Evolution of the Raphe within the Diatom Subclass Eunotiophycidae

24 Introduction . 25 Materials and methods . 27 Results . 33 Discussion . 37 Conclusion . 47 5 References . 49 Chapter III: CHARACTERS AND TAXA INCLUDED IN ANALYSIS . 50 Introduction . 50 Taxa included in analysis . 51 Characters included in analysis . 58 1. Central nodule characters . 62 2. Central sternum characters . 62 3. Costae and Fibulae characters . 64 4. Face-Mantle Junction (FMJ) characters . 64 5. Girdle Band characters . 67 6. Mantle characters . 68 7. Ornamentation characters . 69 8. Pore Field characters . 70 9. Punctae characters . 71 10. Raphe characters . 73 11. Rimoportula characters . 78 12. Striae characters . 80 13. Valve Outline characters . 82 6 14. Z-outline characters . 85 Chapter IV: PHYLOGENY OF THE EUNOTIOPHYCIDAE . 87 Introduction . 87 Methods . 90 Phylogenetic Analyses . 93 Conclusions . 120 Future Research . 124 REFERENCES . 126 APPENDIX. 134 7 List of Tables Table 2.1. Characters and states adapted from the hypothesis presented in Burliga et al. (2013). 28 Table 2.2. Taxonomic matrix adapted from the hypothesis presented in Burliga et al. (2013) . 29 Table 2.3. Reproduction of characters and states used in analysis by Williams and Reid (2006a, Table 2) . 30 Table 2.4. Taxonomic matrix using taxa considered in Burliga et al. (2013) and character states presented by Williams and Reid (2006a, Table 2) . 31 Table 2.5. Combined characters and states from first two analyses. Duplicated characters were reduced to a single character . 32 Table 2.6. Combined taxonomic matrix including taxa and characters from both analyses and newly described Eunotioid genera since the publication of Burliga et al. (2013) . 33 Table 2.7. List of taxa included in analysis with references for original description and concept references used to code morphological features . 35 Table 3.1 List of all taxa included in the analysis, including nomenclatural references, and the taxonomic reference(s) or material used to carry out observations. Images for Actinella mirabilis and two Eunotia species collected from Japan are found in Appendix . 52 8 Table 3.2 Taxa included in the phylogenetic analysis grouped by presence or absence of rimoportulae or a raphe, and the coincidence of the raphe with a central sternum in raphid taxa . 56 10 List of Figures Figure 1.1 A whole diatom frustule with general structural parts labelled . 15 Figure 1.2 Example of a size diminution series of one diatom species, Eunotia arcuoides Foged (1977) . 16 Figure 1.3 Morphology of Pseudohimantidium pacificum as illustrated by Round et al. (1990) . 16 Figure 1.4 Morphology of the genus Peronia. One valve in each frustule has a centrally located raphe with rimoportulae at each apex, while the other has a reduced raphe and only one rimoportula (Round et al. 1990) . 17 Figure 1.5 Inset of 3-gene molecular clock phylogeny targeting the araphid pennate sister clades to the raphid taxa and the Eunotioid taxa. 20 Figure 2.1. Strict consensus tree for taxa and characters presented in Burliga et al. (2013) . 37 Figure 2.2. Majority rules tree for taxa and characters presented in Burliga et al. (2013) . 38 Figure 2.3. Strict consensus tree for taxa presented in Burliga et al. (2013) using the character matrix presented in Williams and Reid (2006a) . 39 Figure 2.4. Majority rules tree for taxa presented in Burliga et al. (2013) using the character matrix presented in Williams and Reid (2006a) . 39 Figure 2.5. Strict consensus tree for the combined data set using taxa and characters from both Burliga et al. (2013) and Williams and Reid (2006a) . 40 11 Figure 2.6. Majority rules tree for the combined data set using taxa and characters from both Burliga et al. (2013) and Williams and Reid (2006a) . 41 Figure 2.7 “Immaculate Raphe” Hypothesis . 43 Figure 2.8 Minimum evolutionary sequence with Peronia as basal raphid lineage when heterovalvy is accounted for . 44 Figure 2.9 Three step evolutionary sequence for a monophyletic raphe origin . 46 Figure 2.10 Evolutionary sequences for a multiply derived raphe origin . 47 Figure 4.1 Majority rules consensus tree based on original 124 characters and 60 taxa. 95 Figure 4.2 Majority rules consensus tree of the analysis coding the raphe as internal and external fissures with the raphe reduced and present characters merged.96 Figure 4.3 Majority rules consensus tree excluding central nodule characters based on 124 characters and 60 taxa. 98 Figure 4.4 Majority rules consensus tree excluding central sternum characters based on 119 characters and 60 taxa. 99 Figure 4.5 Majority rules consensus tree excluding costae and fibulae characters based on 122 characters and 60 taxa . 100 Figure 4.6 Majority rules consensus tree excluding face-mantle junction characters based on 119 characters and 60 taxa. 101 12 Figure 4.7 Major