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The Uses of Molecular Dating Analyses in Evolutionary Studies, with Examples from the Angiosperms

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The Uses of Molecular Dating Analyses in Evolutionary Studies, with Examples from the Angiosperms Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2006 The uses of molecular dating analyses in evolutionary studies, with examples from the angiosperms Rutschmann, Frank Kaspar Abstract: Die sechs Kapitel der vorliegenden Dissertation befassen sich alle mit verschiedenen Aspekten von molekularen Datierungsmethoden, englisch molecular dating methods genannt. Dabei reicht die Spannweite der behandelten Themen von experimentellen Untersuchungen der Methoden selbst bis hin zur praktischen Anwendung der molekularen Altersbestimmung für die Aufklärung von biologischen und evolutionsgeschichtlichen Fragen bei verschiedenen Gruppen von Blütenpflanzen (Angiospermen). The six chapters that compose this dissertation are all related to various aspects of molecular dating, ranging from more methodological and experimental work to the application of different methods in the context of biological and evolutionary questions and hypotheses related to different groups of flowering plants (Angiosperms). Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-163459 Dissertation Published Version Originally published at: Rutschmann, Frank Kaspar. The uses of molecular dating analyses in evolutionary studies, with examples from the angiosperms. 2006, University of Zurich, Faculty of Science. The Uses of Molecular Dating Analyses in Evolutionary Studies, with Examples from the Angiosperms Dissertation zur Erlangung der naturwissenschaftlichen Doktorwürde (Dr. sc. nat.) vorgelegt der Mathematisch-naturwissenschaftlichen Fakultt der niversitt Zürich von Frank Kaspar Rutschmann von Zürich ZH Promotionskomitee: Prof. Dr. Elena Conti ()orsitz) Prof. Dr. Peter Linder Dr. Torsten Eriksson Zürich 200. Acknowledgements First of all, I would like to express my gratitude towards my supervisor, Elena Conti. The last four years would not have been as exciting and fruitful without your full support. I really appreciate your style of supervision which gave me the freedom to explore the things I was fascinated about. I am very impressed by your enthusiasm and your dedication to all sorts of biological uestions, but especially by your social empathy. Your office door was always open for all kinds of uestions - even beyond biology. I would also like to thank Peter Linder - it was a great pleasure to collaborate with you, and your sense of humor made the struggle with statistics and manuscripts much more fun. A great deal of laughter was also initiated by my fantastic and very patient office mates Merran Matthews, Josephine Jacksch and (abriele Salvo, who often supplied me with mental and physical calories. But also Timo van der Niet, Sandro ,agen, -s.fia /ock and P0ter S12v0nyi, Evelin Pfeifer, 3rs Landergott, Brigitte Mara11i, Claudia ,inteler, Chlo0 (alley, Rolf Rutishauser, Niklaus M5ller, Alex Bernhard, Jakob Schneller, Burgi Liebst, Melanie Ranft, Rosemarie Sigrist, Reto Nyffeler, Daniel /ein1mann, J5rg Sch2nenberger, Maria von Baltha1ar, and many other members of the institute contributed to an en7oyable atmosphere and many cheerful discussions. The staff of the secretariat, the library, and the botanical garden made every 7ourney outside the office a pleasure and provided an efficient working environment, especially Corinne Burlet, Claudio Brun, Barbara Seit1, Elena Benetti, Nadine 8ofmehl, Elisabeth Schneeberger, and Daniel Schlagenhauf. Finally, I would like to thank my family and friends, who supported me in many different ways. Thank you so much, Corinne Furrer, Anne and Christian Rutschmann, Dieter Rutschmann, Annette and Jochen ,ild, Andri Schl9pfer and Linda -ehnder, Renata and /ans72rg Schlaepfer, Philip Moline and Saskia Lampert, Nikolaus Amrhein, Annemarie and Niklaus 8ohler-Pfister, Frances Athanasiou, Torsten Eriksson, Stephan Lange, 8aren /il1inger, Christoph Eichenberger, Beat Seiler, Lilo Michel, Lukas and Thomas Furrer, Domini ue Sirena, Corsin M5ller, Florian Steiner, and Jonas ,ittwer. Last but not least I owe much to my parents who have supported me in all conceivable ways. I can sincerely say that without you, this pro7ect would not have been possible. I therefore would like to dedicate this work to my mother, Margrit Rutschmann, and my late father, Peter Rutschmann. Ta le of Contents Pu lication list ......................................................................................................... 4 General introduction ............................................................................................. 5 Chapters: I. Molecular dating of phylogenetic trees: A brief review of current methods that estimate divergence times .................... 13 II. Did Crypteroniaceae really disperse out-of-India; Molecular dating evidence from rbcL, ndhF, and rpl16 intron se uences ........ 47 III. Calibration of molecular clocks and the biogeographic history of Crypteroniaceae: A reply to Moyle ............................................................... 85 I,. Tempo and mode of diversification in the African Penaeaceae and related taxa .................................................................................................. 93 ,. Assessing calibration uncertainty in molecular dating: The assignment of fossils to alternative calibration points .............................. 137 ,I. Taxon sampling effects in molecular clock dating: An example from the African Restionaceae .................................................... 187 General summary .............................................................................................. .19 /usammenfassung ............................................................................................ ..1 0e enslauf ............................................................................................................ ..5 Pu lication list The following publications stem from my years as a Ph.D. student at the Institute of Systematic Botany, 3niversity of -urich, Swit1erland (2002-2006). They represent ten articles, of which I have written five as a first or single author. Four papers are already published. The most recent work is listed first. Rutschmann, F., J. Sch2nenberger, /.P. Linder, and E. Conti. Tempo and mode of diversification in the African Penaeaceae and related taxa. In preparation. Barker N.P., P./. ,eston, and F. Rutschmann. Molecular dating of the radiation of the Proteaceae is only partially congruent with the breakup of (ondwana. In preparation. Rutschmann F., T. Eriksson, 8. Abu Salim, and E. Conti. Assessing calibration uncertainty in molecular dating: The assignment of fossils to alternative calibration points. Submitted to Systematic Biology. Schlaepfer /. and F. Rutschmann. Deriving species responses from vegetation relev0s: an iterative approach. Submitted to Botanica Helvetica. Sch2nenberger, J., E. Conti, F. Rutschmann, and R. Dahlgren. Penaeaceae in 8. 8ubit1ki, ed. The families and genera of vascular plants. Col. D. Springer, Berlin. In press. Rutschmann F. 2006. Molecular dating of phylogenetic trees: A brief review of current methods that estimate divergence times. Diversity and Distributions 12: E5-48. Linder /.P., C. R. /ardy, and F. Rutschmann. 2005. Taxon sampling effects in molecular clock dating: An example from the African Restionaceae. Molecular Phylogenetics and Evolution 35: 56DH582. Conti E., F. Rutschmann, T. Eriksson, 8. Sytsma, and D. Baum. 2004. Calibration of molecular clocks and the biogeographic history of Crypteroniaceae: A reply to Robert (. Moyle. Evolution 58 (8): 18I4-18I6. Rutschmann F. 2005. Bayesian molecular dating using PAML/multidivtime. A step-by-step manual, version 1.5 (July 2005). 3niversity of -urich, Swit1erland. Available at http://www.plant.ch. Rutschmann F., T. Eriksson, J. Sch2nenberger, and E. Conti. 2004. Did Crypteroniaceae really disperse out-of-India; Molecular dating evidence from rbcL, ndhF, and rpl16 intron se uences. International Journal o Plant Sciences 165(4 Suppl.): 6D-8E. 4 General introduction In the uest of understanding evolutionary mechanisms and processes, accurate information about the timing of specific events in the past is needed. For example, it is important to know how fast retroviruses like the human immunodeficiency virus (/IC) change their genotype, in order to design new drugs or vaccines that will work also for future strains (8orber et al., 2000). Or, to mention another fascinating example, it is of general interest - even beyond the life sciences - to know when the first humans started to diverge from the chimpan1ees (between 6.E and 5.4 million years agoL Patterson et al., 2006). 3ntil forty years ago, information about the timing of past evolutionary events was only available in the form of fossils. Fossils are usually dated based on age estimates of the stratigraphic layer in which they are found, and they can be assigned to modern taxa by comparing the morphological characters preserved in the fossil with the traits of extant species (/ennig, 1D6DL Doyle and Donoghue, 1DDE). /owever, most organisms that once populated our planet have not been preserved in the fossil record, or their fossils have not been detected so far (Darwin, 185D). This implies that for most organisms, no direct information about their phylogenetic age is available. In 1D65, -uckerkandl and Pauling postulated that the amount of difference between the DNA molecules of two species is a function of the time since their evolutionary separation. This was shown by comparing
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