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20,299 results for “Systematic”
Data from: Ultraconserved yet informative for species delimitation: UCEs resolve long-standing systematic enigma in Central European bees
Accurate and testable species delimitation hypotheses are essential for measuring, surveying and managing biodiversity. Today, taxonomists often rely on mitochondrial DNA barcoding to complement morphological species delimitations. Although COI barcoding has largely proven successful in assisting identifications for most animal taxa, there are nevertheless numerous cases where mitochondrial barcodes do not necessarily reflect the species history. For instance, what is regarded as one single species can be associated with two distinct DNA barcodes, which can point either to cryptic diversity or to deep within-species mitochondrial divergences with no reproductive isolation. In contrast, two or more species can share barcodes, for instance due to mitochondrial introgression. These intrinsic limitations of mitochondrial DNA barcoding can only be addressed with nuclear genomic markers, which are expensive, labour intensive, poorly repeatable, and often require high-quality DNA. To overcome these limitations, we examined the use of ultraconserved nuclear genetic elements (UCEs) as a quick and robust genomic approach to address such problematic cases of species delimitation. This genomic method was assessed using six different bee species complexes suspected to harbour cryptic diversity, mitochondrial introgression, or mitochondrial paraphyly. The sequencing of UCEs recovered between 686 and 1860 homologous nuclear loci and provided explicit species delimitation hypotheses in all investigated species complexes. These results provide strong evidence for the suitability of UCEs as a fast method for species delimitation even in recently diverged lineages. Furthermore, this study provided the first conclusive evidence for both mitochondrial introgression among distinct species, and mitochondrial paraphyly within a single bee species.
A large-scale systematic framework of Chinese snakes based on a unified multilocus marker system
Snakes are one of the most diverse groups of terrestrial vertebrates, with approximately 3500 extant species, some of which are closely related to human life. A robust phylogeny and taxonomy of snakes is crucial for us to know, study, protect and make use of them. For a large group such as snakes, cross-study data utilization is important which can be facilitated by standardization of the loci used for systematic analyses. In this study, we combined 5 mitochondrial markers, 19 vertebrate-universal nuclear protein coding (NPC) markers and 72 snake-specific noncoding intron markers, and generated a unified multilocus marker system for studies of snake systematics. This marker system is an addition to the squamate conserved locus set compiled for large-scale sequence capture experiments. We applied this marker system to over 440 snake samples and constructed the currently most comprehensive systematics framework of the snakes in China. Robust snake phylogenetic relationships were recovered at both deep and shallow evolutionary depths, demonstrating the usefulness of this multilocus marker system. Discordance was revealed by a parallel comparison between the snake tree based on our multilocus marker system and that based on only the mitochondrial loci, highlighting the necessity of using multiple marker types to better understand the snake evolutionary histories. The divergence times of different snake groups were estimated with the multilocus data set. Our comprehensive snake tree not only confirms many important nodes inferred in previous studies but also contributes new insights into the phylogenetic relationships among snakes. Suggestions are made for the current snake taxonomy.
Agile Global Software Development: A Systematic Literature Review
<p>Global Software Development (GSD) continues to grow substantially and it is fast becoming the norm and fundamentally different from local Software Engineering development. Withal, agile software development (ASD) has become an appealing choice for companies attempting to improve their performance although its methods were originally designed for small and individual teams. The current literature does not provide a cohesive picture of how the agile practices are taken into account in the distributed nature of software development: how to do it, who, and what works in practice. This study aims to highlight how ASD practices are applied in the context of GSD in order to develop a set of techniques that can be relevant in both research and practice. To answer the research question, "how are agile practices adopted in agile global software development teams?'" We conducted a systematic literature review of the ASD and GSD literature. A synthesis of solutions found in seventy-six studies provided 48 distinct practices that organizations can implement, including "collaboration among teams", "agile architecture'", "coaching", "system demo" and "test automation". These implementable practices go some way towards providing solutions to manage GSD teams, and thus to embrace agility.</p>
data sets and trees for the Rasplus et al paper "Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)" Cladistics (2020)
<p>Data sets and trees for the Rasplus <em>et al</em>. paper "Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus <em>Ficus</em> (Moraceae)" Cladistics (2020). Preprint = https://www.biorxiv.org/content/10.1101/2020.04.15.042259v1</p> <p><strong>*.phy = Data sets (phylip format) [see Table 2 of the paper for more details].</strong></p> <p>- <strong>mergeR1R2.phy</strong> : complete data set (530 RAD loci shared by 75% of the samples + assembly of forward & reverse reads)<br> - <strong>mergeR1R2_GCinfmean.phy</strong> : loci with GC content inferior or equal to mean GC content<br> - <strong>mergeR1R2_GCsupmean.phy</strong> : loci with GC content strictly superior to mean GC content<br> - <strong>mergeR1R2_LS3.phy</strong> : loci that evolve at a homogeneous rate across clades of interest (Clade1= sect. Pharmacosycea; Clade2=subg. Urostigma, Clade3=sect. Oreosycea, Clade4= "gynodioecious clade")<br> - <strong>mergeR1R2_PCA.phy</strong> : loci for which difference between Long Branch (LB) scores for sect. Pharmacosycea and other ingroups was not significant according to our custom iterative PCA approach</p> <p> <br> <strong>Fig*.nwk : Trees (newick format) that were obtained for the different data sets.</strong></p> <p>Trees are also included as Figures or Supplementary Figures of the paper. Note that you may visualize these nwk trees in FigTree (open FigTree. Upload the FigS1A_RAxML_mergeR1R2_inclfigtreeannot.nex first and then open the other trees - do not close FigTree in between !- Annotations included in the first file will be automatically used to annotate other trees). </p> <p><strong>Appendix S2 : Morphological matrix + morphological tree + 4 competing molecular trees. </strong></p> <p>This file can be opened in Mesquite to get reconstruction of ancestral character states</p>
Sample Records. Citizen Science and Citizen Energy Communities: A Systematic Review of Potential Alliances for SDGs
<p>Sample Records. Citizen Science and Citizen Energy Communities: A Systematic Review of Potential Alliances for SDGs</p>
Systematic reanalysis of co-fractionation mass spectrometry data: predicted interactomes
<p>This upload contains predicted interactomes for 27 species or clades: 17 individual organisms with at least three published CF-MS experiments, and 9 phylogenetic groupings of those organisms. </p> <p>The following individual organisms are represented:</p> <ul> <li>Arabidopsis thaliana</li> <li>Brassica oleracea</li> <li>Caenorhabditis elegans</li> <li>Chaetomium thermophilum</li> <li>Chlamydomonas reinhardtii</li> <li>Dictyostelium discoideum</li> <li>Drosophila melanogaster</li> <li>Nematostella vectensis</li> <li>Homo sapiens</li> <li>Mus musculus</li> <li>Oryza sativa</li> <li>Plasmodium berghei</li> <li>Plasmodium falciparum</li> <li>Plasmodium knowlesi</li> <li>Strongylocentrotus purpuratus</li> <li>Triticum aestivum</li> <li>Trypanosoma brucei</li> <li>Xenopus laevis</li> </ul> <p>The following clades are also represented:</p> <ul> <li>BOP clade</li> <li>Deuterostomia</li> <li>Eucharontoglires</li> <li>Eukaryota</li> <li>Mesangiospermae</li> <li>Opiskothonta</li> <li>Plasmodium</li> <li>Tetrapoda</li> <li>Viridaplantae</li> </ul> <p>The interactomes are provided in two forms. Files in the 'All interactions' directory include the complete classifier scores for every possible protein pair (sorted in descending order). Files in the '50% precision' directory include only those interactions identified above 50% precision, for convenience. </p> <p>Proteins were mapped to orthogroups using eggNOG. Maps from eggNOG orthogroups to UniProt accessions are available from https://github.com/skinnider/CF-MS-analysis/tree/master/data/resources/eggNOG. The phylogenetic tree used to group species into clades is also available from https://github.com/skinnider/CF-MS-analysis/tree/master/data/resources/TimeTree/species.nwk.</p> <p>The third and final directory, 'Human', contains the consensus CF-MS human interactome, in which proteins were merged across 46 human experiments by their gene names, rather than based on eggNOG orthogroups. The directory contains both complete classifier scores (file 'classifier-scores.tsv.gz') and the consensus CF-MS interactome, at 50% precision (file 'CF-MS-interactome.tsv').</p>
The influence of thin as compared to thick peri-implant soft tissues on esthetic outcomes. A systematic review and meta-analysis.
<p>Dataset for all analyses in the paper.</p>
The new systematics of Scleractinia: integrating molecular and morphological evidence
<p>Phylogenetic data matrix of 12 DNA markers and BEAST input file for time-calibrated trees of 576 Scleractinia species</p>
Systematic Literature Review results: PRISMA Statement Phases for Education and Communication based on Circular Economy and Bioenergy Literature
<p>Results of each phase of the prisma statement of the flow Diagram.</p>
A Systematic Review on Software Robustness Assessment - Dataset
<p>Dataset supporting the paper entitled "A Systematic Review on Software Robustness Assessment".</p>
Supporting dataset – A systematic review of automated journalism scholarship: guidelines and suggestions for future research
<p>This dataset supports the following article, conditionally accepted for publication in Open Research Europe:</p> <p>"A systematic review of automated journalism scholarship: guidelines and suggestions for future research."</p> <p> </p> <p> </p>
Characterizing Technical Debt and Antipatterns in AI-Based Systems: A Systematic Mapping Study
<p>All artifacts related to a systematic mapping study on technical debt and antipatterns in AI-based systems; the data consists of an Excel file (00-all-data.xlsx) which includes a tab for all important constructs plus a separate CSV file per construct:</p> <ul> <li>List of primary studies (01-primary-studies.csv)</li> <li>Established types of technical debt (02-established-td-types.csv)</li> <li>New types of technical debt (03-new-td-types.csv)</li> <li>Affected software quality attributes (04-affected-qas.csv)</li> <li>Identified antipatterns (05-antipatterns.csv)</li> <li>Reported solutions to address technical debt or antipatterns (06-solutions.csv)</li> </ul> <p> </p>
Quality Evaluation Models or Frameworks for Open Source Software: A Systematic Literature Review (Article Pool)
<p>This pdf includes all of the articles that analyzed in the study: "Quality Evaluation Models or Frameworks for Open Source Software: A Systematic Literature Review".</p>
A systematic literature assessment on the effects of human-altered soundscapes on marine life
<p>A dataset containing the results of a systematic assessment of the literature on the effects of human-altered soundscapes on marine life. This identified 538 peer-reviewed papers that consider how changes in anthrophony, geophony, and biophony affect marine fauna. Papers on the effects of anthrophony are categorised by species, taxonomic group, effect category, statistical outcome, and whether mitigation strategies were tested. Papers considering changes in bio- or geo-phony contain details on the ecosystem where responses were measured, the effect shown, and the statistical outcome. </p>
Anatomy of the nasal and auditory regions of the fossil lagomorph Palaeolagus haydeni: systematic and evolutionary implications
<p>Palaeolagus, a late Eocene to early Miocene North American lagomorph genus, represented by numerous and well-preserved specimens, has been long considered a basal leporid, although it is currently understood as a stem lagomorph. Based on micro-computed tomography (μCT) data and 3D reconstructions, here we present the first description of intracranial structures of the nasal and auditory regions of a complete skull of Palaeolagus haydeni from the early Oligocene of Nebraska. Although Palaeolagus haydeni shows a puzzling mixture of extant leporid and ochotonid characters, it helps to polarize and re-evaluate already known lagomorph intracranial characters based on outgroup comparison with Rodentia and Scandentia. Common derived features of Palaeolagus haydeni and extant Lagomorpha are the dendritic maxilloturbinal and the excavated nasoturbinal that contacts the lamina semicircularis. Generally, Palaeolagus haydeni and Leporidae have several characters in common, some of which are certainly plesiomorphic (e.g., thin wall of bulla tympani and flat conic cochlea). Palaeolagus haydeni resembles Leporidae in having an interturbinal between the two frontoturbinals, and three ethmoturbinals plus one interturbinal between ethmoturbinal I and II. Now, this should also be regarded as a plesiomorphic grundplan pattern for Leporidae whereas ochotonids are derived from the lagomorph grundplan as concerns the number of frontoturbinals. Concerning the middle ear, Palaeolagus haydeni significantly contributes to the polarization of the anterior anchoring of the malleus in extant lagomorphs. Palaeolagus haydeni resembles the pattern observed in early ontogenetic stages of Ochotonidae, i.e., the attachment of the malleus to the ectotympanic via a short processus anterior. The patterns in adult ochotonids and leporids now can be regarded as two different and apomorphic character states. Autapomorphic characters of Palaeolagus haydeni are the reduced frontoturbinal 2 and the additional anterolaterally oriented process of the lamina semicircularis. Interestingly, among the investigated intracranial structures the loss of the secondary crus commune is the only apomorphic grundplan character of crown Lagomorpha.</p> <p> </p>
Data from: Systematic revision of Symbiodiniaceae highlights the antiquity and diversity of coral endosymbionts
The advent of molecular data has transformed the science of organizing and studying life on Earth. Genetics-based evidence provides fundamental insights into the diversity, ecology, and origins of many biological systems, including the mutualisms between metazoan hosts and their micro-algal partners. A well-known example is the dinoflagellate endosymbionts ("zooxanthellae") that power the growth of stony corals and coral reef ecosystems. Once assumed to encompass a single panmictic species, genetic evidence has revealed a divergent and rich diversity within the zooxanthella genus Symbiodinium. Despite decades of reporting on the significance of this diversity, the formal systematics of these eukaryotic microbes have not kept pace, and a major revision is long overdue. With the consideration of molecular, morphological, physiological, and ecological data, we propose that evolutionarily divergent Symbiodinium "clades" are equivalent to genera in the family Symbiodiniaceae, and we provide formal descriptions for seven of them. Additionally, we recalibrate the molecular clock for the group and amend the date for the earliest diversification of this family to the middle of the Mesozoic Era (∼160 mya). This timing corresponds with the adaptive radiation of analogs to modern shallow-water stony corals during the Jurassic Period and connects the rise of these symbiotic dinoflagellates with the emergence and evolutionary success of reef-building corals. This improved framework acknowledges the Symbiodiniaceae's long evolutionary history while filling a pronounced taxonomic gap. Its adoption will facilitate scientific dialog and future research on the physiology, ecology, and evolution of these important micro-algae.
Image 1. Puntius rubrotinctus Neotype, 71.8 in Systematic status of Systomus rubrotinctus Jerdon (Teleostei: Cyprinidae) with notes on the Puntius arulius group of fishes
Image 1. Puntius rubrotinctus Neotype, 71.8 mm SL, ZSI/SRS F.8373
Figure 4 in Systematics, bionomy, and metamorphosis of Coleoptera (Insecta): Papers celebrating the 80 birthday of Cleide Costa
Figure 4. Coleoptera Immature Collection (CIC-MZUSP). (A) Notebook with daily records of Coleoptera immatures in the laboratory; (B-D) Sergio Ide, Leopoldina Pascher and Adriana Pires working on the collection; (E) Sônia Casari and Maria Eulina Jorge; (F) Adriana Pires and Sergio Ide; (G) Cleide Costa and Wanessa Zorzan; (H) Cabinets of the Coleoptera Immature Collection-MZUSP.
Figure 3 in Systematics, bionomy, and metamorphosis of Coleoptera (Insecta): Papers celebrating the 80 birthday of Cleide Costa
Figure 3. Cleide Costa's drawing process. (A) Drafts to final art of adult and larva of Glyptolopus quadricostatus Heinze, 1944 (Cerylonidae), from Costa et al., 1996. (B) Pencil draft and final art of Scraptia triangularis Champion, 1916 (Scraptiidae), from Vanin et al., 1996.
Figure 2 in Systematics, bionomy, and metamorphosis of Coleoptera (Insecta): Papers celebrating the 80 birthday of Cleide Costa
Figure 2. Correspondences between Dr.Cleide Costa and Dr. Ubirajara Martins during her first studies of beetles.These letters were the beginning of their contributions.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.