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The Origins of Multicellularity: Correlation Between Morphological and Genomic Complexity in Microorganisms

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The Origins of Multicellularity: Correlation Between Morphological and Genomic Complexity in Microorganisms The Origins of Multicellularity: Correlation between Morphological and Genomic Complexity in Microorganisms by Ben Qin, BS A Dissertation In Biology Submitted to the Graduate Faculty of Texas Tech University in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Approved Sean Rice Chair of Committee Michael San-Francisco Zhixin Xie John Zak Kai Zhang Mark Sheridan Dean of the Graduate School May 2017 Copyright 2017, Ben Qin Texas Tech University, Ben Qin, May 2017 Acknowledgements This work is generated with the immense help from my advisor, Dr. Sean Rice, who directed me to lay down the framework of this research, walked me through the evolutionary theories behind the numbers collected, and encouraged me to overcome obstacles in the research process. I also want to thank my other committee, Dr. Michael San-Francisco, Dr. Zhixin Xie, Dr. John Zak, and Dr. Kai Zhang, for all of their insightful instructions from a professional microbiology perspective. My friends from our lab and departments enlightened me with their novel ideas. Especially, Ryan Vazquez showed me how to use the random sampling to test the origins of multicellularity. This statistical problem puzzled me for years and his suggestion gave a beautiful answer. ii Texas Tech University, Ben Qin, May 2017 Table of Contents Acknowledgements .................................................................................. ii Abstract ................................................................................................. vii List of Tables ............................................................................................ x List of Figures .......................................................................................... xi List of Abbreviations .............................................................................. xv 1. Introduction ......................................................................................... 1 1.1 The origin of the question ............................................................................... 1 1.2 PIC does not support Ne as an explanation ...................................................... 2 1.3 Could morphological complexity play a role? .................................................. 7 1.4 Differences between prokaryotes and eukaryotes .......................................... 8 1.5 How did multicellularity evolve in eukaryotes? ............................................... 9 2. Prokaryotes ........................................................................................ 12 2.1 Cell type justification criteria ........................................................................ 12 2.2 Data mining .................................................................................................. 14 2.3 Phylogenies .................................................................................................. 15 2.4 Raw data comparison ................................................................................... 18 2.5 Diagnostic test .............................................................................................. 25 iii Texas Tech University, Ben Qin, May 2017 2.6 Correlation ................................................................................................... 26 2.7 Regressions of cell types on genomic traits ................................................... 28 2.8 Discussion ..................................................................................................... 31 3. Eukaryotes ......................................................................................... 32 3.1 Cell type justification criteria ........................................................................ 32 3.2 Data mining .................................................................................................. 33 3.3 Phylogenies .................................................................................................. 34 3.4 Raw data comparison ................................................................................... 37 3.5 Diagnostic test .............................................................................................. 41 3.6 Correlation ................................................................................................... 42 3.7 Regressions of cell types on genomic traits ................................................... 43 3.8 Discussion ..................................................................................................... 45 4. Eukaryotic Multicellularity .................................................................. 47 4.1 Two different paths to multicellularity .......................................................... 47 4.2 Independent origins of divisional multicellularity ......................................... 48 4.2.1 Fungi .............................................................................................................. 48 4.2.2 Animals & Choanoflagellates ........................................................................ 49 4.2.3 Stramenopiles ............................................................................................... 50 4.2.4 Green algae and plants ................................................................................. 51 4.2.5 Red algae ....................................................................................................... 53 iv Texas Tech University, Ben Qin, May 2017 4.3 Independent origins of aggregative multicellularity ...................................... 53 4.3.1 Capsaspora .................................................................................................... 54 4.3.2 Fonticula ........................................................................................................ 55 4.3.3 Dictyostelium ................................................................................................ 56 4.3.4 Copromyxa .................................................................................................... 57 4.3.5 Acrasis ........................................................................................................... 58 4.3.6 Sorogena ....................................................................................................... 59 4.3.7 Guttulinopsis ................................................................................................. 60 4.3.8 Sorodiplophrys .............................................................................................. 61 4.4 Phylogenies .................................................................................................. 61 4.5 Data comparison .......................................................................................... 63 4.6 Statistical analysis ......................................................................................... 67 4.7 Discussions ................................................................................................... 69 4.7.1 Divisional multicellularity arises from the simplest unicellular ancestors. ... 69 4.7.2 Aggregation and division based multicellularity show different patterns. ... 69 5. Conclusion .......................................................................................... 71 5.1 What is new in this research ......................................................................... 71 5.2 Prokaryotes and eukaryotes ......................................................................... 72 5.3 Eukaryote multicellularity ............................................................................. 73 5.4 Future study ................................................................................................. 74 v Texas Tech University, Ben Qin, May 2017 5.4.1 Incorporating more data ............................................................................... 74 5.4.2 Prokaryotic multicellularity ........................................................................... 75 5.4.3 Evolution of cooperation .............................................................................. 75 5.5 Concluding remarks ...................................................................................... 76 Bibliography ........................................................................................... 77 Appendices A. Cell Type Number of Prokaryotes ....................................................... 82 B. Genomic Data of Prokaryotes ............................................................. 92 C. Cell Type Number of Eukaryotes ......................................................... 99 D. Genomic Data of Eukaryotes ............................................................ 106 E. Branch Values for Resampling Test ................................................... 110 F. References for Cell Types .................................................................. 117 vi Texas Tech University, Ben Qin, May 2017 Abstract The earth's remarkable biodiversity is a testament to the evolution of organismal complexity. The fact that some kinds of complexity, including multicellularity, have arisen many times suggests that there are repeating selection pressure to become more complex, but our current knowledge of the mechanisms allowing for increased complexity is still far from complete. Most of the work that has been done focused on a few groups, primarily multicellular animals and plants. In this work, I study the evolution of phenotypic complexity across the entire tree
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