1,720,976 research outputs found
Dataset for tree congruence: quantifying similarity between dendrogram topologies
No full textThis dataset comprises 40 simulated dendrograms generated from MRPs and retaining suboptimal trees. There are four sets of dendrograms, each set comprises 10 dendrograms. The sets of dendrograms have 11, 21, 31 and 41 terminal nodes respectively. The sets of dendrograms were analysed using CRI (Vidovic & Martill 2017), MASTxCF (New), CF (Colless 1980), R-F (Robinson & Foulds 1981), Mickevich’s CIM (Mickevich 1980), Rohlf’s CI1 (Rohlf 1982), Weighted CF (Colless 1980), and SPR distances (Goloboff 2008). Additionally, Kendall’s tau-b was used to measure the concordance between the 1,620 results and Spearman’s rho was used to confirm those findings.
CF, MASTxCF, Weighted CF, CIM and CI1 were generated in PAUP. MASTxCF was manually calculated from information obtained in PAUP but an R script was subsequently written and the results were recalculated, as were the CF indices. The SPR distances, one of the R-F metrics, and distortion coefficient were calculted in TNT. The CRI and R-F distances were calculated in R only. The procedures for the CRI, MASTxCF, CF and R-F are given.</span
COAF Open Access block grant return 2018-2019 University of Southampton
No full textList of articles that UoS paid for with COAF OA fund monies during 01/10/2018 to 30/09/2019. Contains financial information, Grant numbers, dates of acceptance/publication, DOIs and licence details
Tree congruence: quantifying similarity between dendrogram topologies
No full textTree congruence metrics are typically global indices that describe the similarity or dissimilarity between dendrograms. This study principally focuses on topological congruence metrics that quantify similarity between two dendrograms and can give a normalised score between 0 and 1. Specifically, this article describes and tests two metrics the Clade Retention Index (CRI) and the MASTxCF which is derived from the combined information available from a maximum agreement subtree and a strict consensus. The two metrics were developed to study differences between evolutionary trees, but their applications are multidisciplinary and can be used on hierarchical cluster diagrams derived from analyses in science, technology, maths or social sciences disciplines. A comprehensive, but non-exhaustive review of other tree congruence metrics is provided and nine metrics are further analysed. 1,620 pairwise analyses of simulated dendrograms (which could be derived from any type of analysis) were conducted and are compared in Pac-man piechart matrices. Kendalls tau-b is used to demonstrate the concordance of the different metrics and Spearmans rho ranked correlations are used to support these findings. The results support the use of the CRI and MASTxCF as part of a suite of metrics, but it is recommended that permutation metrics such as SPR distances and weighted metrics are disregarded for the specific purpose of measuring similarity
Is open access tarnished?
No full textAs open access terms have split into colour-coded brands, not all allow totally unrestricted access and reuse. Among these, “bronze OA” stands out as a potentially damaging misnomer, writes Steven Vidovi
University of Southampton APCs for COAF 2017-2018
No full textDetails of the University of Southampton Article Processing Charges (APCs) for 1 September 2017 to 31 August 2018 using Charities Open Access Fund (COAF) administered by the library. Other papers may have been made open access using other budgets within the university or by co-authors at other HEIs and are not included here.</span
Cladistic revision of Cretaceous Brachylepadomorpha and Verrucomorpha dataset
No full textThis dataset supports the publication by Andy S. Gale & S U. Vidovic "The origins of major sessile cirripede groups; a revision of Cretaceous Brachylepadomorpha and Verrucomorpha" in Journal of Systematic Palaeontology
DOI: 10.1080/14772019.2023.2258370
This dataset comprises the TNT script to run a cladistic analysis of sessile cirripede groups and bootstrap resampling with 1000 replicates; the output files from TNT; the supporting Nexus file; and an R script for post-analysis of the tree to calculate the Gap Excess Ratio (GER).
The cladistic analysis comprises 48 characters, one of which is continuous, all others were treated as unordered with equal weights. The TNT script also contains instructions to run an implied weights analysis.
To successfully execute the TNT script, the user will need to include the correct file path to their own copy of Stats.run, a TNT script for calculating the ensemble consistency index and retention index.
TNT scripts can be given a .tnt extension and can be read by TNT and Mesquite. Nexus files can be given a .nex extension and can be read by Mesquite and TNT. R files can be given a .r extension and can be run in RStudio. The output log can be read in plain text, .tre and .nex output files can be opened by all the software used in this study.
Contributions to this dataset:
Gale made intellectual contributions with respect to the anatomy, systematics and stratigraphic occurrence of sessile cirripede groups. Gale: co-designed the analysis; wrote the characters; coded the matrix.
Vidovic made intellectual contributions with respect to cladistic analysis and post-analysis. Vidovic: wrote the dataset; co-designed and executed the analysis; wrote the scripts and functions; created the files; edited the characters; coded the matrix.</span
University of Southampton Reproducible and Transparent Practices Map
No full textThe University of Southampton has numerous pockets of excellence practicing reproducible and transparent research best practices, broadly contributing to Open Research, Research Integrity, and Research Culture. Here we attempt to "map" those pockets of excellence, considering tools, training, activities, infrastructure, networks etc. which create, promote, and enable these practices
University of Southampton - Response to Guidance on the Implementation of Plan S
No full textThe responses to the questions below comprise feedback to cOAlition S on the Plan S guidance from the University of Southampton. These points are based on discussion at the University Open Research Group and consultation with professional and academic staff in all Faculties. The University wholly embraces the idea of a fully open future for research and the general principle of beginning to deliver on these goals from January 2020. We, as an institution, have been deeply involved in the progress to Open Access (OA), developing EPrints open source software for institutional and subject repositories of which ePrints Soton was an early example. Overall, we are supportive of innovation and disrupting the publishing market, but we are aware of a complex and varied publishing environment
The origins of major sessile cirripede groups; a revision of Cretaceous Brachylepadomorpha and Verrucomorpha
No full textThe taxonomy of Cretaceous cirripedes referred to the sessile orders Brachylepadomorpha and Verrucomorpha is revised. New taxa include the brachylepadid genera Crithmumlepas (type species C. hoensis sp. nov., C. aycliffensis sp. nov.) and Calvatilepas (type species C. recurvus sp. nov.). The family Pycnolepadidae nov. is established (constituent genera Pycnolepas, Faxelepas) and Pycnolepas batchelorum sp. nov. is described; a new eoverrucid species, E. barringtonensis sp. nov. is erected. Cladistic analysis of 48 characters of 18 operational taxonomic units, including 16 in-group sessile taxa yielded a consensus tree showing the strongly supported monophyly of Brachylepadomorpha + Verrucomorpha + Balanomorpha. It is recommended that the Order Brachylepadomorpha is abandoned, and its constituent families are identified as, respectively, stem group Verrucomorpha (Pycnolepadidae) and stem group Balanomorpha (Brachylepadidae). The sister-group relationship of Verrucomorpha and Balanomorpha, identified from many molecular studies, is confirmed from shell morphological data. The Neolepadoidea are shown to closely parallel the sessile adaptations of verrucomorphs and balanomorphs. The fossil record of key segments of cirripede evolution is demonstrated to be remarkably, and surprisingly, complete. http://zoobank.org/urn:lsid:zoobank.org:pub:8F450F22-94BA-49D3-BAF9-A8377359D0E8.</p
Pterodactylus scolopaciceps Meyer, 1860 (Pterosauria, Pterodactyloidea) from the Upper Jurassic of Bavaria, Germany:the problem of Cryptic Pterosaur Taxa in early ontogeny
Full text linkThe taxonomy of the Late Jurassic pterodactyloid pterosaur Pterodactylus scolopaciceps Meyer, 1860 from the Solnhofen Limestone Formation of Bavaria, Germany is reviewed. Its nomenclatural history is long and complex, having been synonymised with both P. kochi (Wagner, 1837), and P. antiquus (Sömmerring, 1812). The majority of pterosaur species from the Solnhofen Limestone, including P. scolopaciceps are represented by juveniles. Consequently, specimens can appear remarkably similar due to juvenile characteristics detracting from taxonomic differences that are exaggerated in later ontogeny. Previous morphological and morphometric analyses have failed to separate species or even genera due to this problem, and as a result many species have been subsumed into a single taxon. A hypodigm for P. scolopaciceps, comprising of the holotype (BSP AS V 29 a/b) and material Broili referred to the taxon is described. P. scolopaciceps is found to be a valid taxon, but placement within Pterodactylus is inappropriate. Consequently, the new genus Aerodactylus is erected to accommodate it. Aerodactylus can be diagnosed on account of a unique suite of characters including jaws containing 16 teeth per-jaw, per-side, which are more sparsely distributed caudally and terminate rostral to the nasoantorbital fenestra; dorsal surface of the skull is subtly depressed rostral of the cranial table; rostrum very elongate (RI = ∼7), terminating in a point; orbits correspondingly low and elongate; elongate cervical vertebrae (approximately three times the length of their width); wing-metacarpal elongate, but still shorter than the ulna and first wing-phalanx; and pteroid approximately 65% of the total length of the ulna, straight and extremely thin (less than one third the width of the ulna). A cladistic analysis demonstrates that Aerodactylus is distinct from Pterodactylus, but close to Cycnorhamphus Seeley, 1870, Ardeadactylus Bennett, 2013a and Aurorazhdarcho Frey, Meyer and Tischlinger, 2011, consequently we erect the inclusive taxon Aurorazhdarchidae for their reception
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