cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rt1385v
title: Data from: The cranium of Proviverra typica (Mammalia, Hyaenodonta) and its impact on hyaenodont phylogeny and endocranial evolution

description: We describe the first endocast reconstruction of a hyaenodont mammal based
 on X‐ray microtomography. The endocast belongs to the type material of the
 European hyaenodont Proviverra typica. We performed phylogenetic analysis
 to contextualize the evolution of endocranial size and complexity in
 Hyaenodonta. We added several European hyaenodonts and modified several
 codings of the most recent character–taxon matrix established to question
 the relationships within Hyaenodonta. Including these new species in a
 phylogenetic analysis reveals a new clade: Hyaenodontoidea. Comparisons
 with several previously described endocasts show that there was an
 increase in complexity in the convolutions of the encephalon within
 Hyaenodontidae history. Moreover, the analysis of the encephalization
 quotient reveals that the endocranium of the Hyaenodonta is not smaller
 than those of fossil Carnivora or some extant Carnivora. Therefore, the
 extinction of Hyaenodonta may not be linked to the relative size of
 hyaenodont brains.
description: Supplementary data
 1List
 of all the taxa and specimens added to the matrix of Borths & Stevens
 (2017), along with information on age and locality
 data.Supplementary data
 2List
 of the modifications to the matrix of Borths & Stevens
 (2017)Supplementary data
 3Descriptions of
 characters and character states used in the phylogenetic
 analysis.Supplementary data
 4Input file for the
 Bayesian phylogenetic analysis, formatted for MrBayes.Supplementary Data
 5‘Allcompat’ summary tree
 formatted for FigTree.
DOI: 10.5061/dryad.f1f0q44
title: Data from: Natural selection and repeated patterns of molecular evolution following allopatric divergence

description: Background: Geographic speciation is a major force in generating
 biodiversity. However, how genomes diverge over time after geographic
 isolation has halted gene flow has remained unclear. We examine
 genome-wide divergence of putatively single-copy orthologous genes (POGs)
 from transcriptomes in 20 allopatric species/variety pairs from diverse
 angiosperm clades. Sixteen of these pairs reflect the well-known eastern
 Asia – eastern North America floristic disjunction; these species have
 been isolated for different lengths of time, from the Miocene to
 Pleistocene. Results: Molecular evolutionary analyses revealed that
 &gt;90% of the genes examined are under purifying selection and
 &lt;10% are under positive selection, and this pattern was observed
 for all taxon pairs, despite differences in divergence time. The
 divergence level at synonymous sites shared by most POGs in each taxon
 pair predicts the divergence time between the species/varieties.
 Divergence time estimates were positively correlated with abundance of
 genes under moderate purifying selection, but negatively correlated with
 abundance of genes under strong purifying selection. We identified 200
 genes under strong positive selection across the species pairs, with 14
 shared by 10-15 pairs and one shared by all taxon pairs. An additional 15
 loci annotated to biological processes responding to various stimuli were
 present in 1-3 pairs.Conclusions: Our results suggest a common “most genes
 conserved–few genes adaptive” genomic architecture for the taxon pairs,
 which may be a key for maintaining a balance between the ability to
 conserve ancestral functions and the ability to evolve new features
 beneficial for new adaptations. As geographic isolation proceeds through
 time, the evolutionary trajectory of some genes changed from strong
 purifying selection to more relaxed selection. The allopatric divergence
 of these taxon pairs involved both neutral and adaptive evolution of
 functional genes.
description: Orthologous single copy
 genes positive selectionOne zip file contains 40
 species orthologous singe copy genes prior to EST scan and one dn/ds excel
 file.Single_copy_orthologs.zip
DOI: 10.5061/dryad.6p55sp3
title: Data from: A Darwinian uncertainty principle

description: Reconstructing ancestral characters and traits along a phylogenetic tree
 is central to evolutionary biology. It is the key to understanding
 morphology changes among species, inferring ancestral biochemical
 properties of life, or recovering migration routes in phylogeography. The
 goal is twofold: to reconstruct the character state at the tree root (e.g.
 the region of origin of some species), and to understand the process of
 state changes along the tree (e.g. species flow between countries). We
 deal here with discrete characters, which are `unique', as opposed to
 sequence characters (nucleotides or amino-acids), where we assume the same
 model for all the characters (or for large classes of characters with
 site-dependent models) and thus benefit from multiple information sources.
 In this framework, we use mathematics and simulations to demonstrate that
 although each goal can be achieved with high accuracy individually, it is
 generally impossible to accurately estimate both the root state and the
 rates of state changes along the tree branches, from the observed data at
 the tips of the tree. This is because the global rates of state changes
 along the branches that are optimal for the two estimation tasks have
 opposite trends, leading to a fundamental trade-off in accuracy. This
 inherent `Darwinian uncertainty principle' concerning the
 simultaneous estimation of `patterns' and `processes' governs
 ancestral reconstructions in biology. For certain tree shapes (typically
 speciation trees) the uncertainty of simultaneous estimation is reduced
 when more tips are present, however, for other tree shapes it does not
 (e.g. coalescent trees used in population genetics).
description: Online Appendix -
 Mathematical ResultsOnline appendix:
 statements and proofs of TheoremsOnlineAppendixRevised_GascuelSteel_USYB-2019-012.pdf
DOI: 10.5061/dryad.61sr186
title: Data from: Colonization and extinction dynamics among the plant species at tree bases in Paris (France)

description: 1. In cities, trees growing along streets could play an important
 ecological role for spontaneous plants that grow at their bases. For
 example, these trees could represent corridors that allow species to move
 in the urban matrix by potentially connecting large green spaces (e.g.,
 parks, gardens, etc.) We considered sets of urban trees in 15 streets as
 metapopulations for 15 plant species. Our objective was to determine the
 factors influencing the dynamics of colonization and extinction of
 populations based on the distance of the streets from green spaces and the
 biological traits of each species. 2. The species in 1,324 tree bases of
 the Bercy district of Paris were surveyed annually from 2009 to 2015. For
 each species and each street, we used SPOMSIM software to identify the
 best-fit metapopulation model: the propagule rain model (PRM), Levins
 model (LM), and the PRM and LM with a fixed extinction or a rescue effect.
 3. The results demonstrated that the species more often conformed to the
 PRM in streets near green spaces, which suggested that green spaces could
 act as the sources for the populations in those streets. Species with
 seeds with long-term persistence more often conformed to the PRM,
 indicating that a soil seed bank helps species invade entire streets.
 Finally, a higher percentage of species with a short height conformed to
 models with a rescue effect, which indicated that those species resisted
 the effects of weeding by the city technical services more often than
 taller species. 4. Synthesis and applications. This study showed how the
 biological traits of species and the geography of the district determine
 the dynamics of the plants in the streets, and the results may provide
 important information for biodiversity management in cities.
description: Data of the results of
 SPOMSIM modelingFeatures of the 15
 species and 15 streets for which population dynamics was modeled and
 SPOMSIM modeling results.
DOI: 10.5061/dryad.rg3587h
title: Data from: Introgression between non-sister species of honeyeaters (Aves: Meliphagidae) several million years after speciation

description: We reassessed whether two parapatric non-sister Australian honeyeater
 species (Aves: Meliphagidae), varied and mangrove honeyeaters (Gavicalis
 versicolor and G. fasciogularis, respectively), that diverged from a
 common ancestor c. 2.5 Mya intergrade in the Townsville area of
 north-eastern Queensland. Consistent with a previous specimenbased study,
 by using genomics methods we show one-way gene flow for autosomal but not
 Z-linked markers from varied into mangrove honeyeaters. Introgression
 barely extends south of the area of parapatry in and around the city of
 Townsville. While demonstrating the long-term porosity of species
 boundaries over several million years, our data also suggest a clear role
 of sex chromosomes in maintaining reproductive isolation.
description: Gavicalis autosomal
 structure fileThis file contains
 genotypes for 9 Varied Honeyeaters and 25 Mangrove Honeyeaters scored at
 5667 autosomal ddRAD-seq loci. It is formatted for the program STRUCTURE,
 and missing data are coded as '-9'.HOEA.5667A.N34.struGavicalis Z-linked structure fileThis file contains genotypes for 9 Varied Honeyeaters and 25 Mangrove Honeyeaters scored at 267 Z-linked ddRAD-seq loci. The data are formatted for the program STRUCTURE, and missing data are coded as '-9'. For diploid males, alleles for each locus were randomly assigned to two pseudohaplotypes.HOEA.267Z.N55haploid.struGavicalis Sampling InformationA list of samples, including sampling locations, sampling date, age, and sex, for the 9 Varied and 25 Mangrove Honeyeaters included in this study.Gavicalis_sample_info.xlsxGavicalis GenePop fileGenePop file modified for the software SPAGEDI containing genotypes at 3767 variable autosomal loci for 9 Varied and 25 Mangrove Honeyeaters. Data were obtained from ddRAD-seq.HOEA.N34.3767var.spagedi.txtGavicalis FASTA filesThis zipped folder contains individual FASTA files for each of 5667 autosomal and 267 Z-linked loci for 9 Varied and 25 Mangrove Honeyeaters. All data were obtained using ddRAD-seq.HOEA.fasta_files.zipGavicalis Concatenated FASTA FilesThis zipped folder contains three files consisting of concatenated ddRAD-seq data for 9 Varied and 25 Mangrove honeyeaters. The files include, (1) 5667 concatenated autosomal loci, (2) 267 concatenated Z-linked loci, and (3) 5934 concatenated autosomal + Z-linked loci. Alleles were randomly assigned to pseudohaplotypes.HOEA.Concatenated.FASTA.zip
DOI: 10.5061/dryad.2cb0g0h
title: Data from: Comparative static (anoxic) and shaking culture of metabolite derived from Methyl Red degradation by Lysinibacillus fusiformis strain W1B6

description: This paper reports on the comparative characteristics and properties of
 the metabolites derived from Methyl Red decolorization by Lysinibacillus
 fusiformis strain W1B6 under static and shaking conditions. The batch
 culture system was used to investigate the effect of aeration on the
 azoreductase activity in biodegradation process, transformation of color
 removal and the metabolite products. Biodegradation analysis was monitored
 using Fourier transform infrared spectroscopy and high-performance liquid
 chromatography while metabolites were determined using gas
 chromatography-mass spectroscopy. Phytotoxicity and anti-microbial test
 were also conducted to detect the toxicity of metabolites. The results
 showed that this strain grows higher in shaking while the azoreductase
 activity increased more rapidly in static condition. Despite that, no
 significant difference in the decolorization was observed under both
 static and shaking conditions with up to 96% and 93.6% decolorization
 achieved respectively within 4 h of incubation. The Methyl Red was
 degraded into two fragmented compounds i.e. benzoic acid, 2- amino and
 1.4-benzenediamine, N,N-dimethyl-. The concentration of both compounds was
 higher in shaking due to the biotransformation of benzoic acid, 2- amino
 into methyl anthranilate was probably more rapidly in static condition.
 Other metabolites were also detected as intermediate biotransformation and
 by-products. Less or no toxic effect was found in metabolite degradation
 products from both culture conditions.
description: sequence of
 Lysinibacillus fusiformisThis bacteria was
 isolated in Malaysia and used for this studysequence.fastaGCMS resultsContain of GCMS results of Control (without dye) and Treatments using dye (in Static and Shaking culture)FTIR resultsFTIR results of Untreatment dye and Dye treatment (in Static and Shaking culture of bacteria)HPLC resultsHPLC results of Standard (Methyl red, DMPD and ABA) and Result of dye treatment (under Static and Shaking culture)Microbial ToxicityRepresentative picture of microbial toxicity experimentPhytotoxicity pictureRepresentative picture of Phytotoxicity experiment
DOI: 10.5061/dryad.2vr4152
title: Data from: From limb to fin: an Eocene protocetid forelimb from Senegal sheds new light on the early locomotor evolution of cetaceans

description: Cetaceans constitute a textbook example of the secondary adaptation of
 tetrapods to aquatic life. This major event in the evolutionary history of
 mammals is often linked in the literature to the limb‐to‐fin transition.
 Paradoxically, limb bones are scarce in the fossil record of early
 cetaceans, and the transition from a limb‐adapted morphology for an
 amphibious life in shallow water to a fin‐adapted morphology for a pelagic
 lifestyle remains poorly documented. Here, we describe new protocetid
 remains from the upper Lutetian of Senegal, including a nearly complete
 articulated forelimb. A cladistic analysis including 24 taxa and 137
 morphological characters recovers the new African specimen close to
 Carolinacetus. It also confirms that cetacean dispersal to the New World
 was not the result of a single colonization event. A 3D model of the
 forelimb was reconstructed. Anatomical comparisons suggest that it is
 unlikely that the Senegalese forelimb was used as a rigid pectoral flipper
 for steering as in basilosaurids and modern cetaceans. Instead, we suggest
 that the hand was actively used during swimming. This challenges previous
 reconstructions of protocetids as mainly foot‐powered swimmers, and
 suggests that swimming specializations of early cetaceans were probably
 more diverse than previously considered.
description: Supplemental data
 1Character
 listSupplemental data
 2Data
 matrixSupplemental data
 3Character distribution
 on the strict consensus cladogram: unambiguous
 synapomorphies
DOI: 10.5061/dryad.jq44b1r
title: Data from: A human subcortical network underlying social avoidance revealed by risky economic choices

description: Social interactions have a major impact on well-being. While many
 individuals actively seek social situations, others avoid them, at great
 cost to their private and professional life. The neural mechanisms
 underlying individual differences in social approach or avoidance
 tendencies are poorly understood. Here we estimated people's
 subjective value of engaging in a social situation. In each trial, more or
 less socially anxious participants chose between an interaction with a
 human partner providing social feedback and a monetary amount. With
 increasing social anxiety, the subjective value of social engagement
 decreased; amygdala BOLD response during decision-making and when
 experiencing social feedback increased; ventral striatum BOLD response to
 positive social feedback decreased; and connectivity between these regions
 during decision-making increased. Amygdala response was negatively related
 to the subjective value of social engagement. These findings suggest a
 relation between trait social anxiety / social avoidance and activity in a
 subcortical network during social decision-making.
description: BehaviouralDataThe behavioural data collected in Study 1 and 2, and the behavioural data collected during the fMRI part of Study 2. Rows are participants, columns are different behavioural variables. See manuscript for details.BehavData.xlsxParameterEstimatesMainAnalysisParameter estimates from the GLM fit to the fMRI data. Data are averaged across voxels with each region of interest stated as sheet name. Rows are participants, columns are experiment conditions.BetasMainRFX_revised.xlsxParameterEstimatesConnectivityAnalysisThe parameter estimates generated during the functional connectivity analysis of the fMRI data. Conventions as in the main parameter estimates file.BetasPPI_revised.xlsxfMRIdecodingAccuracyAmyRThe decoding accuracy obtained in the right Amygdala ROI for each participant.fMRI_DecodingAmyR.csv
DOI: 10.5061/dryad.24h5f33
title: Data from: Is age more than manual material handling associated with lumbar vertebral body and disc changes? A cross-sectional multicenter MRI study

description: Objective Conflicting evidence exists to what extent manual material
 handling (MMH) causes lumbar disc disease, lack of evidence exist that
 this effect takes place especially at L5-S1 level, where the greatest
 moment occurs. The aim was to assess if lumbar vertebral body and disc
 changes are more common in people whose job involves significant MMH and,
 if so, to evaluate if lumbar vertebral body and disc changes are more
 prevalent in the lower part of the lumbar spine (L4-L5 and L5-S1). Design
 Observational, cross-sectional, with quasi-random recruitment. Setting
 Outpatient radiology units of three large hospitals in northern (Bologna
 and Brescia) and southern (Bari) Italy. Participants 183 consecutive adult
 subjects (89 males, 94 females) aged 20-70 years referred by the General
 Practitioner (GP) or a specialist for Magnetic Resonance Imaging (MRI) of
 the lumbar spine. Primary and secondary outcome measures:
 Neuroradiologists (blind to clinical assessment) evaluated the prevalence
 of intervertebral disc and vertebral body changes in standardized magnetic
 resonance imaging (MRI) examinations. History of personal and family
 musculoskeletal diseases and injuries, current and past manual material
 handling at work and during leisure time were assessed by interview and
 self-administered questionnaire. Results Participants were classified
 according their occupational exposure to MMH. No association was found
 between MMH and vertebral body and intervertebral disc changes, whereas
 age over 45 years was consistently associated with more DEBIT changes,
 Pfirrmann changes, osteophytes and Modic changes: the association was
 statistically significant at the conventional 5% level. Conclusions Age,
 and not MMH, seems to primarily affect the presence of intervertebral disc
 changes; prospective studies are needed to better explore the relationship
 between MMH and the possible presence (and level) of lumbar vertebral body
 and/or disc changes.
description: Dataset of the
 studyDataset to replicate the
 analysisDataset.xlsx
DOI: 10.5061/dryad.jc3mk77
title: Data from: Stethoscope disinfection is rarely done in Ethiopia: what are the associated factors?

description: Introduction: The stethoscope, which is non-critical medical devices and a
 symbol of healthcare, is likely to be contaminated by pathogenic
 microorganisms and can play a contributory role in the transmission of
 hospital-acquired infection. And regular cleaning of the diaphragm of the
 stethoscope with a suitable disinfectant is decisive. However, in the
 resource-constrained setting like many healthcare facilities in Ethiopia
 healthcare provider’s stethoscope disinfection practice and its associated
 factors have not been well studied so far. Therefore, this study sought to
 determine stethoscope disinfection practice and associated factors among
 the healthcare providers in Addis Ababa, Ethiopia. Methods: A
 facility-based cross-sectional study was carried out between April and May
 2016. For this study, 576 healthcare providers (physicians, health
 officers, nurses, midwives, and anesthesiologist) were included from 21
 healthcare facilities in Addis Ababa. A pre-tested structured
 questionnaire was used for data collection. Descriptive statistics were
 computed. Bivariate and multivariable logistic regression analyses were
 used to identify factors that were significantly associated with
 stethoscope disinfection after every use. Results: A total of 546
 healthcare providers participated in this study, for a response rate of
 94.7%. Two-fifths, 39.7% (95%CI: 35.9, 44.0%) of healthcare providers
 disinfecting their stethoscope after every use. And a significant number
 of participants 34.6% (95%CI: 30.8, 38.5%) never disinfect their
 stethoscope. Three out of four (76.0%) healthcare providers believe that
 stethoscope contamination can contribute to the transmission of
 infections. Safe infection prevention practice (AOR = 3.79, 95%CI:
 2.45–5.84), awareness on infection prevention guideline (AOR = 1.93;
 95%CI: 1.31, 2.82), and favorable attitude towards infection prevention
 (AOR = 1.73, 95%CI: 1.02, 2.93) were significantly associated with
 stethoscope disinfection after every use. The study also found that the
 odds of stethoscope disinfection were likely to be reduced by 79% among
 physicians than nurses (AOR = 0.21; 95%CI: 0.09, 0.49).Conclusions: Only a
 small proportion of healthcare providers disinfect their stethoscopes
 after every use. Factors such as safe infection prevention practice,
 awareness on infection prevention guidelines, and favorable attitude
 towards infection prevention were the independent predictors of
 stethoscopes disinfection after every use. Hence, promotion of stethoscope
 hygiene along with an educational program to enhance disinfection
 compliance in healthcare facilities may have a positive effect.
description: Stethoscope disinfection
 in EthiopiaSPSS data on stethoscope
 disinfectionStethoscope
 disinfection_Data.sav
DOI: 10.5061/dryad.fg80hp6
title: Data from: Reduced metabolism supports hypoxic flight in the high-flying bar-headed goose (Anser indicus)

description: The bar-headed goose is famed for migratory flight at extreme altitude. To
 better understand the physiology underlying this remarkable behavior, we
 imprinted and trained geese, collecting the first cardiorespiratory
 measurements of bar-headed geese flying at simulated altitude in a wind
 tunnel. Metabolic rate during flight increased 16-fold from rest,
 supported by an increase in the estimated amount of O2 transported per
 heartbeat and a modest increase in heart rate. The geese appear to have
 ample cardiac reserves, as heart rate during hypoxic flights was not
 higher than in normoxic flights. We conclude that flight in hypoxia is
 largely achieved via the reduction in metabolic rate compared to normoxia.
 Arterial was maintained throughout flights. Mixed venous PO2 decreased
 during the initial portion of flights in hypoxia, indicative of increased
 tissue O2 extraction. We also discovered that mixed venous temperature
 decreased during flight, which may significantly increase oxygen loading
 to hemoglobin.
description: Data files and R script
 used for analysisThis file contains .csv
 files with data as well as R script that was used in the linear mixed
 model analysis of Meir et al, "Reduced metabolism and increased O2
 pulse support hypoxic flight in the bar-headed goose (Anser
 indicus)"Meiretal.zip