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The Pennsylvania State University the Graduate School College Of The Pennsylvania State University The Graduate School College of Agricultural Sciences A PHYLOGEOGRAPHIC STUDY OF ANASTREPHA OBLIQUA AND A. LUDENS (DIPTERA: TEPHRITIDAE) A Dissertation in Entomology by Raul Ruiz © 2010 Raul Ruiz Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy December 2010 The dissertation of Raul Ruiz was reviewed and approved by the following: Bruce A. McPheron Professor of Entomology Dean for the College of Agriculture Dissertation Adviser Chair of Committee Michael Saunders Professor of Entomology Shelby Fleischer Professor of Entomology David M. Geiser Associate Professor of Plant Pathology Norman B. Barr Molecular Biologist Special Member USDA APHIS Center for Plant Health Science and Technology Gary W. Felton Graduate Program Office for Department of Entomology Signatures are on file in the Graduate School. ii ABSTRACT This thesis examines the phylogeographic variation of two economically important Tephritid pest species, Anastrepha ludens (Mexican fruit fly) and A. obliqua (West Indian fruit fly). Both of these species are formidable fruit pests that are associated with many plants and are considered economically important pests. Both species have a wide geographic distribution with occasional infestations occurring in the US. This research evaluates the utility of a sequence-based approach for two mitochondrial genes and nuclear markers. We assess these markers as genetic tools for revealing historical processes, for delineating populations, and examining for population structure. The Mexican fruit fly is a major pest of orange and grapefruit occurring in Mexico and C. America. I analyzed 543 A. ludens individuals from 67 geographic collections and found one predominant haplotype occurring in the majority of specimens. I observed 68 haplotypes in all and see a substantial difference among haplotypes belonging to northern and southern groups of collections. The results show that COI and ND6 are useful for phylogeographic studies of A. ludens and may be used for pathway analysis. The West Indian fruit fly is a major pest of mango and plum contributing to millions of dollars in damage each year throughout its geographic range. The current geographic distribution for A. obliqua includes areas stretching from N. Mexico, C. America, and S. America as far and N. Argentina, as well as the Caribbean. West Indian fruit fly specimens were examined for genetic variation at two spatial scales. The first study is of specimens gathered from five different host species over three years in the Mexican state of Veracruz represent those geographic collections examined at a local scale. Additional collections gathered from throughout the geographic range represent the second study of this species. iii In Veracuz, numerous specimens were examined for variation that may be due to the influence by ecological factors using mtDNA and nuclear markers. Here, five species of infested fruit was collected over three years and fruit fly larvae were allowed to emerge and mature to adults. I sequenced two genes (COI and NDI) and used 17 nuclear loci from these flies and revealed that the populations examined in Veracruz represent one panmictic population. The value of this information is especially important to the management of this pest because it reveals that one management strategy is sufficient. Additionally, this information is used in knowing the diversity of this pest at this window in time. Fifty-four collections of A. obliqua were sequenced in a broader geographic study. Mitochondrial regions from the COI and ND6 genes reveal six populations throughout the distribution of this fly. I recovered 61 haplotypes from the 349 individuals gathered from 54 localities. Many of these haplotypes were either site specific or region specific making this a useful tool for pathway analysis. There were substantial differences seen among the lineages represented by the haplogroups. The amount of divergence seen among these four haplogroups is in line with differences seen among other closely related taxa I analyzed. This would suggest that a review of taxanomic keys is needed. Also, additional analyses perhaps with unlinked loci are needed to evaluate the level of interaction among different lineages that co-occur. iv TABLE OF CONTENTS LIST OF FIGURES ----------------------------------------------------------------------------------------------------------------------- VII LIST OF TABLES -------------------------------------------------------------------------------------------------------------------------- IX ACKNOWLEDGMENTS ---------------------------------------------------------------------------------------------------------------- XII CHAPTER 1: INTRODUCTION ---------------------------------------------------------------------------------------------------------- 1 THE IMPORTANCE OF ANASTREPHA ------------------------------------------------------------------------------------------------------ 1 USE OF MOLECULAR METHODS --------------------------------------------------------------------------------------------------------- 3 JUSTIFYING THE NEED FOR DIAGNOSTIC MARKERS ---------------------------------------------------------------------------------- 4 REFERENCES -------------------------------------------------------------------------------------------------------------------------------- 6 CHAPTER 2: Phylogeographic analysis of Mexican fruit fly (Diptera: Tephritidae) using mitochondrial dna sequence data ---------------------------------------------------------------------------------------------------------------------------------------------10 ABSTRACT ------------------------------------------------------------------------------------------------------------------------------10 MATERIALS AND METHODS -------------------------------------------------------------------------------------------------------------13 Sample Collection. ------------------------------------------------------------------------------------------------------------- 13 DNA Extraction, PCR Amplification, and Sequencing. ------------------------------------------------------------------ 16 Data Analysis. ------------------------------------------------------------------------------------------------------------------ 17 RESULTS -----------------------------------------------------------------------------------------------------------------------------------19 Mitochondrial Variability in Anastrepha ludens. --------------------------------------------------------------------------- 19 Population Structure, Neutrality Tests and Demographic Inferences. ---------------------------------------------------- 25 DISCUSSION --------------------------------------------------------------------------------------------------------------------------------34 ACKNOWLEDGEMENTS -------------------------------------------------------------------------------------------------------------------37 REFERENCES CITED ----------------------------------------------------------------------------------------------------------------------37 CHAPTER 3: Genetic variation in Anastrepha obliqua (Diptera: Tephritidae) in geographic collections from the Mexican state of Veracruz ------------------------------------------------------------------------------------------------------------------43 ABSTRACT ---------------------------------------------------------------------------------------------------------------------------------43 INTRODUCTION ----------------------------------------------------------------------------------------------------------------------------44 MATERIALS AND METHODS -------------------------------------------------------------------------------------------------------------47 Collections and DNA extraction. --------------------------------------------------------------------------------------------------47 Mitochondrial DNA PCR and sequencing analysis. ----------------------------------------------------------------------------51 mtDNA phylogenetic reconstruction ----------------------------------------------------------------------------------------------53 mtDNA phylogeographic analysis -------------------------------------------------------------------------------------------------53 Microsatellite PCR and fragment analysis ---------------------------------------------------------------------------------------54 Microsatellite data analyses ---------------------------------------------------------------------------------------------------------57 RESULTS -----------------------------------------------------------------------------------------------------------------------------------58 Sequence variation -------------------------------------------------------------------------------------------------------------------58 Phylogenetic reconstruction with mtDNA ---------------------------------------------------------------------------------------62 Phylogeographic analysis of mtDNA ---------------------------------------------------------------------------------------------63 Microsatellite analyses---------------------------------------------------------------------------------------------------------------71 DISCUSSION --------------------------------------------------------------------------------------------------------------------------------77 Diversity among collections --------------------------------------------------------------------------------------------------------77 Population structure with mtDNA -------------------------------------------------------------------------------------------------78
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