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2. Tree congruence: quantifying similarity between dendrogram topologies

Author

Vidovic, Steven U.

Subjects
Mathematics - General Topology, Quantitative Biology - Populations and Evolution, Quantitative Biology - Quantitative Methods, Statistics - Methodology
Abstract

Tree 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., Comment: 17 pages, 4 figures, 3 tables, 1 linked dataset

Published
2019

4. The taxonomy and phylogeny of Diopecephalus kochi (Wagner, 1837) and 'Germanodactylus rhamphastinus' (Wagner, 1851): Taxonomy of Diopecephalus and Germanodactylus

Author

Vidovic, Steven U. and Martill, David M.

Abstract

The Solnhofen pterosaurs Pterodactylus antiquus, Aerodactylusscolopaciceps, Diopecephalus kochi, Germanodactylus cristatus and Germanodactylus rhamphastinus all have complicated taxonomic histories. Species originally placed in the genus Pterodactylus, such as Aerodactylus scolopaciceps, Ardeadactylus longicollum, Cycnorhamphus suevicus and Germanodactylus cristatus possess apomorphies not observed in the type species of Pterodactylus, and consequently have been placed in new genera. The affinities of another Solnhofen pterosaur previously placed in Pterodactylus, Diopecephalus kochi, are less clear. It has been proposed that D. kochi is a juvenile specimen of Pterodactylus antiquus, or perhaps “Germanodactylus rhamphastinus” specimens are mature examples of D. kochi. Furthermore, studies have suggested that “Germanodactylus rhamphastinus” is not congeneric with the type species of Germanodactylus. Geometric morphometric analysis of prepubes and a cladistic analysis of the Pterosauria elucidate plesiomorphic and apomorphic conditions for basal Jurassic pterodactyloids. Germanodactylus is found to be a monotypic genus and Pterodactylus, Diopecephalus, and “G. rhamphastinus” are found as distinct taxa belonging in individual genera, diagnosable using a combination of characters. Thus, Diopecephalus kochi is not demonstrated to be congeneric with Germanodactylus or Pterodactylus and is maintained as a valid taxon. “G. rhamphastinus” is readily distinguishable from other Solnhofen pterosaur taxa, and a new genus is erected for its reception.

Published
2018

10. The taxonomy and phylogeny of Diopecephalus kochi(Wagner, 1837) and ‘Germanodactylus rhamphastinus’ (Wagner, 1851)

Author

Vidovic, Steven U. and Martill, David M.

Abstract

The Solnhofen pterosaurs Pterodactylus antiquus, Aerodactylus scolopaciceps, Diopecephalus kochi, Germanodactylus cristatusand Germanodactylus rhamphastinusall have complicated taxonomic histories. Species originally placed in the genus Pterodactylus, such as Aerodactylus scolopaciceps, Ardeadactylus longicollum, Cycnorhamphus suevicusand Germanodactylus cristatuspossess apomorphies not observed in the type species of Pterodactylus, and consequently have been placed in new genera. The affinities of another Solnhofen pterosaur previously placed in Pterodactylus, Diopecephalus kochi, are less clear. It has been proposed that D. kochiis a juvenile specimen of Pterodactylus antiquus, or perhaps ‘Germanodactylus rhamphastinus’ specimens are mature examples of D. kochi. Furthermore, studies have suggested that ‘Germanodactylus rhamphastinus’ is not congeneric with the type species of Germanodactylus.Geometric morphometric analysis of prepubes and a cladistic analysis of the Pterosauria elucidate plesiomorphic and apomorphic conditions for basal Jurassic pterodactyloids. Germanodactylusis found to be a monotypic genus and Pterodactylus, Diopecephalus, and ‘G. rhamphastinus’ are found as distinct taxa belonging in individual genera, diagnosable using a combination of characters. Thus, Diopecephalus kochiis not demonstrated to be congeneric with Germanodactylusor Pterodactylusand is maintained as a valid taxon. ‘G. rhamphastinus’ is readily distinguishable from other Solnhofen pterosaur taxa, and a new genus is erected for its reception.

Published
2018
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11. A new bernissartiid crocodyliform from the Lower Cretaceous Wessex Formation (Wealden Group, Barremian) of the Isle of Wight, southern England.

Author

SWEETMAN, STEVEN C., PEDREIRA-SEGADE, ULYSSE, and VIDOVIC, STEVEN U.

Subjects
CROCODILIANS, FOSSIL crocodilians, SKULL, CRETACEOUS paleontology, DENTAL anthropology, ANATOMY
Abstract

A substantially complete skull of a small crocodyliform recently found on the foreshore near Yaverland on the southeast coast of the Isle of Wight, southern England is described. The locality, mode of preservation and associated matrix indicate that it is derived from one of the plant debris beds of the Lower Cretaceous Wessex Formation (Barremian, Wealden Group). The dentition, unique among crocodyliforms, serves to confirm that the specimen is referable to the, until now, monotypic family Bernissartiidae. Apomorphies, including placement of the choana entirely within the pterygoids and disposition of cranial sutures demonstrate that the Isle of Wight skull cannot be referred to Bernissartia fagesii, known from contemporaneous strata. Furthermore, these characters indicate that the specimen should not be referred to a new species of Bernissartia. It is therefore placed in a new genus and species, Koumpiodontosuchus aprosdokiti. The systematic position of Bernissartiidae, and characters used to diagnose Eusuchia, including placement of the choana(e) within the prerygoids, are discussed. Until recently this condition was thought to be restricted to Eusuchia with all non-eusuchian neosuchian crorocdiliforms possessing choanae bounded posteriorly by the pterygoids and anteriorly by the palatines. While the choana of Koumpiodontosuchus aprosdokiti gen. et sp. nov. is entirely bounded by the pterygoids it differs from the choanae of eusuchians in lacking a median septum, being anteroposteriorly elongate and in its anterior placement. [ABSTRACT FROM AUTHOR]

Published
2015
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