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Phylogeny and Systematic History of Early Salamanders

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Phylogeny and Systematic History of Early Salamanders Phylogeny and systematic history of early salamanders Marianne Pearson University College London PhD in Palaeobiology I, Marianne Rose Pearson, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis 13 July 2016 2 Abstract Prevalent paedomorphy and convergence in salamander morphology has made it difficult to resolve relationships using purely morphological characters. However, many new fully articulated fossil salamanders have emerged, especially from China, and it is important to be able to place them within a phylogenetic framework to better understand the origin and radiation patterns of early salamanders. This study looks at the phylogeny of extant taxa using both molecular and morphological datasets. In deciphering the phylogeny of modern day taxa the limitations and caveats of the data were explored. The extent of the influence homoplasy and convergence have on the phylogenetic topology has been assessed using methods designed to identify and/or down-weight homoplasy in morphological characters. Once characters had been identified as potentially homoplasious and removed from the dataset, further analyses were performed on reduced datasets. Fossils were simulated by creating subsets of characters (those commonly found in the fossil record) for extant taxa. Analyses using parsimony and Bayesian inference were performed to test the robustness of the placements of these simulated fossils. The impact of missing data caused by poor preservation and incomplete specimens was tested by simulating reduced/limited character scores for living taxa, and then comparing the phylogenetic placement of these artificially degraded taxa with their ‘true’ position based on complete data. This paves the way for the inclusion of the fossils. While this study has not resolved the relationships between salamander families it has allowed a deeper understanding of the data, and assesses the confidence with which the placement of key fossils can be made in a new way. This novel method has further implications for the fitting of fossils within a phylogenetic framework in other problem clades. Biogeographic hypotheses can then be tested. 3 Contents 1.1 Project Aims ...................................................................................................................................11 1.2 Introduction to Salamanders ..........................................................................................................12 1.2.1 Is it possible to correct for the signal caused by convergence in the morphological data? .......... 13 1.3 The Origins of Salamanders ............................................................................................................14 1.4 Previous Phylogenies......................................................................................................................18 1.4.1 Do soft body characters give a more reliable and congruent signal relative to molecular results than the signal from the osteological data? .......................................................................................... 30 1.5 The Mesozoic Fossil Record ............................................................................................................30 1.6 Biogeography 1.6.1 Introduction to biogeography ........................................................................37 1.6.2 Salamander geographic distribution ............................................................................................. 37 1.6.2.1 Gondwana ............................................................................................................................. 38 1.6.2.2 Laurasia .................................................................................................................................. 38 1.6.2.3 What is the position of Sirenidae in relation to other salamanders? Are the enigmatic Gondwanan fossils (Kababisha and Noterpeton) related to Sirenidae? ........................................... 40 1.6.2.4 Can fossils be placed robustly at a Family and/or Salamandroidea/Cryptobranchoidea level? ........................................................................................................................................................... 41 2.1 Introduction: ..................................................................................................................................43 2.2 Materials and Methods ..................................................................................................................44 2.2.1 Molecular data .............................................................................................................................. 44 2.2.2 Morphological data ...................................................................................................................... 48 2.2.3 Combined Molecular and Morphological data ............................................................................. 53 2.2.4 Tree comparisons .......................................................................................................................... 53 2.2.5 Character mapping ....................................................................................................................... 53 2.3 Results............................................................................................................................................54 2.3.1.2 Nuclear DNA phylogeny ......................................................................................................... 55 2.3.1.3 Mitochondrial DNA phylogeny .............................................................................................. 56 2.3.2 Morphological Results 2.3.2.1 Full Morphological dataset with extant outgroups ...................... 57 2.3.3 Full Morphological dataset with fossil outgroups ......................................................................... 59 2.3.2.2 Morphological phylogeny (osteological) ............................................................................... 62 2.3.2.3 Morphological phylogeny (soft body) ................................................................................... 64 2.3.3 Molecular and Morphological data 2.3.3.1 Combined molecular data with all morphological data ........................................................................................................................................................ 67 2.4 Discussion 2.4.1 Molecular discussion ............................................................................................67 2.4.2 Morphological discussion .............................................................................................................. 69 2.4.3 Total evidence discussion .............................................................................................................. 71 4 2.5 Conclusions ....................................................................................................................................71 3.1 Introduction ...................................................................................................................................74 3.1.1 Homology within the dataset........................................................................................................ 74 3.1.2 Problems with fitting fossils .......................................................................................................... 74 3.2 Material and Methods ....................................................................................................................75 3.2.1 Tree dependent character evaluation ........................................................................................... 75 3.2.1.1 Retention Index ..................................................................................................................... 75 3.2.1.2 RI dataset ............................................................................................................................... 76 3.2.2 Tree independent character evaluation ........................................................................................ 77 3.2.2.1 Le Quesne Probability randomisation test ................................................................................. 77 3.2.2.2 The Le Quesne dataset ............................................................................................................... 78 3.2.2.3 Tree comparison statistics ......................................................................................................... 78 3.2.2.4 Simulating fossils ....................................................................................................................... 79 3.3 Results............................................................................................................................................79 3.3.1 Tree dependent phylogeny results ................................................................................................ 79 3.3.2 Tree independent results............................................................................................................... 82 3.3.3 Tree comparison results ................................................................................................................ 86 3.3.4 Simulated fossils using RI subset ..................................................................................................
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