STUDIES IN POPULATION GENETICS Edited by M. Carmen Fusté Studies in Population Genetics Edited by M. Carmen Fusté 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. 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Publishing Process Manager Silvia Vlase Technical Editor Teodora Smiljanic Cover Designer InTech Design Team First published August, 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@intechopen.com Studies in Population Genetics, Edited by M. Carmen Fusté p. cm. ISBN 978-953-51-0588-6 Contents Preface VII Chapter 1 Piecing the punicus Puzzle 1 Byron Baron Chapter 2 The Evolution of Plant Mating System: Is It Time for a Synthesis? 17 Cheptou Pierre-Olivier Chapter 3 Population Genetics of the“Aeromonas hydrophila Species Complex” 39 Mª Carmen Fusté, Maribel Farfán, David Miñana-Galbis, Vicenta Albarral, Ariadna Sanglas and José Gaspar Lorén Chapter 4 Minisatellite DNA Markers in Population Studies 55 Svetlana Limborska, Andrey Khrunin and Dmitry Verbenko Chapter 5 Polymorphism 85 Oliver Mayo Chapter 6 Speciation in Brazilian AtlanticForest Mosquitoes: A Mini-Review of the Anopheles cruzii Species Complex 105 Luísa D.P. Rona, Carlos J. Carvalho-Pinto and Alexandre A. Peixoto 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 Shuhua Xu and Wenfei Jin 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 [...]... inconsistent forces in natural populations, thus casting doubt about the general applications of theoretical “purging” studies to natural populations 3.3 Inferring mating system parameters in natural populations How population genetics parameters vary with inbreeding and more specifically selffertilization has been central in population genetics theory until its foundation (Malécot, 1948) The intensive use... alleles, inbreeding depression is expected to decrease with inbreeding regime The reason is that regular inbreeding will expose recessive mutations to selection by producing homozygotes and thus lower the frequencies of deleterious alleles This process known as the “purging process” has been central in population genetics studies analyzing inbreeding depression Influential theoretical studies in the... between inbreeding depression and selffertilisation, though weak, in accordance with expectations However, a more complete compilation of data did were not able to find a significant decrease of inbreeding depression 24 Studies in Population Genetics with selfing (Winn et al, 2011) Analysing specifically the possibility of purging in populations, Byers and Waller (1999) conclude that purging is an inconsistent... way the magnitude of inbreeding depression varies with the selfing regime under the partial dominance hypothesis and under the overdominance hypothesis is the exact opposite If inbreeding depression is mainly due to overdominant alleles, inbreeding depression increases with selfing as a consequence the higher proportion of homozygote loci in inbred lines On the contrary, if inbreeding depression is caused... the population selfing rate Thus, selfing rates related to selfing rate as can be easily inferred from genotyping a sample of individuals in a population While this method is simple, Fis can be potentially inflated by other sources of inbreeding (biparental inbreeding) thus biasing upward the estimated selfing rates 3.3.2 Inference from progeny array analysis Another classical method to estimate selfing... genetic drift in populations as consequence of the joint sampling of gametes In diploid populations, male and female gametes are sampled independently under random mating, which results in an effective population size of twice the number of individuals Because both female and male gametes are sampled together in individuals of a complete selfing population, the effective populations the population is... complete selfing, thus departing to the classical Hardy-Weinberg equilibrium under random mating In a quantitative genetics perspective, selfing substantially affect the distribution of additive 22 Studies in Population Genetics variance in a way that increases between-lines genetic variance and decreasing within line genetic variance as a consequence of the purity of the lines (Falconer, 1981) Self-fertilization... documenting the deleterious effects of inbreeding in 57 species Interestingly, he anticipated a number of evolutionary trends, such as the relationship between inbreeding depression values and mating system of populations, which was to be confirmed by population genetics theory hundred years later Beyond the empirical results reported in various organisms by empiricists, the rise of population genetics in. .. not depends on whether populations are regular inbreeders or not While complete outcrossing is often viewed as a way to avoid inbreeding depression, the magnitude of inbreeding depression is in itself (measured as the difference in fitness in selfed and outcrossed offsprings) is not constant and vary with the inbreeding regime as a consequence of mutation selection balance in the populations Importantly,... variation in the chloroplast genome (Schoen et al 1997) In gray: branch giving rise to inbred lines, in black branch giving rise to cross-pollinated lines (the ancestor is supposed to cross-pollinated) Photos: left, the crosspollinator A furcata and right self-pollinating species A Vernicosa Courtesy of Daniel J Schoen (McGill University, Canada) In a recent study, Goldberg et al (2009) have demonstrated in . STUDIES IN POPULATION GENETICS Edited by M. Carmen Fusté Studies in Population Genetics Edited by M. Carmen Fusté Published by InTech Janeza Trdine 9, 51000. Sardinian haplotype, which was found in almost half the sampled Sardinian individuals. This means that the population inhabiting Corsica most probably crossed over from Sardinia. Similarly in. the insular populations. These analyses indicated that the Sardinian population separated from the common ancestor population in North Africa during the early Pleistocene while the Corsican populations