ANALYSIS OF GENETIC VARIATION IN ANIMALS Edited by Mahmut Çalişkan Analysis of Genetic Variation in Animals Edited by Mahmut Çalişkan 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 orders@intechweb.org Analysis of Genetic Variation in Animals, Edited by Mahmut Çalişkan p. cm. ISBN 978-953-51-0093-5 Contents Preface IX Part 1 Molecular Phylogenetics 1 Chapter 1 Genetic Characterization of Albanian Sheep Breeds by Microsatellite Markers 3 Anila Hoda and Paolo Ajmone Marsan Chapter 2 Genetic Characterization of Romanian Local Breeds Using Microsatellite Markers 27 Georgescu Sergiu Emil and Costache Marieta Chapter 3 Spatial Variation of Genetic Diversity in Drosophila Species from Two Different South American Environments 45 Luciana P. B. Machado, Daniele C. Silva, Daiane P. Simão and Rogério P. Mateus Chapter 4 Interspecific and Intraspecific Genetic Diversity of Thunnus Species 63 Mei-Chen Tseng, Chuen-Tan Jean, Peter J. Smith and Yin-Huei Hung Chapter 5 Molecular Approaches for the Study of Genetic Diversity in Microflora of Poultry Gastrointestinal Tract 83 Alireza Seidavi Chapter 6 Molecular Markers and Genetic Diversity in Neotropical Felids 105 Alexeia Barufatti Grisolia and Vanessa Roma Moreno-Cotulio Chapter 7 Genetic Diversity and Evolution of Marine Animals Isolated in Marine Lakes 121 Naoto Hanzawa, Ryo O. Gotoh, Hidekatsu Sekimoto, Tadasuke V. Goto, Satoru N. Chiba, Kaoru Kuriiwa and Hidetoshi B. Tamate VI Contents Chapter 8 Genetic Diversity and Genetic Heterogeneity of Bigfin Reef Squid “Sepioteuthis lessoniana” Species Complex in Northwestern Pacific Ocean 151 Hideyuki Imai and Misuzu Aoki Chapter 9 Genetic Variation of Host Immune Response Genes and Their Effect on Hepatitis C Infection and Treatment Outcome 167 Pooja Deshpande, Michaela Lucas and Silvana Gaudieri Part 2 Conservation of Genetic Resources 187 Chapter 10 Landscape Genomics in Livestock 189 Lorraine Pariset, Stephane Joost, Maria Gargani and Alessio Valentini Chapter 11 Managing the Genetic Resources in the Intensive Stock Enhancement Program Carried out on Black Sea Bream in Hiroshima Bay, Japan 217 Enrique Blanco Gonzalez and Tetsuya Umino Chapter 12 Loss of Genetic Diversity in Wild Populations 231 Shawn Larson Chapter 13 Low Danube Sturgeon Identification Using DNA Markers 243 Marieta Costache, Andreea Dudu and Sergiu Emil Georgescu Chapter 14 Shark DNA Forensics: Applications and Impacts on Genetic Diversity 269 Luis Fernando Rodrigues-Filho, Danillo Pinhal, Davidson Sodré and Marcelo Vallinoto Chapter 15 Molecular Biodiversity Inventory of the Ichthyofauna of the Czech Republic 287 Jan Mendel, Eva Marešová, Ivo Papoušek, Karel Halačka, Lukáš Vetešník, Radek Šanda, Milena Koníčková and Soňa Urbánková Chapter 16 Aquatic Introductions and Genetic Founder Effects: How do Parasites Compare to Hosts? 315 April M. H. Blakeslee and Amy E. Fowler Chapter 17 Estimating the Worth of Traits of Indigenous Breeds of Cattle in Ethiopia 337 Girma T. Kassie, Awudu Abdulai and Clemens Wollny Preface 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) derive from a common ancestor, provides a rational framework for organizing the vast array of biological knowledge. Through evolution, new species arise via a 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 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 these recent extinctions. Most species that become extinct are never scientifically documented, with some scientists estimating that up to half of all presently existing species may become extinct by 2100. The leading evolutionary forces such as mutation, natural selection, and genetic drift have created a vast diversity of animals which ended in the formation of many well- defined breeds with different levels of performance. The knowledge of the genetic variability and process that underlie the livestock’s origins and maintenance has crucial importance to provide critical insights into the structure and dynamics of livestock populations. Genetic diversity is a requirement 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 the 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. Detailed knowledge of genetic variation within and among different breeds is very important for understanding and improving traits of economic X Preface importance. Hence, the future improvement is dependent on genetic variation present within breeds and between breed variation. The purpose of Analysis of Genetic Variation in Animals is to provide a glimpse into the dynamic process of genetic variation by presenting the thoughts of some of the scientists who are engaged in the development of new tools and ideas used to reveal genetic variation, often from very different perspectives. I would like to express my deepest gratitude to all the authors who contributed to this book by sharing their valuable works with us. This book should prove useful to students, researchers, and experts in the area of conservation biology, genetic diversity, and molecular biology. The year 2010 was celebrated as the international year of biodiversity by the United Nations and it has been a unique opportunity to realize the vital role that biodiversity plays in sustaining the life on Earth. Let us all wish much success to all projects and initiatives dealing with the conservation of diversity of life because rich genetic resources are a prerequisite for future generations to be able to breed crop varieties and face new challenges. Prof Dr. Mahmut Calıskan Mustafa Kemal University, Tayfur Sokmen Campus Fen-Edebiyat Faculty, Biology Dept. Antakya-Hatay Turkey . purpose of Analysis of Genetic Variation in Animals is to provide a glimpse into the dynamic process of genetic variation by presenting the thoughts of some of the scientists who are engaged in. ANALYSIS OF GENETIC VARIATION IN ANIMALS Edited by Mahmut Çalişkan Analysis of Genetic Variation in Animals Edited by Mahmut Çalişkan Published by InTech. A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from orders@intechweb.org Analysis of Genetic Variation in Animals, Edited