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Differentiation of Gene Expression in Behaviorally Isolated

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Differentiation of Gene Expression in Behaviorally Isolated DIFFERENTIATION OF GENE EXPRESSION IN BEHAVIORALLY ISOLATED BLACK AND BROWN MORPHS OF DROSOPHILA ELEGANS by DAIJU HOSHINO Presented to the Faculty of the Graduate School of The University of Texas at Arlington in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE IN BIOLOGY THE UNIVERSITY OF TEXAS AT ARLINGTON May 2007 Copyright © by DAIJU HOSHINO 2007 All Rights Reserved ACKNOWLEDGEMENTS This research was supported by a UTA’s Research Enhancement Program grant (awarded to Pawel Michalak), and an Animal Behaviour Society grant (awarded to John H. Malone). I thank my primary advisor Pawel Michalak for substantial support for my research and academic career, a PhD candidate student at our laboratory John H. Malone for intensive support for research and discussion, an undergraduate student research assistant Ivan T. Lee for help of fly mating experiments and mRNA extraction, a graduate student Daina Ma for help with flies, two of great committee members Esther Betrán and Jaroslaw Krzywinski for help with master thesis editing, all members from Genome Biology Group for giving me ideas on research, and my family and fiancée for supporting my academic career and growth throughout entire college education. April 17, 2007 iii ABSTRACT DIFFERENTIATION OF GENE EXPRESSION IN BEHAVIORALLY ISOLATED BLACK AND BROWN MORPHS OF DROSOPHILA ELEGANS Publication No. ______ DAIJU HOSHINO, M.S. The University of Texas at Arlington, 2007 Supervising Professor: Pawel Michalak Pre-zygotic isolation has been recognized as the primary form of incipient speciation, with behavioral isolation as one of its most significant manifestations. In spite of intensive research on behavioral isolation, its molecular mechanism is still poorly understood. We present microarray data from two morphs, black (OH) and brown (HK), of Drosophila elegans. Since only OH females show strong preference to mate with same type of males, these two morphs provide a model system for investigations into the incipient stage of speciation. We analyzed the expression profiles from heads of mated OH females and non- mated females of both morphs. Subsequent analysis of candidate genes by GoMiner showed that OH unique genes were enriched in the visual system related categories, and iv these categories were still enriched with candidate genes whose expression levels were modified after mating. These results suggest that Drosophila elegans might use visual cues mainly as mate recognition. v TABLE OF CONTENTS ACKNOWLEDGEMENTS................................................................................... iii ABSTRACT ......................................................................................................... iv LIST OF ILLUSTRATIONS................................................................................. viii LIST OF TABLES................................................................................................ ix Chapter 1. INTRODUCTION..................................................................................... 1 1.1 Introduction..................................................................................... 1 2. MATERIALS AND METHODS............................................................... 4 2.1 Flies................................................................................................ 4 2.2 Mating Experiment.......................................................................... 4 2.3 RNA Collection............................................................................... 4 2.4 Affymetrix Drosophila GeneChip® Profiles ................................... 5 2.5 Statistical Analysis.......................................................................... 6 3. RESULTS ................................................................................................. 9 3.1 Mate-By-Female Choice Test.......................................................... 9 3.2 Differentially Expressed Genes Between OH Female and HK Female............................................................. 10 3.3 Differentially Expressed Gene in OH Female Due to Mating Effect ....................................................................... 18 vi 3.4 Overlap of Candidate Genes Among the Group I, II, III, and IV.............................................................. 24 4. DISCUSSION........................................................................................... 27 4.1 Does HK Female Also Show Mating Preference? ........................... 27 4.2 Sequence Divergence Between D. elegans and D. melanogaster ........................................................................ 28 4.3 Some OH Strain-Unique Candidate Genes Are Involved in the Visual System ........................................................ 30 4.4 Gene Involved in the Visual System Are Still Up-Regulated in Mated OH Female ........................................ 31 4.5 OH Unique Genes Are Significantly Enriched in Biochemical Process................................................................... 32 4.6 Transcriptional Changes Associated With Mating ........................... 32 4.7 Biochemical Process Profile in Neural Circuit in Drosophila elegans Is Modified by Mating................................. 35 4.8 Problems Need to Be Addressed...................................................... 36 4.9 Conclusion and Future Direction..................................................... 37 Appendix A. A PUBLISHED PREVIOUS WORK......................................................... 38 REFERENCES ..................................................................................................... 72 BIOGRAPHICAL INFORMATION..................................................................... 76 vii LIST OF ILLUSTRATIONS Figure Page 4.1 Multiple Female Choice Mating Reveals That OH Females Have a Strong Preference to Mate With Own Males..................................... 28 viii LIST OF TABLES Table Page 3.1 Summary of multiple female choice tests ..................................................... 9 3.2 Total G and all of the each replicate show the significance non-random mating by OH female ............................................................... 10 3.3 Total G and only the replicate 4 show the significance non-random mating by HK female ............................................................... 10 3.4 Summary of the number of genes differentially expressed in each contrast ............................................................................ 11 3.5 Group I: Up-regulated genes in non-mated OH compared to non-mated HK.......................................................................... 11 3.6 Group II: Down-regulated genes in non-mated OH compared to non-mated HK.......................................................................... 13 3.7 D. elegans between species (OH and HK), enriched GO categories of overexpressed genes in nMOH (Group I)................................. 15 3.8 D. elegans between species (OH and HK), enriched GO categories of underexpressed genes in OH (Group II)................................... 17 3.9 Group III: Up-regulated genes in non-mated OH compared to mated OH................................................................................. 18 3.10 Group IV: Down-regulated genes in non-mated OH compared to mated OH................................................................................. 20 3.11 D. elegans mating effect, enriched GO categories of overexpressed genes in non-mated OH (Group III)....................................... 21 3.12 D. elegans mating effect, enriched GO categories of underexpressed genes in non-mated OH (Group IV)..................................... 22 ix 3.13 Genes overlapping between Group I and Group IV ...................................... 25 3.14 GO categories shown to be enriched by both enriched GO categories of Group I and those of Group IV ................................................ 25 4.1 Estimation of Ks by Kumar method. Calculation was done by MEGA 4 .................................................................................. 29 4.2 Genes overlapping with McGraw’s candidate genes..................................... 33 x CHAPTER 1 INTRODUCTION 1.1 Introduction The new developments in comparative genetics and genomics hold promise for providing answers to many questions about the origin of new species (speciation). Reproductive isolation between species has been recognized as the essential step to speciation (Dobzhansky 1937; Mayr 1963). While post-zygotic isolation has been widely accepted as the main cause of evolutionary divergence of species, pre-zygotic isolation is considered to be involved in incipient speciation (Coyne and Orr 1998). Several theoretical models of pre-mating isolation have been proposed, with assortative mating by direct mate choice playing a central role (Rundle et al. 2005). Mate discrimination has been observed in many closely related species, including Drosophila melanogaster. Zimbabwe and Cosmopolitan morphs of D. melanogaster provide a good model to investigate asymmetrical mating that results in prezygotic isolation. However, in spite of the intensive effort of many researchers, the genetic mechanism of this mating discrimination needs yet to be resolved (Chenoweth and Blows 2006). Here we use Drosophila elegans, another Drosophila system that shows partial sexual isolation between two different morphs (Hirai and Kimura, 1997; Ishii et al, 2001; Ishii et al, 2002; Kopp and True 2002).
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