cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6b09786
title: Data from: A maladaptive combination of traits contributes to the maintenance of a Drosophila hybrid zone

description: Drosophila teissieri and D. yakuba diverged approximately 3 mya and are
 thought to share a large, ancestral, African range [1, 2, 3]. These
 species now co-occur in parts of continental Africa and in west Africa on
 the island of Bioko [1, 4]. While D. yakuba is a human commensal, D.
 teissieri seems to be associated with Parinari fruits, restricting its
 range to forests [4, 5, 6]. Genome data indicate introgression, despite no
 evidence of contemporary hybridization. Here we report the discovery of D.
 yakuba-D. teissieri hybrids at the interface of secondary forests and
 disturbed, open habitats on Bioko. We demonstrate that hybrids are the F1
 progeny of D. yakuba females and D. teissieri males. At high temperatures
 like those found on Bioko, D. teissieri females are generally less
 receptive to mating, and in combination with temperature effects on egg
 lay and egg-to-adult viability, this decreases the potential for gene flow
 between female D. teissieri and male D. yakuba relative to the reciprocal
 cross. Field and laboratory experiments demonstrate that F1 hybrids have a
 maladaptive combination of D. yakuba behavior and D. teissieri physiology,
 generating additional barriers to gene flow. Nevertheless, analysis of
 introgressed and non-introgressed regions of the genome indicate that,
 while rare, gene flow is relatively recent. Our observations identify
 precise intrinsic and extrinsic factors that, along with hybrid male
 sterility, limit gene flow and maintain these species. These data
 contribute to a growing body of literature that suggests the Gulf of
 Guinea may be a hotspot for hybridization.
description: Cooper et al. data
 packageThis .zip file contains
 all the data files for Cooper et al. 2018.dryad_package.zip
DOI: 10.5061/dryad.16h8j
title: Data from: Risk factors of falls in inpatients and their practical use in identifying high-risk persons at admission, Fukushima Medical University Hospital cohort study

description: Objectives: To clarify the risk factors for falls in hospital settings and
 to propose the use of such factors to identify high-risk persons at
 admission. Design: Prospective cohort study. Setting: Fukushima Medical
 University Hospital, Japan, from August 2008 and September 2009.
 Participants: 9957 adult consecutive inpatients admitted to our hospital.
 Methods: Information was collected at admission from clinical records
 obtained from a structured questionnaire conducted in face-to-face
 interviews with subjects by nurses and doctors and fall events were
 collected from clinical records.Results: The proportion of patients who
 fell during follow-up was 2.5% and the incidence of falls was 3.28 per 100
 person-days. There were significant differences in age, history of
 falling, cognitive dysfunction, planned surgery, wheelchair use, need for
 help to move, use of a remote caring system, rehabilitation, use of
 laxative, hypnotic or psychotropic medications and need for help with
 activities of daily living (ADL) between patients who did and did not
 fall. Multivariable adjusted ORs for falls showed that age, history of
 falls and need for help with ADL were common risk factors in both men and
 women. Using psychotropic medication also increased the risk of falling in
 men while cognitive dysfunction and use of hypnotic medication increased
 the risk of falling in women. Planned surgery was associated with a low
 risk of falls in women. Conclusions: To prevent falls in inpatients it is
 important to identify high-risk persons. Age, history of falling and the
 need for help with ADL are the most important pieces of information to be
 obtained at admission. Care plans for patients including fall prevention
 should be clear and considered.
description: analysisdata_140628This data is SPSS.analysisdata_140723_3.sav
DOI: 10.5061/dryad.dm98k
title: Data from: Genome-wide gene-associated microsatellite markers for the model invasive ascidian, Ciona intestinalis species complex

description: The vase tunicate, Ciona intestinalis species complex, has become a good
 model for ecological and evolutionary studies, especially those focusing
 on microevolution associated with rapidly changing environments. However,
 genome-wide genetic markers are still lacking. Here we characterized a
 large set of genome-wide gene-associated microsatellite markers for C.
 intestinalis spA (= C. robusta). Bioinformatic analysis identified 4654
 microsatellites from expressed sequence tags (ESTs), 2126 of which
 successfully assigned to chromosomes were selected for further analysis.
 Based on the distribution evenness on chromosomes, function annotation and
 suitability for primer design, we chose 545 candidate microsatellites for
 further characterization. After amplification validation and variation
 assessment, 218 loci were polymorphic in at least one of the two
 populations collected from the coast of Arenys de Mar, Spain (N = 24 - 48)
 and Cape Town, South Africa (N = 24 - 33). The number of alleles, observed
 heterozygosity and expected heterozygosity ranged from two to 11, 0 to
 0.833 and 0.021 to 0.818, and from two to 10, 0 to 0.879 and 0.031 to
 0.845 for the Spanish and African populations, respectively. When all
 microsatellites were tested for cross-species utility, only 60 loci
 (25.8%) could be successfully amplified and all loci were polymorphic in
 C. intestinalis spB. A high level of genome-wide polymorphism is likely
 responsible for the low transferability. The large set of microsatellite
 markers characterized here is expected to provide a useful genome-wide
 resource for ecological and evolutionary studies using C. intestinalis as
 a model.
description: Raw microsatellite
 genotype dataRaw genotyping data for
 both Ciona intestinalis spA and spB.
DOI: 10.5061/dryad.v057n
title: Data from: Community traits affect plant–plant interactions across climatic gradients

description: Plant abundances and demography often vary along gradients of
 environmental stress, and neighboring plants can amplify or diminish such
 variation. We asked to what degree the effects of neighboring plants on a
 focal species can be explained by the traits and abundances of species in
 the surrounding community. We studied a common understory herb, Trientalis
 latifolia, across climatic gradients created by topography in the Siskiyou
 Mountains, southwestern Oregon. We compared Trientalis fitness along these
 gradients with and without neighbor removal, and asked whether the effects
 of neighboring plants could be predicted by their community-weighted trait
 values and abundances. Environmental conditions alone did not explain
 whether neighbors had competitive or facilitative effects on Trientalis.
 However, the environment interacted with neighbor traits and biomass to
 influence neighbor effects: at cool, higher elevations, high neighbor
 biomass was associated with stronger facilitative effects, while at warm,
 lower elevations, high neighbor dissimilarity from Trientalis was
 associated with stronger competitive effects. We suggest that covariation
 and interactions among environmental and community characteristics are key
 to understanding species performance along climatic gradients.
description: Core_DatasetThis datasheet contains the core data by individual and plot for the manuscript, including environmental data, Trientalis traits, and community traits. See the Core_Dataset_Metadata.csv for details.Core_Dataset_MetadataMetadata with column definitions and units for Core_Dataset.csvRII_TraitThis file contains relative interaction data and traits by plot. See RII_Trait_Metadata.csv for details.RII_Trait_MetadataMetadata file with column descriptions and units for the RII_Traits.csv file.
DOI: 10.5061/dryad.d1vg6
title: Data from: Delimitation of the Thoracosphaeraceae (Dinophyceae), including the calcareous dinoflagellates, based on large amounts of ribosomal RNA sequence data

description: The phylogenetic relationships of the Dinophyceae (Alveolata) are not
 sufficiently resolved at present. The Thoracosphaeraceae (Peridiniales)
 are the only group of the Alveolata that include members with calcareous
 coccoid stages; this trait is considered apomorphic. Although the coccoid
 stage apparently is not calcareous, Bysmatrum has been assigned to the
 Thoracosphaeraceae based on thecal morphology. We tested the monophyly of
 the Thoracosphaeraceae using large sets of ribosomal RNA sequence data of
 the Alveolata including the Dinophyceae. Phylogenetic analyses were
 performed using Maximum Likelihood and Bayesian approaches. The
 Thoracosphaeraceae were monophyletic, but included also a number of
 non-calcareous dinophytes (such as Ensiculifera and Pfiesteria) and even
 parasites (such as Duboscquodinium and Tintinnophagus). Bysmatrum had an
 isolated and uncertain phylogenetic position outside the
 Thoracosphaeraceae. The phylogenetic relationships among calcareous
 dinophytes appear complex, and the assumption of the single origin of the
 potential to produce calcareous structures is challenged. The application
 of concatenated ribosomal RNA sequence data may prove promising for
 phylogenetic reconstructions of the Dinophyceae in future.
description: Gottschling_etal_Protist_2011Gottschling_Soehner_etal_Protist_2011.zip
DOI: 10.5061/dryad.pm870
title: Data from: Past climate change drives current genetic structure of an endangered freshwater mussel species

description: Historical-to-recent climate change and anthropogenic disturbance affect
 species distributions and genetic structure. The Rio Grande watershed of
 the United States and Mexico encompasses ecosystems that are intensively
 exploited, resulting in substantial degradation of aquatic habitats. While
 significant anthropogenic disturbances in the Rio Grande are recent,
 inhospitable conditions for freshwater organisms likely existed prior to
 such disturbances. A combination of anthropogenic and past climate factors
 may contribute to current distributions of aquatic fauna in the Rio Grande
 basin. We used mitochondrial DNA and 18 microsatellite loci to infer
 evolutionary history and genetic structure of an endangered freshwater
 mussel, Popenaias popeii, throughout the Rio Grande drainage. We estimated
 spatial connectivity and gene flow across extant populations of P. popeii
 and used ecological niche models (ENMs) and approximate Bayesian
 computation (ABC) to infer its evolutionary history during the
 Pleistocene. structure results recovered regional and local population
 clusters in the Rio Grande. ENMs predicted drastic reductions in suitable
 habitat during the last glacial maximum. ABC analyses suggested that
 regional population structure likely arose in this species during the
 mid-to-late Pleistocene and was followed by a late Pleistocene population
 bottleneck in New Mexico populations. The local population structure arose
 relatively recently, perhaps due to anthropogenic factors. Popenaias
 popeii, one of the few freshwater mussel species native to the Rio Grande
 basin, is a case study for understanding how both geological and
 anthropogenic factors shape current population genetic structure.
 Conservation strategies for this species should account for the fragmented
 nature of contemporary populations.
description: Popenaias popeii
 specimen informationList of specimen
 information (species, DNA ID, locality, collection date, GenBank accession
 number for COI, number of microsatellite loci successfully genotyped) used
 in the study. Blanks in the GenBank accession number column indicate
 unsuccessful sequencing.Ppopeii_locality_information.xlsxMicrosatellite genotype dataMicrosatellite genotype data in Genepop format.Ppopeii_microsatellites_GenePop.txtInput and parameter files for STRUCTUREMicrosatellite genotype data in STRUCTURE format.Structure.zipAligned mtDNA sequences in FASTA formatPpopeii_COII_COI.fasta
DOI: 10.5061/dryad.3181p74
title: Data from: The personal and social experiences of community-dwelling younger adults after stroke in Australia: a qualitative interview study

description: Objectives: To examine the personal and social experiences of younger
 adults after stroke. Design: Qualitative study design involving in-depth
 semi-structured interviews and rigorous qualitative descriptive analysis
 informed by social constructionism. Participants: Nineteen young stroke
 survivors aged 18 to 55 at the time of their first-ever stroke. Setting:
 Participants were recruited from urban and rural settings across
 Australia. Interviews took place in a clinic room of the Florey Institute
 of Neuroscience and Mental Health (Melbourne, Australia), over an online
 conference platform or by telephone. Results: Four main themes emerged
 from the discourses: (1) psycho-emotional experiences after young stroke;
 (2) losing pre-stroke life construct and relationships; (3) recovering and
 adapting after young stroke; and (4) invalidated by the old-age, physical
 concept of stroke. While these themes ran through the narratives of all
 participants, data analysis also drew out interesting variation between
 individual experiences. Conclusions: For many younger adults, stroke is an
 unexpected and devastating life event that profoundly diverts their
 biography and presents complex and continued challenges to fulfilling
 age-normative roles. While adaptation, resilience and post-traumatic
 growth are common, this study suggests that more bespoke support is needed
 for younger adults after stroke. Increasing public awareness of young
 stroke is also important, as is increased research attention to this
 problem.
description: Additional thematised
 quotationsSupplemental participant
 quotations organised into themes and sub-themes to provide further support
 for the study results.Interview topic
 guideQuestions related to the
 personal and social experiences of younger stroke survivors extracted from
 the topic guide of the larger qualitative study.
DOI: 10.5061/dryad.016gp34
title: Data from: All-trans retinoic acid disrupts development in ex vivo cultured fetal rat testes. II: modulation of mono-(2-ethylhexyl) phthalate toxicity

description: Humans are universally exposed to low levels of phthalate esters
 (phthalates), which are used to plasticize polyvinyl chloride. Phthalates
 exert adverse effects on the development of seminiferous cords in the
 fetal testis through unknown toxicity pathways. To investigate the
 hypothesis that phthalates alter seminiferous cord development by
 disrupting retinoic acid signaling in the fetal testis, gestational day 15
 fetal rat testes were exposed for 1-3 days to 10-6 M all-trans retinoic
 acid (ATRA) alone or in combination with 10-6 to 10-4 M
 mono-(2-ethylhexyl) phthalate (MEHP) in ex vivo culture. As previously
 reported, exogenous ATRA reduced seminiferous cord number. This effect was
 attenuated in a concentration-dependent fashion by MEHP co-exposure. ATRA
 and MEHP-exposed testes were depleted of DDX4-positive germ cells but not
 Sertoli cells. MEHP alone enhanced the expression of the retinoic acid
 receptor target Rbp1 and the ovary development-associated genes Wnt4 and
 Nr0b1, and suppressed expression of the Leydig cell marker, Star, and the
 germ cell markers, Ddx4 and Pou5f1. In co-exposures, MEHP predominantly
 enhanced the gene expression effects of ATRA, but the Wnt4 and Nr0b1
 concentration-responses were non-linear. Similarly, ATRA increased the
 number of cells expressing the granulosa cell marker FOXL2 in testis
 cultures, but this induction was attenuated by addition of MEHP. These
 results indicate that MEHP can both enhance and inhibit actions of ATRA
 during fetal testis development and provide evidence that retinoic acid
 signaling is a target for phthalate toxicity in the fetal testis.
description: Supplemental
 MaterialsSupplemental Methods,
 Supplemental Figure S1, Supplemental Tables S1 and S2Spade_et_al-ATRA_MEHP-supplement.pdf
DOI: 10.5061/dryad.7vs0v
title: Data from: Historical data to plan the recovery of the European eel

description: 1. Long-term perspectives are critical to understand contemporary
 ecological systems. However, historical data on the distribution of
 biodiversity have only rarely been used in applied environmental sciences.
 2. Here, we use historical sources to reconstruct the historical range of
 the European eel, a critically endangered species. We then use this
 baseline range to set range targets for the recovery of the European eel,
 as opposed to the abundance-based targets established by the European
 Union, which are constrained by the poor information on pre-collapse
 stocks. 3. We collected over 10 000 historical freshwater fish records
 from Spain in the 19th and 16th centuries, as well as over 25 000 records
 from the global biodiversity information facility (GBIF) to characterize
 historical and current European eel distribution in the Iberian Peninsula.
 We converted fish records into an eel presence–absence data set using
 subcatchment as spatial unit of analysis and modelled eel distribution in
 the different historical periods. 4. The eel was historically widespread
 throughout the Iberian Peninsula, but it has lost over 80% of its original
 range, mainly due to river fragmentation by dams. Distribution models
 applied to 16th- and 19th-century data showed a high agreement, supporting
 the use of the 19th-century estimated distribution as a baseline range. We
 identified the number and identity of dams that should be made passable
 for accomplishing specific range recovery targets, for example showing
 that acting upon 20 dams would make available 60% of the baseline eel
 range. 5. Synthesis and applications. This work exemplifies how insights
 gained from historical ecology can support and guide present-day
 management of migratory fishes. Similar approaches could be developed
 throughout Europe to plan the recovery of the eel, since there are large
 amounts of historical eel records. Historical baseline ranges for the eel
 range should be incorporated into the European Union legal mandates aimed
 at the recovery of the species.
description: data
 MADOZ-RELACIONESMS Excel file with two
 sheets, one for the 19th century Madoz Dictonary (MADOZ) and the other for
 the 16th century Relaciones Topográficas. Both sheets give the
 geographical position (in decimal degrees) of localities with information
 on freshwater fish included in the two historical sources. A "1"
 is given to localities citing the eel, while "0" is assigned to
 localities in which freshwater fish were identified by specific or
 genus-level names, but the eel was not cited
DOI: 10.5061/dryad.49vj1
title: Data from: Fighting over food unites the birds of North America in a continental dominance hierarchy

description: Members of different species often engage in aggressive contests over
 resources. This series of aggressive contests between species may result
 in an interspecific dominance hierarchy. Such hierarchies are of interest
 because they could be used to address a variety of research questions, for
 example, do similarly ranked species tend to avoid each other in time or
 space, and what will happen when such species come into contact as
 climates change? Here, we propose a method for creating a
 continental-scale hierarchy, and we make initial analyses based on this
 hierarchy. Leveraging the existing network of citizen scientists from
 Project FeederWatch, we collected the data with which to create a
 continent-spanning interspecific dominance hierarchy that included species
 that do not currently have overlapping geographic distributions. We
 quantified the extent of intransitivities (rock-paper-scissors
 relationships) in the hierarchy, as intransitivities can promote local
 species’ coexistence. Overall, the hierarchy was nearly linear, and
 largely predicted by body mass, although there were clade-specific
 deviations from the average mass–dominance relationship. Warblers and
 orioles, for instance, were more dominant than expected based on their
 body mass, while buntings, grosbeaks, and doves were less dominant than
 expected. Intransitive relationships were rare. Few interactions were
 reported between close relatives and ecological competitors like Mountain
 and Black-capped Chickadees, as such species often have only marginally
 overlapping geographic distributions, restricting opportunity for
 observation. Yet, these species’ ranks—emergent properties of the
 network—were often in agreement with targeted studies of dominance
 relationships between them.
description: FeederWatch
 interactionsThe 7,685 interspecific
 displacements used in our Behavioral Ecology paper to create a dominance
 hierarchy of North American feeder birds.forDryad.csv
DOI: 10.5061/dryad.c8t42
title: Data from: Ancestral origins and invasion pathways in a globally invasive bird correlate with climate and influences from bird trade

description: Invasive species present a major threat to global biodiversity.
 Understanding genetic patterns and evolutionary processes that reinforce
 successful establishment is paramount for elucidating mechanisms
 underlying biological invasions. Among birds, the ring-necked parakeet
 (Psittacula krameri) is one of the most successful invasive species,
 established in over 35 countries. However, little is known about the
 evolutionary genetic origins of this species and what population genetic
 signatures tell us about patterns of invasion. We reveal the ancestral
 origins of populations across the invasive range and explore the potential
 influence of climate and propagule pressure from the pet trade on observed
 genetic patterns. Ring-necked parakeet samples representing the ancestral
 native range (n = 96) were collected from museum specimens, and modern
 samples from the invasive range (n = 855) were gathered from across
 Europe, Mauritius and Seychelles, and sequenced for two mitochondrial DNA
 markers comprising 868 bp of cytochrome b and control region, and
 genotyped at 10 microsatellite loci. Invasive populations comprise birds
 that originate predominantly from Pakistan and northern areas of India.
 Haplotypes associated with more northerly distribution limits in the
 ancestral native range were more prevalent in invasive populations in
 Europe, and the predominance of Asian haplotypes in Europe is consistent
 with the higher number of Asian birds transported by the pet trade outside
 the native range. Successful establishment of invasive species is likely
 to be underpinned by a combination of environmental and anthropogenic
 influences.
description: Psittacula krameri
 genotypes from 10 Microsatellite lociGenotypes for
 ring-necked parakeets across the native and invasive
 ranges.Psittacula krameri genotypes 10
 Msat loci.xlsxPsittacula krameri 74
 mtDNA Haplotypes (control region and cyt.b)Mitochondrial haplotypes
 based on 868bp of control region and cytochrome b, found across the native
 and invasive rangesPsittacula krameri mtDNA
 Haplotype frequenciesHaplotypes for each
 individual in each invasive population and across the native
 range.