ANALYSIS OF GENETIC
VARIATION IN ANIMALS

Edited by Mahmut Çalişkan
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Analysis of Genetic Variation in Animals
Edited by Mahmut Çalişkan


Published by InTech
Janeza Trdine 9, 51000 Rijeka, Croatia

Copyright © 2012 InTech
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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


Analysis of Genetic Variation in Animals, Edited by Mahmut Çalişkan
p. cm.
ISBN 978-953-51-0093-5

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Contents
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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



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Preface
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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




Part 1
Molecular Phylogenetics