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Genome Evolution in Parasitic Wasps: Comparisons of Sexual and Asexual Species

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Genome Evolution in Parasitic Wasps: Comparisons of Sexual and Asexual Species University of Iowa Iowa Research Online Theses and Dissertations Summer 2018 Genome evolution in parasitic wasps: comparisons of sexual and asexual species Eric S. Tvedte University of Iowa Follow this and additional works at: https://ir.uiowa.edu/etd Part of the Biology Commons Copyright © 2018 Eric S. Tvedte This dissertation is available at Iowa Research Online: https://ir.uiowa.edu/etd/6516 Recommended Citation Tvedte, Eric S.. "Genome evolution in parasitic wasps: comparisons of sexual and asexual species." PhD (Doctor of Philosophy) thesis, University of Iowa, 2018. https://doi.org/10.17077/etd.kgdbnt2x Follow this and additional works at: https://ir.uiowa.edu/etd Part of the Biology Commons GENOME EVOLUTION IN PARASITIC WASPS: COMPARISONS OF SEXUAL AND ASEXUAL SPECIES by Eric S. Tvedte A thesis submitted in partial fulfillment of the requirements for the Doctor of Philosophy degree in Biology in the Graduate College of The University of Iowa August 2018 Thesis Supervisors: Associate Professor John M. Logsdon, Jr. Associate Professor Andrew Forbes Copyright by Eric S. Tvedte 2018 All Rights Reserved Graduate College The University of Iowa Iowa City, Iowa CERTIFICATE OF APPROVAL ____________________________ PH.D. THESIS _________________ This is to certify that the Ph.D. thesis of Eric Tvedte has been approved by the Examining Committee for the thesis requirement for the Doctor of Philosophy degree in Biology at the August 2018 graduation. Thesis Committee: ____________________________________________ John M. Logsdon, Jr., Thesis Supervisor ____________________________________________ Andrew Forbes, Thesis Supervisor ____________________________________________ Maurine Neiman ____________________________________________ Bryant McAllister ____________________________________________ Todd Scheetz ____________________________________________ Andrew Kitchen ACKNOWLEDGEMENTS I would like to thank my advisors, John Logsdon and Andrew Forbes for their immense contribution to my professional and personal growth. I’d also like to thank my committee members, Maurine Neiman, Bryant McAllister, Todd Scheetz, and Andrew Kitchen for their advising and engagement with the project. I thank past and present colleagues in the Logsdon & Forbes labs, particularly Joe Jalinsky, Cindy Toll, Chris Rice, Alaine Hippee, Anna Ward, Heather Widmayer, Robin Bagley, Sarah Hanson, Elizabeth Savelkoul, Gaby Hamerlinck, and Amanda Nelson for your collaboration, guidance, and pizza-eating on Fridays. I also thank Neiman lab folks, especially Kyle McElroy, Laura Bankers, and Joel Sharbrough, for talks about sex. My thesis work was greatly aided by the contributions from high school students and undergraduates, including Austin Ward, Austin Paden, Samuel Cummings, Breana Rinker, and Ethan Nelson-Moore. I am also grateful for the assistance of the administrators and staff in the Biology Department, past and present. I am particularly thankful to Phil Ecklund, Tom Koeppel, Eileen Sullivan, and Gery Hehman for their various roles during my tenure. Last but not least, I’d like to thank my friends and family for their steadfast support. I would especially like to thank my girlfriend, Zoey, whose serenity, thoughtfulness, and laughter has given me so much inspiration over the past year. ii ABSTRACT The fate of any lineage is contingent on the rate at which its genome changes over time. Genome dynamics are influenced by patterns of mutation and recombination. Mutations as the raw force of variation can be acted on independently during exchanges of homologous genetic regions via meiotic recombination. While molecular evolution in sexual lineages is impacted by both mutation and recombination, asexual lineage fate is primarily influenced by the mutation rate; recombination is often altered or absent in asexuals. Although multiple studies show accelerated mutation accumulation in asexual lineages that have lost recombination, virtually nothing is known about rate patterns when meiosis is retained. Here, I use parasitic wasps in genus Diachasma to investigate genome evolution in a recently-derived asexual lineage. I provide evidence that asexual Diachasma possess a canonical set of meiosis genes as well as high levels of genomic homozygosity. Taken together, these observations support an active, albeit modified, form of meiosis in this asexual lineage. In addition, I present the first documentation of accelerated mutation accumulation in the nuclear genome of a naturally-occurring, meiotically- reproducing organism. If harmful, these mutations could impede asexual lineage persistence and contribute strong support for the long-term benefits of sex. iii PUBLIC ABSTRACT Reproduction is a core organismal trait, and transitions between reproductive strategies may influence the evolutionary trajectory of a species. Sex is a costly reproductive strategy, yet it is ubiquitous in nature. The predominance of sex may be explained in part by passage of genetic material across generations during meiosis, particularly segregation and recombination. Sex enables parents to transmit genetic material without harmful mutations to offspring. Loss of sex may increase the accumulation of mutations in the genome. If harmful, these mutations could lead to the eventual extinction of an asexual lineage. A recent loss-of-sex event in Diachasma parasitic wasps offers a promising opportunity to compare patterns of genome-wide mutations between sexual and asexual species. I used newly sequenced genomes from sexual and asexual Diachasma to investigate whether sex loss in an asexual wasp is associated with changes in meiosis genes. I identified a complete meiosis gene set in the asexual speices D. muliebre, supporting meiotic egg production despite sex loss. To assess whether reproductive mode influences Diachasma evolution more broadly, I retrieved a genome-wide dataset to calculate evolutionary rates between wasp species. I found evidence for greater mutation accumulation in asexual Diachasma, suggesting the modification of meiosis has an effect on the generation and maintenance of genetic variation. Future studies are needed to determine the extent to which this could affect the organism’s ability to survive in nature. iv TABLE OF CONTENTS LIST OF TABLES ........................................................................................................... viii LIST OF FIGURES ........................................................................................................... ix PREFACE .......................................................................................................................... xi CHAPTER 1: INTRODUCTION ....................................................................................... 1 The problem of sex ...................................................................................................... 1 Evolution of meiosis genes in asexual lineages........................................................... 1 Genome evolution in asexual lineages ........................................................................ 4 Diachasma wasps: a promising model for the study of sex loss ................................. 6 Thesis aims .................................................................................................................. 8 REFERENCES ............................................................................................................... 9 CHAPTER 2: DESCRIPTIVE ANALYSES OF THE GENOME OF THE PARASITIC WASP DIACHASMA ALLOEUM, AN EMERGING MODEL FOR ECOLOGICAL SPECIATION AND TRANSITIONS TO ASEXUAL REPRODUCTION ............................................................................................................ 15 ABSTRACT .................................................................................................................. 15 INTRODUCTION ........................................................................................................ 16 MATERIALS & METHODS ....................................................................................... 18 Biological material .................................................................................................... 18 DNA isolation, library preparation, sequencing, and genome assembly ................... 18 RNA isolation, RNAseq library preparation, sequencing, assembly, and annotation............................................................................................................ 20 Characterization of ultraconserved elements using BUSCO ..................................... 21 Identification of orthologous gene clusters using OrthoVenn ................................... 22 Manual gene annotation ............................................................................................. 23 RESULTS & DISCUSSION ........................................................................................ 27 Quality assessment of genome assembly ................................................................... 27 Annotation of repertoire of intact oxidative phosphorylation genes in D. alloeum .. 28 Ortholog groups are shared between D. alloeum and other hymenopterans ............. 30 Expansion of species-specific chemosensory genes in D. alloeum ........................... 31 D. alloeum contains canonical genes involved in reproduction and sex determination ................................................................................................ 40 Acknowledgements ..................................................................................................
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