cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g1m5k70
title: Data from: Elevated precipitation alters the community structure of spring ephemerals by changing dominant species density in Central Asia

description: Global climate change is one of the most pressing conservation challenges;
 in particular, changes in precipitation regimes have already substantially
 influenced terrestrial ecosystems. However, the mechanisms influencing
 precipitation changes on individual plants and the plant communities in
 desert grasslands have yet to be fully elucidated. We therefore examine
 the influence of increased precipitation on plant community compositions
 in the Gurbantunggut Desert, Xinjiang, northwestern China from 2005 to
 2009. We found that growth of all plant species and the community
 productivities increased markedly with enhanced water input. Cover of
 ephemeral synusia also significantly increased due to increased
 precipitation, implying that the role of the ephemeral community for
 stabilization of sand dunes was strengthened by increased precipitation.
 The response of plant community compositions to increased precipitation
 was primarily reflected as changes in plant density, while increased
 precipitation did not affect plant species richness and the diversity
 index. Dominant species drove the response of plant density to increasing
 precipitation during the five-year study period. However, the relative
 responses of rare species were stronger than those of the dominant
 species, thereby potentially driving species turnover with long-term
 increased precipitation. This finding improved our understanding of how
 increased precipitation drives the changes in plant community composition
 in desert grasslands and will help to better predict changes in the
 community composition of ephemerals under future global climate change
 scenarios.
description: Data.Elevated
 precipitation alters the community structure of spring ephemerals by
 changing dominant species density in Central Asia
DOI: 10.5061/dryad.3185h66
title: Data from: Mate fidelity in a polygamous shorebird, the snowy plover (Charadrius nivosus)

description: Social monogamy has evolved multiple times and is particularly common in
 birds. However, it is not well understood why some species live in
 long-lasting monogamous partnerships while others change mates between
 breeding attempts. Here, we investigate mate fidelity in a sequential
 polygamous shorebird, the snowy plover (Charadrius nivosus), a species in
 which both males and females may have several breeding attempts within a
 breeding season with the same or different mates. Using six years of data
 from a well-monitored population in Bahía de Ceuta, Mexico, we
 investigated predictors and fitness implications of mate fidelity both
 within and between years. We show that in order to maximize reproductive
 success within a season, individuals divorce after successful nesting and
 re-mate with the same partner after nest failure. Therefore, divorced
 plovers, counterintuitively, achieve higher reproductive success than
 individuals that retain their mate. We also show that different mating
 decisions between sexes predict different breeding dispersal patterns.
 Taken together, our findings imply that divorce is an adaptive strategy to
 improve reproductive success in a stochastic environment. Understanding
 mate fidelity is important for the evolution of monogamy and polygamy, and
 these mating behaviours have implications for reproductive success and
 population productivity.
description: Halimubieke et al
 2019_Ecology&Evolution dataThis file contains 9
 different datasets for different scientific questions raised in the
 manuscript. (1)To test the relationship between mate fidelity and nesting
 success within years, please refer to data named
 "Within_year_groups_new", for between years, please refer to
 "female_early_early_new", "female_late_early_new",
 "male_early_early_new" and "male_late_early_new".(2)
 To test reproductive success and mate fidelity within years, please refer
 to "Within year full", for between years, please refer to
 "early early_1" and "late early_1".(3) To breeding
 dispersal and mate fidelity within years, please refer to
 "Within_year_groups_new", and for between years, please refer to
 "early early_1" and "late early_1". (4) to test
 re-mating time and mate fidelity, please refer to "remate
 time".Halimubieke et al 2019 ecology
 and evolution data.zip
DOI: 10.5061/dryad.77hs873
title: Data from: Social foraging extends associative odor-food memory expression in an automated learning assay for Drosophila melanogaster

description: Animals socially interact during foraging and share information
 about the quality and location of food sources. The mechanisms of
 social information transfer during foraging have been mostly
 studied at the behavioral level, and its underlying neural
 mechanisms are largely unknown. Fruit flies have become a model
 for studying the neural bases of social information
 transfer, because they provide a large genetic toolbox to monitor
 and manipulate neuronal activity, and they show a rich repertoire
 of social behaviors. Fruit flies aggregate, they use social
 information for choosing a suitable mating partner
 and oviposition site, and they show better aversive learning when
 in groups. However, the effects of social interactions on
 associative odor–food learning have not yet been investigated.
 Here, we present an automated learning and memory assay for
 walking flies that allows the study of the effect of group size
 on social interactions and on the formation and expression of
 associative odor–food memories. We found that both inter-fly
 attraction and the duration of odor–food memory expression
 increase with group size. This study opens up opportunities to
 investigate how social interactions during foraging are relayed
 in the neural circuitry of learning and memory expression.
description: Data_S1Data S1: Tracking data. The CSV file contains 5350149 rows. The 15 columns contain the following information per column: 1) The video recording file name. 2) The experimental phase, either Conditioning or Test. 3) The location of the arena that the fly was video recorded in, either top left (TL), bottom left (BL), bottom right (BR) or top right (TR). 4) The group size in the arena, either Single (1 fly), Pair (2 flies), Small group (3-4 flies) or Large group (7-8 flies). 5) The number of flies in the group. 6) The track identification number for each fly per video recording during the test. Identities of the flies were not obtained for the conditioning dataset. 7) The video frame number. Videos were recorded at 15 frames per second in both the conditioning and test. 8) The x coordinate of the fly. 9) The y coordinate of the fly. 10) The x coordinate of the CS+. 11) The y coordinate of the CS+. 12) The x coordinate of the CS-. 13) The y coordinate of the CS-. 14) The x coordinate of the center of the arena. 15) The y coordinate of the center of the arena. 16) The theta polar coordinate of the fly (centralized to the arena location and normalized by the distance between the CS+ and the CS-, applies to all polar coordinates). 17) The radius polar coordinate of the fly. 18) The theta polar coordinate of the CS+. 19) The radius polar coordinate of the CS+. 20) The theta polar coordinate of the CS-. 21) The radius polar coordinate of the CS-.
DOI: 10.5061/dryad.6d5d302
title: Data from: Temperature amplifies the effect of high CO2 on the photosynthesis, respiration and calcification of the coralline algae Phymatolithon lusitanicum

description: The combination of ocean acidification (OA) and global warming is expected
 to have a significant effect on the diversity and functioning of marine
 ecosystems, particularly on calcifying algae such as rhodoliths (maërl)
 that form extensive beds worldwide, from polar to tropical regions. In
 addition, the increasing frequency of extreme events, such as heatwaves,
 threaten coastal ecosystems and may affect their capacity to fix blue
 carbon. The few studies where the simultaneous effects of both temperature
 and CO2 were investigated have revealed contradictory results. To assess
 the effect that high temperature spells can have on the maërl beds under
 OA, we tested the short-time effects of temperature and CO2 on the net
 photosynthesis, respiration and calcification of the recently described
 species Phymatolithon lusitanicum, the most common maërl species of
 southern Portugal. Photosynthesis, calcification and respiration increased
 with temperature, and the differences among treatments were enhanced under
 high CO2. We found that in the short term, the metabolic rates of
 Phymatolithon lusitanicum will increase with CO2 and temperature as will
 the coupling between calcification and photosynthesis. However, under high
 CO2, this coupling will favor photosynthesis over calcification, which, in
 the long term, can have a negative effect on the blue carbon fixing
 capacity of the maërl beds from southern Portugal.
description: Data_SordoetalData of Net and gross production and respiration under control and high CO2 conditions (Excel sheet 1), Data of light and dark calcification under control and high CO2 conditions (Excel sheet 2), Carbonate system parameters in each treatment. Salinity, temperature (T), total alkalinity (TA) and pH (NBS scale) were measured, while dissolved inorganic carbon (DIC) and saturation state of seawater with respect to aragonite (ΩAR) were calculated using the programe CO2SYS (Excel sheet 3)
DOI: 10.5061/dryad.54m0128
title: Data from: Genetic diversity and demographic history of introduced sika deer on the Delmarva Peninsula

description: The introduction of non-native species can have long-term effects on
 native plant and animal communities. Introduced populations are
 occasionally not well understood and offer opportunities to evaluate
 changes in genetic structure through time and major population changes
 such as bottleneck and or founder events. Invasive species can often
 evolve rapidly in new and novel environments, which could be essential to
 their long-term success. Sika deer are native to East Asia, and their
 introduction and establishment to the Delmarva Peninsula, USA is poorly
 documented, but probably involved ≥1 founder and/or bottleneck events. We
 quantified neutral genetic diversity in the introduced population and
 compared genetic differentiation and diversity to the presumed source
 population from Yakushima Island, Japan, and a captive population of sika
 deer in Harrington, Delaware, USA. Based on data from 10 microsatellite
 DNA loci, we observed reduced genetic variation attributable to founder
 events, support for historic hybridization events, and evidence that the
 population did originate from Yakushima Island stocks. Estimates of
 population structure through Bayesian clustering and demographic history
 derived from Approximate Bayesian Computation (ABC), were consistent with
 the hypothesized founder history of the introduced population in both
 timing and effective population size (approximately 5 effective breeding
 individuals, an estimated 36 generations ago). Our ABC results further
 supported a single introduction into the wild happening before sika deer
 spread throughout the Delmarva. We conclude that free-ranging sika deer on
 Delmarva are descended from ca. 5 individuals introduced about 100 years
 ago from captive stocks of deer maintained in the United Kingdom.
 Free-ranging sika deer on Delmarva have lost neutral diversity due to
 founder and bottleneck events, yet populations have expanded in recent
 decades and show no evidence of abnormalities associated with inbreeding.
 We suggest management practices including increasing harvest areas and
 specifically managing sika deer outside of Maryland.
description: Sikadata.Dryad.7.2019Sika deer allelic diversity across 4 study populations based in Delmarva Peninsula, USA and Yakushima Island Japan.
DOI: 10.5061/dryad.453dg14
title: Knee function through finite element analysis and the role of Miocene hominoids in our understanding of the origin of antipronograde behaviours: the Pierolapithecus catalaunicus patella as a case study

description: Although extensive research has been carried out in recent years on human
 bipedalism origin and evolution, a full understanding of this question is
 far to be achieved. In this regard, the role of Miocene hominoids emerges
 as key to better comprehend the locomotor types observed in living apes
 and humans. Pierolapithecus catalaunicus, an extinct stem great ape from
 the middle Miocene (c. 12.0 Ma) of the Vallès-Penedès Basin (NE Iberian
 Peninsula), is the first undoubted hominoid with an orthograde (erected)
 body plan. Its locomotor repertoire included above-branch quadrupedalism
 and other antipronograde behaviours. Elucidating the adaptive features
 present in the Pierolapithecus skeleton and its associated biomechanics
 helps us to better understand the origin of hominoid orthogrady. This work
 represents a new biomechanical perspective on the Pierolapithecus
 locomotion, by studying its patella among a large sample of extant
 anthropoids. This is the first time that the biomechanical patellar
 performance in living non-human anthropoids and a stem hominid is studied
 through Finite Element Analysis (FEA). Differences in stress distribution
 are found depending on body plan and the presence/absence of a distal
 apex, probably due to dissimilar biomechanical performances.
 Pierolapithecus’ biomechanical response mainly resembles that of great
 apes, suggesting a similar knee joint use in mechanical terms. These
 results underpin previous studies on Pierolapithecus, favouring the idea
 that a relevant degree of some antipronograde behaviour may have made up
 part of its locomotor repertoire. Moreover, our results corroborate the
 presence of modern great ape-like knee biomechanical performances back in
 the Miocene.
description: CAD models figure, von
 Mises stress values, validation test, and statistical results
 The data file
 contains additional information for this study including: S1) patellae CAD
 model images (figure); S2) von Mises stress values obtained for points A-E
 (table); S3-S5) validation test: explanatory text (S3), von Mises stress
 colour maps at the patellar medialateral midsection (figure; S4), and
 patellar models' information and von Mises stress values (table; S5);
 S6) ANOVA and MANOVA significance results derived from PCA (table); S7)
 PCA variables loadings (table); S8) PCA eigenvalues by taxon
 (table). Pina et al
 2019_SOM.pdf
DOI: 10.5061/dryad.kp32qr6
title: Data from: Population structure, connectivity and demographic history of an apex marine predator, the bull shark Carcharhinus leucas

description: Knowledge of population structure, connectivity and effective population
 size remains limited for many marine apex predators, including the bull
 shark Carcharhinus leucas. This large-bodied coastal shark is distributed
 worldwide in warm temperate and tropical waters, and uses estuaries and
 rivers as nurseries. As an apex predator, the bull shark likely plays a
 vital ecological role within marine food webs, but is at risk due to
 inshore habitat degradation and various fishing pressures. We investigated
 the bull shark’s global population structure and demographic history by
 analysing the genetic diversity of 370 individuals from 11 different
 locations using 25 microsatellite loci and three mitochondrial genes (CR,
 nd4, cytb). Both types of markers revealed clustering between sharks from
 the Western Atlantic and those from the Western Pacific and the Western
 Indian Ocean, with no contemporary gene flow. Microsatellite data
 suggested low differentiation between the Western Indian Ocean and the
 Western Pacific, but substantial differentiation was found using
 mitochondrial DN A. Integrating information from both types of markers and
 using Bayesian computation with a random forest procedure (ABC-RF), this
 discordance was found to be due to a complete lack of contemporary gene
 flow. High genetic connectivity was found both within the Western Indian
 Ocean and within the Western Pacific. In conclusion, these results suggest
 important structuring of bull shark populations globally with important
 gene flow occurring along coastlines , highlighting the need for
 management and conservation plans on regional scales rather than oceanic
 basin scale.
description: Microsatellite genotypes
 of the bull shark samples Sampling information are
 indicated for each individual (date of sampling, sampling locality, sex,
 total length) as well as the identified mitochondrial haplotypes for each
 gene (control region, nicotinamide adenine dinucleotide dehydrogenase
 subunit 4, cytochrome b) and the concatenated mitochondrial haplotype
 (CR-nd4-cytb). Microsatellite genotypes for the 25 loci are also indicated
 (2 alleles per locus, 3-digits per allele). Missing data are indicated by
 "NA" or by a question mark. microsatellite
 genotypes.xlsx
DOI: 10.5061/dryad.83ng085
title: Populus euphratica WRKY1 binds the promoter of PeHA1 to enhance gene expression and salt tolerance

description: Plasma membrane proton pumps play a crucial role in maintaining ionic
 homeostasis in salt-resistant Populus euphratica under saline conditions.
 High levels of NaCl (200 mM) induced PeHA1 expression in P. euphratica
 roots and leaves. We isolated a 2022-bp promoter fragment upstream of the
 translational start of PeHA1 from P. euphratica. The promoter-reporter
 construct PeHA1-pro::GUS was transferred to tobacco plants, demonstrating
 that β-glucuronidase activities increased in root, leaf, and stem tissues
 under salt stress. DNA affinity purification sequencing revealed that
 PeWRKY1 protein targeted the PeHA1 gene. We assessed the salt-induced
 transcriptional response of PeWRKY1 and its interaction with PeHA1 in P.
 euphratica. PeWRKY1 binding to the PeHA1 W-box in promoter region was
 verified by a yeast one-hybrid assay, electrophoretic mobility shift
 assay, luciferase reporter assay, and virus-induced gene silencing.
 Transgenic tobacco plants overexpressing PeWRKY1 had improved expression
 of NtHA4, which has a cis-acting W-box in the regulatory region, and H+
 pumping activity in both in vivo and in vitro assays. We conclude that
 salt stress upregulated PeHA1 transcription due to the binding of PeWRKY1
 to the W-box in the promoter region of PeHA1. Thus, we conclude that
 enhanced H+ pumping activity enabled salt-stressed plants to retain Na+
 homeostasis.
description: Figure S1. Promoter sequence analysis of <i>Populus euphratica</i> <i>PeHA1</i>. Figure S2. Semi-quantitative RT-PCR analysis of <i>PeWRKY1</i> in wild-type (WT) tobacco and transgenic lines L1–L15. Figure S3. Phenotype tests of wild-type (WT) tobacco and <i>PeWRKY1</i>-transgenic plants. Figure S4. Na<sup>+</sup> concentrations and fluxes in roots of wild-type (WT) tobacco and <i>PeWRKY1</i>-transgenic plants. Figure S5. Promoter sequence analysis of<i> </i>tobacco<i> NtHA4</i>. Figure S6. Promoter sequence analysis of<i> </i>tobacco<i> NtHA</i><i>2</i>. Table S1. Primer sets used for quantitative real-time PCR. Table S2. Primers used for cloning the promoters of <i>Populus euphratica</i> <i>PeHA1</i> and <i>Nicotiana tabacum </i>L. <i>NtHA2 </i>and<i> NtHA4</i>. Table S3. PeWRKY1 DAP-seq peaks located upstream of the transcription start site (TSS) of the <i>PeHA1</i> gene.
DOI: 10.5061/dryad.8t3g361
title: Data from: Tracheostomy and long-term mortality in ICU patients undergoing prolonged mechanical ventilation

description: Introduction. In critically ill patients undergoing prolonged mechanical
 ventilation (MV), the difference in long-term outcomes between patients
 with or without tracheostomy remains unexplored. Methods. Ancillary study
 of a prospective international multicentre observational cohort in 21
 centres in France and Belgium, including 2087 patients, with a one-year
 follow-up after admission. We included patients with a MV duration ≥10
 days, with or without tracheostomy. We explored the one-year mortality
 with a classical Cox regression model (adjustment on age, SAPS II,
 baseline diagnosis and withdrawal of life-sustaining therapies) and a Cox
 regression model using tracheostomy as a time-dependant variable. Results.
 29.5% patients underwent prolonged MV, out of which 25.6% received
 tracheostomy and 74.4% did not. At one-year, 45.2% patients had died in
 the tracheostomy group and 51.5% patients had died in the group without
 tracheostomy (p=0.001). In the Cox-adjusted regression model, tracheostomy
 was not associated with improved one-year outcome (HR CI95 0.7
 [0.5-1.001], p=0.051), as well as in the model using tracheostomy as a
 time-dependent variable (OR CI 95 1 [0.7-1.4], p=0.9). Conclusions. In our
 study, there was no statistically significant difference in the one-year
 mortality of patients undergoing prolonged MV when receiving tracheostomy
 or not.
description: Classic
 selection Cox model with Tracheo
 as traditional variable   
 Time
 dependant Cox model with
 tracheostomy as time-dependant variable   
 Time and
 effect Cox model with
 trachesotomy as an effect-dependant variable   
 Time and effect
 dependant variable Cox Cox model with
 tracheostomy as time and effect-dependant variable   
 Supporting Information
 WLST R script. Sensitivity
 analysis when excluding patients with WLST   
 HADS Dataset with HADS
 data   
 Tracheo_dryad
 Dataset
     
 Variable
 trachéo Creation of new
 data   
 Survival
 Standard
 survival analysis   
 QUALY SF36, IES-R and HADS
 analysis   
 Propensity
DOI: 10.5061/dryad.6222780
title: Data from: Lower breeding success in the invaded range: no evidence for the enemy release hypothesis in South American Barn Swallows

description: It is widely assumed that colonizing species thrive because they lack
 natural enemies in their new range, increasing their survival and
 reproductive success. Barn Swallows (Hirundo rustica) started to breed in
 South America around 1980 and since have increased dramatically their
 population size and geographic range, in stark contrast with the decline
 of the source population in North America. The reasons behind the growth
 of the South American population are unknown. However, because this
 species had never bred in this area in recorded times, the lack of natural
 predators, parasites or pathogens could lead to higher breeding success,
 as predicted by the enemy release hypothesis. Here we test whether
 breeding success is higher in the newly colonized range than in the native
 range to test the enemy release hypothesis. We studied the breeding
 biology of South American Barn Swallows quantifying seven breeding
 parameters: clutch size, overall breeding success, offspring mortality by
 predation and ectoparasites, number of fledglings per breeding attempt,
 number of breeding attempts per breeding season, and total number of
 fledglings produced per pair per breeding season. Additionally, we
 compared these parameters with published information from North American
 populations using meta-analyses. We found that, while clutch size did not
 differ between North and South American populations, the southern
 population overall had lower breeding success, with higher mortality from
 predation and ectoparasites. An egg laid in South America was 2.6 times
 more likely to fail than one laid in North America, which resulted on
 average in 1.1 fewer fledglings per pair per breeding season for the South
 American breeding population. These results, demonstrating lower breeding
 success in a newly colonized range, do not support the enemy release
 hypothesis and indicate that the growth of the South American Barn Swallow
 population is most likely caused by other demographic factors.
description: Gandoy et al
 DataData used to perform the
 Generalized Linear Mixed Model