cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.63xsj3v2j
title: Perception of dead conspecifics increases reproductive investment in fruit flies

description: Adaptive plasticity in life-history traits is often critical to maximize
 fitness in the face of environmental heterogeneity. For example, many
 organisms respond to a threat to their survival (and hence residual
 reproductive value) by adaptively increasing their investment into current
 reproduction (i.e. “terminal investment”).  A key to successful
 terminal investment is the use of adequate environmental cues to extrinsic
 mortality sources. In species that live at high population densities, the
 presence of dead conspecifics could potentially act as a reliable cue to
 extrinsic mortality sources (e.g. via pathogens). We experimentally tested
 this idea using the model organism Drosophila melanogaster, a pest species
 that experiences marked demographic shifts. We monitored the reproductive
 output of young mated females during repeated bouts of egg-laying in the
 presence (i.e. dead-exposed) or absence (i.e. controls) of dead
 conspecifics, interspersed by mating periods where dead conspecifics were
 always absent. Dead-exposed females produced more offspring than controls
 when in the presence of dead conspecifics but fewer offspring than
 controls when dead conspecifics were subsequently removed (i.e. during
 mating periods). These changes were repeatable across time, and are thus
 indicative of high plasticity in reproductive behaviour. Flies responded
 equally to starvation-induced and flash-frozen dead conspecifics,
 indicating that the cause of death is irrelevant to trigger the plastic
 response observed, and that females respond to the presence of dead
 conspecifics per se. Finally, we found that dead-exposed females produced
 heavier daughters (but not sons) than controls when in the presence of
 dead conspecifics, but not during mating periods (when dead conspecifics
 were absent). In this species body size correlates more strongly with
 female (than male) fitness, so higher investment in daughter weight is
 congruent with terminal investment.   Altogether, our results
 show that perception of dead conspecifics leads to highly plastic
 life-history adjustments in the form of increased investment in both the
 quantity and the quality of offspring. We discuss these results in the
 context of terminal investment and other alternative hypotheses.
DOI: 10.5061/dryad.rxwdbrv8m
title: Invasion history shapes host transcriptomic response to a body-snatching parasite

description: By shuffling biogeographic distributions, biological invasions can both
 disrupt long-standing associations between hosts and parasites and
 establish new ones. This creates natural experiments with which to study
 the ecology and evolution of host-parasite interactions. In estuaries of
 the Gulf of Mexico, the white-fingered mud crab (Rhithropanopeus harrisii)
 is infected by a native parasitic barnacle Loxothylacus panopaei
 (Rhizocephala), which manipulates host physiology and behavior. In the
 1960s, L. panopaei was introduced to the Chesapeake Bay and has since
 expanded along the southeastern Atlantic coast, while host populations in
 the northeast have so far been spared. We use this system to test the
 host’s transcriptomic response to parasitic infection and investigate how
 this response varies with the parasite’s invasion history, comparing
 populations representing (1) long-term sympatry between host and parasite,
 (2) new associations where the parasite has invaded during the last sixty
 years, and (3) naïve hosts without prior exposure. A comparison of
 parasitized and control crabs revealed a core response, with widespread
 downregulation of transcripts involved in immunity and molting. The
 transcriptional response differed between hosts from the parasite’s native
 range and where it is absent, consistent with previous observations of
 increased susceptibility in populations lacking exposure to the parasite.
 Crabs from the parasite’s introduced range, where prevalence is highest,
 displayed the most dissimilar response, possibly reflecting immune
 priming. These results provide molecular evidence for parasitic
 manipulation of host phenotype and the role of gene regulation in
 mediating host-parasite interactions.
description: mRNA-seq of tissue from experiments described in Tepolt et al
 2020 "Recent introductions reveal differential susceptibility to
 parasitism across an evolutionary mosaic", <em>Evolutionary
 Applications. </em>13<em>(3), </em>545-558. Host
 (<em>Rhithropanopeus harrisii</em>) and parasite
 (<em>Loxothylacus panopaei</em>) transcriptomes were assembled
 using Trinity v2.8.5. Expression matrices constructed using utility
 scripts within Trinity and were filtered using R. All processing/analysis
 are contained within a corresponding GitHub repository
 (https://github.com/tepoltlab/RhithroLoxo_DE).
description: See publication supplement for sample metadata.
DOI: 10.5061/dryad.xgxd254gr
title: A phylogeny of Antirrhinum reveals parallel evolution of alpine morphology

description: • Parallel evolution of similar morphologies in closely related lineages
 provides insight into the repeatability and predictability of evolution.
 In the genus Antirrhinum (snapdragons), as in other plants, a suite of
 morphological characters are associated with adaptation to alpine
 environments. • We test for parallel trait evolution in Antirrhinum by
 investigating phylogenetic relationships using Restriction-site associated
 DNA (RAD) sequencing. We then associate phenotypic information to our
 phylogeny to reconstruct patterns of morphological evolution and relate
 this to evidence for hybridization between emergent lineages. •
 Phylogenetic analyses show that the alpine character syndrome is present
 in multiple groups, suggesting that Antirrhinum has repeatedly colonised
 alpine habitats. Dispersal to novel environments happened in the presence
 of intraspecific and interspecific gene flow. • We find support for a
 model of parallel evolution in Antirrhinum. Hybridisation in natural
 populations, and a complex genetic architecture underlying the alpine
 morphology syndrome, support an important role of natural selection in
 maintaining species divergence in the face of gene flow.
description: Raw reads were
 demultiplexed using the <i>process_radtags</i> script from the
 Stacks software (Catchen <i>et al.</i>, 2013). Trimmomatic
 0.36 (Bolger <i>et al.</i>, 2014) was used to remove adaptor
 sequences, clip sequences with a phred score of ≤20 and remove any read
 shorter than 30 bp. Filtered reads were mapped to the <i>A.
 majus</i> genome (Li <i>et al.</i>, 2019) using Bowtie2
 (Langmead & Salzberg, 2012) and duplicate sequences removed using
 Picard tools (Broad Institute, 2018). SNPs were called using samtools 1.6
 and the multiallelic caller implemented in bcftools 1.4 (Li, 2011),
 retaining invariant sites. This dataset was then filtered by mapping
 quality (≥40), depth (≥3x) and missing data, both per taxon (removing
 individuals with &gt;70% missing data) and per site (removing sites
 present in less than 50% of individuals). The final data included
 16,061,293 sites from 86 samples corresponding to 24 taxa. To root the phylogenetic trees we
 used available whole genome sequence data from <i>Misopates orontium
 </i>(A. Whibley and E. Coen, unpublished).
 <i>Misopates</i> has been shown to belong to the
 <i>Antirrhinum</i> clade, and diverged from the genus
 <i>Antirrhinum</i> in the last 10-15 million years (Ogutcen
 and Vamosi, 2016). Variant calling was done as above retaining only the
 loci present in the alignment of <i>Antirrhinum</i>
 samples.
DOI: 10.5061/dryad.wdbrv15p8
title: A sit-and-wait predator, but not an active-pursuit predator, alters pollinator-mediated selection on floral traits

description: Indirect species interactions are ubiquitous in nature, often outnumbering
 direct species interactions. Yet despite evidence that indirect
 interactions have strong ecological effects, relatively little is known
 about whether they can shape adaptive evolution by altering the strength
 and/or direction of natural selection. We tested whether indirect
 interactions affect the strength and direction of pollinator-mediated
 selection on floral traits of the bumble-bee pollinated wildflower Lobelia
 siphilitica. We estimated the indirect effects of two pollinator predators
 with contrasting hunting modes: dragonflies (Aeshnidae and Corduliidae)
 and ambush bugs (Phymata americana, Reduviidae). Because dragonflies are
 active pursuit predators, we hypothesized that they would strengthen
 pollinator-mediated selection by weakening plant-pollinator interactions
 (i.e. a density-mediated indirect effect). In contrast, because ambush
 bugs are sit-and-wait predators, we hypothesized that they would weaken or
 reverse the direction of pollinator-mediated selection by altering
 pollinator foraging behavior (i.e. a trait-mediated indirect effect).
 Specifically, if ambush bugs hunt from plants with traits that attract
 pollinators (i.e. prey), then pollinators will spend less time visiting
 those plants, weakening or reversing the direction of selection on
 attractive floral traits. We did not find evidence that high dragonfly
 abundance strengthened selection on floral traits via a density-mediated
 indirect effect: neither pollen limitation (a proxy for the strength of
 plant-pollinator interactions) nor directional selection on floral traits
 of L. siphilitica differed significantly between high- and low-dragonfly
 abundance treatments. In contrast, we did find evidence that ambush bug
 presence affected selection on floral traits via a trait-mediated indirect
 effect: ambush bugs hunted from L. siphilitica plants with larger daily
 floral displays, reversing the direction of pollinator-mediated selection
 on daily display size. These results suggest that indirect species
 interactions have the potential to shape adaptive evolution by altering
 natural selection.
DOI: 10.5061/dryad.jsxksn09c
title: A shift to shorter cuticular hydrocarbons accompanies sexual isolation among Drosophila americana group populations

description: Because sensory signals often evolve rapidly, they could be instrumental
 in the emergence of reproductive isolation between species. However,
 pinpointing their specific contribution to isolating barriers, and the
 mechanisms underlying their divergence, remains challenging. Here we
 demonstrate sexual isolation due to divergence in chemical signals between
 two populations of Drosophila americana (SC and NE) and one population of
 D. novamexicana, and dissect its underlying phenotypic and genetic
 mechanisms. Mating trials revealed strong sexual isolation between
 Drosophila novamexicana males and SC Drosophila americana females, as well
 as more moderate bi-directional isolation between D. americana
 populations. Mating behavior data indicates SC D. americana males have the
 highest courtship efficiency and, unlike males of the other populations,
 are accepted by females of all species. Quantification of cuticular
 hydrocarbon (CHC) profiles—chemosensory signals that are used for species
 recognition and mate finding in Drosophila—shows that the SC D. americana
 population differs from the other populations primarily on the basis of
 compound carbon chain-length. Moreover, manipulation of male CHC
 composition via heterospecific perfuming—specifically perfuming D.
 novamexicana males with SC D. americana males—abolishes their sexual
 isolation from these D. americana females. Of a set of candidates, a
 single gene—elongase CG17821—had patterns of gene expression consistent
 with a role in CHC differences between species. Sequence comparisons
 indicate D. novamexicana and our Nebraska (NE) D. americana population
 share a derived CG17821 truncation mutation that could also contribute to
 their shared “short” CHC phenotype. Together, these data suggest an
 evolutionary model for the origin and spread of this allele and its
 consequences for CHC divergence and sexual isolation in this group.
description: Methods can be found in the publication associated with this
 work.
description: Seee ReadMe file for usage notes for this dataset.
DOI: 10.25338/b8sd14
title: Data from: Feather chemicals contain information about the major histocompatibility complex in a highly scented seabird

description: Mate choice informed by the immune genes of the Major Histocompatibility
 Complex (MHC) may provide fitness benefits including offspring with
 increased immunocompetence. Olfactory cues are considered the primary
 mechanism organisms use to evaluate the MHC of potential mates, yet this
 idea has received limited attention in birds. Motivated by a finding of
 MHC-dependent mate choice in the Leach’s storm-petrel (Oceanodroma
 leucorhoa), we examined whether the chemical profiles of this highly
 scented seabird contain information about MHC genes. Whereas previous
 studies in birds examined non-volatile compounds, we used gas
 chromatography-mass spectrometry to measure the volatile compounds emitted
 from feathers that potentially serve as olfactory infochemicals about MHC
 and coupled this with locus-specific genotyping of MHC IIB genes. We found
 that feather chemicals reflected individual MHC diversity through
 interactions with sex and breeding status. Furthermore, similarity in MHC
 genotype was correlated with similarity in chemical profiles within
 female-female and male-female dyads. We provide the first evidence that
 volatile chemicals from bird feathers can encode information about MHC.
 Our findings suggest that olfaction likely aids MHC-based mate choice in
 this species, and highlight a role for chemicals in mediating genetic mate
 choice in birds where this mode of communication has been largely
 overlooked.
description: We gathered blood samples
 and feather samples from 60 Leach’s storm-petrels (<i>Oceanodroma
 leucorhoa</i>) breeding on Bon Portage Island in Nova Scotia,
 Canada. We
 extracted DNA from the blood samples and used PCR-based cloning and
 sequencing to determine the MHC class IIB genotypes of
 individuals. We
 identified and quantified the volatile chemicals associated with the
 feather samples using headspace gas-chromatography mass-spectrometry to
 describe the chemical profiles of individuals. We used the resulting data to
 test whether information about MHC genotype is reflected in the scent of
 Leach’s storm-petrel plumage. Detailed methods about how the
 data were generated can be found in the corresponding
 publication.
description: This data package includes
 the data files and code (R programming language) needed to reproduce the
 analysis, results, and figures for the corresponding
 publication. Please see README file for
 detailed descriptions of all files and variables.
DOI: 10.5061/dryad.1g1jwstwg
title: A long tail of truth and beauty: a simple rule of pattern formation explains symmetry, complexity and beauty in the peacock’s tail

description: Darwin’s theory of sexual selection by female choice has become a standard
 explanation for exaggerated sexually dimorphic traits, such as the
 peacock’s (Pavo cristatus) long tail. Eyespot beauty-based female choice
 requires genetic variation in female preference and the number of
 eyespots, as well as a genetic correlation between the two. However,
 little genetic variation has been documented in either of these traits in
 natural and feral peacock populations. We examined the anatomical plan
 underlying feather development and discovered that eyespot feather
 follicles originate in alternating rows of 10/11, which uniquely
 determines the train’s feather complexity, bilateral symmetry, and eyespot
 arrangement and beauty. This pattern precludes intrinsic variation in
 eyespot number, resulting in a fixed number of total eyespots in fully
 mature individuals. Since number of eyespots and tail length are
 independent traits and function of the age of the animal, the only
 variation available in these trats is also function of age. We propose an
 alternate, male drive, hypothesis in which females choose males based on
 their overall dominance (size, vigour, call, courting), and beauty of the
 train may (or may not) be a factor in female choice but it cannot affect
 the train length.  This hypothesis can explain all known results.
description: Collected from museum specimens of peacock's tail.
description: Missing data values (indicated by "-" sign) are due to
 poor quality of the specimen.
DOI: 10.5061/dryad.m37pvmd2f
title: Too many to count: Using orthophotography to census an unharvested beaver (Castor canadensis) population in Ontario

description: Various field methods exist to monitor wildlife populations and estimate
 trends in their distribution and abundance. For American beaver (Castor
 canadensis), aerial surveys provide a means to obtain abundance data over
 large areas and typically involve observers searching watercourses and
 shorelines for active beaver presence. Here, we describe a systematic
 aerial photo census we designed and executed in autumn to quantify annual
 beaver abundance on the 184 km2 Michipicoten Island, Ontario from
 2015–2019. Aerial photos were stitched together into orthophoto mosaics
 after each census and visually searched for beaver food caches, with each
 food cache representing an independent beaver colony. Our methods revealed
 that beaver colony abundance declined substantially from a peak of 6.1
 colonies/km2 in 2015, the highest reported across North America, to 0.4
 colonies/km2 in 2018. Beaver abundance remained low through 2019. Though
 photographing the entire isolated study area required relatively little
 time and effort, even when beaver density was very high, post-census
 processing work was time-consuming. Lessons learned will improve the
 efficiencies of our future censuses and aid other researchers. Our method
 is advantageous over traditional aerial wildlife surveys in that it
 provides a digital and visual record that can be used for additional
 analyses. 
description: Counts of American beaver food caches and active and inactive
 lodges over 4 years (2015, 2017, 2018, 2019) from aerial photos taken
 during transect censuses.
DOI: 10.7280/d17x15
title: Oak woodland health assessment in Orange County metrics

description: Oak woodlands are declining in Orange County (OC) due to habitat
 destruction and climate change, along with increased drought and weather
 extremes, fire frequency, and the recent invasion by goldspotted oak
 borers (GSOB). The Center for Environmental Biology (CEB) has been
 conducting a long-term oak woodland health monitoring program in OC for
 the goals of restoration. In this project, we analyzed oak monitoring data
 on demographics and pathogens collected from 2010 to 2020 and incorporated
 fire frequency and GSOB data to create a health-based oak woodland ranking
 system to make recommendations for restoration. Here we show our
 three-level recommendations of restoration priority: 1) Level 1: Blind
 Canyon (BLI) and Boy Scout Camp (BSC); 2) Level 2: Limestone Canyon (LSC)
 and Oak Flat (OF); 3) Level 3: Fremont Canyon (FMC), Gypsum Canyon (GYP),
 and Irvine Mesa (IRM). Increased fire frequency was positively correlated
 with declining health. We also assessed remote sensing data (Normalized
 Difference Vegetation Index, NDVI) against on the ground data for its
 potential to identify declining oak woodlands. NDVI was an imperfect
 indicator of declining oak woodland health, but may be useful for larger
 woodlands or with improved imagery resolution. Our work will inform local
 stakeholders in future restoration projects of OC oak woodlands.
description: Sampling protocol (from CEB Oak Monitoring Report Feb 29 2020):
 Within each woodland, random sections, or “reaches,” were identified for
 sampling. Each reach included clusters of trees that were monitored.
 Individual Coast Live Oak trees were sampled in “Y” shaped clusters that
 included three trees that surrounded one randomly selected “sentinel”
 tree. Clusters were located in woodlands in the coastal and inland
 protected open space within Orange CountyData processing:
 Data from raw CEB data set were cleaned in Excel by removing
 inappropriate nonnumeric characters and correcting any other errors.
 Analysis using cleaned data set was performed in R.
description: Please see ReadMe file.
DOI: 10.15468/dl.7xvnwq
title: Occurrence Download

description: A dataset containing 99989 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Trachemys scripta elegans"
 ]
}

 The dataset includes 99989 records from 476 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002873-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2g3uuk
title: Occurrence Download

description: A dataset containing 312 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Grammostola rosea (Walckenaer, 1837)"
 ]
}

 The dataset includes 312 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009991-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7txgse
title: Occurrence Download

description: A dataset containing 812 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lonicera tatarica",
 "Country is Czechia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 812 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049576-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.774t2e
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lonicera tatarica",
 "Country is Croatia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049575-250811113504898/datasets/export for details.
DOI: 10.15468/dl.b54nx5
title: Occurrence Download

description: A dataset containing 118357 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Schoenoplectus lacustris"
 ]
}

 The dataset includes 118357 records from 1003 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049495-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mttdza
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pueraria phaseoloides",
 "Country is Papua New Guinea",
 "HasCoordinate is true"
 ]
}

 The dataset includes 37 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024846-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2d3v5j
title: Occurrence Download

description: A dataset containing 879233 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Potentilla erecta"
 ]
}

 The dataset includes 879233 records from 1882 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024776-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.29218346
title: Additional file 1 for Beyond Diagnoses: Identifying Functional Subgroups Among Adults with Chronic Conditions Using NHANES Data

description: Additional file 1. Table S1. NHANES variable mapping for functional tasks and chronic conditions across studies. Table S2. NHANES variables from Knisely et al. 2021 that were excluded from this study.