cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f5r163j
title: Data from: Introduced garden plants are strong competitors of native and alien residents under simulated climate change

description: 1) Most invasive plants have been originally introduced for horticultural
 purposes. Still, most alien garden plants have not naturalized yet,
 probably due in part to inadequate climatic conditions. Climate change may
 alter this, but few experimental studies have addressed this for
 non-naturalized alien garden plants, and those that have, addressed only
 singular aspects of climate change. 2) In a greenhouse experiment, we
 examined the performance of nine non-naturalized alien herbaceous garden
 plants of varying climatic origins in response to simulated climate
 warming and reduced water availability, in a factorial design, as
 projected for southern Germany. To assess their invasion potential, we
 grew the species in competition with resident native and
 already-naturalized alien species. 3) Reduced watering negatively affected
 non-naturalized garden plants, as well as the native and naturalized
 competitors, particularly at higher temperatures. However, non-naturalized
 aliens performed better relative to competitors when temperatures
 increased. Naturalized and native resident competitor responses to climate
 change were both negative, but across climate treatments, non-naturalized
 aliens, irrespective of their climatic origins, performed better against
 native than against naturalized competitors. 4) Synthesis. We conclude
 that relative performance compared to resident species may increase for
 non-naturalized alien garden plants under climate change, as resident
 species become less competitive. Ongoing climate change is therefore
 likely to promote naturalization of commonly-planted alien herbaceous
 species.
description: Haeuseretal_Dryad_uploadZip file containing all data for Haeuser et all. 2018 JEcol.
DOI: 10.5061/dryad.1978
title: Data from: Complex phylogeographic patterns in the freshwater alga Synura provide new insights on ubiquity versus endemism in microbial eukaryotes

description: The global distribution, abundance, and diversity of microscopic
 freshwater algae demonstrate an ability to overcome significant barriers
 such as dry land and oceans by exploiting a range of biotic and abiotic
 colonization vectors. If these vectors are considered unlimited and
 colonization occurs in proportion to population size, then globally
 ubiquitous distributions are predicted to arise. This model contrasts with
 observations that many freshwater microalgal taxa possess true
 biogeographies. Here, using a concatenated multi-gene dataset, we study
 the phylogeography of the freshwater heterokont alga Synura petersenii
 sensu lato. Our results suggest that this Synura morphotaxon contains both
 cosmopolitan and regionally endemic cryptic species, co-occurring in some
 cases, and masked by a common ultrastructural morphology. Phylogenies
 based on both proteins (seven protein-coding plastid and mitochondrial
 genes) and DNA (nine genes including ITS and 18S rDNA) reveal pronounced
 biogeographic delineations within phylotypes of this cryptic species
 complex, while retaining one clade that is globally distributed. Relaxed
 molecular clock calculations, constrained by fossil records, suggest that
 the genus Synura is considerably older than currently proposed. The
 availability of tectonically-relevant geological time (10^7-10^8 years)
 has enabled the development of the observed, complex biogeographic
 patterns. Our comprehensive analysis of freshwater algal biogeography
 suggests that neither ubiquity nor endemism wholly explain global patterns
 of microbial eukaryote distribution, and that processes of dispersal
 remain poorly understood.
description: 7-protein sequence
 alignment of Synura peterseniiThe concatenated
 7-protein alignment of Synura petersenii (plastid: PSAA, PSBA, PSBC, RBCL;
 mitochondrion: COB, COX1, COX3) with five closely related Synura and other
 heterokonts as outgroup taxa that used for the phylogeny
 analysis.Syn_7AA_2009Nov25.nex9-gene DNA sequence aligment of Synura peterseniiThe concatenated 9-gene alignment of Synura petersenii (plastid: PSAA, PSBA, PSBC, RBCL; mitochondrion: COB, COX1, COX3; nuclear: ITS, 18S rDNA) with five closely related Synura and other heterokonts as outgroup taxa that used for the phylogeny analysis.9Syn106.nex
DOI: 10.5061/dryad.q91784t
title: Data from: Heterochromatin-enriched assemblies reveal the sequence and organization of the Drosophila melanogaster Y chromosome

description: Heterochromatic regions of the genome are repeat-rich and poor in protein
 coding genes, and are therefore underrepresented in even the best genome
 assemblies. One of the most difficult regions of the genome to assemble
 are sex-limited chromosomes. The Drosophila melanogaster Y chromosome is
 entirely heterochromatic, yet has wide-ranging effects on male fertility,
 fitness, and genome-wide gene expression. The genetic basis of this
 phenotypic variation is difficult to study, in part because we do not know
 the detailed organization of the Y chromosome. To study Y chromosome
 organization in D. melanogaster, we develop an assembly strategy involving
 the in silico enrichment of heterochromatic long single-molecule reads and
 use these reads to create targeted de novo assemblies of heterochromatic
 sequences. We assigned contigs to the Y chromosome using Illumina reads to
 identify male-specific sequences. Our pipeline extends the D. melanogaster
 reference genome by 11.9 Mb, closes 43.8% of the gaps, and improves
 overall contiguity. The addition of 10.6 MB of Y-linked sequence permitted
 us to study the organization of repeats and genes along the Y chromosome.
 We detected a high rate of duplication to the pericentric regions of the Y
 chromosome from other regions in the genome. Most of these duplicated
 genes exist in multiple copies. We detail the evolutionary history of one
 sex-linked gene family—crystal-Stellate. While the Y chromosome does not
 undergo crossing over, we observed high gene conversion rates within and
 between members of the crystal-Stellate gene family, Su(Ste), and PCKR,
 compared to genome-wide estimates. Our results suggest that gene
 conversion and gene duplication play an important role in the evolution of
 Y-linked genes.
description: Dryad.Chang.Larracuente.Genetics.11.12.2018
DOI: 10.5061/dryad.p05t5d0
title: Data from: Habitat amount hypothesis and passive sampling explain mammal species composition in Amazonian river islands

description: Nested structures of species assemblages have been frequently associated
 with patch size and isolation, leading to the conclusion that
 colonization-extinction dynamics drives nestedness. The ‘passive sampling’
 model states that the regional abundance of species randomly determines
 their occurrence in patches. The ‘habitat amount hypothesis’ also
 challenges patch size and isolation effects, arguing that they occur
 because of a 'sample area effect'. Here we (1) ask whether the
 structure of the mammal assemblages of fluvial islands shows a nested
 pattern, (2) test whether species’ regional abundance predicts species’
 occurrence on islands, and (3) ask whether habitat amount in the landscape
 and matrix resistance to biological flow predict the islands’ species
 composition. We quantified nestedness and tested its significance using
 null models. We used a regression model to analyze whether a species’
 relative regional abundance predicts its incidence on islands. We accessed
 islands’ species composition by an NMDS ordination and used multiple
 regression to evaluate how species composition responds to habitat amount
 and matrix resistance. The degree of nestedness did not differ from that
 expected by the passive sampling hypothesis. Likewise, species’ regional
 abundance predicted its occurrence on islands. Habitat amount successfully
 predicted the species composition on islands, whereas matrix resistance
 did not. We suggest the application of habitat amount hypothesis for
 predicting species composition in other patchy systems. Although the
 island biogeography perspective has dominated the literature, we suggest
 that the passive sampling perspective is more appropriate for explaining
 the assemblages’ structure in this and other non-equilibrium patch
 systems.
description: Rabelo_mammals-in-islands_dataThese data are a product of Rafael Rabelo’s Master thesis, conducted at the Ecology Graduate Program of Brazil´s National Institute for Amazon Research (INPA), with logistical and financial support from Mamirauá Institute for Sustainable Development (IDSM-OS/MCTIC). The aim of the research was to evaluate the pattern of mammal distribution in fluvial islands and to understand the factors that drive species distribution.doi:10.5063/F1V12310This link redirects to the dataset archived at KNB repository.
DOI: 10.5061/dryad.r2dm56s
title: Data from: Two-year bee, or not two-year bee? How voltinism is affected by temperature and season length in a high-elevation solitary bee

description: Organisms must often make developmental decisions without complete
 information about future conditions. This uncertainty—for example, about
 the duration of conditions favorable for growth—can favor bet-hedging
 strategies. Here, we investigated the causes of life-cycle variation in
 Osmia iridis, a bee exhibiting a possible bet-hedging strategy with
 co-occurring one- and two-year life cycles. One-year bees reach adulthood
 quickly but die if they fail to complete pupation before winter; two-year
 bees adopt a low-risk, low-reward strategy of postponing pupation until
 the second summer. We reared larval bees in incubators in various
 experimental conditions and found that warmer—but not longer—summers, and
 early birth dates, increased the frequency of one-year life cycles. Using
 in situ temperature measurements and developmental trajectories of
 laboratory- and field-reared bees, we estimated degree-days required to
 reach adulthood in a single year. Local long-term (1950–2015) climate
 records reveal that this heat requirement is met in only ~7% of summers,
 suggesting that the observed distribution of life cycles is adaptive.
 Warming summers will likely decrease average generation times in these
 populations. Nevertheless, survival of bees attempting one-year life
 cycles—particularly those developing from late-laid eggs—will be
 &lt;100%; consequently, we expect the life-cycle polymorphism to
 persist.
description: Osmia_iridis_summer_duration_expt_2013-14Please see README file.Osmia_iridis_summer_duration_expt_2014-15Please see README file.Osmia_iridis_2015_summer_incubator_exptData used to generate Fig. 3A-B. Please see README file for details.Osmia_iridis_2016_summer_incubator_exptData used to generate Fig. 3C-D. Please see README file for details.Osmia_iridis_development_by_DD_2015-16Data used to generate Fig. 4. Please see README file for details.NOAA_CB_dataProcessed data from NOAA's Crested Butte weather station. Please see README file for details.NOAA_CB_DD12_1950-2015Please see README file.NOAA_CB_DD12_1950-2015_by_dayData used to generate Fig. 5. Please see README file for details.Osmia_iridis_parsivoltinism_statsData used to generate Fig. 6. Please see README file for details.Forrest_HOBO_data_May2013-Dec2016Temperature data from field sites. Please see README file for details.
DOI: 10.5061/dryad.4vc0rg0
title: Data from: Genetic diversity and population divergences of an indigenous tree (Coffea mauritiana) in Reunion Island: role of climatic and geographical factors

description: Oceanic islands are commonly considered as natural laboratories for
 studies on evolution and speciation. The evolutionary specificities of
 islands associated with species biology provide unique scenarios to study
 the role of geography and climate in driving population divergence.
 However, few studies have addressed this subject in small oceanic islands
 with heterogeneous climates. Being widely distributed in Reunion Island
 forest, Coffea mauritiana represents an interesting model case for
 investigating patterns of within-island differentiation at small spatial
 scale. In this study, we examined the genetic diversity and population
 divergences of C. mauritiana using SNP markers obtained from 323
 individuals across 34 locations in Reunion Island. Using redundancy
 analysis, we further evaluated the contribution of geographic and climatic
 factors to shaping genetic divergence among populations. Genetic diversity
 analyses revealed that accessions clustered according to the source
 population, with further grouping in regional clusters. Genetic
 relationships among the regional clusters underlined a recent process of
 expansion in the form of step-by-step colonization on both sides of the
 island. Divergence among source populations was mostly driven by the joint
 effect of geographic distance and climatic heterogeneity. The pattern of
 isolation-by-geography was in accordance with the dispersal
 characteristics of the species, while isolation-by-environment was mostly
 explained by the heterogeneous rainfall patterns, probably associated with
 an asynchronous flowering among populations. These findings advance our
 knowledge on the patterns of genetic diversity and factors of population
 differentiation of species native to Reunion Island, and will also
 usefully guide forest management for conservation.
description: Data_Dryad_HDY-18-A0272RSNP data obtained by Dart sequencing from collected samples in Reunion Island
DOI: 10.5061/dryad.5tb3312
title: Data from: Condition-dependent foraging strategies in a coastal seabird: evidence that the rich get richer

description: The degree to which foraging individuals are able to appropriately modify
 their behaviors in response to dynamic environmental conditions and
 associated resource availability can have important fitness consequences.
 Despite an increasingly refined understanding of differences in foraging
 behavior between individuals, we still lack detailed characterizations of
 within-individual variation over space and time, and what factors may
 drive this variability. From 2014-2017, we used GPS transmitters and
 accelerometers to document foraging movements by breeding adult Brown
 Pelicans (Pelecanus occidentalis) in the northern Gulf of Mexico, where
 the prey landscape is patchy and dynamic at various scales. Assessments of
 traditional foraging metrics such as trip distance, linearity, or duration
 did not yield significant relationships between individuals. However, we
 did observe lower site fidelity and less variation in energy expenditure
 in birds of higher body condition, despite a population-level trend of
 increased fidelity as the breeding season progressed. These findings
 suggest that high-quality individuals are both more variable and more
 efficient in their foraging behaviors during a period of high energetic
 demand, consistent with a 'rich get richer' scenario in which
 individuals in better condition are able to invest in more costly
 behaviors that provide higher returns. This work highlights the importance
 of considering behavioral variation at multiple scales, with particular
 reference to within-individual variation, to improve our understanding of
 foraging ecology in wild populations.
description: Brown pelican (Pelecanus
 occidentalis) GPS telemetry data, 2014-2017Raw GPS telemetry data
 collected from 30 adult brown pelicans nesting on Raccoon Island in the
 northern Gulf of Mexico. All dates and times are in GMT/UTC, and are
 presented in 24-hour format. Birds are identified by their GPS tag
 numbers, which do not carry any quantitative significance. Further
 information on these individuals can be found in Supplementary Tables 1
 and 2 of the article.Geary_etal_BEHECO-2018-0101_BRPE_telemetry_data_2014-2017.csv
DOI: 10.5061/dryad.h1542kr
title: Data from: Patterns of transposable element variation and clinality in Drosophila

description: Natural populations often exist in spatially diverse environments and may
 experience variation in the strength and targets of natural selection
 across their ranges. Drosophila provides an excellent opportunity to study
 the effects of spatially varying selection in natural populations, as both
 D. melanogaster and D. simulans live across a wide range of environments
 in North America. Here, we characterize patterns of variation in
 transposable elements (TEs) from six populations of D. melanogaster and
 nine populations of D. simulans sampled from multiple latitudes across
 North America. We find a nearly two-fold excess of TEs in D. melanogaster
 relative to D. simulans, with this difference largely driven by TEs
 segregating at the lowest and highest allele frequencies. We find no
 effect of latitude on either total TE abundance or average TE allele
 frequencies in either species. Moreover, we show that, as a class of
 mutations, the most common patterns of TE variation do not coincide with
 the sampled latitudinal gradient, nor are they consistent with local
 adaptation acting on environmental differences found in the most extreme
 latitudes. We also do not find a cline in ancestry for North American D.
 melanogaster—for either TEs or SNPs—suggesting a limited role for
 demography in shaping patterns of TE variation. Though we find little
 evidence for widespread clinality among TEs in Drosophila, this does not
 necessarily imply a limited role for TEs in adaptation. We discuss the
 need for improved models of adaptation to large-scale environmental
 heterogeneity, and how these might be applied to T
description: dmel_na_teCallsTE calls for North American Dmeldsim_na_teCallsTE calls for North American Dsimdmel_afrEur_teCallsTE calls for Dmel from Africa and Europete_database_creationFiles and code needed to create the TE databaserunning_teflonFiles and code needed to run TEFLoNrunning_popoolation2Files and code needed to run PoPoolation2README
DOI: 10.5061/dryad.qc90qb4
title: Data from: Multi-perspective predictive modeling for acute kidney injury in general hospital populations using electronic medical records

description: Objective: Acute kidney injury (AKI) in hospitalized patients puts them at
 much higher risk for developing future health problems such as chronic
 kidney disease, stroke, and heart disease. Accurate AKI prediction would
 allow timely prevention and intervention. However, current AKI prediction
 researches pay less attention to model building strategies that meet
 complex clinical application scenario. This study aims to build and
 evaluate AKI prediction models from multiple perspectives that reflect
 different clinical applications. Material and Methods: A retrospective
 cohort of 76,957 encounters and relevant clinical variables were extracted
 from a tertiary care, academic hospital electronic medical record (EMR)
 system between November 2007 and December 2016. Five machine learning
 methods were used to build prediction models. Prediction tasks from four
 clinical perspectives with different modeling and evaluation strategies
 were designed to build and evaluate the models. Results: Experimental
 analysis of the AKI prediction models built from four different clinical
 perspectives suggest a realistic prediction performance in cross-validated
 AUC ranging from 0.720 to 0.764. Discussion: Results show that models
 built at admission is effective for predicting AKI events in the next day;
 models built using data with a fixed lead time to AKI onset is still
 effective in the dynamic clinical application scenario in which each
 patient’s lead time to AKI onset is different. Conclusion: To our best
 knowledge, this is the first systematic study to explore multiple clinical
 perspectives in building predictive models for AKI in the general
 inpatient population to reflect real performance in clinical application.
description: AKI_Prediction_Scrubbed_EMR
DOI: 10.34894/7p3daf
title: Openarch Dutch death certificates

description: Cleaned, deduplicated and (partially) standardized version of Dutch death certificates (c. 1811-1960), retrieved from &lt;a href="https://www.openarch.nl/exports/5cfb55ebaf9fe5aaf216f6da1229c632/"&gt;openarch.nl&lt;/a&gt;. The csv files per archive, used to create this dataset, were retrieved in January 2020. Scripts used to create this dataset are available &lt;a href="https://github.com/CLARIAH/wp4-civreg"&gt;at Github/wp4-civreg &lt;/a&gt;(version 1.0).
description: Note that deduplication may still be imperfect, especially for stillbirths without a full name.
DOI: 10.5061/dryad.g28t010
title: Data from: A songbird compensates for wing molt during escape flights by reducing the molt gap and increasing angle-of-attack

description: During molt, birds replace their feathers to retain feather quality and
 maintain flight performance. However, wing gaps inherent of this process
 can also reduce flight capacities, which could be detrimental when
 foraging or escaping predators. Still, many bird species will not stop
 their normal activities when molting. In this study, we investigated
 whether and how birds adjust their escape flight behavior to compensate
 for the reduction in performance when flying with wing gaps. Using
 stereoscopic high-speed videography, we filmed 146 upward-directed escape
 flights of 19 and 22 pied flycatchers (Ficedula hypoleuca) with and
 without simulated molt gaps, respectively. We then reconstructed the
 three-dimensional body and wing movements throughout each maneuver. By
 comparing flights with and without gaps, we determined how wing molt gaps
 affected wing morphology, escape flight performance, and how the birds
 adjusted their flight kinematics in order to negate possible negative
 aerodynamic effects. Our manipulations resulted in a lower
 second-moment-of-area of the wings, but flight speed and net aerodynamic
 force production did not differ between the two groups. We found that in
 manipulated birds, the size of the gap was reduced as the flight feathers
 adjacent to the gap had moved towards each other. Moreover, the
 experimental decrease in second-moment-of-area was associated with an
 increase in angle-of-attack, whereas changes in wingbeat-induced speeds
 were associated with variations in aerodynamic force production. This
 suggests that the control of escape flight in molting birds might be
 modular, allowing relatively simple flight control, thus reducing the
 burden on the neuro-muscular flight control system.
description: Database
 S1Body, tail and wingbeat
 kinematics for all analyzed flight sequences, stored in MATLAB (MathWorks,
 Inc.) binary data container format. Each flight sequence is identified by
 the combination calendar date and sequence number; treatment information
 consists of treatment group (‘control’ or ‘molt’), bird ID number and
 frames per second of the video. The movement dynamics of each digitized
 body, wing and tail marker throughout the flight is defined as its {x,y,z}
 position throughout time (t) and normalized time (tau). See Figure 1A for
 the {x,y,z} coordinate system, and Figure 1C and Table 1 for the
 definition of the natural body, wing and tail markers.DatabaseS1.mat