the relationships between fish assemblages and benthic
 composition (α-diversity). At the γ-diversity level, a total of 438 marine
 fish species were detected across methods. eDNA exhibits an extraordinary
 power to explore the regional species pool given sufficient replication, a
 power which is unachievable by DOV and UVC. At the β-diversity level, all
 the methods successfully revealed the same spatial patterns of beta
 diversity and the distance decay of similarity in fish assemblages. At the
 α-diversity level, none of the methods is capable of investigating the
 entire resident fish fauna, but visual surveys are more suitable for
 scrutinizing interactions between fish and benthos. Instead of
 undiscriminatingly recommending a combination of eDNA with traditional
 survey methods, we suggest implementing specific surveys in accordance
 with the ecological questions of interest.
description: Full details on sample collection and analyses are available in
 the published manuscript.
description: See README file.