The effects of natural selection on human Y chromosome amplicons by Levi S. Teitz Bachelor of Science, Biological Sciences University of Maryland, College Park, 2013 SUBMITTED TO THE DEPARTMENT OF BIOLOGY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN BIOLOGY AT THE MASSACHUSETTS INSTITUTE OF TECHNOLOGY JUNE 2018 ©2018 Massachusetts Institute of Technology. All rights reserved. Signature of Author: _______________________________________________________ Department of Biology May 29, 2018 Certified by: _____________________________________________________________ David C. Page Professor of Biology Thesis Supervisor Accepted by: _____________________________________________________________ Amy E. Keating Professor of Biology Co-Chair, Biology Graduate Committee The effects of natural selection on human Y chromosome amplicons by Levi S. Teitz Submitted to the Department of Biology on May 29, 2018 in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biology ABSTRACT The Y chromosome is unique among the mammalian chromosomes: it determines sex, and is therefore normally present in a single copy, unlike all other chromosomes that can recombine with an identical homolog. These two facts have had profound effects on the fate of the Y chromosome, subjecting it to unique evolutionary pressures that caused the loss of most of its genes. Because of this lack of functional genes, speculation abounded that natural selection is ineffective on a chromosome that lacks a homolog with which to recombine, and that the Y chromosome is doomed to eventually fade away. In recent years, evidence has been building that the Y chromosome is indeed shaped by evolutionary forces acting to maintain its functional genes. However, these studies bypassed the amplicons—large, highly identical segmental duplications—which are a prominent feature of mammalian Y chromosomes and contain many genes crucial for spermatogenesis. In this thesis, we present evidence that natural selection acts on the ampliconic regions of the human Y chromosome. We first develop computational tools to detect amplicon copy number changes from whole genome sequencing data of 1216 men, and find that many men have such changes. By projecting those changes onto a phylogenetic tree of the analyzed Y chromosomes, we find that the reference copy number of each amplicon is ancestral to all modern human Y chromosomes. We then use simulations and novel analytical methods to demonstrate that the ancestral copy number of each amplicon is maintained by selection within diverse human lineages, even in the face of extremely high rates of mutation. Finally, we find that deleted amplicons are preferentially restored to their previous copy number by subsequent duplications. These results are another step forward in the ongoing reframing the history of the mammalian Y chromosome: the Y chromosome is not the victim of random neutral processes, but is the carefully calibrated result of complex interplay between various selective forces. Thesis Supervisor: David C. Page Title: Professor of Biology 3 4 To Grandma, Grandpa, Sabba, and Savta 5 6 בס״ד ACKNOWLEDGEMENTS First and foremost, thank you to my advisor, David Page, for your endless encouragement and faith in me. You are a true mentor, always looking to guide me and help me grow as a scientist. Your meticulous approach to research and the conscientious philosophy with which you run your lab are models that I can only hope to emulate in the future, wherever it takes me. I joined the Page lab not just because of the science but also because of the people, who have created an amazingly warm, collaborative, and intellectually challenging atmosphere. Special thanks to Helen Skaletsky, for constantly sharing your incredible expertise and helping my science reach new heights; Tatyana Pyntikova, for helping me break my streak of doing no non-computational experiments, and for the tremendous amount of work you put in to assist me with my research; Laura Brown, for your kindness and care that shine through while sitting next to you every day; and Katherine Romer, for your friendship in sharing board game nights, puzzle hunts, and much more with me. And thank you to Winston Bellott. From the time I was your rotation student until today, you have happily acted as my sounding board and proofreader, taught me a tremendous amount through our countless conversations on every topic, kept me up to date on various rocket launches (from both Earth and Kerbin), and answered literally thousands of my questions. Your unending enthusiasm for and knowledge of both science and everything else is inspiring. Thank you as well to the members of my thesis committee: Dave Bartel, Jing-Ke Weng, and Andy Clark, for your generous and valuable advice. To my friends, in Cambridge, Somerville, and elsewhere: the meals, movies, cooking sessions, songs, games, shows, visits, phone calls, and more that we’ve shared have kept me going over the past five years. Without you, none of this work would have been possible. And finally, to my family. I love you, and thank you for everything. 7 8 CONTENTS CHAPTER 1: INTRODUCTION .................................................................................... 11 PART I: THE Y CHROMOSOME IN THE PRE-GENOMIC ERA .................................................13 PART II: COMPLETE SEQUENCE OF Y CHROMOSOMES ......................................................22 PART III: Y CHROMOSOME VARIATION ............................................................................35 PART IV: CURRENT OPINIONS ON Y CHROMOSOME AMPLICONS ......................................48 ACKNOWLEDGEMENTS ....................................................................................................50 REFERENCES ....................................................................................................................50 CHAPTER 2: SELECTION HAS COUNTERED HIGH MUTABILITY TO PRESERVE THE ANCESTRAL COPY NUMBER OF Y CHROMOSOME AMPLICONS IN DIVERSE HUMAN LINEAGES ....................................................................................... 61 SUMMARY ........................................................................................................................63 INTRODUCTION ................................................................................................................64 RESULTS ..........................................................................................................................70 DISCUSSION .....................................................................................................................99 MATERIAL AND METHODS .............................................................................................105 ACKNOWLEDGEMENTS ..................................................................................................116 REFERENCES ..................................................................................................................116 SUPPLEMENTAL MATERIAL AND METHODS ....................................................................123 SUPPLEMENTAL FIGURES AND TABLES ...........................................................................129 CHAPTER 3: CONCLUSIONS AND FUTURE WORK .............................................141 CONCLUSIONS ................................................................................................................143 FUTURE WORK ...............................................................................................................145 ACKNOWLEDGEMENTS ..................................................................................................150 REFERENCES ..................................................................................................................150 9 10 CHAPTER 1 INTRODUCTION ______________________________________ 11 12 PART I: THE Y CHROMOSOME IN THE PRE-GENOMIC ERA THE DISCOVERY OF THE Y CHROMOSOME The first Y chromosome was discovered in 1905. Two studies observed via light microscopy that several insect species have a male-specific chromosome: each species has the same number of chromosomes in male and female, but in males one chromosome is significantly smaller than the rest (Stevens, 1905; Wilson, 1905). Until that point, scientists had only been aware of the X chromosome, of which one copy is absent in males (Henking, 1891; Sutton, 1902). Due to its male-specific nature, the Y chromosome was hypothesized to play a role in sex determination (Stevens, 1905; Wilson, 1905). This hypothesis ended up being partially true: exceptions include fruit flies, whose sex is determined by the ratio of X chromosomes to autosomes, but which require the Y chromosome for male fertility (Bridges, 1916). While most early sex chromosome research was done in insects, studies identifying human and other mammalian Y chromosomes followed (Painter, 1921). However, the mammalian Y chromosome’s role in sex determination remained unclear until 1959, when studies of men with Klinefelter syndrome, who have two X chromosomes and one Y chromosome, and women with Turner syndrome, who have just a single X chromosome, demonstrated that maleness in humans depends on the presence or absence of the Y chromosome (Ford et al., 1959; Jacobs and Strong, 1959). Y CHROMOSOME EVOLUTIONARY THEORY In his studies of fly genetics, Hermann Muller noted that many traits exhibited the pattern of X-chromosome linkage, but none had been linked to the Y chromosome 13 (Muller,