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Taxonomic Diversity of Some Rusts and Smuts of Khyber Pakhtunkhwa and Adjacent Hills of Pakistan.Pdf Taxonomic Diversity of Some Rusts and Smuts of Khyber Pakhtunkhwa and Adjacent Hills of Pakistan A dissertation submitted to the University of the Punjab in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY IN BOTANY BY AAMNA ISHAQ DEPARTMENT OF BOTANY UNIVERSITY OF THE PUNJAB LAHORE, PAKISTAN February, 2017 Taxonomic Diversity of Some Rusts and Smuts of Khyber Pakhtunkhwa and Adjacent Hills of Pakistan A dissertation submitted to the University of the Punjab in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY In Botany BY AAMNA ISHAQ Supervisors Prof. Dr. Abdul Nasir Khalid Dr. Najam-ul-Sehar Afshan DEPARTMENT OF BOATNY UNIVERSITY OF THE PUNJAB LAHORE-PAKISTAN Dedicated to My loving Parents and My Sisters Without whom none of my success would be possible APPROVAL CERTIFICATE I certify that the research work described in this thesis submitted by Aamna Ishaq d/o Muhammad Ishaq Malik has been carried out under my direct supervision. I have personally gone through all the data reported in the manuscript and certify their authenticity. I also certify that the thesis has been prepared according to the prescribed format. I recommend it to be processed for evaluation by the external examiner for the award PhD degree in Botany. Prof. Dr. Abdul Nasir Khalid Department of Botany University of the Punjab, Lahore, Pakistan. ACKNOWLEDGEMENTS First of all, I would like to thank almighty Allah Subhanahu Wa Ta'ala for giving me strength to start and successfully complete this work. I would like to pay my heartiest gratitude to my respected teacher and PhD supervisor, Dr. Abdul Nasir Khalid for his continuous advices, guidance, kindness, support, and patience throughout the duration of my research work. Thanks are also due to my co-supervisor Dr. Najam-ul-Sehar Afshan (Assistant Professor, Center for Undergraduate Studies, PU, Lahore) for her supervision, skills, scholarly guidance and inspiring advices throughout the progress of my research work. Thanks are also due to Dr. Abdul Rehman Khan Niazi (Associate Professor, Department of Botany, PU, Lahore) for his moral support, kindness and especially for his assistance in field tours. I am thankful to Prof. Dr. Firdaus-e-Bareen, chairperson, Prof. Dr. Muhammad Saleem and Prof. Dr. Khan Rass Masood, Ex-Chairmen Department of Botany, University of the Punjab, Lahore for providing me conducive environment and facilities for carrying out this research project. I am indebted to Higher Education Commission of Pakistan (HEC) for funding this research project and awarding me the scholarships under indigenous 5000 fellowships (Batch VI) and IRSIP (International Research Support Initiative Program). I am thankful to my foreign supervisor, Prof. Dr. Catherine Aime, Director, Botany and Plant Pathology, Purdue University USA for allowing me to work in her Lab under her guidance, valuable suggestions and giving me access to Arthur Fungarium (PUR) and Kriebel Herbarium (PUL) specimens and literature for improvement of my work and publications. My sincere thanks to Dr. Mehardad Abbasi (Acting Curator, Arthur Herbarium) for his valueable suggestions in identifitacions and Mr. John F. Klimek (Herbarium Manager) for his help in Phylogenetic part of my research. I want to thank my foreign lab fellows Ms. Rachel i A. Koch and Mr. Teeratas Kijpornyongpan (PhD Scholars, Purdue University, USA) for their continuous help in completion of my work during my stay in Purdue University, USA. I am thankful to Director, Department of Physics, University of Peshawar, Peshawar, Pakistan for facilitating the Scanning Electron Microscopy (SEM). I would like to acknowledge staff of Soil survey of Punjab, Lahore and Pakistan Meteorological Department (PMD) for giving me necessary data and information of the study area needed for the research work. Special thanks to Ms. Sana Ishaq (GIS Specialist, Urban Unit, Lahore) for generous help in mapping and distribution analysis of data. I wish to thank Dr. Kálman Vánky (Honorary Member of Hungarian Academy of Science), Prof. Dr. Cvetomir M. Denchev (Bulgarian Academy of Sciences, Bulgaria), Prof. Dr. Reinhard Burndt (Department of Biology, ETH, Zurich) for verification of some of the samples and reviewing the manuscripts. I highly acknowledge my dearest friends, Dr. Nousheen Yousaf (Lecturer, Government College University, Lahore), Dr. Sana Jabeen (Lecturer, University of Education, Faisalabad) and Ms. Nusrat Majeed for always being there for me with their great support and cheerful company. I want to thank my seniors in research Laboratory, Dr. Muhammad Hanif (GCU, Lahore), Dr. Samina Sarwar (LCWU, Lahore), Dr. Tayyaba Ashraf (Govt. college for women, Sheikhupura), Dr. Abdul Razzaq (UVAS, Lahore), Dr. Sobia Razzaq (LCWU, Lahore) and Dr. Syeda Bint-e- Zahra (Govt. college for woment, Salamat Pura, Lahore) for always acknowledging my efforts. I also acknowledge all my friends and lab fellows especially Dr. Malka Saba (Gujrat University), Ms. Arooj Naseer (Center for Undergraduate Studies, PU, Lahore), Ms. Hira Bashir, Ms. Munazza Kiran, Ms. Tayyeba Qasim, MS. Memoona Khan (Govt. Post graduate college for women, Muzang, Lahore), Ms. Annum Razzaq, Ms. KhushBakht and Mr. Muhammad Usman for their support and help in finishing of this project and cheerful company throughout the session. ii My sincere thanks to my research collaborators Dr. Muhammad Fiaz (Assistant Professor, Hazara University, Mansehra) and Mr. Sadiqullah (Hazara University, Mansehra) for sharing some of their specimens generously. I am thankful to Dr. Ishtiaq Ahmad (Govt. College, Matta, Swat) and Dr. Shah Hussain (Hazara University, Mansehra) for arranging wonderful field trips in different regions of Pakistan. My special thanks to Mr. Akbar Shah (Lab assistant) for his help both in field and in laboratory. This piece of research would have been impossible without the prayers and support of my sweet parents. I am thankful to my sisters, Saira, Hina, Tibra and Sakeena for their moral support and love. Aamna Ishaq iii Table of Contents Page No. Acknowledgment ....................................................................................................... i List of Tables ............................................................................................................. iv List of Figures ............................................................................................................ vii Abstract ...................................................................................................................... xii CHAPTER 1 Introduction ............................................................................................................... 1 CHAPTER 2 Literature Review ..................................................................................................... 5 Aims and Objectives of Study .................................................................................. 11 CHAPTER 3 Materials and Methods ............................................................................................. 12 3.1. Description of sampling site .................................................................... 12 3.2. Sample collection ..................................................................................... 12 3.3. Preservation of samples ........................................................................... 12 3.4. Identification of host plants ..................................................................... 12 3.5. Microscopic analysis ................................................................................ 20 3.6. Identification of Fungi ............................................................................. 20 3.7. Molecular Characterization ...................................................................... 21 3.7.1. Genomic DNA Extraction......................................................... 21 3.7.2. Polymerase Chain Reaction (PCR) ........................................... 21 3.7.3. Analyses of Molecular Data ...................................................... 22 3.8. Biodiversity Analysis ............................................................................... 23 3.8.1. Species Richness (S) ................................................................. 23 3.8.2. Margalef diversity index (D) .................................................... 23 3.8.3. Shannon Index (H) .................................................................... 24 3.8.4. Shannon‟s Equitability (EH ) ..................................................... 24 3.5.5. Simpson Index (D) .................................................................... 25 3.8.5. Simpson‟s Reciprocal Index (1/D)............................................ 25 3.9. Dendrogram cluster analysis .................................................................... 25 iv 3.10. Distribution Mapping and Predictive Modeling .................................... 26 CHAPTER 4 Results ........................................................................................................................ 27 4.1. Taxonomy ................................................................................................ 28 4.2. Biodiversity Analysis ............................................................................... 212 4.2.1. Diversity of fungal taxa ............................................................ 212 4.2.2. Shannon and Simpson Indices .................................................. 212 4.2.3.
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