cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9k862c8
title: Data from: Last generation genome – environment associations reveal the genetic basis of heat tolerance in common bean (Phaseolus vulgaris L.)

description: Genome-Environment Associations (GEA) are a powerful strategy for the
 study of adaptive traits in wild plant populations, yet they still lack
 behind in the use of modern statistical methods as the ones suggested for
 Genome-Wide Association Studies (GWAS). In order to bridge this gap, we
 couple GEA with last generation GWAS algorithms in common bean to identify
 novel sources of heat tolerance across naturally heterogeneous ecosystems.
 Common bean (Phaseolus vulgaris L.) is the most important legume for human
 consumption, and breeding it for resistance to heat stress is key because
 annual increases in atmospheric temperature are causing decreases in yield
 of up to 9% for every 1°C. A total of 78 geo-referenced wild accessions,
 spanning the two gene pools of common bean, were Genotyped by Sequencing
 (GBS) leading to the discovery of 23,373 SNP markers. Three indices of
 heat stress were developed for each accession and inputted in last
 generation algorithms (i.e. SUPER, FARMCPU and BLINK) to identify putative
 associated loci with the environmental heterogeneity in heat stress.
 Best-fit models revealed 120 significantly associated alleles distributed
 in all 11 common bean chromosomes. Flanking candidate genes were
 identified using 1kb genomic windows centered in each associated SNP
 marker. Some of these genes were directly linked to heat-responsive
 pathways, such as the activation of heat shock proteins (MED23, MED25,
 HSFB1, HSP40 and HSP20). We also found protein domains related to thermo
 stability in plants such as S1 and Zinc finger A20 & AN1. Other
 genes were related to biological processes that may correlate with plant
 tolerance to high temperature, such as time to flowering (MED25, MBD9 and
 PAP), germination and seedling development (Pkinase_Tyr, Ankyrin-B and
 Family Glicosil-hydrolase), cell wall stability (GAE6), and signaling
 pathway of abiotic stress via Abscisic Acid (Histone-like transcription
 factors NFYB and phospholipase C) and Auxin (Auxin response factor and
 AUX_IAA). This work offers putative associated loci for marker-assisted
 and genomic selection for heat tolerance in common bean. It also
 demonstrates that it is feasible to identify genome-wide environmental
 associations with modest sample sizes by using a combination of various
 carefully chosen environmental indices and last generation GWAS
 algorithms.
description: Genetic and
 environmental data, and R codeGenetic and
 environmental data, and R codeLopez.zip
DOI: 10.5061/dryad.th70gn0
title: Data from: Energetics meets sexual conflict: the phenology of hibernation in Tasmanian echidnas (Tachyglossus aculeatus setosus)

description: 1. Echidnas are egg-laying mammals found across Australia and in Tasmania
 they hibernate resulting in a most unusual mating system: males enter
 hibernation in late summer-early autumn and arouse in late autumn-early
 winter to mate, although females are still hibernating. Groups of males
 compete for matings and both males and females mate with multiple
 partners. Females that mate early return to hibernation even when
 pregnant, and males continue to mate with pregnant females. We asked to
 what extent to can the bizarre combination of behavioural and
 physiological features that characterize reproduction of Tasmanian
 echidnas be attributed to their phylogeny, and how much is a consequence
 of their ecology? 2. To understand the interaction between energetics and
 the echidna mating system in determining the timing of echidna hibernation
 we analysed data from an 18-year study of a wild population of Tasmanian
 echidnas 3. Males with high fat reserves arouse earliest and seek out
 suitable females, and females that mate early in the mating season
 re-enter hibernation while pregnant. 4. Competition between males drives
 early mating and while mating with males in the best condition could be
 advantageous for females and their young, egg-laying in winter is
 potentially disadvantageous, and post-mating hibernation by females is a
 means of delaying hatching of young until environmental conditions are
 more favourable. This post-mating hibernation by females is usually
 disrupted by males which mate with them although they are already
 pregnant. 5. Comparisons with other echidna populations suggests that a
 decreased activity period due to hibernation has not increased male-male
 competition. 6. Similar competition between groups of males for access to
 females is seen in chlamyphorid armadillos, which occupy a similar
 ecological niche to echidnas.
description: echidna
 dataImmergence and emergence
 dates, masses and reproductive activity and Observation
 history
DOI: 10.15468/dl.7kt82b
title: Occurrence Download

description: A dataset containing 293518 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is United States of America",
 "HasCoordinate is true",
 "TaxonKey is Clangula",
 "Year 2020-2026"
 ]
}

 The dataset includes 293518 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001822-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.bs03tq7
title: Data from: Post K-Pg diversification of the mammalian order Eulipotyphla as suggested by phylogenomic analyses of ultra-conserved elements

description: The origin of the mammalian order Eulipotyphla has been debated
 intensively with arguments around whether they began diversifying before
 or after the Cretaceous-Palaeogene (K-Pg) boundary at 66 Ma. Here, we used
 an in-solution nucleotide capture method and next generation DNA
 sequencing to determine the sequence of hundreds of ultra-conserved
 elements (UCEs), and conducted phylogenomic and molecular dating analyses
 for the four extant eulipotyphlan lineages—Erinaceidae, Solenodontidae,
 Soricidae, and Talpidae. Concatenated maximum-likelihood analyses with
 single or partitioned models and a coalescent species-tree analysis showed
 that divergences among the four major eulipotyphlan lineages occurred
 within a short period of evolutionary time, but did not resolve the
 interrelationships among them. Alternative suboptimal phylogenetic
 hypotheses received consistently the same amount of support from different
 UCE loci, and were not significantly different from the maximum likelihood
 tree topology, suggesting the prevalence of stochastic lineage sorting.
 Molecular dating analyses that incorporated among-lineage evolutionary
 rate differences supported a scenario where the four eulipotyphlan
 families diversified between 57.8 and 63.2 Ma. Given short branch lengths
 with low support values, traces of rampant genome-wide stochastic lineage
 sorting, and post K-Pg diversification, we concluded that the crown
 eulipotyphlan lineages arose through a rapid diversification after the
 K-Pg boundary when novel niches were created by the mass extinction of
 species.
description: mafft-nexus-edge-trimmed-clean-50p_noPartitionTaxonsetsNexus file for phylogenetic analysesmafft-nexus-edge-trimmed-clean-75p-8Nexus file for molecular dating
DOI: 10.5061/dryad.j133192
title: Data from: Ancient mitochondrial gene transfer between fungi and the orchids

description: The mitochondrial genomes (mitogenomes) of plants are known to incorporate
 and accumulate DNA from intra- and extracellular donors. Despite the
 intimate relationships formed between flowing plants (angiosperms) and
 fungi, lengthy fungal-like sequence has not been identified in angiosperm
 mitogenomes to date. Here we present multiple lines of evidence
 documenting horizontal gene transfer (HGT) between the mitogenomes of
 fungi and the ancestors of the orchids, plants that are obligate parasites
 of fungi during their early development. We show that the ancestor of the
 orchids acquired an approximately 270 bp fungal mitogenomic region
 containing three transfer RNA genes. We propose that the short HGT was
 later replaced by a second HGT event transferring more than 8 kb and 14
 genes from a fungal mitogenome to that of the ancestor of the largest
 orchid subfamily, Epidendroideae. Our results represent the first evidence
 of genomic-scale HGT between fungal and angiosperm mitogenomes and
 demonstrate that the length intergenic spacer regions of angiosperm
 mitogenomes can effectively fossilize the genomic remains of ancient,
 non-plant organisms.
description: Alignment of orchid HGT
 extentsAlignment of orchid
 mitochondrial sequences representing the extent of the fungal HGT region
 for each taxon, as identified via BLAST.Orchid_HGT_extents_alignment_FINAL.phyFungal and orchid atp6 alignmentAlignment of fungal and orchid atp6 sequences. Genbank accession number are appended to names of fungal sequences.atp6_orchid_fungi_alignment_curated.phyUstilago maydis coxI and Dendrobium catenatum fungal coxI alignmentAlignment of coxI of Ustilago maydis and the fungal-derived coxI remnant of the Dendrobium catenatum mitogenome.dendrobium_ustilago_cox1_alignment.fastaAlignment of Erycina pusilla mitogenomic BACsAlignment of four Genbank-archived BACs representing mitogenomic sequences of Erycina pusilla. Each sequence is named using its GenBank accession number.Erycina_mito_HGT_BAC_clones alignment.phyHexalectris brevicaulis vs. NCBI Basidiomycete RefSeq Genomes BLAST ResultBLAST result summary of Hexalectris brevicaulis fungal-derived sequence extent queried against the NCBI RefSeq Genomes database. Search conducted 13 March 2019.NCBI Blast_Hexa_brev_extent_vs_Basidiomycota_RefSeq_Genomes.pdfCorallorhiza striata var. striata 187MT Kraken2 resultsKraken2 results of 100bp segments of long range PCR of mitogenomic sequence of Corallorhiza striata var. striata (187MT) containing fungal-derived sequence.C_striata_187MT_100bp_interval_IDs.txtAlignment of tRNA region common across orchid fungal-derived regionsAlignment of fungal-derived sequence containing the same tRNA genes across orchid taxa sampled.HGT_core_tRNAs_aligned_genera.phy
DOI: 10.5061/dryad.679m4q2
title: Data from: From strategy to action: A qualitative study on salient factors influencing knowledge transfer in project-based experiential learning in healthcare organizations in Kenya

description: Objectives Knowledge transfer is recognized as a key determinant of
 organizational competitiveness. Existing literature on the transfer of
 knowledge and skills imply diminutive return on investment in training and
 development due to the low application of learned knowledge to the work
 environment. Following devolution of health services provision to new
 counties in Kenya in 2013, Strathmore Business School designed an
 experiential facility improvement project-based leadership training
 programme for healthcare managers in the new counties. Selected healthcare
 management teams participated in the leadership training to improve health
 systems performance in the devolved counties in Kenya.Despite similar
 training, the projects implementation contexts were different, leading to
 different implementation completion rates. The aim of this study was to
 investigate the reasons for this disparity and then recommend solutions.
 Design A qualitative study using semi-structured interviews. A thematic
 framework approach was used in data analysis. Setting and participants
 Thirty-nine projects team constituting; 33 successful and 6 unsuccessful
 project teams, were purposively selected based on their project
 implementation success rates at the end of the leadership training. The
 managers had undertaken a team-based institutional improvement project.
 The prioritized projects were housed within; 23 public, 10 faith-based and
 6 private health facilities in 19 counties in Kenya. Results Our findings
 indicate projects completion rates were influenced by (training design,
 work environment climate, trainee characteristics, team-based coaching
 and, leveraging on occurring opportunities). Transfer barriers were
 (inadequate management support, inadequate support, high staff-turn over,
 misalignment of board’s verses manager’s priorities, lack of technical
 expertise, endemic strikes, negative politics and, poor communication).
 Recommendations (needs-driven curriculum, effective allocation and
 efficient utilization of resources, proper prioritization, effective
 communication, longitudinal coaching and, work-teams recruitment).
 Conclusion The findings reveal that unless training interventions are
 informed by a need-driven curriculum customized to real-world work teams,
 the potential knowledge and skill transfer can be thwarted.
description: In-depth interview data
 summaryThe qualitative data
 obtained from the in-depth interviews have been summarised in an excel
 worksheet. The summary presents the study background information, factors
 which could have led to success or failure in the implementation of the
 projects at the workplace. In addition, the work-environment specific
 enablers and barriers of knowledge transfer, and how these factors could
 be reinforced or mitigated for better results, are presented in the form
 of illustrative quotes.From Strategy to Action
 Qualitative Data summary- Chelagat
 Tecla.xlsx
DOI: 10.5061/dryad.3mc4265
title: Data from: Genome-wide association mapping of date palm fruit traits

description: Date palms (Phoenix dactylifera) are an important fruit crop of arid
 regions of the Middle East and North Africa. Despite its importance, few
 genomic resources exist for date palms, hampering evolutionary genomic
 studies of this perennial crop species. Here we report an improved
 long-read genome assembly for P. dactylifera that is 772.3 Mb in length,
 with contig N50 of 897.2 Kb, and use this to perform GWAS mapping of the
 sex determining region and 21 fruit traits. We find a fruit color GWAS at
 the R2R3-MYB transcription factor (VIRESCENS) gene and identify functional
 alleles that include a retrotransposon insertion and start codon mutation.
 We also find a GWAS peak for sugar composition spanning deletion
 polymorphisms in multiple linked invertase genes. MYB transcription
 factors and invertase are implicated in fruit color and sugar composition
 in other crop species, demonstrating the importance of parallel evolution
 in the evolutionary diversification of domesticated species.
description: SNP callset used in GWAS
 (gwas.snp1.8c.vcf.gz)Single nucleotide
 polymorphisms (SNPs) in Variant Call Format (VCF) used in the Genomewide
 Association Study. See the README file for additional
 details.gwas.snp1.8c.vcf.gz
DOI: 10.5061/dryad.pk05kf2
title: Data from: Aster rupestris (Asteraceae, Astereae), a new species from Guizhou, China: Evidence from morphological, molecular and cytological date

description: [No abstract entered]
description: Appendix_1_Table_A1Appendix 1: separate Excel-file with Genbank accession numbers and Table A1.
DOI: 10.5061/dryad.0jj7sf0
title: Data from: Predictors of return to work after kidney transplantation: a 12-month cohort of the Japan Academic Consortium of Kidney Transplantation (JACK) study

description: Objectives: To investigate the cumulative return-to-work rate and to
 identify predictors of employment after kidney transplantation. Design:
 Retrospective, outpatient-based cohort study. Setting: This was a
 single-center study of the largest Japanese kidney transplant center.
 Participants: We selected Japanese kidney transplant recipients aged 20-64
 years who were employed in paid jobs at the time of transplantation and
 who visited an outpatient clinic from December 2017 to March 2018. From
 797 patients, we evaluated 515 in this study. Interventions: We
 interviewed patients at an outpatient clinic and investigated the timing
 and predictors of return to work using logistic regression models. Primary
 and secondary outcome measures: The primary outcome was the cumulative
 return-to-work rate, and the secondary outcome was to investigate the
 predictors of return to work after kidney transplantation. Results: Among
 the 515 included recipients, the cumulative overall partial/full return to
 work rates at 2, 4, 6, and 12 months were 22.3%, 59.0%, 77.1%, and 85.0%,
 respectively. The median duration from transplantation to return to work
 was 4 months. Regarding partial/full return to work, according to the
 multivariable analysis including all variables, male sex was a greater
 predictor for return to work than female sex (odds ratio [OR]: 2.05, 95%
 confidence interval [CI] 1.32-3.20); a managerial position was a greater
 predictor than a non-managerial position (OR: 2.23, 95% CI 1.42-3.52).
 Regarding full return to work, male sex (OR: 1.95, 95% CI 1.25-3.06) and
 managerial position (OR: 1.95, 95% CI 1.25-3.06) were also good
 predictors. Conclusions: The cumulative return-to-work rate was 85.0% 1
 year post-transplantation. Given that cumulative return-to-work rates
 varied by sex and position, transplant and occupational physicians should
 support kidney transplant recipients in the aspect of returning to work.
description: dry
DOI: 10.5061/dryad.37g6d40
title: Data from: The conservation genomics of the endangered distylous gypsophile Oreocarya crassipes (Boraginaceae)

description: The Chihuahuan Desert includes many endemic angiosperm species, some
 having very restricted geographic ranges. One of these species is
 Oreocarya crassipes (I. M. Johnst.) Hasenstab & M. G. Simpson, an
 endangered distylous gypsophile from the Trans-Pecos region in southern
 Brewster County, Texas, USA. The species is known from 10 populations, and
 this small number of populations, human development in the area, a
 distylous breeding system, and edaphic requirements threaten the long-term
 viability of the species. Using both hundreds of single nucleotide
 polymorphisms identified via tunable genotyping-by-sequencing (tGBS) and
 10 microsatellite loci, patterns of genetic diversity, demography,
 selection, and migration were examined for 192 individuals from four
 populations of O. crassipes. From the sampled individuals, two populations
 (clusters) were identified via multiple methodologies and with both types
 of data. With SNP data, population substructure was further resolved among
 one of these populations to identify two distinct groups of individuals.
 Multiple individuals recognized as having mixed ancestry, along with Fst
 values and AMOVA results, provide evidence of genetic exchange among
 populations, which is less common for gypsophiles than non-gypsophiles,
 and the rate of migration among populations has been increasing recently.
 The Fst values for O. crassipes are more similar to those of other rare
 species than to other gypsophiles. Additionally, while distyly
 specifically does not necessarily impact the population genetics of the
 species, allogamy, which is facilitated by distyly, seems to have played a
 role in the genetic structure of O. crassipes.
description: SNP file - 10% missing
 dataStructure file with 238
 SNPs and up to 10% missing data generated via tunable
 Genotyping-by-SequencingOreocarya.LMD10.snps.genotype_STRUCTURE.txtSNP file - 50% missing dataStructure file with 238 SNPs and up to 10% missing data generated via tunable Genotyping-by-SequencingOreocarya.LMD50.snps.genotype.STRUCTURE.strMicrosatellite dataStructure file with 10 microsatellite lociOREOCARYA MICROSAT DATA.str
DOI: 10.5061/dryad.v67m4f0
title: Data from: Limited gene exchange between two sister species of leaf beetles within a hybrid zone in the Alps

description: Analysing genomic variation within and between sister species is a first
 step towards understanding species boundaries. We focused on two sister
 species of cold-resistant leaf beetles, Gonioctena quinquepunctata and G.
 intermedia, whose ranges overlap in the Alps. A previous study of DNA
 sequence variation had revealed multiple instances of mitochondrial genome
 introgression in this region, suggesting recent hybridizations between the
 two species. To evaluate the extent of gene exchange resulting from these
 hybridization events, we sampled individuals of both species inside and
 outside the hybrid zone and analysed genomic variation among them using
 RAD-seq markers. Individual levels of introgression in the nuclear genome
 were estimated first by defining species-specific SNPs (displaying a fixed
 difference between species) a priori, and second by using model-based
 methods. Both types of analyses indicated little gene exchange, if any,
 between species at the level of the nuclear genome. While the first method
 suggested slightly more gene flow, we argue that it has likely
 overestimated introgression in the phylogeographic context of this study.
 We conclude that strong intrinsic barriers prevent genetic exchange at the
 level of the nuclear genome between the two species. The apparent
 discrepancy observed between introgression occurring in the nuclear and
 mitochondrial genomes could be explained by selection acting in favour of
 the latter. Also, these results have consequences for the phylogeographic
 study of each species, since we can assume that genetic diversity in the
 overlapping portion of their ranges is not the product of introgression.
description: stacks_results_m10_M3_n3_batch_1_maxDP500_p0_5.vcfData set Astacks_results_m10_M8_n8_batch_1_maxDP500_p0_5.vcfData set B
DOI: 10.5061/dryad.2t6t1fd
title: Data from: Stochastic dynamics of three competing clones: conditions and times for invasion, coexistence and fixation

description: In large clonal populations, several clones generally compete which
 results in complex evolutionary and ecological dynamics: experiments show
 successive selective sweeps of favorable mutations as well as long-term
 coexistence of multiple clonal strains. The mechanisms underlying either
 coexistence or fixation of several competing strains have rarely been
 studied altogether. Conditions for coexistence has mostly been studied by
 population and community ecology, while rates of invasion and fixation
 have mostly been studied by population genetics. In order to provide a
 global understanding of the complexity of the dynamics observed in large
 clonal populations, we develop a stochastic model where three clones
 compete. Competitive interactions can be intransitive and we suppose that
 strains enter the population via mutations or rare immigrations. We first
 describe all possible final states of the population, including stable
 coexistence of two or three strains, or the fixation of a single strain.
 Second, we give estimate of the invasion and fixation times of a favorable
 mutant (or immigrants) entering the population in a single copy. We
 especially show that invasion and fixation can be slower or faster when
 considering complex competitive interactions. Third, we explore the
 parameter space assuming prior distributions of reproduction, death and
 competitive rates and we estimate the likeliness of the possible dynamics.
 We especially show that when mutations can affect competitive
 interactions, even slightly, stable coexistence is likely. We discuss our
 results in the context of the evolutionary dynamics of large clonal
 populations.
description: Posterior
 distributionContains the mathematica
 notebooks used to calculate the posterior distribution of all possible
 final statesSimulation
 programCode source for the
 stochastic simulations. The random number generator is not included
 because of license limitation. It can however be freely downloaded (web
 address within the README.txt file)