The largest phylogenetic analysis of ichthyosaurs to date is presented, with 114 ingroup taxa coded at species level. Completeness of the taxa included varied from > 98% to < 2%; 10 taxa were removed a priori using Concatabominations due to incompleteness and taxonomic uncertainty. The data were analysed using three widely used optimization criteria, maximum parsimony, maximum likelihood and Bayesian inference; while similar, each criterion produced different topologies, support and levels of resolution. Maximum parsimony found a poorly-resolved consensus tree with moderate improvement from a posteriori pruning of unstable taxa; however, general support remained low. Tree resolution was reduced more by taxa that lacked codings from phylogenetically important regions of the tree, rather than by those that simply lacked many codings. Resolution present in the most likely tree is poorly supported; sister relationships cannot be confirmed, although similarities are found to the most parsimonious tree. Bayesian inference found poorly resolved consensus trees. While more resolved, an equal-distribution rate prior is significantly worse than the null gamma-distribution rate prior for morphological data, but suggests rate heterogeneity across ichthyosaur phylogeny. Tree comparisons under each analytical criterion failed to select a single best tree; however, the Bayesian inference tree with gamma-distribution rate prior is selected as the best tree based on recent analyses showing improved accuracy using this criterion. Unequivocally resolved clades include Ichthyopterygia, Ichthyosauria, Shastasauria, Euichthyosauria, Parvipelvia and Neoichthyosauria, but with variation in their taxonomic components. Mixosauridae and Ophthalmosauridae are similarly recovered, but their definitions are modified to stem-based definitions to prevent substantial variation of included taxa. Several genera are not monophyletic: Brachypterygius, Leptonectes, Mixosaurus, Ophthalmosaurus, Paraophthalmosaurus, Phalarodon, Platypterygius, Stenopterygius, Temnodontosaurus and Undorosaurus. Complex and variable relationships suggest the need for new characters and a re-evaluation of the state of ichthyosaur phylogenetics.
- Bayesian inference
- maximum likelihood
- maximum parsimony
- tree selection
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27 Sep 2016
Student thesis: Doctoral Thesis › Doctor of Philosophy (PhD)File
Polly E Eccleston (Other), Simon H Atack (Other), D A G Williams (Manager), Sadaf R Alam (Manager) & Steven A Chapman (Manager)