Total Evidence: A Test of Principle Using the Malacostraca
Ni Dhubhghaill, C., 2012. Total Evidence: A Test of Principle Using the Malacostraca. Thesis (Doctor of Philosophy (PhD)). University of Bath.
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The phylogeny of Eumalacostraca (Crustacea) has remained elusive, despite over a century of morphological and more recently molecular studies. Prior to this, no large scale combined evidence analyses of all eumalacostracan orders has been carried out. Evidence from four nuclear ribosomal and mitochondrial loci (18S rRNA, 28S rRNA, 16S rRNA, and cytochrome c oxidase subunit I) were combined with a newly synthesized morphological dataset to examine the utility of available data. With an aim to resolve conflict in the morphological dataset, fossils were added to the morphological dataset and their effects examined. The stratigraphic congruence of crustaceans was examined to determine the quality of existing trees. A modified protocol was developed to generate new molecular markers for the investigation of eumalacostracan phylogeny. Finally the effects of the new data on existing datasets were examined in a combined evidence approach. Significant conflict was detected between data partitions, especially between morphology and molecules. The addition of fossil data revealed the morphological dataset to be very sensitive to taxon sampling. Stratigraphic congruence was found to be poor for the five crustacean groups examined. Histone 3 and alanyl-tRNA synthetase were shown to be capable of successfully recovering relationships at the level of genus and above. Glutamyl-prolyl-tRNA synthetase failed to recover monophyletic groupings when analysed alone. Combining all molecular data produced well-supported phylogenies, but significant conflict between data partitions was identified and trees were very sensitive to taxon sampling. Rate heterogeneity and conflict between data partitions mean that the total sum of molecular and morphological evidence as presented here is currently unable to resolve a wellsupported eumalacostracan phylogeny. We recommend additional taxon sampling and further sampling of novel markers using the modified protocol developed here as well as the addition of fossil data and the exploitation of next generation sequencing technologies.
|Item Type||Thesis (Doctor of Philosophy (PhD))|
|Creators||Ni Dhubhghaill, C.|
|Uncontrolled Keywords||eumalcostraca, total evidence, phylogenetics|
|Departments||Faculty of Science > Biology & Biochemistry|
|Publisher Statement||UnivBath_PhD_2012_C_Ni_Dhubhghaill.pdf: © The Author|
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