**Meet the editor**

Dr M. Carmen Fusté graduated in Biology at the University of Barcelona, where she completed her PhD in 1980. Since then she has worked in different aspects of Microbiology including bacterial genetics, physiology and bacterial polysaccharide production. Her research in bacterial population genetics began in 1991 with the application of MLEE analysis to the study of different

pathogenic and environmental bacteria such as Escherichia coli, Neisseria meningitidis, Haemophilus influenzae, Vibrio cholerae, Pseudomonas stutzeri and Aeromonas. More recently, she has taken advantage of new sequencing techniques to determine the population genetics structure of a group of Aeromonas strains belonging to the "A.hydrophila complex". This work, which has helped clarify this group of species, constitutes one of the chapters of this book.

Contents

**Preface VII** 

Chapter 2 **The Evolution of Plant** 

Chapter 3 **Population Genetics of** 

Chapter 1 **Piecing the** *punicus* **Puzzle 1**  Byron Baron

Cheptou Pierre-Olivier

and Dmitry Verbenko

Chapter 6 **Speciation in Brazilian AtlanticForest Mosquitoes: A Mini-Review of** 

and Alexandre A. Peixoto

Shuhua Xu and Wenfei Jin

Chapter 5 **Polymorphism 85**  Oliver Mayo

Mª Carmen Fusté, Maribel Farfán, David Miñana-Galbis, Vicenta Albarral, Ariadna Sanglas and José Gaspar Lorén

Svetlana Limborska, Andrey Khrunin

**Mating System: Is It Time for a Synthesis? 17** 

**the"***Aeromonas hydrophila* **Species Complex" 39** 

Chapter 4 **Minisatellite DNA Markers in Population Studies 55** 

**the** *Anopheles cruzii* **Species Complex 105**  Luísa D.P. Rona, Carlos J. Carvalho-Pinto

Chapter 7 **The Next Step in Understanding Population Dynamics: Comprehensive Numerical Simulation 117** 

John C. Sanford and Chase W. Nelson

Chapter 8 **Population Genetics in the Genomic Era 137** 

## Contents

#### **Preface XI**


Preface

Population geneticists study the genetic composition and variability of natural populations as well as the theories that explain this variability in terms of natural selection, mutation, recombination, genetic drift and gene flow. Population genetics was first developed among eukaryotes in an attempt to reconcile Darwin's theory of evolution by natural selection and Mendelian genetics. When Darwin postulated that natural selection is the main force of evolutionary change, a great controversy was created. As Darwin did not fully understand the inheritance mechanism, he was unable to answer one of the main criticisms of his thesis. If selection is gradually to modify a population, the individuals that constitute this population have to vary, because if all the members are identical, no selection can occur. This controversy would eventually be solved thanks to Mendel's inheritance theory, even though the early Mendelians did not accept an important role for natural selection in evolution.

The foundations of population genetics were established in the 1920s and 1930s when R.A. Fisher, J.B.S. Haldane and S. Wright elaborated mathematical models to explain how Darwin's theory of natural selection (and other evolutionary forces) could modify the genetic composition of a population over time. Since then, research in this field has been mainly focused on eukaryote species and only to a small extent on the prokaryotes, to which population genetics was first applied in the 1970s. The classical analysis of multilocus enzyme electrophoresis (MLEE) has been substituted by new gene sequencing technology, which, being highly reproducible and exportable, has

The aim of this book has been to reflect the diversity of applications of population genetics. The chapters take a variety of approaches, including general and theoretical, while others report studies on animals, plants and bacteria. Here follows a summary

Minisatellite markers are revisited, a classic in genetic studies that are back in fashion since their polymorphic nature and high mutation rate allow not only the determination of population divergence over long periods, but also the relatively recent ethnic history of populations. In the search for a comprehensive view of population dynamics, a highly advanced numerical simulation program, which is readily accessible to both students and teachers, is presented. The advantages of using

allowed the comparison of data among different laboratories.

of the different contributions,

## Preface

Population geneticists study the genetic composition and variability of natural populations as well as the theories that explain this variability in terms of natural selection, mutation, recombination, genetic drift and gene flow. Population genetics was first developed among eukaryotes in an attempt to reconcile Darwin's theory of evolution by natural selection and Mendelian genetics. When Darwin postulated that natural selection is the main force of evolutionary change, a great controversy was created. As Darwin did not fully understand the inheritance mechanism, he was unable to answer one of the main criticisms of his thesis. If selection is gradually to modify a population, the individuals that constitute this population have to vary, because if all the members are identical, no selection can occur. This controversy would eventually be solved thanks to Mendel's inheritance theory, even though the early Mendelians did not accept an important role for natural selection in evolution.

The foundations of population genetics were established in the 1920s and 1930s when R.A. Fisher, J.B.S. Haldane and S. Wright elaborated mathematical models to explain how Darwin's theory of natural selection (and other evolutionary forces) could modify the genetic composition of a population over time. Since then, research in this field has been mainly focused on eukaryote species and only to a small extent on the prokaryotes, to which population genetics was first applied in the 1970s. The classical analysis of multilocus enzyme electrophoresis (MLEE) has been substituted by new gene sequencing technology, which, being highly reproducible and exportable, has allowed the comparison of data among different laboratories.

The aim of this book has been to reflect the diversity of applications of population genetics. The chapters take a variety of approaches, including general and theoretical, while others report studies on animals, plants and bacteria. Here follows a summary of the different contributions,

Minisatellite markers are revisited, a classic in genetic studies that are back in fashion since their polymorphic nature and high mutation rate allow not only the determination of population divergence over long periods, but also the relatively recent ethnic history of populations. In the search for a comprehensive view of population dynamics, a highly advanced numerical simulation program, which is readily accessible to both students and teachers, is presented. The advantages of using

#### VIII Preface

genomic data for population genetics analysis, which has greatly improved our knowledge of mechanisms of mutation and recombination, and adaptation to local environments, is the theme of another contribution. A population genetics study of a Mediterranean species of bat found on the Maltese Islands aims to understand its possible origin and promote its conservation. The goal of another study is to determine the impact of climate change on the evolution and speciation of Brazilian Atlantic Forest Mosquitoes As new techniques for revealing polymorphism have been developed, one chapter comprehensively describes this phenomenon and its use in studying a variety of biological problems, giving extensive examples. An overview of concepts, techniques and empirical data development in plant mating systems is presented in another chapter with a special focus on the evolution of self fertilization in hermaphroditic plants

Finally, a population genetics study sheds light on the doubts about the existence of true species in bacteria. The analysis of several strains included in the "Aeromonas hydrophila species complex" has confirmed that the entities phenotypically described as bacterial species form cohesive groups in which genetic recombination plays a limited role in reducing genetic variation and can therefore be defined as biological species.

> **Dr M. Carmen Fusté**  Department of Health Microbiology and Parasitology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain

VIII Preface

in hermaphroditic plants

species.

genomic data for population genetics analysis, which has greatly improved our knowledge of mechanisms of mutation and recombination, and adaptation to local environments, is the theme of another contribution. A population genetics study of a Mediterranean species of bat found on the Maltese Islands aims to understand its possible origin and promote its conservation. The goal of another study is to determine the impact of climate change on the evolution and speciation of Brazilian Atlantic Forest Mosquitoes As new techniques for revealing polymorphism have been developed, one chapter comprehensively describes this phenomenon and its use in studying a variety of biological problems, giving extensive examples. An overview of concepts, techniques and empirical data development in plant mating systems is presented in another chapter with a special focus on the evolution of self fertilization

Finally, a population genetics study sheds light on the doubts about the existence of true species in bacteria. The analysis of several strains included in the "Aeromonas hydrophila species complex" has confirmed that the entities phenotypically described as bacterial species form cohesive groups in which genetic recombination plays a limited role in reducing genetic variation and can therefore be defined as biological

Department of Health Microbiology and Parasitology, Faculty of Pharmacy,

**Dr M. Carmen Fusté** 

Spain

University of Barcelona, Barcelona,

**1** 

Byron Baron

*Malta* 

*AnGen Labs, Marsascala,* 

**Piecing the** *punicus* **Puzzle** 

The occurrence of *Myotis* species in the Mediterranean region has been documented for a very long time. At present, 15 *Myotis* species are known to inhabit the Mediterranean region (Temple & Cuttelod, 2009). However the classification of some of these species has been continuously shifting and somewhat difficult to determine. One such species has been what is now referred to as *Myotis punicus* Felten, 1977 (Castella *et al.*, 2000). Until the late 1990s *Myotis punicus* was generally thought to be an insular variant of either *Myotis myotis* or *Myotis blythii*, mostly because both these species are distributed throughout the Mediterranean region. It was considered to be either a smaller variant of *Myotis myotis* (Gulia, 1913; Ellerman & Morrison-Scott, 1966; Benda & Horácek, 1995), or a larger variant of *Myotis blythii* (Lanza, 1959; Strelkov, 1972; Felten *et al.*, 1977; Bogan *et al.*, 1978; Corbet, 1978). In Malta, some authors also attributed particular individuals to other species including *Myotis daubentoni* (Gulia, 1913), *Myotis capaccinii* (Gulia, 1913) and *Myotis oxygnathus* (Lanfranco, 1969). However, several authors have commented on the differences observed from individuals of *Myotis myotis* and *Myotis blythii* across the rest of their distribution range and expressed doubt as to the correct classification (Strinati, 1951; Strelkov, 1972; Felten *et al.*, 1977; Gaisler, 1983; Menu & Popelard, 1987; Borg *et al.*, 1990;

The distinguishing features of *Myotis punicus* were first reported through comparative analyses of morphometric data (Benda & Horácek, 1995; Arlettaz *et al*., 1997). Cranial morphometrics in conjunction with measurements of forearm and ear length presented a distinct cluster of individuals from the Mediterranean region intermediate in size between *Myotis myotis* and *Myotis blythii*. It was also noted that this intermediate cluster lacked the white spot of hair on the forehead, which is typical of *Myotis blythii* (Arlettaz *et al*., 1997). Among the distinctive features of *Myotis punicus* are its large size (comparable to *Myotis myotis*), the plagiopatagium (wing membrane) starting at the base of the toes, a lancet shaped tragus and distinct dorsal (light brown) and ventral (white) fur coloration (Dietz &

However, genetic analysis was required to solve this riddle and obtaining the samples required for such analyses was the first hurdle. In order to carry out research on a protected species such as *Myotis punicus*, which is protected, together with all other European bats

**1. Introduction** 

Courtois *et al.*, 1992).

von Helversen, 2004).

**2. The appropriate sampling method** 
