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Genome Size Diversity and Evolution in the Crustacea

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Genome Size Diversity and Evolution in the Crustacea by Nicholas W. Jeffery A Thesis Presented to The Faculty of Graduate Studies of The University of Guelph In partial fulfillment of requirements for the degree of Doctor of Philosophy in Integrative Biology Guelph, Ontario, Canada © Nicholas W. Jeffery, September 2015 ABSTRACT GENOME SIZE DIVERSITY AND EVOLUTION IN THE CRUSTACEA Nicholas W. Jeffery Advisor: Dr. T. Ryan Gregory University of Guelph, 2015 The study of genome size, also known as the C-value in diploid organisms, began in the late 1940’s and has become increasingly efficient and prevalent in the current world of molecular biology and whole-genome sequencing. As of the start of this thesis, genome size estimates were available for a mere 318 crustaceans, representing less than 1% of the known species diversity (and certainly a much smaller fraction of the true species diversity). Even with this limited sample size, some patterns began to emerge when comparing genome size to various biological and ecological parameters within the Crustacea. This thesis first reviews the genome size literature, then develops methodologies for estimating genome size specifically in crustaceans using two common methods and different preservation techniques. I also undertook a large genome size survey of 401 species of Crustacea and how this relates to their overall life history, including body size, developmental mode, climate and habitat, and overall diversity. Finally I take an in-depth look at genome size diversity in the amphipod genus Hyalella from both North and South America, and investigate how genome size may have contributed to lineage proliferation within these groups. This study more than doubles the number of crustacean genome size estimates generated over the past 60 years, and will help shed light on the C-value enigma, which aims to determine why genome size is so variable among organisms. Acknowledgements I first came to the Gregory lab in the winter 2009 semester as an undergraduate working on methods for genome size estimation in preserved invertebrates. While this project largely turned out to provide little in the way of results, it launched me forward into my MSc in the lab where I was able to pick a project that combined my love for the ocean and all things aquatic, and my newfound interest in molecular biology and genetics. I was given the opportunity to upgrade to my PhD in January 2011, which, while at first I was somewhat hesitant, has now been realized as one of the best decisions of my life. Because of this I have a lot of people to thank. Throughout these past (nearly) 6 years I was able to see and conduct fieldwork at some locations that I probably otherwise would not get to see, and I will always consider myself lucky for this. This included a 3-week trip to Churchill, Manitoba in July 2009, a 4-week trip to the Bamfield Marine Sciences Centre and Haida Gwaii (formerly the Queen Charlotte Islands) in May and June 2010 (where we were robbed halfway through the trip, losing all of our clothes, though luckily nothing we couldn’t replace!), and a 2-week road trip through the Yukon Territory and Alaska in July 2010. I also got the opportunity to return to the Huntsman Marine Science Centre in St. Andrews, New Brunswick, in 2011, and took a road trip to the Halanych lab in Auburn, Alabama in 2012. First and foremost I owe thanks to Ryan Gregory for the opportunity to be in his lab and for allowing me to pursue a research path and group of animals that interests me. Thanks for the guidance but also the chance to work on my own. Thanks also to my advisory committee Sally Adamowicz and Jonathan Witt for their help with ideas, DNA sequencing and obtaining specimens to make this a better project. A very special thank you to all the members of the Gregory, Hebert, Crease and Adamowicz labs, past and present, that helped me with lab work, iii writing and overall having a good time. Specifically, thanks to Tyler “Tyler-man” Elliott, Brent Saylor, João Lima, Brandon Laforest, Paola Pierossi, Amanda Winegardner, Kelly Hadfield, Syed Omar, Kara Layton, Gillian Martin, Liz Boyle, Claudia Bertrand, Liz Martinez and Anne Chambers. Kelly Mulligan was a great volunteer and helped me get through a large number of samples as I started to drown in lab work, and I’m grateful for the help she gave me. Also thanks to the Flow Cytometry Discussion group and the “Flowdeos” to discuss and compare methods during the early years of my grad work. I am indebted to Christy Carr for her help with the entire DNA barcoding process and being patient with me learning all of the details of sequencing DNA, as well as for several summers of enjoyable field work teaching me collection techniques and how to be a better marine biologist. More thanks go to Dr. Jim Bogart for his tips, suggestions and methods on producing karyotypes and his advice once I finally was able to produce karyotypes after hundreds of trials. The administrative secretaries (Monica, Lori and Debbie) were always there to help with a smile, and I’m also very grateful for their advice and help over the years. Last but not least from the IBIO department I would like to thank Sheri Hincks as the lab coordinator for the Invertebrate Zoology labs that I TA’d with at least 1 semester each year of my work here. Sheri helped me become a better TA each time I helped with the course and as a result I began to really enjoy teaching and helping students, and still enjoy it more each time. Much gratitude also goes to my many collaborators who provided me with many species I would not be able to obtain otherwise, as well as general advice to make my thesis that much better. Specifically thanks to the following people for providing specimens: Grace Wyngaard, the British Antarctic Survey (including Melody Clark and Geraint Tarling), Jean-Yves Toullec and the French Polar Institute, the Synalpheus snapping shrimp group (Kristin Hultgren, Dustin iv Rubenstein, Emmett Duffy, Solomon Chak), Nataša Mori, Sarah Fernald, France Dufresne, Melania Cristescu, Björn von Reumont, Teresa Crease, Tom Cronin, Sheila Patek, Erica Staaterman, Adriana Radulovici, Gary Saunders, Lev Yampolsky, Tom Iliffe, José García, Max Rampin, Acacia Alcivar-Warren, Georg Mayer, Emily Ellis, Ken Halanych, Scott Santos, Keith Crandall, Dag Hessen, and Carla Hurt. Finally I’d like to thank my friends and my mom, dad, and sister for their love and support throughout my 10 years at the University of Guelph. My wife (as of about 2 weeks ago!) Erin always helped me keep on track and pushed me forward, and I am very grateful for her support. v Table of Contents Acknowledgements ..................................................................................................................................... iii List of Tables ................................................................................................................................................ ix List of Figures ................................................................................................................................................ x List of Abbreviations ................................................................................................................................ xii Chapter One.................................................................................................................................................. 1 An Introduction to Crustacean Genome Size Diversity ............................................................................... 1 Abstract ........................................................................................................................................................ 2 General Crustacean Biology ......................................................................................................................... 3 Crustacean Phylogeny and Diversity ............................................................................................................. 5 An Introduction to Genome Size.................................................................................................................. 7 The Current State of Knowledge of Crustacean Genome Sizes .................................................................. 8 History and Overview of Crustacean Genome Size Study ............................................................................. 8 Taxonomic Breakdown of Existing Genome Size Knowledge in Crustaceans .......................................... 12 Branchiopods .............................................................................................................................................. 12 Copepods ..................................................................................................................................................... 14 Crabs, Shrimps, and Mantis Shrimps........................................................................................................... 17 Amphipods and Isopods (Superorder Peracarida) ...................................................................................... 18 Ostracods .................................................................................................................................................... 20 Crustacean Genome Composition: Knowledge of Noncoding DNA ......................................................... 21 Thesis Objectives .......................................................................................................................................
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