cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kh189323s
title: Data from: Innate and adaptive immune proteins in the preen gland secretions of male house sparrows

description: Recent studies have demonstrated that preen oil acts to reduce or
 eliminate feather-associated bacteria. The mechanisms underlying this
 antibacterial activity, however, are incompletely understood. In addition
 to the activity of alcohols (i.e. 3,7-dimethyloctan-1-ol), recent research
 has suggested that antimicrobial peptides may underlie the antibacterial
 activity of preen oil. Here, we document the presence of innate and
 adaptive immune proteins, lysozyme and immunoglobulin Y (IgY), in the
 preen oil of house sparrows (Passer domesticus). We suggest lysozyme
 functions as an antimicrobial agent, with potentially important impacts
 against Gram-positive feather degrading bacteria. Furthermore, both
 lysozyme and IgY likely act in local immune defence of the preen gland,
 and may also play a role in regulating the local microbiome, with
 potentially important consequences for chemical communication and
 signalling. Our findings suggest that the preen gland and its secretions
 should be considered an integral part of the body’s first line of defence
 against invading infections.
description: Preen gland secretions were collected from male house sparrows
 and measures of lysozyme and IgY were obtained through laboratory assays.
 Morphology data was collected from males before they were
 released.
description: Individual ID is based on ring number of each male.
 Capture time and Sampling time are calculated as minutes since
 00.00 on the day of sampling. Time_diff_minutes is the amount of time
 between capture and sampling. Preen gland length,
 width, and depth are based on the mean of three measurements taken for
 each dimension. Lysozyme concentration is measured in
 μg ml−1. IgY concentration is measured using an ELISA assay and the
 resulting optical density values (absorbance units) reflect
 concentration. Body condition was calculated as the
 scaled mass index following Peig and Green 2009, using tarsus length as
 the morphology measure of body size.
DOI: 10.5061/dryad.s7h44j153
title: Micronutrients enhance macronutrient effects in a meta-analysis of grassland arthropod abundance

description: Aim: Ongoing alterations to Earth’s biogeochemical cycles (e.g. via
 fertilization, burning of fossil fuels, and pollution) are expected to
 impact plants, plant consumers, and all subsequent trophic levels. While
 fertilization experiments often reveal arthropod nutrient limitation by
 nitrogen and phosphorus via effects on plant nutrient density and biomass,
 these macronutrients are only two of many nutrients important to arthropod
 fitness. Micronutrients are key to osmoregulation and enzyme function and
 can interact synergistically with macronutrients to shape the geography of
 arthropod abundance. We examine arthropod response to macro- and
 micronutrient fertilization as a function of nutrient type, application
 amount, duration, frequency, and plant responses to fertilization with the
 goal of addressing how ongoing alterations to biogeochemical cycles will
 shape future grassland food webs. Location: Global. Time period:
 1987-2018. Major taxa studied: Invertebrates. Methods: We compiled a
 database of 62 studies to test the response of six arthropod trophic
 groups to multiple fertilizer types (compositions of varying macro- and
 micronutrients), quantities, application frequencies, and application
 durations. Additionally, we examined the role of plant nutrient content
 and biomass in mediating arthropod responses to fertilization. Results:
 Micronutrients applied alone had no effects on plant biomass nor arthropod
 abundance. However, when added with macronutrients, micronutrients
 amplified the effect of N, P, and K in promoting arthropod abundance, a
 synergy which did not affect plant biomass. Micronutrients thus catalyzed
 the ability of macronutrients to promote arthropod abundance across all
 guilds studied. Main conclusions: In grasslands, the rules governing the
 abundance of autotrophs and their consumers appear to differ fundamentally
 in their response to Earth’s changing biogeochemistry. By revealing the
 importance of micronutrients for arthropods using a global dataset, we
 highlight a stoichiometric disjunction between limits of plants and
 arthropods for metal cations whose biogeochemistry, along with N and P,
 are being actively rearranged in the Anthropocene.
description: Meta-data includes variable names, descriptions, and data
 type. Data includes all data collected for
 meta-analysis. If a value was missing the cell has "NA" in
 it.
DOI: 10.5061/dryad.9w0vt4bd1
title: Power and limitations of environmental DNA metabarcoding for surveying leaf litter eukaryotic communities

description: Leaf litter habitats shelter a great variety of organisms, which play an
 important role in ecosystem dynamics. However, monitoring species in leaf
 litter is challenging, especially in highly diverse environments such as
 tropical forests, because individuals may easily camouflage themselves or
 hide in the litter layer. Identifying species based on environmental DNA
 (eDNA) would allow us to assess biodiversity in this microhabitat, without
 the need for direct observation of individuals. We applied eDNA
 metabarcoding to analyze large amounts of leaf litter (1 kg per sample)
 collected in the Brazilian Atlantic forest. We compared two DNA extraction
 methods, one total and one extracellular, and amplified a fragment of the
 mitochondrial 18S rRNA gene common to all eukaryotes, to assess the
 performance of eDNA from leaf litter samples in identifying different
 eukaryotic taxonomic groups. We also amplified two fragments of the
 mitochondrial 12S rRNA gene to specifically test the power of this
 approach for monitoring vertebrate species, with a focus on anurans. Most
 of the eukaryote sequence reads obtained were classified as Fungi,
 followed by Metazoa, and Viridiplantae. Most vertebrate sequences were
 assigned to Homo sapiens; only two sequences assigned to the genus
 Phyllomedusa and the species Euparkerella brasiliensis can be considered
 true detections of anurans in our eDNA samples. The detection of taxa
 varied depending on the DNA extraction method applied. Our results
 demonstrate that the analysis of eDNA from leaf litter samples has low
 power for monitoring vertebrate species, and should be preferentially
 applied to describe active and abundant taxa in terrestrial communities,
 such as Fungi and invertebrates.
DOI: 10.5061/dryad.1vhhmgqr4
title: Non-adaptive host-use specificity in tropical armored scale insects

description: Most herbivorous insects are diet specialists in spite of the apparent
 advantages of being a generalist. This conundrum might be explained by
 fitness trade-offs on alternative host plants, yet evidence of such
 trade-offs has been elusive. Another hypothesis is that specialization is
 non-adaptive, evolving through neutral population genetic processes and
 within the bounds of historical constraints. Here we report on a striking
 lack of evidence for the adaptiveness of specificity in tropical canopy
 communities of armored scale insects. We find evidence of pervasive diet
 specialization, and find that host-use is phylogenetically conservative,
 but also find that more-specialized species occur on fewer of their
 potential hosts than do less-specialized species, and are no more abundant
 where they do occur. Of course local communities might not reflect
 regional diversity patterns. But based on our samples, comprising hundreds
 of species of hosts and armored scale insects at two widely separated
 sites, more specialized species do not appear to outperform more
 generalist species.
description: Tropical armored scale insect communities were sampled from
 canopy cranes.
DOI: 10.5061/dryad.98sf7m0h1
title: Hydrothermal physiology and climate vulnerability in amphibians

description: All relevant data and code for the analysis from: Greenberg DA, Palen WJ.
 2021 Hydrothermal physiology and climate vulnerability in amphibians.
 Proc. R. Soc. B 20202273. https://doi.org/10.1098/rspb.2020.2273 Data on
 jump performance (jump_performance_trials.csv), water loss rates and water
 conservation behaviour in Pacific chorus frogs (treefrog_waterloss.csv),
 and estimated hours of climate restriction based on thermal physiology and
 hydothermal physiology (physiological_limits_activity.csv) for three
 species of anurans from the Pacific Northwest. All R code to conduct each
 analysis is also included.
DOI: 10.5061/dryad.g79cnp5np
title: Sequential organization of birdsong: Relationships with individual quality and fitness

description: Many vocalizing animals produce the discrete elements of their acoustic
 signals in a specific sequential order, but we know little about the
 biological relevance of this ordering. For that, we must characterize the
 degree by which individuals differ in how they organize their signals
 sequentially and relate these differences to variation in quality and
 fitness. In this study, we fulfilled these tasks in male collared
 flycatchers (Ficedula albicollis). We characterized the sequential order
 of syllables with a network analysis approach and studied the consistency
 of network variables on distinct time-scales (within-day, between-day, and
 between-year), and assessed their relationship with such quality
 indicators as age, body condition, arrival date, and fitness-related
 proxies like survival to the next year and pairing success. We found that
 the syllables were associated non-randomly with one another and both the
 frequency differences of consecutive syllables and the number of motif
 types were higher in the original than in randomized syllable sequences.
 Average degree and small-worldness showed considerable among-individual
 differences and decreasing repeatability with increasing time-scale.
 Furthermore, we found relationships between male age and average degree
 among and within individuals. Accordingly, older males produce syllable
 sequences by using common syllables less often than younger individuals.
 However, the network variables showed no relationship with fitness-related
 variables. In conclusion, the sequential organization of birdsong has the
 potential to encode individual-specific characteristics, which thus could
 be used as signals in social interactions and thus potentially could be
 subject to sexual selection.
description: Data based on field recordings, segmented and manually clustered
 syllables from the song of collared flycatcher. We also included repeated
 recordings from the same individuals from the same day, different days, or
 from different years. Based on the syllables sequence, we generated
 directed unweighted networks and calculated 4 network measure variables
 for all recordings: average degree, average minimum path, clustering
 coefficient, and small-worldness. We also searched for the motifs with
 different lengths. Furthermore, we calculated the frequency differences
 between the consecutive syllables. The details of the processing are
 provided in the manuscript.
description: 4 datasets are included in 1 Excel file: 
 data_176ind - the network measures and male traits for 176
 individuals data_repeatability - the network measures
 for repeated recordings data_acoustic - the mean
 frequency differences of consecutive syllables for original and randomized
 sequences data_motifs - the number of motif
 types  In dataset, each row represents
 data for one recording.
DOI: 10.5061/dryad.bnzs7h489
title: Genomic and chemical evidence for local adaptation in resistance to different herbivores in Datura stramonium

description: Since most species are collections of genetically variable populations
 distributed to habitats differing in their abiotic/biotic environmental
 factors and community composition, the pattern and strength of natural
 selection imposed by species on each others' traits are also expected
 to be highly spatially variable. Here, we used genomic and quantitative
 genetic approaches to understand how spatially variable selection operates
 on the genetic basis of plant defenses to herbivores. To this end, an F2
 progeny was generated by crossing Datura stramonium (Solanaceae) parents
 from two populations differing in their level of chemical defense. This F2
 progeny was reciprocally transplanted into the parental plants’ habitats
 and by measuring the Identity by Descent (IBD) relationship of each F2
 plant to each parent, we were able to elucidate how spatially variable
 selection imposed by herbivores operated on the genetic background (IBD)
 of resistance to herbivory, promoting local adaptation. The results
 highlight that plants possessing the highest total alkaloid concentrations
 (sum of all alkaloid classes) were not the most well-defended or fit.
 Instead, specific alkaloids and their linked loci/alleles were favored by
 selection imposed by different herbivores. This has led to population
 differentiation in plant defenses and thus, to local adaptation driven by
 plant-herbivore interactions.
DOI: 10.5061/dryad.wwpzgmsh8
title: Genetic and phenotypic diversity of guppy population pre- and post-flood disturbance

description: Rare extreme “black swan” disturbances can impact ecosystems in many ways,
 such as destroying habitats, depleting resources, and causing high
 mortality. In rivers, for instance, exceptional floods that occur
 infrequently (e.g., so-called “50-year floods”) can strongly impact the
 abundance of fishes and other aquatic organisms. Beyond such ecological
 effects, these floods could also impact intraspecific diversity by
 elevating genetic drift or dispersal and by imposing strong selection,
 which could then influence the population’s ability to recover from
 disturbance. And yet, natural systems might be resistant (show little
 change) or resilient (show rapid recovery) even to rare extreme events –
 perhaps as a result of selection due to past events. We considered these
 possibilities in two rivers where native guppies experienced two extreme
 floods - one in 2005 and another in 2016. For each river, we selected four
 sites and used archived “historical” samples to compare levels of genetic
 diversity and phenotypic mean traits before versus after floods. Genetic
 diversity was represented by 33 neutral microsatellite markers, and
 phenotypic diversity was represented by body length and male melanic
 (black) color. We found that genetic diversity and population structure
 was mostly resistant to even these extreme floods; whereas the larger
 impacts on phenotypic diversity were short-lived, suggesting additional
 resilience. We discuss the determinants of these two outcomes for guppies
 facing floods, and then consider the general implications for the
 resistance and resilience of intraspecific variation to black swan
 disturbances.
description: This dataset contains genotypes for 1221 guppies at 33
 microsatellites. These fish were collected before (2004, 2016) and after
 (2005, 2017) disturbance. The second spreadsheet
 contains the body length of the same individuals, with a few missing
 values.
DOI: 10.5061/dryad.fj6q573s8
title: Temperature alone is insufficient to understand hibernation energetics

description: Energy conservation has long been a focal point in hibernation research. A
 long-standing assumption is that ambient temperature (Ta) largely defines
 the rate of energy expenditure because of well-known relationships between
 Ta, metabolic rate and frequency of arousal from torpor. Body condition
 and humidity also affect energy expenditure but are usually considered
 secondary factors. We held tricolored bats (Perimyotis subflavus) in
 captivity under multiple environmental conditions to directly compare the
 importance of Ta, fat mass and humidity for hibernation energy
 expenditure. Fat mass was the best predictor of female mass loss, followed
 by Ta and humidity. However, males had less fat and adopted a more
 energetically conservative hibernation strategy. Our results demonstrate
 that understanding the evolution of behavior, physiology and ecology of
 hibernation requires disentangling the relative contributions of multiple
 drivers of hibernation energetics, and that Ta is not always the most
 important factor driving energy expenditure.
DOI: 10.5061/dryad.kh189323t
title: Separating direct and indirect effects of rising temperatures on biogenic volatile emissions in the Arctic

description: Volatile organic compounds (VOCs) are released from biogenic sources in a
 temperature-dependent manner. Consequently, Arctic ecosystems are expected
 to greatly increase their VOC emissions with ongoing climate warming,
 which is proceeding at twice the rate of global temperature rise. Here, we
 show that ongoing warming has strong, increasing effects on Arctic VOC
 emissions. Using a combination of statistical modelling on data from
 several warming experiments in the Arctic tundra and dynamic ecosystem
 modelling, we separate the impacts of temperature and soil moisture into
 direct effects and indirect effects through vegetation composition and
 biomass alterations. The indirect effects of warming on VOC emissions were
 significant, but smaller than the direct effects. Furthermore, vegetation
 changes also cause shifts in the chemical speciation of the emissions.
 Both direct and indirect effects result in large geographic differences in
 VOC emission responses in the warming Arctic, depending on the local
 vegetation cover and the climate dynamics. Our results outline complex
 links between local climate, vegetation, and ecosystem-atmosphere
 interactions, with likely local-to-regional impacts on the atmospheric
 composition.
DOI: 10.25338/b8k349
title: Data from: Taxonomic revision of the New World members of the Trapdoor spider genus Ummidia Thorell (Araneae,: Mygalomorphae,: Halonoproctidae )

description: This study documents a comprehensive taxonomic treatment of the New World
 Ummidia species. At the onset of this work the genus comprised 27 species
 and one subspecies with a cosmopolitan distribution that includes North
 America, South America, Asia, Northern Africa, and Europe; of these
 species the majority of the nominal diversity can be attributed to the New
 World where 20 species have been previously described. Ummidia oaxacana
 (Chamberlin, 1925) is considered a nomen dubium; U. tuobita (Chamberlin,
 1917) and U. absoluta (Gertsch and Mulaik, 1940) are both considered
 junior synonyms of U. audouini (Lucas, 1835); the subspecies U. carabivora
 emarginata (Atkinson, 1886) is considered a junior synonym of U.
 carabivora (Atkinson, 1886); U. pygmaea (Chamberlin and Ivie, 1945) is
 considered a junior synonym of U. beatula (Gertsch and Mulaik, 1940 ); U.
 celsa (Gertsch and Mulaik, 1940) is considered a junior synonym of U.
 funerea (Gertsch, 1936); Hebestatis lanthanus (Valerio, 1987) is
 considered a junior synonym of U. rugosa (Karsch, 1880). Thirty-three new
 species are described: U. neilgaimani, U. gingoteague, U. rongodwini, U.
 okefenokee, U. richmond, U. macarthuri, U. colemanae, U. rosillos, U.
 mercedesburnsae, U. paulacushingae, U. waunekaae, U. gertschi, U.
 timcotai, U. gabrieli, U. pesiou, U. rodeo, U. huascazaloya, U. anaya, U.
 cuicatec, U. brandicarlileae, U. riverai, U. frankellerae, U. hondurena,
 U. yojoa, U. matagalpa, U. carlosviquezi, U. varablanca, U. quepoa, U.
 cerrohoya, U. quijichacaca, U. tibacuy, U. neblina, U. tunapuna. 
 Atkinson G (1886) Descriptions of some new trapdoor spiders; their nests
 and food habits. Entomological American 2: 109–137. Chamberlin RV (1917)
 New spiders of the family Aviculariidae. Bulletin of the Museum of
 Comparative Zoology 61: 25–75. Chamberlin RV (1925) Diagnoses of new
 American Arachnida. Bulletin of the Museum of Comparative Zoology 67: 40.
 Gertsch WJ (1936) Further diagnoses of new American spiders. American
 Museum Novitates 852: 1–27. Gertsch WJ, Mulaik S (1940) The Spiders of
 Texas. I. Bulletin of the American Museum of Natural History 77: 307–340.
 Karsch F (1880) Arachnologische Blatter (Decas I). Zeitschrift fur die
 Gesammten Naturwissenschaften, Dritte Folge 5: 373–409. Lucas H (1835)
 Genre Pachyloscelis Lucas. Magasin de Zoologie 6: 1–6. Valerio CE (1987) A
 Species of Hebestatis (Araneae, Ctenizidae) from Costa Rica. The Journal
 of Arachnology 15: 227–230.
DOI: 10.5061/dryad.pg4f4qrmr
title: Code and data from: A mobile sex-determining region, male-specific haplotypes, and rearing environment influence age at maturity in Chinook salmon.

description: Variation in age at maturity is an important contributor to life history
 and demographic variation within and among species. The optimal age at
 maturity can vary by sex, and the ability of each sex to evolve towards
 its fitness optimum depends on the genetic architecture of maturation.
 Using GWAS of RAD sequencing data, we show that age at maturity in Chinook
 salmon exhibits sex-specific genetic architecture, with age at maturity in
 males governed by large (up to 20Mb) male-specific haplotypes. These
 regions showed no such effect in females. We also provide evidence for
 translocation of the sex-determining gene between two different
 chromosomes. This has important implications for sexually antagonistic
 selection, particularly that sex-linkage of adaptive genes may differ
 within and among populations based on chromosomal location of the
 sex-determining gene. Our findings will facilitate research into the
 genetic causes of shifting demography in Chinook salmon as well as a
 better understanding of sex-determination in this species and Pacific
 salmon in general.
description: RADseq data for Chinook salmon, using sbfI enzyme for digestion. 
 DNA was sequenced on a HiSeq 2000 or HiSeq 2500 and processed with
 STACKS.
description: Code and VCF files to replicate analyses from "A mobile
 sex-determining region, male-specific haplotypes, and rearing environment
 influence age at maturity in Chinook salmon." Descriptions of files
 are included in the README.  AnalysisCode.R contains all code to run
 analyses.
DOI: 10.5061/dryad.ffbg79csd
title: Dataset for Longitudinal metabolic alterations in plasma of rats exposed to low doses of high linear energy transfer radiation

description: Astronauts embarking on deep space missions are at high risk of long-term
 exposure to low doses of high linear energy transfer (LET) radiation,
 which can contribute to the development of cancer and multiple
 degenerative diseases. However, long term effects of exposure to low doses
 of high LET radiation in plasma metabolite profiles have not been
 elucidated. We utilized an untargeted metabolomics and lipidomics approach
 to analyze plasma obtained from adult male Long Evans rats to determine
 the longitudinal effects of low-dose proton and low-dose oxygen ion
 whole-body irradiation on metabolic pathways. Our findings reveal that
 radiation exposure induced modest changes in the metabolic profiles in
 plasma, 7 months after exposure. Furthermore, we identified some common
 metabolite dysregulations between protons and oxygen ions, which may
 indicate a similar mechanism of action for both radiation types.