DISENTANGLING THE GENETICS OF COEVOLUTION IN POTAMOPYRGUS ANTIPODARUM AND MICROPHALLUS SP. By CHRISTINA E JENKINS A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY WASHINGTON STATE UNIVERSITY School of Biological Sciences JULY 2016 © Copyright by CHRISTINA E JENKINS, 2016 All Rights Reserved © Copyright by CHRISTINA E JENKINS, 2016 All Rights Reserved To the Faculty of Washington State University: The members of the Committee appointed to examine the dissertation of CHRISTINA E JENKINS find it satisfactory and recommend that it be accepted. Mark Dybdahl, Ph.D., Chair Scott Nuismer, Ph.D. Joanna Kelley, Ph.D. Jeb Owen, Ph.D. ii Acknowledgement First and foremost, I need to thank my committee, Mark Dybdahl, Scott Nuismer, Joanna Kelley and Jeb Owen. They have put in a considerable amount of time helping me grow and learn as a scientist, and have consistently challenged me to be better during my Ph.D. studies. I cannot find words to thank them enough, so for now, “thank you” will need to suffice. I especially thank Mark and Scott; coadvising was an adventure and one I embarked on gladly. Thank you for all the input and effort, even when it made all three of us cranky. I need to thank the undergraduates and field assistants that have worked for and with me to collect data, process samples, plan field seasons and generally make my life easier. Thanks to Jared and Caitlin for their tireless work (seriously, hours upon hours of their time) running flow cytometry to answer questions about polyploidy. Thank you to Meredith and Jordan for collecting snails, through sand flies, rain, hangovers, and occasionally hypothermia. And especially to Jordan: it is not easy traveling with someone for 6 weeks at a time on the far side of the world, but he made our trips productive and fun. I need to thank all of my lab mates, from both the Nuismer lab at University of Idaho: Ailene McPherson, ET Thornquiste, Anahi Espindola, Virginie Poullain and Bob Week; and from the Dybdahl lab at Washington State University: Jennifer Madrid Thorson, Jon Finger (DIJON!) and Mark Smithson. Being in two different labs is a lot like having two families. Neither of them knows much about each other, and there isn’t much interaction as a whole unit. But similar to having two families, I cannot imagine going through the last six years without the endless support from every one of them. I need to thank my friends in the graduate student and postdoc community on the Palouse. Six years is a long time to slog through a Ph.D. and I have met some amazing people, iii many of whom I now consider family. The non-exhaustive list of people I need to thank: Emily Jones, Katie Shine, Diego Morales, Simon Uribe-Convers, Kayla Hardwick, Travis Hagey, Tim McGuin, Natalie Gage, Hannah Marx, Roxy Hickey, Matt Pennell, Matt Singer, Daniel Beck, Tyler Heather, Gen Metzger, TATE (just Tate), Wesly Loftie-Eaton, Thibault Stadler, Amy Worthington, Maribeth Latvis, Sarah Jacobs, Marius Myrvold, Urs Weber, Andy Kramer, Ben Weideback, Chloe Stenkamp-Strahm, Erin Weise and many more. Thank you for supporting me, for taking care of me, for encouraging me, and for believing in me. Especially when I wasn’t able to do any of these things for myself. I need to thank a few people who have acted in the role of “partner” over the last few years. First, I need to thank Bobbi Johnson. I don’t know how I convinced the coolest person on the planet to be friends with me, but I’m sure glad I did. If I had half of the life skills that she does, I could take over the world, and I’m amazed every day that she hasn’t done so already. Thank you for taking care of all the things I am entirely incapable of. Kimberly Lackey and I undertook the impossible and succeeded. We were asked to teach a course for which there was no course. We wrote all the labs, the quizzes, the lectures, the exams and any other relevant material. We met constantly for two years, spoke many times a day, produced a cohesive class, and published a text book together. I could not have done this with anyone else, and I will forever be grateful for our partnership. Finally, I need to thank my “domestic partner” Hannah Marx. We have a wine club membership, a CSA, a storage unit together and have the keys to each other’s apartment. We have done “romantic weekends” in Paris, McCall, Seattle, and many more. I can’t imagine not having you in my life, and can’t wait for our adventures in the future. iv A Ph.D. takes a long time, and I simply would not have been able to undertake it without the support of my family and friends, who I would like to thank a million times. Especially my baby niece, Annie Grace, who makes me smile a little bit every day. v DISENTANGLING THE GENETICS OF COEVOLUTION IN POTAMOPYRGUS ANTIPODARUM AND MICROPHALLUS SP. Abstract by Christina E. Jenkins, Ph.D. Washington State University July 2016 Chair: Mark Dybdahl Host-parasite coevolution is potentially important for many evolutionary transitions such as the evolution of sexual reproduction, ploidy, and the evolution of mating systems according to mathematical models of coevolution. In these models, host-parasite interaction is characterized by host resistance and parasites’ infectivity which is assumed to be based on a matrix of genotype by genotype specificity (GxG). Importantly, a recent trend has demonstrated that the GxG matrix assumed in a given theoretical model will drastically alter the outcome of the above evolutionary transitions. Consequently, determining the form of genetic interaction matrices in natural populations is crucial to both understanding coevolution and the resulting evolutionary transitions. In this dissertation, I explore the genetics of host-parasite interactions in three different ways. First, using the New Zealand snail, Potamopyrgus antipodarum and its undescribed trematode parasite Microphallus sp., I tested the fit of different genetic models by comparing the resistance of triploid and tetraploid hosts, which differ in gene dosage, heterozygosity, and abundance of novel alleles. In my second chapter, I explored the molecular and genetic basis of traits associated with infection by assembling and annotating a transcriptome for Microphallus sp. and comparing the results with other similar parasites. First, to facilitate vi comparisons, I determined the phylogenetic placement of Microphallus sp. among the trematode parasites. Second, I compared the genes expressed in Microphallus sp. with those of other well- studied trematode parasites. Finally, because trematodes infect both snail and vertebrate hosts in their life cycle, I used further comparative analyses to determine whether Microphallus sp. are expressing genes to evade the vertebrate or invertebrate immune system. Finally, in my third chapter, I developed a technique for finding the genomic regions involved in coevolution. Using genomic data, we can look for SNPs that covary spatially between the host and parasite, as these will likely mark regions involved in local adaptation. I tested the efficacy of this technique using simulated populations of hosts and parasites with coevolving and neutral loci. I altered models of infection, evolutionary and statistical parameters to determine when we are able to detect coevolving loci. vii TABLE OF CONTENTS Page Abstract ...................................................................................................................................... vi TABLE OF CONTENTS ......................................................................................................... viii LIST OF TABLES ...................................................................................................................... x LIST OF FIGURES ................................................................................................................... xi Dedication ................................................................................................................................ xiii Introduction ................................................................................................................................. 1 The role of ploidy in host resistance ........................................................................................... 8 Abstract: .................................................................................................................................. 8 Introduction ............................................................................................................................. 9 Materials and Methods .......................................................................................................... 12 Results ................................................................................................................................... 16 Discussion ............................................................................................................................. 17 Acknowledgements ............................................................................................................... 19 The Microphallus sp. transcriptome and an analysis of its taxonomic relationship to other Digenea parasites ...................................................................................................................... 24 Abstract ................................................................................................................................. 24 Introduction ..........................................................................................................................