GENETIC DIVERSITY IN MICROORGANISMS Edited by Mahmut Caliskan Genetic Diversity in Microorganisms Edited by Mahmut Caliskan Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2012 InTech All chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. As for readers, this license allows users to download, copy and build upon published chapters even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. Notice Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Publishing Process Manager Marina Jozipovic Technical Editor Teodora Smiljanic Cover Designer InTech Design Team First published February, 2012 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from [email protected] Genetic Diversity in Microorganisms, Edited by Mahmut Caliskan p. cm. ISBN 978-953-51-0064-5 Contents Preface IX Part 1 Microbial Genetic Diversity 1 Chapter 1 Diversity of Heterolobosea 3 Tomáš Pánek and Ivan Čepička Chapter 2 Archaeal Diversity and Their Biotechnological Potential 27 Birgül Özcan Chapter 3 Genotyping Techniques for Determining the Diversity of Microorganisms 53 Katarzyna Wolska and Piotr Szweda Chapter 4 DNA Based Techniques for Studying Genetic Diversity 95 Ahmed L. Abdel-Mawgood Chapter 5 Patterns of Microbial Genetic Diversity and the Correlation Between Bacterial Demographic History and Geohistory 123 Pei-Chun Liao and Shong Huang Chapter 6 Microsatellites as Tools for Genetic Diversity Analysis 149 Andrea Akemi Hoshino, Juliana Pereira Bravo, Paula Macedo Nobile and Karina Alessandra Morelli Chapter 7 HIV-1 Diversity and Its Implications in Diagnosis, Transmission, Disease Progression, and Antiretroviral Therapy 171 Inês Bártolo and Nuno Taveira VI Contents Chapter 8 Using Retroviral Iterative Genetic Algorithm to Solve Constraint Global Optimization Problems 215 Renato Simões Moreira, Otávio Noura Teixeira, Walter Avelino da Luz Lobato, Hitoshi Seki Yanaguibashi and Roberto Célio Limão de Oliveira Part 2 Phylogenetics 233 Chapter 9 Genetically Related Listeria Monocytogenes Strains Isolated from Lethal Human Cases and Wild Animals 235 Ruslan Adgamov, Elena Zaytseva, Jean-Michel Thiberge, Sylvain Brisse and Svetlana Ermolaeva Chapter 10 Issues Associated with Genetic Diversity Studies of the Liver Fluke, Fasciola Heptica (Platyhelminthes, Digenea, Fasciolidae) 251 Denitsa Teofanova, Peter Hristov, Aneliya Yoveva and Georgi Radoslavov Chapter 11 Genetic Diversity of Brazilian Cyanobacteria Revealed by Phylogenetic Analysis 275 Maria do Carmo Bittencourt-Oliveira and Viviane Piccin-Santos Chapter 12 Pre-Columbian Male Ancestors for the American Continent, Molecular Y-Chromosome Insight 291 Graciela Bailliet, Marina Muzzio, Virginia Ramallo, Laura S. Jurado Medina, Emma L. Alfaro, José E. Dipierri and Claudio M. Bravi Chapter 13 Approaches for Dissection of the Genetic Basis of Complex Disease Development in Humans 309 Nicole J. Lake, Kiymet Bozaoglu, Abdul W. Khan and Jeremy B. M. Jowett Chapter 14 Genetic Diversity and the Human Immunodeficiency Virus Type-1: Implications and Impact 339 Orville Heslop Preface So far as we know all life in the universe exists at or near the surface of planet Earth. The life forms on Earth connected through shared history are a DNA-based life. Reconstruction of this history, known as phylogeny, is one of the most difficult challenges in contemporary biology. However it is well worth the effort, because of the considerable benefits that robust phylogenetic hypotheses can provide for diverse fields of biology, both basic and applied. Because even distantly related life forms are perfectly similar genetically and share the same regulatory genes, it would be counterproductive not to take advantage of the full range of variation produced by this great experiment conducted over billions of years. Robust phylogenetic trees are essential tools for displaying this variation efficiently. Genetics, the science of heredity, deals with the factors that are responsible for the similarities and differences between life forms and generations. These factors affect form and function at every level, from the molecules that compose each living cell, through the organismal and population levels of biological organization. The concepts of genetics are therefore fundamental to all biological disciplines and serve as the unifying core in the study of modern biology. Biological evolution is the dual process of genetic change and diversification of organisms through time. By this process related populations can diverge from one another in their genetic characteristics and give rise to new species. The idea that populations can change over time and produce different species, and that all present day species (approximately 2100 million species) were derived in this manner from a common ancestor, provides a rational framework for organizing the vast array of biological knowledge. Through evolution, new species arise through the process of speciation. New varieties of organisms arise and thrive when they have the ability to find and exploit an ecological niche, however, species become extinct when they are no longer able to survive in changing conditions or against superior competition. Most of extinctions have occurred naturally and it is estimated that 99.9% of all species that have ever existed are now extinct. Mass extinctions are relatively rare events. However, isolated extinctions are quite common and scientists have become alarmed at the high rates of recent extinctions. Most species that become extinct are never scientifically documented. Some scientists estimate that up to half of presently existing X Preface species may become extinct by 2100. Genetic diversity is required for populations to evolve and cope with environmental changes, new diseases, and pest epidemics. Genetic variability also provides the opportunity for tracing the history of populations, species, and their ancestors. Therefore, the assessment of genetic variation in species and among populations is important for conservation of genetic resources. The genetic diversity determination can be based on morphological, biochemical, and molecular types of data. As a matter of fact, molecular markers (RFLP, RAPD, mtDNA, RFLP, SNP etc.) are superior to both morphological and biochemical markers because they are relatively simple to detect, abundant throughout the genome, completely independent of environmental conditions, and can be detected at virtually any stage of development. Genetic diversity is the fundamental source of biodiversity. In 1989, the World Wildlife Fund defined biodiversity as “the richness of life on Earth – millions of plants, animals and microorganisms, including the genes which they carry, and complex ecosystems that create the environment”. Currently, the issue of maintaining the genetic diversity as a component of the conservation of biodiversity has been accepted at an international level. FAO has included the issue of conservation, evaluation, and use of animal genetic resources, in its fields of interest since 1970s. In this context, one of the main concerns of scientific research activities is conserving the genetic diversity of local breeds, especially those of economic interest. Genetic diversity among individuals reflects the presence of different alleles in the gene pool, and hence, different genotypes within populations. Genetic diversity should be distinguished from genetic variability, which describes the tendency of genetic traits found within populations to vary. There is a considerable genetic variability within or between natural populations. Population geneticists attempt to determine the extent of this variability by identifying the alleles at each locus and measuring their respective frequencies. This variability provides a genomic flexibility that can be used as a raw material for adaptation. On the other hand, one of the consequences of low genetic variability could be inability to cope with abiotic and biotic stresses. From the growing knowledge on the genome sequences of organisms it becomes evident that all forms of diversity have their origin at genetic level. In this context genetic diversity analysis provides vital and powerful data that helps for better understanding of genetic variation and improved conservation strategies. The purpose of these books is to provide a glimpse into the dynamic process of genetic variation by presenting the thoughts of some of the scientists who are