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Thesis Draft Examination of the population structure of darkbarbel catfish (Pelteobagrus vachelli) in the Upper Yangtze River Basin, China, using novel microsatellite markers By Adrienne Powell A thesis submitted to the Department of Biology in conformity with the requirements for the degree of Master of Science Queen’s University Kingston, Ontario, Canada June, 2012 Copyright © Adrienne Powell, 2012 ii Abstract: The darkbarbel catfish (Peltoebagrus vachelli) is a small bodied benthic fish that inhabits the Yangtze River in China and is commercially valued as food. The objectives of this project were to develop the first set of microsatellite primers specific to P. vachelli and use them to examine the levels of genetic variability and population structure of three populations collected at three sites (Yibin, Luzhou, and Song Ji) along an unfragmented stretch of the upper Yangtze River. Microsatellite primers were designed from an enriched library of genomic DNA and a total of eight primer pairs were optimized to produce reliable polymorphic PCR amplicons on a LI-COR 4200 IR2 platform. A high level of variability was detected amongst the isolated loci with the number of alleles per locus ranging from 14 – 29 and mean observed and expected heterozygosity values of 0.84 and 0.90 respectively across the entire sample set. Overall levels of genetic diversity were high within the three populations with mean observed and expected heterozygosities ranging from 0.823 – 0.869 and 0.864 – 0.921 respectively. Little evidence of genetic structure was detected (global FST = 0.0065, p < 0.05) within the sampled region and pairwise tests of differentiation were not significant (all FST p > 0.05). These results imply historically large populations of P. vachelli in the upper portion of the Yangtze River that, in the absence of artificial barriers, are part of a single panmictic unit. As plans have been put forth for construction of hydroelectric installations within the sampled region, this study provides a baseline estimate of the levels of genetic variation present in P. vachelli within the remaining undammed stretch of the Upper Yangtze River which will serve as a foundation for future analyses on the iii effects of river fragmentation within this region. Additionally the isolation and characterization of the microsatellites will provide useful molecular markers for a variety of other applications in this and closely related species such as parentage analysis, determination of stocks, and maintenance of genetic variation in stocking practices. iv Acknowledgements: I would like to thank my supervisors, Drs. Peter Boag and Yu-Xiang Wang, without whom this project would not have been possible. My appreciation also goes to Dr. John Casselman as an integral member of my committee who gave support and insightful comments throughout the process of completing my Master’s degree. Dr. Brent Murray from the University of Northern British Columbia was instrumental in the designing, planning, and carrying out the sampling of specimens used in this study. Thank you also to the students who helped with the sample collection: Bo-Jian Chen, Lily Yao, Yong-Peng Chen, and Dr. Shi-Jian Fu from Chongqing Normal University as well as Mi Wang, Hong Qing and Xiang Chang from Southwestern University. I would also like to express my sincere gratitude to Zhengxin Sun for providing me with the protocol for the microsatellite library development and guiding me through the process as well as locating supplies necessary to complete the task. I appreciate the support and encouragement that you extended over the years. Thank you to also to members of the Boag lab including Candace Scott for designing the primers and providing invaluable knowledge with regards to laboratory methods amongst other things. Other members of the lab including Christopher Harris, Stephanie McCormack, Ozge Danisment, and Jesse Lai provided technical support and laboratory assistance during the data collection process. v From the Wang lab, I would like to extend my appreciation to Victoria Kopf, Dr. Yi-Ping Luo, Mingzhi Qu and various other office buddies for their company and random conversations along the way. I would also like to express my appreciation to Dr. Peter Van Cooverden deGroot for his support, encouragement, and advise on a variety of issues. Others in the department including Anne Curtis, Amy Chabot, Andy Wong, Sharilyn Hoobin, Roxane Razavi, and Lori Parker provided knowledge and support along the way. I would also like to thank my family, particularly my grandmothers, my parents and my many brothers and sister as well as my friends for their support throughout this often challenging process. vi Table of Contents: Abstract ii Acknowledgements iv List of Tables ix List of Figures and Illustrations x List of Abbreviations xi Chapter 1: Introduction and Literature Review 1 River Fragmentation 1 Genetic Consequences of River Fragmentation 1 Biodiversity in the Yangtze River 2 High Levels of Biodiversity in the Upper Yangtze River 3 Dam Development in the Yangtze Basin 3 Consequences of Dam Construction along the Yangtze River 4 Case Study: The Chinese Sturgeon 6 Population Structure in the Yangtze River 7 Genetic Impacts of Fragmentation along the Yangtze 8 Molecular Tools Applicable to Fisheries Biology 8 Microsatellites 9 Catfish Evolutionary History 10 Siluriformes 11 Catfish Phylogeny 12 The Family Bagridae 12 Genera of the Family Bagridae 13 The study species: Pelteobagrus vachelli 14 Population Structure of Pelteobagrus vachelli 16 Effects of Dam Construction on Pelteobagrus vachelli 17 Purpose of This Study 18 Chapter 2: Materials and Methods 20 The Study Area: The Yangtze River 20 The Upper Yangtze 20 Sample Collection 22 Microsatellite Library Development 22 Isolation of Genomic DNA 22 Restriction Enzyme Digestion of Genomic DNA 24 Preparation of Double Stranded SNX Linkers 25 Ligation of DNA Fragments to SNX Linkers and Verification 26 vii Enrichment of the Microsatellite gDNA-Linker with Biotin-oligos 26 PCR to Test the Results of the Enrichment 28 Dot Blot of the Enriched Microsatellite gDNA-Linker 29 Ligation of Enriched Microsatellite gDNA-Linker to TOPO TA Vector 31 Identification of Positive Colonies by Hybridization with Probes 32 Growth of Positive Colonies 34 Plasmid Isolation and Sequencing of Inserts 35 Primer Design 35 Primer Optimization 35 Multiplex PCR Optimization 37 Genomic DNA Isolation of the Sample Set 37 PCR Amplification of Loci 38 Amplification Error Estimation 38 Data Analysis 40 Chapter 3: Results 43 Microsatellite Library Construction and Optimization 43 Genotyping Error Estimates 43 Microsatellite Genotyping 44 Assessment of Genotyping Technical Errors 44 Genetic Variability of the Optimized Alleles 44 Tests of Linkage Disequilibrium across Populations 46 Private Alleles 46 Genetic Variation within Populations 46 Deviations from Hardy-Weinberg equilibrium within Populations 49 Linkage Disequilibrium between Pairs of Loci within Populations 50 Population Structure 51 Chapter 4: Discussion 55 Microsatellite Variability 55 Comparisons with Other Bagrid Species 56 High Levels of Genetic Diversity 57 Population Structure 59 Models of Gene Flow 61 High Variability and Lack of Population Differentiation 62 Limitations of this Study 65 Final Considerations 66 Literature Cited 67 Appendix 1: Allele frequencies per population 82 Appendix 2: Three dimensional plot of the principle coordinates analysis 85 viii Appendix 3: Literature summary of the size range of microsatellite alleles 86 Appendix 4: Literature summary of levels of heterozygisty in fish species 87 ix List of Tables: Table 1: Sampling sites, GPS coordinates, the number of individual Pelteobagrus 23 vachelli sampled, and the range of fork length (FL) in cm from the three locations along the Upper Yangtze River, China. Table 2: Microsatellite loci isolated in this experiment with the locus specific 39 forward and reverse primer sequences, the optimized annealing temperature (Tm), whether or not it was amplified as part of a multiplex, and the expected allele size. MgCl2 concentration was 1.5 mM in all cases. Table 3: Summary statistics per locus and averages across loci including the 45 number of alleles, standardized allelic richness (AR), range in allele size (in base pairs), expected heterozygosity (He), observed heterozygosity (Ho), and the polymorphic information content of each locus (PIC) and the averages across loci for the 61 samples included in the analyses. Table 4: Number of private alleles (P), total number of alleles (A) and the 47 percentage (%) of the total identified for each locus within the Song Ji, Luzhou, and Yibin populations and over all populations. Table 5: Genetic diversity at eight microsatellite loci for three populations along 48 the upper Yangtze River, China, including the total number of alleles (A), allelic richness (AR) standardized to 20 individuals per population, expected heterozygosity (HE), observed heterozygosity (HO), and the p-value associated with the exact test for deviation from Hardy-Weinberg equilibrium. Table 6: AMOVA analysis averaged across loci. Global FST = 0.00648 over all loci 52 (distance matrix calculated from the number of different alleles), 95% C.I. (0.00137 – 0.01110), P (rand > obs value) = 0.04703. Table 7: Pairwise FST values among the three populations (above the diagonal) 53 with the corresponding p-values (below the diagonal). x List of Figures and Illustrations: Figure 1: Map of the upper Yangtze River system where: XLD represents Xiluodu;
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