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Insights on Reticulate Evolution in Ferns, with Special Emphasis on the Genus Ceratopteris

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Insights on Reticulate Evolution in Ferns, with Special Emphasis on the Genus Ceratopteris Utah State University DigitalCommons@USU All Graduate Theses and Dissertations Graduate Studies 8-2021 Insights on Reticulate Evolution in Ferns, with Special Emphasis on the Genus Ceratopteris Sylvia P. Kinosian Utah State University Follow this and additional works at: https://digitalcommons.usu.edu/etd Part of the Ecology and Evolutionary Biology Commons Recommended Citation Kinosian, Sylvia P., "Insights on Reticulate Evolution in Ferns, with Special Emphasis on the Genus Ceratopteris" (2021). All Graduate Theses and Dissertations. 8159. https://digitalcommons.usu.edu/etd/8159 This Dissertation is brought to you for free and open access by the Graduate Studies at DigitalCommons@USU. It has been accepted for inclusion in All Graduate Theses and Dissertations by an authorized administrator of DigitalCommons@USU. For more information, please contact [email protected]. INSIGHTS ON RETICULATE EVOLUTION IN FERNS, WITH SPECIAL EMPHASIS ON THE GENUS CERATOPTERIS by Sylvia P. Kinosian A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in Ecology Approved: Zachariah Gompert, Ph.D. Paul G. Wolf, Ph.D. Major Professor Committee Member William D. Pearse, Ph.D. Karen Mock, Ph.D Committee Member Committee Member Karen Kaphiem, Ph.D Michael Sundue, Ph.D. Committee Member Committee Member D. Richard Cutler, Ph.D. Interim Vice Provost of Graduate Studies UTAH STATE UNIVERSITY Logan, Utah 2021 ii Copyright © Sylvia P. Kinosian 2021 All Rights Reserved iii ABSTRACT Insights on reticulate evolution in ferns, with special emphasis on the genus Ceratopteris by Sylvia P. Kinosian, Doctor of Philosophy Utah State University, 2021 Major Professor: Zachariah Gompert, Ph.D. Department: Biology The history of life is often viewed as a bifurcating tree; however, in reality it is more like a tangled hedgerow. Many groups of organisms are known to have such a reticulate evolutionary history, but it is particularly common in ferns and lycophytes (also known as pteridophytes). This dissertation investigates the role of polyploidy and hybridization in pteridophyte evolution, with a special emphasis on the model fern Ceratopteris. Population genomic analyses are used to understand hybridization across large evolutionary distances in Dryopteris; in addition, evolutionary network and hybridization detection analyses infer cryptic species and reticulate evolution in Ceratopteris. Finally, a close look is taken at the model fern species C. richardii, also known as the C-fern. Ceratopteris richardii has been an important part of pteridophyte research since the 1980s, but no wild specimens of the C-fern have been included in an evolutionary context. This work presents the first evidence that C. richardii is a hybrid species, or potentially a mix of morphotypes derived from different pairs of species, all under the same name. These findings are important to consider for future research using C. richardii and any of its genomic resources. (197 pages) iv PUBLIC ABSTRACT Insights on reticulate evolution in ferns, with special emphasis on the genus Ceratopteris Sylvia P. Kinosian The history of life is often viewed as a evenly branching tree; however, in reality it is more like a tangled hedgerow. Many groups of organisms are known to have such a net-like or reticulate evolutionary history, but it is particularly common in ferns and lycophytes (also known as pteridophytes). This dissertation investigates how net-like evolution affects different groups of ferns, with a special emphasis on the model species C-fern (Ceratopteris richardii, also called the antler or water sprite fern). Genomic data are utilized to under- stand hybridization, cryptic species and reticulate evolution in two groups of ferns. The C-fern is shown to be a potential hybrid species, which has important implications for future research using this model organism. v To my grandmothers, Ann Hinman Lilley and Dr. Mary Jane Kinosian. vi ACKNOWLEDGMENTS I am grateful to advisors my Paul Wolf and Will Pearse. Paul was instrumental in the development of my dissertation, and Will provided immeasurable help actualizing each chapter. I am indebted to Dave Barrington and Cathy Paris for introducing me to the world of ferns. The opportunity to do research as an undergrad in the Barrington Lab changed my career trajectory, and has lead my to some of the most memorable experiences of my life. Thank you to parents, Margaret and Henry, for introducing me to the natural world, and supporting me unconditionally throughout my academic endeavors. Thank you to Jacob Suissa for many thoughtful discussions and endless encouragement. I'm looking forward to many more years of collaboration and tropical field work. To my friends in Logan, I couldn't have done this without you. All of you made life so much more fun with many awesome trips, big and small. Whenever I needed break, an excuse to go outside, or just space to vent, someone was always there. And finally, I am so grateful to Ian Burbidge, has been the most supportive partner as I figured out how to be a scientist. Sylvia P. Kinosian vii CONTENTS Page ABSTRACT :::::::::::::::::::::::::::::::::::::::::::::::::::::: iii PUBLIC ABSTRACT ::::::::::::::::::::::::::::::::::::::::::::::: iv ACKNOWLEDGMENTS :::::::::::::::::::::::::::::::::::::::::::: vi LIST OF TABLES ::::::::::::::::::::::::::::::::::::::::::::::::: x LIST OF FIGURES :::::::::::::::::::::::::::::::::::::::::::::::: xi 1 Introduction ::::::::::::::::::::::::::::::::::::::::::::::::::: 1 1.1 History of reticulate evolution in ferns.....................1 1.2 Behind the research: people of reticulate evolution in pteridology......2 1.3 History of the model fern genus Ceratopteris .................3 1.3.1 Ceratopteris as a model organism....................4 1.3.2 Taxonomic history............................5 1.4 Dissertation summary..............................6 2 Mothers of Pteridology :::::::::::::::::::::::::::::::::::::::::::: 17 2.1 Abstract...................................... 17 2.2 Introduction.................................... 18 2.3 Historical women in pteridology: Premise................... 19 2.4 Historical women in pteridology: Biographies................. 19 2.4.1 Margaretta Riley (1804 - 1899)..................... 19 2.4.2 Sarah \Sadie" Frances Price (1849-1903)................ 21 2.4.3 Elizabeth Gertrude Knight Britton (1858 - 1934)........... 24 2.4.4 Alma Gracey Stokey (1877 - 1968)................... 26 2.4.5 Norma E. Pfeiffer (1878 - 1978)..................... 28 2.4.6 Irene Manton (1904 - 1988)....................... 29 2.4.7 Alice Faber Tryon (1920 - 2009).................... 30 2.4.8 Barbara Joe Hoshizaki (1928 - 2012).................. 33 2.4.9 Florence Wagner (1919 - 2020)..................... 34 2.5 Conclusion.................................... 34 3 Using RAD data to confirm parentage of polyploids in a reticulate complex of ferns 43 3.1 Abstract...................................... 43 3.2 Introduction.................................... 44 3.3 Materials and Methods.............................. 47 3.3.1 Taxon sampling and DNA extraction.................. 48 3.3.2 ddRAD library preparation and sequencing.............. 48 3.3.3 Data cleaning............................... 50 3.3.4 Data analysis............................... 50 viii 3.4 Results....................................... 53 3.5 Discussion..................................... 54 3.5.1 Dryopteris campyloptera clade..................... 54 3.5.2 Dryopteris celsa clade.......................... 56 3.5.3 RAD data and analysis of polyploid complexes............ 57 3.5.4 Summary and future directions..................... 59 4 Cryptic diversity in the model fern genus Ceratopteris (Pteridaceae) :::::::::: 66 4.1 Abstract...................................... 66 4.2 Introduction.................................... 67 4.3 Materials and methods.............................. 70 4.3.1 Taxon sampling.............................. 70 4.3.2 DNA extraction............................. 72 4.3.3 Library construction and sequencing.................. 72 4.3.4 Species tree inference.......................... 72 4.3.5 Polyploidy analysis............................ 73 4.3.6 Simulated RADseq analysis of the Ceratopteris richardii genome.. 74 4.4 Results....................................... 74 4.4.1 Population and genomic structure analysis............... 74 4.4.2 Species tree inference.......................... 77 4.4.3 Ploidy assignment across species.................... 77 4.4.4 Analysis of simulated RADseq data.................. 79 4.5 Discussion..................................... 81 4.5.1 Species boundaries in Ceratopteris ................... 81 4.5.2 Evolutionary drivers in Ceratopteris .................. 87 4.6 Conclusion.................................... 89 5 There and back again: Reticulate evolution in Ceratopteris ::::::::::::::::: 99 5.1 Abstract...................................... 99 5.2 Introduction.................................... 100 5.3 Material and Methods.............................. 102 5.3.1 Sampling................................. 102 5.3.2 DNA extraction and sequencing..................... 104 5.3.3 Data processing.............................. 104 5.3.4 Estimation of interspecies gene flow.................. 105 5.3.5 Phylogenetic network analysis...................... 105 5.4 Results....................................... 107 5.5 Discussion..................................... 111 5.5.1 Hybridization in context for a model system.............. 111 5.5.2
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