cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qnk98sfg2
title: Data from: Population genomics of the 'Arcanum' species group in wild tomatoes: evidence for separate origins of two self-compatible lineages

description: Given their diverse mating systems and recent divergence, wild tomatoes
 (Solanum section Lycopersicon) have become an attractive model system to
 study ecological divergence, the build-up of reproductive barriers, and
 the causes and consequences of the breakdown of self-incompatibility. Here
 we report on a lesser-studied group of species known as the ‘Arcanum’
 group, comprising the nominal species Solanum arcanum, S. chmielewskii and
 S. neorickii. The latter two taxa are self-compatible but are thought to
 self-fertilize at different rates, given their distinct manifestations of
 the morphological ‘selfing syndrome’. Based on experimental crossings and
 transcriptome sequencing of a total of 39 plants representing each
 species’ geographic range, we provide compelling evidence for deep
 genealogical divisions within S. arcanum; only the self-incompatible
 lineage known as ‘var. marañón’ has close genealogical ties to the two
 self-compatible species. Moreover, there is evidence under multiple
 inference schemes for different geographic subsets of S. arcanum var.
 marañón being closest to S. chmielewskii and S. neorickii, respectively.
 To broadly characterize the population-genomic consequences of these
 recent mating-system transitions and their associated speciation events,
 we fit demographic models indicating strong reductions in effective
 population size, congruent with reduced nucleotide and S-locus diversity
 in the two independently derived self-compatible species.
DOI: 10.5061/dryad.63xsj3v1v
title: Observational evidence of herbivore-specific associational effects between neighboring conspecifics in natural, dimorphic populations of Datura wrightii

description: Associational effects – in which the vulnerability of a plant to
 herbivores is influenced by its neighbors – have been widely implicated in
 mediating plant-herbivore interactions. Studies of associational effects
 typically focus on interspecific interactions or pest-crop dynamics.
 However, associational effects may also be important for species with
 intraspecific variation in defensive traits. In this study, we observed
 hundreds of Datura wrightii – which exhibits dimorphism in its trichome
 phenotype – from over 30 dimorphic populations across California. Our aim
 was to determine whether a relationship existed between the trichome
 phenotype of neighboring conspecifics and the likelihood of being damaged
 by four species of herbivorous insects. We visited plants at three
 timepoints to assess how these effects vary both within and between
 growing seasons. We hypothesized that the pattern of associational effects
 would provide rare-morphs (i.e. focal plants that are a different morph
 than their neighbors) with an advantage in the form of reduced herbivory,
 thereby contributing to the negative frequency-dependent selection
 previously documented in this system. We found the best predictor of
 herbivory/herbivore presence on focal plants was the phenotype of the
 focal plant. However, we also found some important neighborhood effects.
 The total number of plants near a focal individual predicted the
 likelihood and/or magnitude of herbivory by Tupiochoris notatus, Lema
 daturaphila, and Manduca sexta. We also found that velvety focal plants
 with primarily sticky neighbors are more susceptible to infestation by
 Tupiochoris notatus and Lema daturaphila. This does not align with the
 hypothesis that associational effects at the near-neighbor scale
 contribute to a rare-morph advantage in this system. Overall the results
 of our study show that the number and trichome-morph composition of
 neighboring conspecifics impact interactions between D. wrightii and
 insect herbivores.
description: Dataset was collected by observing herbivores/herbivory on Datura
 wrightii plants in populations across Central and Southern California.
 Populations were visited in 2017 (Summer, July/aug) and 2018 (Spring,
 April/May; and Summer, July/Aug). Herbivory (all .dmg
 variables) was measured via observer (JKG) estimation from 0% (undamaged)
 to 100% (complete defoliation). Herbivore presence was recorded as a
 binary (0 = no occurence; 1 = occurence). Herbivore occurence was not
 recorded during Spring 2018. Species of herbivore
 observed: ms: Manduca sexta lema:
 Lema daturaphila gh: Grasshoppers (rare
 generalist) fb: flea beetles (Epitrix sp.)
 mirids: Tupiochoris notatus tc: Trichobaris
 compacta (only observed in Summer 2018)
DOI: 10.15468/dl.w5kuwd
title: Occurrence Download

description: A dataset containing 159 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Erythrophleum fordii"
 ]
}

 The dataset includes 159 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002823-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3j9kd51hg
title: A behavioral syndrome linking boldness and flexibility facilitates invasion success in sticklebacks

description: Understanding the factors that allow a species to expand their range and
 adapt to changing habitats is essential for mitigating anthropogenic
 change. We evaluated how behavior and cognition facilitate colonization of
 new environments and evolve post establishment during natural biological
 invasions. Marine threespined sticklebacks are expert colonists with a
 penchant for invading freshwater environments and rapidly adapting to
 them. However, the role of behavior in facilitating rapid adaptation in
 this system has received little attention. By rearing replicate
 populations of sticklebacks under common garden conditions in the lab, we
 tested the hypothesis that boldness is favored in dispersers and that
 neophilia and flexibility are favored in recently-arrived immigrants. We
 found that dispersing populations comprised bold individuals, while
 sticklebacks from the invaded region were flexible in their behavior.
 Moreover, boldness and flexibility were negatively correlated with each
 another at the individual, family and population levels. Multiple lines of
 evidence suggest that there is a heritable component to boldness and
 flexibility, therefore their divergence is likely to be evolutionary in
 origin. If boldness is favored in invaders during the initial dispersal
 stage, while flexibility is favored in recent immigrants during the
 establishment stage, then the link between boldness and flexibility could
 generate positive correlations between successes during both the dispersal
 and establishment stages, and therefore play a key role in facilitating
 colonization success in this important model organism.
DOI: 10.5061/dryad.000000036
title: Market forces determine the distribution of a leaky function in a simple microbial community

description: Many biological functions are leaky, and organisms that perform them
 contribute some of their products to a community "marketplace"
 where non-performing individuals may compete for them. Leaky functions are
 partitioned unequally in microbial communities, and the evolutionary
 forces determining which species perform them and which become
 beneficiaries are poorly understood. Here we demonstrate that the market
 principle of comparative advantage determines the distribution of a leaky
 antibiotic resistance gene in an environment occupied by two
 "species" - strains of Escherichia coli growing on mutually
 exclusive resources and thus occupying separate niches. Communities
 comprised of antibiotic-resistant cells were rapidly invaded by sensitive
 cells of both types. While the two phenotypes coexisted stably for 500
 generations, in 15/18 replicates, antibiotic sensitivity became fixed in
 one species. Fixation always occurred in the same species, despite both
 species being genetically identical except for their niche-defining
 mutation. In the absence of antibiotic, the fitness cost of resistance was
 identical in both species. However, the intrinsic resistance of the
 species that ultimately became the sole helper was significantly lower,
 and thus its reward for expressing the resistance gene was higher.
 Opportunity cost of resistance, not absolute cost or efficiency of
 antibiotic removal, determined which species became helper, consistent
 with the economic theory of comparative advantage. We present a model that
 suggests that this market-like dynamic is a general property of Black
 Queen systems, and in communities dependent on multiple leaky functions,
 could lead to the spontaneous development of an equitable and efficient
 division of labor.
description: This dataset contains raw data from microbial competition
 experiments; growth curve parameters extracted from microbial growth
 experiments; and R code used to analyze these data statistically as well
 as generate the figures contained in the manuscript. They have been
 minimally processed, with the exception of the growth curve experiments,
 where the raw output from the automated plate reader has been reduced to
 "area under the curve" and "exponential growth rate"
 parameters prior to analysis.
description: A readme file is included with the dataset. We are happy to
 assist you in using the data if you would like to replicate our findings
 -- contact us at evolve@uab.edu.
DOI: 10.5061/dryad.tqjq2bvzb
title: Predicting spatio-temporal population patterns of Borrelia burgdorferi, the Lyme disease pathogen

description: The causative bacterium of Lyme disease, Borrelia burgdorferi, expanded
 from an undetected human pathogen into the etiologic agent of the most
 common vector-borne disease in the United States over the last several
 decades. Systematic field collections of the tick vector reveal increases
 in the geographic range and population size of B. burgdorferi that
 coincided with increases in human Lyme disease incidence across New York
 State. Here we investigate the impact of environmental features on the
 population dynamics of B. burgdorferi. Analytical models developed using
 field collections of nearly 19,000 nymphal Ixodes scapularis and
 spatially- and temporally-explicit environmental features accurately
 explained the variation of B. burgdorferi population sizes across space
 and time. Importantly, the model identified environmental features that
 can be used to predict the biogeographical patterns of B.
 burgdorferi-infected ticks into future years and in previously unsampled
 areas. Forecasting the distribution and abundance of a pathogen at fine
 geographic scales offers a powerful strategy to mitigate a serious public
 health threat.
description: Model selection was performed with R ‘mass’ package. The stepAIC
 function performs stepwise model selection by AIC, searching the range of
 models with the lower component defined as the null model and upper
 component defined as the full model. Model search arguments are set as
 “both” such that search strategy is bi-directional, with steps =1000, and
 k = 2.
description: R codes include two separate files for compiling data and model
 development. Data include tick/pathogen collection data for different
 years, with data grouped by years for training and test data for the
 model.  Relevant R code and tick collection data that
 were previously published can be found at MendeleyData (doi: https://doi.org/10.17632/rtd52gnbyy.1) with further detail in Supplementary Materials in Tran et al. 2020.
DOI: 10.7291/d1rt0q
title: Parallel evolution of phenological isolation across the speciation continuum in serpentine-adapted annual wildflowers

description: Understanding the relative importance of reproductive isolating mechanisms
 across the speciation continuum remains an outstanding challenge in
 evolutionary biology. Here we examine a common isolating mechanism,
 reproductive phenology, between plant sister taxa at different stages of
 adaptive divergence to gain insight into its relative importance during
 speciation. We study 17 plant taxa that have independently adapted to
 inhospitable serpentine soils, and contrast each with a nonserpentine
 sister taxon to form pairs at either ecotypic or species-level divergence.
 We use greenhouse-based reciprocal transplants in field soils to quantify
 how often flowering time (FT) shifts accompany serpentine adaptation, when
 FT shifts evolve during speciation, and the genetic versus plastic basis
 of these shifts. We find that genetically-based shifts in FT in
 serpentine-adapted taxa are pervasive regardless of the stage of
 divergence. Although plasticity increases FT shifts in 5 of the pairs, the
 degree of plasticity does not differ when comparing ecotypic versus
 species-level divergence. FT shifts generally led to significant, but
 incomplete, reproductive isolation that did not vary in strength by stage
 of divergence. Our work shows that adaptation to a novel habitat may
 predictably drive phenological isolation early in the speciation
 process. 
description: All data manipulation and analyses are described and executed in
 the R script. Please refer to the README for details.
DOI: 10.25338/b8tp7g
title: Blueprint for phasing and assembling the genomes of heterozygous polyploids: Application to the octoploid genome of strawberry

description: The challenge of allelic diversity for assembling haplotypes is
 exemplified in polyploid genomes containing homoeologous chromosomes of
 identical ancestry, and significant homologous variation within their
 ancestral subgenomes. Cultivated strawberry (Fragaria × ananassa) and its
 progenitors are outbred octoploids in which up to eight homologous and
 homoeologous alleles are preserved. This introduces significant risk of
 haplotype collapse, switching, and chimeric fusions during assembly. Using
 third generation HiFi sequences from PacBio, we assembled the genome of
 the day-neutral octoploid F. × ananassa hybrid ‘Royal Royce’ from the
 University of California. Our goal was to produce subgenome- and
 haplotype-resolved assemblies of all 56 chromosomes, accurately
 reconstructing the parental haploid chromosome complements. 
 Previous work has demonstrated that partitioning sequences by parental
 phase supports direct assembly of haplotypes in heterozygous diploid
 species. We leveraged the accuracy of HiFi sequence data with
 pedigree-informed sequencing to partition long read sequences by phase,
 and reduce the downstream risk of subgenomic chimeras during assembly. We
 were able to utilize an octoploid strawberry recombination breakpoint map
 containing 3.6 M variants to identify and break chimeric junctions, and
 perform scaffolding of the phase-1 and phase-2 octoploid assemblies. The
 N50 contiguity of the phase-1 and phase-2 assemblies prior to scaffolding
 and gap-filling was 11 Mb. The final haploid assembly represented seven of
 28 chromosomes in a single contiguous sequence, and averaged fewer than
 three gaps per pseudomolecule. Additionally, we re-annotated the octoploid
 genome to produce a custom F. × ananassa repeat library and improved set
 of gene models based on IsoSeq transcript data and an expansive RNA-seq
 expression atlas. Here we present ‘FaRR1’, a gold-standard reference
 genome of F. × ananassa cultivar ‘Royal Royce’ to assist future genomic
 research and molecular breeding of allo-octoploid strawberry.
description: ***WARNING: THIS DATA SUBMISSION CONTAINS FILES ASSOCIATED WITH
 THREE SEPARATE GENOME ASSEMBLIES: -
 files with the prefix
 <em><strong>'farr1.'</strong></em> are
 associated with the Royal Royce synthetic haploid genome (for
 most user applications) - files with the
 prefix
 <em><strong>'farr1_phase1.'</strong></em> are associated with the Royal Royce phase1 (parent haplotype A) genome - files with the prefix <em><strong>'farr1_phase2.'</strong></em> are associated with the Royal Royce phase2 (parent haplotype B) genome
DOI: 10.5061/dryad.rfj6q5797
title: Functional extinction of dugongs in China

description: Dugongs (Dugong dugon) experienced a serious population decline in China
 during the twentieth century, and their regional status is poorly
 understood. To determine their current distribution and status, we
 conducted a large-scale interview survey of marine resource users across
 four Chinese provinces, and reviewed all available historical data
 covering the past distribution of dugongs in China. Only 5% of 788
 respondents reported past dugong sightings, with a mean last-sighting date
 of 23 years earlier, and only three respondents reported sightings from
 within the past five years. Historical records of dugongs peak around
 1960, and then decrease rapidly from 1975 onwards; no records are
 documented after 2008, with no verified field observations after 2000.
 Based on these findings, we are forced to conclude that dugongs have
 experienced rapid population collapse during recent decades and are now
 functionally extinct in China. Our study provides evidence of a new
 regional loss of a charismatic marine megafaunal species, and the first
 reported functional extinction of a large vertebrate in Chinese marine
 waters. This rapid documented population collapse also serves as a
 sobering reminder that extinctions can occur before effective conservation
 actions are developed.
description: This dataset provides the  electronic supplementary material for
 "Functional extinction of dugongs in China".
DOI: 10.15468/dl.6sdk34
title: Occurrence Download

description: A dataset containing 964 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dialium pachyphyllum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 964 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002824-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5x69p8d2h
title: Fire, drought and flooding rains: the effect of climatic extremes on bird species’ responses to time since fire

description: Aim: Climatic extremes and fire affect ecosystems across the globe, yet
 our understanding of how species are influenced by the interaction of
 these broad-scale ecological drivers is poorly understood. Using a
 ten-year dataset, we tested how extreme drought and rainfall interacted
 with time since fire (TSF) to shape bird species’ distributions. Location:
 Semi-arid mallee woodlands of south-eastern Australia. Methods: We
 quantified the effects of climatic extremes on bird species’ occurrence,
 species richness and incidence at 180 sites across three climatic
 periods—an El Niño-associated drought (the ‘Big Dry’), immediately after
 La Niña drought-breaking rainfall (‘Big Wet’), and three years following
 the La Niña event (‘Post-Big Wet’). We then compared species’ responses to
 TSF across the three climatic periods using a chrono-sequence of sites
 from 1-117 years post-fire. Results: La Niña rainfall had sustained
 impacts on species’ occurrence. Over half of species increased
 significantly during the Big Wet. Despite three intervening years of
 below-average rainfall, three quarters of these species remained
 comparably high, Post-Big Wet. By contrast, less than half of threatened
 and declining species benefited from high rainfall. Responses of species
 to TSF were found to differ contingent on climatic conditions: almost
 twice as many species responded to TSF during the Big Wet, and almost
 three times as many Post-Big Wet, compared to the Big Dry. Across climatic
 periods, a majority of species showed preference for mid to older
 post-fire vegetation. Main conclusions: Variation in responses to TSF is
 likely due to the effect of climatic variation on resources. We suggest
 that, at sites of different post-fire age, interactions between TSF and
 climate may differentially influence both the availability and longevity
 of resources. Given climatic extremes are predicted to become increasingly
 severe with climate change, accounting for their influence on fauna-fire
 dynamics will require careful management of fire.
description: Methods for data collection and processing can be found in the
 associated manuscript, Connell et al. Fire, drought and flooding rains:
 the effect of climatic extremes on bird species’ responses to time since
 fire.
description: Connell et al._Occurrence data_Climate fire.csv
 Repeat presence absence data for all bird species at study
 sites across three time periods. Environmental co-variates associated with
 each study site are also listed. Abbreviations are as follows:
 Veg_type - TM = Triodia mallee Veg_type - CM
 = Chenopod mallee TSF_adjusted = time since fire age of
 site during year of survey Connell et al._New
 data.csv New data to which climate + fire GAMMs were
 predicted. Abbreviations as above.
DOI: 10.5061/dryad.6m905qfzs
title: Dietary composition and overlap among small- and medium-sized carnivores in Flanders, Belgium

description: There are increasing concerns about the status and population trends
 carnivores around the world. Carnivores play an important role in
 terrestrial ecosystems, as their interactions influence the composition
 and function of ecological communities. In the context of global change,
 it is essential to understand the interactions and resource use of
 carnivores. In this study, we explore the dietary ecology of six small-
 and medium-sized carnivores (red fox, European badger, European polecat,
 stoat, stone marten and least weasel) to determine their main food
 resources and the degree of food overlap in Flanders, Belgium. The studied
 species differed in their food consumption pattern with some being
 generalist and some more specialist. The dietary composition among the
 species was clearly different, although certain species showed
 considerable overlap for different food types. We also conclude that the
 differences and overlap in dietary habits among the species were
 consistent across seasons. Understanding these relationships among
 species’ populations and their dietary ecology is essential for
 biodiversity conservation and nature management.
DOI: 10.5061/dryad.sn02v6x3j
title: Data from: Clinical presentation and management of SMART syndrome

description: Stroke-like migraine attacks after radiation therapy (SMART) syndrome
 represents a rare but serious condition manifesting years after cranial
 radiation therapy (RT). Characterized by migraine-type headaches,
 stroke-like deficits and/or seizures and MR imaging abnormalities,
 including cortical gyriform enhancement in irradiated brain regions, SMART
 remains diagnostically and therapeutically
 challenging. Distinction from tumor progression is difficult and
 treatment options are limited. Although frequently
 reversible, SMART episodes can recur and effectuate
 persistent neurologic and/or imaging sequelae.