cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25338/b8rh0g
title: Unraveling the complex hybrid ancestry and domestication history of cultivated strawberry

description: Cultivated strawberry (Fragaria × ananassa) is one of our youngest
 domesticates, originating in early eighteenth-century Europe from
 spontaneous hybrids between wild allo-octoploid species (F. chiloensis and
 F. virginiana).  The improvement of horticultural traits by 300
 years of breeding has enabled the global expansion of strawberry
 production.  Here, we describe the genomic history of strawberry
 domestication from the earliest hybrids to modern cultivars.  We
 observed a significant increase in heterozygosity among interspecific
 hybrids and a decrease in heterozygosity among domesticated descendants of
 those hybrids.  Selective sweeps were found across the genome in
 early and modern phases of domestication—59-76% of the selectively swept
 genes originated in the three less dominant ancestral
 subgenomes.  Contrary to the tenet that genetic diversity is
 limited in cultivated strawberry, we found that the octoploid species
 harbor massive allelic diversity and that F. × ananassa harbors as much
 allelic diversity as either wild founder.  We identified 41.8M
 subgenome-specific DNA variants among resequenced wild and domesticated
 individuals.  Strikingly, 98% of common alleles and 73% of total
 alleles were shared between wild and domesticated populations. 
 Moreover, genome-wide estimates of nucleotide diversity were virtually
 identical in F. chiloensis, F. virginiana, and F. × ananassa (π =
 0.0059-0.0060).  We found, however, that nucleotide diversity and
 heterozygosity were significantly lower in modern F. × ananassa
 populations that have experienced significant genetic gains and have
 produced numerous agriculturally important cultivars.
DOI: 10.15468/dl.pxrvf8
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((123.84613956870568 24.101672308243163,124.13018131528524 24.101672308243163,124.13018131528524 24.385714054822724,123.84613956870568 24.385714054822724,123.84613956870568 24.101672308243163))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lygodium microphyllum"
 ]
}

 The dataset includes 39 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002594-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6g4rrt
title: Occurrence Download

description: A dataset listing the 5830 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is Moorea Biocode Project"
 ]
}

 The dataset's 5830 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002577-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.t76hdr7zt
title: Data for: Socially cued anticipatory adjustment of female signalling effort in a moth

description: Juvenile population density has profound effects on subsequent adult
 development, morphology, and reproductive investment. Yet, little is known
 about how the juvenile social environment affects adult investment into
 chemical sexual signalling. Male gumleaf skeletonizer moths, Uraba lugens,
 facultatively increase investment into antennae (pheromone receiving
 structures) when reared at low juvenile population densities, but whether
 there is comparable adjustment by females into pheromone investment is not
 known. We investigate how juvenile population density influences the
 ‘calling’ (pheromone-releasing) behaviour of females, and the
 attractiveness of their pheromones. Female U. lugens adjust their calling
 behaviour in response to socio-sexual cues: adult females reared in high
 juvenile population densities called earlier and for longer than those
 from low juvenile densities. Juvenile density also affected female
 pheromonal attractiveness: y-maze olfactometer assays revealed that males
 prefer pheromones produced by females reared at high juvenile densities.
 This strategic investment in calling behaviour by females, based on
 juvenile cues that anticipate the future socio-sexual environment, likely
 reflects a response to avoid mating failure through competition with
 neighbouring signallers.
description: The R code for analysing this data is contained in the
 Supplementary Materials of the paper.
DOI: 10.15468/dl.rw62xw
title: Occurrence Download

description: A dataset containing 1132 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Phoenix sylvestris"
 ]
}

 The dataset includes 1132 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002596-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.tdz08kpxv
title: Surrounding landscape effect on roadside verges

description: Semi-natural habitats are declining throughout the world, thus the role of
 small anthropogenic habitats in the preservation of plants is becoming
 increasingly appreciated. Here we surveyed the orchid flora of roadside
 verges in five Central European countries (Austria, Hungary, Romania,
 Slovakia and Slovenia) and tested how the surrounding landscape matrix
 affects the overall number of species and individuals, and also different
 functional groups of orchids. We found more than 2000 individuals of 27
 orchid species during our surveys. According to our results, the
 increasing coverage of agricultural and urban areas negatively affect both
 the number of orchid species and individuals on roadsides. Our study
 further suggests, that differences in the surrounding habitats affect
 which species are found on roadsides, since the increasing coverage of
 grasslands or forested areas around orchid occurrences had a significant
 positive effect on the number of grassland or forest-dwelling species and
 individuals, respectively. Most variance in orchid numerosity and
 diversity was explained by the cover of the suitable habitat types of the
 respective taxa in the surrounding landscape of the sampling points. This
 highlights the importance of roadsides acting as refugia for numerous
 species and valuable plant communities as well as supporting biodiversity
 in general.
DOI: 10.5061/dryad.kh189323x
title: Thermal Model for Hyperthermia Treatment of Brain Tumour

description: Code associated to the research article "The interplay of blood flow
 and temperature in regional hyperthermia: A mathematical approach"
 co-authored by Jesús J. Bosque, Gabriel F. Calvo, Víctor M. Pérez-García
 and María Cruz Navarro, to be published in Royal Society Open Science in
 2020. In that article we developed a simple mathematical model for
 hyperthermia treatment of brain tumours and analyse the results. We add
 here the code that we wrote and used to solve the equations and
 draw the conclusions.
description: For more information refer to the original article to be
 published in Royal Society Open Science with the title "The interplay
 of blood flow and temperature in regional hyperthermia: A mathematical
 approach" by the co-authors Jesús J. Bosque, Gabriel F. Calvo, Víctor
 M. Pérez García and María Cruz Navarro.
DOI: 10.15468/dl.3wdfpb
title: Occurrence Download

description: A dataset containing 686 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coregonus nasus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 686 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002595-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.msbcc2fwq
title: Support for a relationship between demography and modeled habitat suitability is scale dependent for the Purple Martin, Progne subis

description: 1. Species distribution models (SDMs) estimate habitat suitability for
 species in geographic space. They are extensively used in conservation
 under the assumption that there is a positive relationship between habitat
 suitability and species success and stability. 2. Given the difficulties
 in obtaining demographic data across a species’ range, this assumption is
 rarely tested. Here we provide a range-wide test of this relationship for
 the eastern subspecies of purple martin (Progne subis subis). 3. We build
 a well-supported SDM for the breeding range of the purple martin, and pair
 it with an unparalleled demographic dataset of nest success and local and
 regional abundance data for the species to test the proposed link between
 habitat suitability and fecundity and demography. 4. We find a positive
 relationship between regional abundance and habitat suitability but no
 relationship between local abundance or fecundity and habitat suitability.
 5. Our data suggest that local success is driven largely by biotic and
 stochastic factors and raise the possibility that purple martins are
 experiencing a time lag in their distribution. More broadly our results
 call for caution in how we interpret SDMs and do not support the
 assumption that areas of high habitat suitability are the best areas for
 species persistence.
description: Puma_samples_10km2.csv - Purple martin occurrence dataset for
 North America from eBird. Dataset was filtered to remove errors and
 thinned to a maximum of 1 record per 10km2
 MartinWatch_nestlevel.csv - Citizen science records of nest
 success between 1995-2016 from the Purple Martin Conservation Association.
 Recording errors and low record numbers are removed as detailed in the
 paper.<br> <br> PMCA_survey.csv - Responses of Purple Martin
 Conservation Association members to a survey regarding management
 practices and nest occupancy. Answers refer to their colony success in the
 year 2016.
DOI: 10.5061/dryad.fqz612jr5
title: Data from: A unique hybodontiform skeleton provides novel insights into Mesozoic chondrichthyan life

description: Asteracanthus apparently was one of the most common Mesozoic hybodontiform
 chondrichthyans, as remains traditionally referred to this genus have been
 reported almost worldwide from Middle Triassic to Late Cretaceous strata
 so far. Asteracanthus was erected by Louis Agassiz for Late Jurassic fin
 spines with stellate tubercles. Later, Arthur Smith Woodward synonymized
 Strophodus, originally introduced by Agassiz for distinctive crushing
 teeth of Triassic to Cretaceous age, with Asteracanthus based on
 associated teeth and spines from the English Middle Jurassic. This
 taxonomic scheme has been accepted for more than 130 years until now,
 although articulated material has never been found. Here, we present a
 unique hybodontiform skeleton from the German Late Jurassic, displaying a
 striking combination of characters: tuberculate dorsal fin spines
 reminiscent of Asteracanthus and multicuspid teeth that markedly differ
 from the crushing teeth previously referred to this genus. Using
 qualitative and quantitative approaches, we compared its fin spines to
 those that were found in association with Agassiz’s Strophodus teeth,
 providing evidence that Asteracanthus and Strophodus in fact represent two
 valid genera distinct from all other hybodontiforms. Morphological
 features that distinguish fin spines of Strophodus from those of all other
 hybodontiforms include a straight anterior border and distally distributed
 posterior denticles. These observations led us to present an emended
 diagnosis for Asteracanthus. Dentally, Asteracanthus shows strong
 resemblance to Hybodus, but it otherwise lacks a palatobasal process on
 the palatoquadrate. Therefore, and in the absence of any reliable
 phylogenetic framework, we recommend treating Asteracanthus as incertae
 familiae until hybodontiform interrelationships are resolved.
DOI: 10.5061/dryad.rr4xgxd6s
title: Data from: Manipulation of cytosine methylation does not remove latitudinal clines in two invasive goldenrod species in Central Europe

description: Invasive species frequently differentiate phenotypically in novel
 environments within a few generations, often even with limited genetic
 variation. For the invasive plants Solidago canadensis and
 S. gigantea, we tested whether such differentiation might have
 happened through heritable epigenetic changes in cytosine methylation. In
 a two-year common-garden experiment, we grew plants from seeds collected
 along a latitudinal gradient in their non-native Central European range to
 test for trait differentiation and whether differentiation disappeared
 when seeds were treated with the demethylation agent zebularine.
 Microsatellite markers revealed no population structure along the
 latitudinal gradient in S. canadensis, but three genetic clusters
 in S. gigantea. Solidago canadensis showed latitudinal
 clines in flowering phenology and growth. In S. gigantea, the
 number of clonal offspring decreased with latitude. Although zebularine
 had a significant effect on early growth, likely through effects on
 cytosine methylation, latitudinal clines remained (or even got stronger)
 in plants raised from seeds treated with zebularine. Thus, our experiment
 provides no evidence that epigenetic mechanisms by selective cytosine
 methylation contribute to the observed phenotypic differentiation in
 invasive goldenrods in Central Europe.
description: <b>Data from: Manipulation of cytosine methylation does not
 remove latitudinal clines in two invasive goldenrod species in Central
 Europe</b>
 EckertHerdenStiftJoshivanKleunen_2020_MolEcol_DryadData.zip
 contains the data from the two-year common-garden experiment
 2015-2016: README.txt contains general
 information on variable description and on data processing.
 EckertHerdenStiftJoshivanKleunen_2020_MolEcol_PlantTraitData.txt
 contains the trait data for both, <em>S. canadensis</em> and
 <em>S. gigantea.</em> 
 EckertHerdenStiftJoshivanKleunen_2020_MolEcol_PlantGrowthData.txt contains the plant growth data for both species from the first year. EckertHerdenStiftJoshivanKleunen_2020_MolEcol_CanadensisMicrosatellitesData.txt contains the microsatellite data for <em>S. canadensis</em>. EckertHerdenStiftJoshivanKleunen_2020_MolEcol_GiganteaMicrosatellitesData.txt contains the microsatellite data for <em>S. gigantea</em>.
DOI: 10.5061/dryad.kh189323z
title: Data on zooplankton species and lake environments from 29 lakes in southern Ontario, Canada

description: The data published here were used to determine temporal variability in the
 drivers of zooplankton community composition, and to identify associations
 between individual species and different environmental metrics. Here, we
 provide two datasets, which are used in the paper by Sinclair et al.
 titled: "Consistent and transient drivers of freshwater zooplankton
 communities". Each dataset is provided as a separate tab in a single
 Excel spreadsheet. The “Info” tab provides more detail on each. The first
 dataset ("Zooplankton community") provides the total abundance
 of each adult zooplankton species detected across 29 lakes from southern
 Ontario, Canada in 2013, 2014, 2015, and 2016. The second dataset
 ("Lake environments") contains information on the depth, area,
 and water chemistry of each sampled lake in each year. Collection methods
 and dates are detailed in the associated article and variable descriptions
 and units are included in the "Info" tab.
description: Please refer to the associated article for data collection
 methods.
description: Please refer to the associated article and attached metadata for
 information on variable transformations and data usage.
DOI: 10.5061/dryad.6djh9w101
title: Data and code for: Male-male contest limits the expression of assortative mate preferences in a polymorphic poison frog

description: Co-divergence of sexual traits and mate preferences can lead to
 assortative mating and subsequently reproductive isolation. However, mate
 choice rarely operates without intrasexual competition, and the effects of
 the latter on speciation are often overlooked. Maintaining trait
 polymorphisms despite gene flow and limiting assortative female
 preferences for less-competitive male phenotypes are two important roles
 that male-male competition may play in the speciation process. Both roles
 rely on the assumption that male-male competition limits the expression of
 divergent female preferences. We tested this assumption in the highly
 color-polymorphic strawberry poison frog (Oophaga pumilio). Females prefer
 males of the local color, suggesting that reproductive isolation may be
 evolving among color morphs. However, this inference does not account for
 male-male competition, which is also color-mediated. We housed females
 with two differently-colored males, and compared reproductive patterns
 when the more attractive male was the territory holder versus when he was
 the non-territorial male. Females mated primarily with the territory
 winner, regardless of coloration, suggesting that when a choice must be
 made between the two, male territoriality overrides female preferences for
 male coloration. Our results highlight the importance of considering the
 combined effects of mate choice and intrasexual competition in shaping
 phenotypic divergence and speciation.
description: The experiments were done in the <em>Oophaga
 pumilio</em> colony at University of Pittsburgh. Behavioral and
 reproductive data was collected by YY and numerous undergrads in the lab,
 curated by YY. Microsatillite analysis and curation was done by YY. R code
 for analysis by YY.
description: The R markdown file contains the code and annotation for all
 analyses and figures presented in the manuscript.
DOI: 10.5061/dryad.1ns1rn8s2
title: Bioaccumulation of the pesticide Imidacloprid in stream organisms and sublethal effects in salamanders in West Virginia

description: Dataset for the article "Bioaccumulation of the Pesticide
 Imidacloprid in Stream Organisms and Sublethal Effects on
 Salamanders."  Contains imidacloprid and metabolite
 concentrations for Desmognathus spp., benthic macroinvertebrates, and
 stream water. Also contains corticosterone concentration data for
 Desmognathus spp. and body condition indices for 5 species of stream
 salamander in relation to water imidacloprid concentrations.Dataset for
 the article "Bioaccumulation of the Pesticide Imidacloprid in Stream
 Organisms and Sublethal Effects on Salamanders."  Contains
 imidacloprid and metabolite concentrations for Desmognathus spp., benthic
 macroinvertebrates, and stream water. Also contains corticosterone
 concentration data for Desmognathus spp. and body condition indices for 5
 species of stream salamander in relation to water imidacloprid
 concentrations.
description: We sampled 48 stream sites in Monongahela National Forest (MNF)
 and two units of the National Park Service (NPS): Gauley River National
 Recreational Area (GARI) and New River Gorge National River (NERI), in
 West Virginia, USA. Of these 48 sites, 27 were adjacent to imidacloprid
 treated hemlock trees and 21 were not.<br> <br> We collected
 water samples from all sites. We extracted imidacloprid from stream water
 and quantified the concentration of imidacloprid in water samples using
 ultra high-performance liquid chromatography-mass spectrometry (UHPLC-MS).
 We also quantified the concentration of imidacloprid metabolites from the
 MNF sites.<br> <br> We sampled salamanders from all 48 sites.
 Captured salamanders were weighed to the nearest 0.1 g with a spring
 scale, and snout-vent length (SVL) and total length were measured to the
 nearest 0.1 mm with dial calipers. We calculated body condition indices
 for each salamander.<br> <br> After sampling salamanders for
 BCI, we collected adult individuals of the salamander genus Desmognathus
 to quantify imidacloprid bioaccumulation and corticosterone levels from 11
 of the 48 sampled sites. A subset of these salamanders was used to
 quantify corticosterone, and these salamanders were decapitated in the
 field and a minimum blood sample of 2 µL was collected within 3 min of
 initial disturbance of the salamander. Plasma samples were assayed for
 corticosterone using radioimmunoassay. Salamander imidacloprid
 concentration was assessed for a subset of salamanders using
 UHPLC-MS.<br> <br> Benthic macroinvertebrates were collected
 from a subset of sites using a D net and imidacloprid concentration within
 composite invertebrate tissues was quantified with UHPLC-MS.
  
description: Users are advised to read the dataset's metadata thoroughly
 to understand appropriate use and data limitations.
DOI: 10.5061/dryad.ffbg79csh
title: Preparatory immunity: Seasonality of mucosal skin defenses and Batrachochytrium infections in Southern leopard frogs

description: Accurately predicting the impacts of climate change on wildlife health
 requires a deeper understanding of seasonal rhythms in host–pathogen
 interactions. The amphibian pathogen, Batrachochytrium dendrobatidis (Bd),
 exhibits seasonality in incidence; however, the role that biological
 rhythms in host defences play in defining this pattern remains largely
 unknown. The aim of this study was to examine whether host immune and
 microbiome defences against Bd correspond with infection risk and seasonal
 fluctuations in temperature and humidity. Over the course of a year, five
 populations of Southern leopard frogs (Rana [Lithobates] sphenocephala) in
 Tennessee, United States, were surveyed for host immunity, microbiome and
 pathogen dynamics. Frogs were swabbed for pathogen load and skin bacterial
 diversity and stimulated to release stored antimicrobial peptides (AMPs).
 Secretions were analysed to estimate total hydrophobic peptide
 concentrations, presence of known AMPs and effectiveness of Bd growth
 inhibition in vitro. The diversity and proportion of bacterial reads with
 a 99% match to sequences of isolates known to inhibit Bd growth in vitro
 were used as an estimate of predicted anti‐Bd function of the skin
 microbiome. Batrachochytrium dendrobatidis dynamics followed the expected
 seasonal fluctuations—peaks in cooler months—which coincided with when
 host mucosal defences were most potent against Bd. Specifically, the
 concentration and expression of stored AMPs cycled synchronously with Bd
 dynamics. Although microbiome changes followed more linear trends over
 time, the proportion of bacteria that can function to inhibit Bd growth
 was greatest when risk of Bd infection was highest. We interpret the
 increase in peptide storage in the fall and the shift to a more anti‐Bd
 microbiome over winter as a preparatory response for subsequent infection
 risk during the colder periods when AMP synthesis and bacterial growth is
 slow and pathogen pressure from this cool‐adapted fungus is high. Given
 that a decrease in stored AMP concentrations as temperatures warm in
 spring likely means greater secretion rates, the subsequent decrease in
 prevalence suggests seasonality of Bd in this host may be in part
 regulated by annual immune rhythms, and dominated by the effects of
 temperature.