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Introduction to Population Biology and Evolution
symptoms they cause (Fig. 1.1; Box 1.1). In many cases, it is no longer adequate to identify a pathogen to the species level; it is often necessary to identify whether a pathogen belongs to a cryptic species or to a subgroup within a species with its own unique biology or pathology. Intraspecific variation may also be evident in other ways, such as the ability to survive between seasons, the time at which a genotype appears during an epidemic, the ability to reproduce sexually, or other traits of biological and epidemiological interest. Moreover, knowledge of biologically relevant genetic variation within pathogen populations has the potential to contribute to better disease management. Understanding the processes by which genetic variation arises and is maintained in populations is one of
Plant pathologists have been aware of genetic diversity and evolution in pathogen populations for more than 100 years, at least since the early descriptions of host specialization and races1 (Barrus, 1911; Stakman and Piemeisel, 1917). Since then, especially in conjunction with the application of a variety of genetic markers in the last 25 years, plant pathologists have discovered a wealth of additional genetic variation in pathogen populations. Molecular genetic markers have made it possible to reliably identify and quantify variation between morphologically similar species of plant pathogens and to uncover remarkable variation within some species. Much of this variation has biological significance, especially variation correlating with pathogenicity, virulence (or “aggressiveness”), or the types of
■ Figure 1.1. Individuals of the same pathogen species may vary in virulence and the type of symptoms they produce when inoculated onto the same host genotype. Some isolates of Fusarium oxysporum f. sp. ciceris are (A) moderately virulent and cause yellowing symptoms in chickpeas (Cicer arietinum), whereas others are (B) highly virulent and cause wilting symptoms (Trapero-Casas and Jiménez-Díaz, 1985). C, The plant on the right is a noninoculated control. (Courtesy R. M. Jiménez-Díaz) 1
Terms in bold text are defined in the glossary.
1
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2 C h a p t e r 1
BOX 1.1
Pathogenicity, Virulence, and Aggressiveness: A Host of Confusing Terms
The terms pathogenicity and virulence have caused much confusion. Sacristán and García-Arenal (2008) summarized the history and use of these terms in plant pathology. The most widely accepted definitions of these terms in plant pathology (Holliday, 1989; D’Arcy et al., 2001) can be traced back to H. H. Whetzel: Pathogenicity is “the ability of an organism to produce disease,” whereas virulence is “the measure of pathogenicity” (Whetzel, 1929). The definition of v irulence has been refined slightly to include the degree of damage infection causes in the host (Holliday, 1989; Sacristán and García-Arenal, 2008). As we have learned more about host–pathogen interactions, the definition of pathogenicity has been refined further to recognize that a microbe may be pathogenic on one host species or host genotype but not on others (Pirofski and Casadevall, 2012). In other words, pathogenicity is a qualitative description of the interaction of pathogen and host genotypes; a microbe is pathogenic or not on a particular host. By contrast, virulence is a quantitative characteristic of a pathogen interacting with a particular host; a pathogen may be highly virulent on one host and less virulent on another. Similarly, one pathogen may be more or less virulent than another on the same host genotype, depending on how much damage it causes the host (Fig. 1.1). Confusion arises in this terminology in the context of gene-for-gene (GFG) systems (Chapter 9) where virulence is often used as a qualitative descriptor of a host–pathogen interaction. In GFG systems, a pathogen inoculated onto a differential cultivar sometimes is scored as virulent or avirulent—a qualitative description implying an all-or-nothing interaction. To confuse matters further, host–pathogen interactions in the context of GFG systems that result in nearly complete inhibition of pathogen development by a hypersensitive response are sometimes called nonpathogenic. In
the overarching goals in population biology. Population biology is an interdisciplinary subject concerning the biological significance of genetic variation at the population level. Ideally, population biology integrates concepts of ecology, evolution, and genetics. The study of population biology of plant pathogens is a combination of plant disease epidemiology and population genetics (Fig. 1.2). Epidemiology is concerned with the ecology
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reaction to the potential confusion caused by the dual use of virulence as a qualitative and quantitative term, Vanderplank (1963) coined the term aggressiveness for the quantitative degree of damage a pathogen causes its host. However, because of the complete redundancy of this definition of aggressiveness to the original definition of virulence and its lack of use outside of plant pathology, the term aggressiveness is not used in this book. Furthermore, not all avirulent interactions in GFG systems completely inhibit disease; some avirulent rust infection types, for example, are better described as low virulence, whereas virulent interactions may be described in comparable, relative terms as high virulence (Chapter 9). The convention adopted for describing GFG systems in this book— despite the potential for confusion—is to use the terms low virulence and high virulence whenever possible; the exception is to use the term virulent race for a pathogen genotype that expresses high virulence on a particular host genotype. The use of the terms pathogenicity and virulence in plant pathology differs from that of some other fields. In animal pathology and evolutionary biology, virulence refers to the reduction in host fitness caused by a pathogen (Read, 1994). This meaning is consistent with its meaning in plant pathology, assuming that the degree of damage caused by infection is correlated with reduction in host fitness. In the ecological literature, infectivity is sometimes used to describe the high-virulence phenotype of a pathogen on a particular host genotype in GFG systems (Tellier and Brown, 2007b; Thrall et al., 2012). The confusion of terminology can hinder communication; therefore, it is essential that terms such as pathogenicity and virulence are defined clearly. It also requires vigilance on the part of readers to be sure they understand how the terms are being used in each context.
of plant pathogens, particularly the dynamics of pathogen population size (and how much disease occurs) over time and space in response to environmental factors (Campbell and Madden, 1990; Cooke et al., 2006; Madden et al., 2007). These ecological dynamics occur on relatively short timescales—days to months, sometimes years. Plant disease epidemiology is a well-established discipline, with roots dating back at least to Vanderplank’s (1963)
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Introduction to Population Biology and Evolution 3
■ Figure 1.2. Population biology of plant pathogens is an interdisciplinary field that integrates plant disease epidemiology and pathogen population genetics, based on concepts of genetics, ecology, and evolution. (Reproduced, by permission of the publisher, from M. Milgroom. 2001. The synthesis of genetics and epidemiology: Contributions of population biology in plant pathology. J. Plant Pathol. 83:57-62. Copyright 2001 Edizioni ETS.)
seminal work, and most plant pathologists are introduced to basic epidemiological concepts in introductory courses. By contrast, population genetics is less well understood by most plant pathologists. As a complement to epidemiology, the emphasis in population genetics is on evolution, particularly changes in the genetic composition of populations. Evolution occurs on timescales as short as days or years; more often, however, these dynamics occur on timescales of decades, centuries, or millennia. Epidemiology and population genetics have common roots in plant pathology, particularly in relation to the evolution of races and deployment of host plant resistance (Vanderplank, 1963; Burdon, 1987; Wolfe and Caten, 1987; Leonard and Fry, 1989). Over the past 25 years, however, these two disciplines have diverged and, for the most part, developed independently. Population genetics emerged as a separate discipline in plant pathology after molecular genetic markers became readily accessible for quantifying selectively neutral genetic variation. Its development was dependent on technological advances, just as epidemiology diverged and became more specialized a decade earlier,
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partly as a consequence of advances in computer technology. Despite their divergence, the two disciplines often address similar questions, although from different conceptual bases, using different tools and terminology (Table 1.1). This close similarity in subject matter argues for thinking of the two as a single holistic discipline. Thus, a more inclusive way to think of population biology is that it comprises both epidemiology and population genetics; it is the synthesis of ecology, evolution, and genetics at the population level (Fig. 1.2). Because the two disciplines have historically been treated independently, for the most part, and because of the wealth of background available elsewhere on plant disease epidemiology, this book focuses mainly on the population genetics and evolutionary components of population biology, with attempts throughout to integrate these concepts with those of epidemiology. This book is aimed at an audience with a basic knowledge of plant pathology but minimal background in evolutionary biology, for example, from introductory biology. This chapter gives a brief introduction to population genetics and evolution, all of which will be explained in more detail throughout the book.
Population Genetics As a component of population biology, we have to consider what population genetics means. The principle aims of population genetics are to understand the inheritance or transmission of genes between generations at the level of populations and the evolutionary and biological significance of genetic variation. To this end, population genetics aims to determine the processes that generate and maintain genetic variation within and among populations. The evolutionary processes shaping populations are often inferred from observed patterns of genetic variation, whether these are allele, genotype, or phenotype frequencies or a variation in nucleotide sequences. Alternatively, evolutionary processes may be studied experimentally by subjecting populations or genotypes to experimental conditions treatments and monitoring changes in allele, genotype, or phenotype frequencies over time. This latter approach has been useful for studying fast-evolving microbes under controlled laboratory conditions where multiple generations occur and evolutionary changes can be detected within a reasonably short time. Evolutionary experiments are much more difficult and less common in greenhouse and field environments, although they have been conducted at times with great success with plant pathogens.
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4 C h a p t e r 1 ■ Table 1.1. Plant disease epidemiology and ecology share many of the same concepts with population genetics of plant pathogens, even though they use different terminology and research methods. Epidemiological or Ecological Concept
Evolutionary or PopulationGenetic Concept
Explanation
Source of inoculum
Migration
Dispersal of individuals from inoculum source to host plants.
Type of inoculum
Recombination
The type of inoculum (e.g., sexual, recombinant inoculum such as ascospores, oospores, or asexual, clonal inoculum [mycelium, conidia]) can sometimes be inferred from patterns of genetic diversity.
Dispersal
Migration
On short timescales, these processes are identical.
Spatial patterns
Migration
Spatial patterns of disease severity/incidence or pathogen genotypes can be used to infer dispersal distances.
Pathogen dormancy
Random genetic drift
Pathogen population size is often markedly reduced in the dormant phase, resulting in bottlenecks and random changes in the genetic composition of the pathogen population in the next generation.
Recombination
Dormancy of some pathogens requires sexual structures, such as eggs or cysts (in nematodes), oospores, teliospores, or ascocarps (e.g., powdery mildew fungi).
Competition
Selection and fitness
Competitive ability between genotypes is a component of fitness and, therefore, may be under selection.
Fungicide resistance
Mutation
Mutations arise that result in fungicide-resistant phenotypes; often mutations occur in single genes, but multiple genes may be involved for some fungicides (e.g., DMI fungicides).
Selection
Application of fungicide increases frequency of resistant phenotypes because of selection.
Mutation
Variation in virulence on particular host genotypes arises by mutation.
Selection
Differential fitness of pathogen genotypes on resistant hosts results in selection for races or genotypes with higher virulence.
Migration
Races or more virulent genotypes can spread among locations.
Coevolution
Host plants evolve mechanisms to detect and inhibit pathogens; pathogens evolve means of evading detection; and plants evolve new mechanisms.
Selection
Differential fitness of genotypes on different hosts results in selection.
Population structure
Selection causes genetic differentiation of pathogen populations on different hosts.
Migration
Movement of individuals from one population to another, often by long-distance dispersal or human activity.
Random genetic drift
Founder effects caused by introduction of relatively few individuals results in populations genetically different and less diverse than the source population.
Mutation and selection
New pathogen phenotypes can arise by mutation that are more virulent or have other traits that are favored by selection.
Recombination, hybridization, and horizontal gene transfer
Exchange of genetic material within and between species can result in pathogens with altered host ranges and/or greater virulence.
Speciation
New species form with unique pathogenic characteristics.
Breakdown or erosion of resistance
Host specialization
Introduced pathogens
Emerging and reemerging pathogens
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Introduction to Population Biology and Evolution 5
In general, three types of questions are addressed in population genetics. The first (alluded to previously) concerns evolutionary processes and demography inferred from population structure, which is defined by patterns of genetic diversity within and between populations—the study of population structure and the inferences that can be drawn from it are major themes throughout this book. This type of approach reveals genome-wide phenomena, in which the entire genome is affected similarly. By contrast, the second type of question addresses the effects of specific genes on phenotypes and evolution; these are locus-specific phenomena. In particular, this type of question relates to genes that are under natural selection. The evolution of fungicide resistance and the emergence of races in gene-for-gene (GFG) systems are examples where single genes under selection can have marked effects on the composition of pathogen populations. The third type of question concerns classification of populations into cryptic species or other closely related taxa and the reconstruction of likely evolutionary pathways that produced them. This type of question could be considered an extension of studies on population structure and genome-wide effects, although it may also involve adaptation and locus-specific phenomena. It is presented here as a distinct question to emphasize evolutionary phenomena at the interface of populations and species. Addressing this latter type of question often combines phylogenetic methods similar to those used in systematics with methods used for analyzing population structure. The rediscovery of Mendel’s laws of inheritance in the early twentieth century, combined with Darwin’s theory of natural selection, culminated in the development of classical population-genetic theory in the 1920s and 1930s. The foundation of classical population genetics was laid long before geneticists understood the physical structure of genes and chromosomes. The discovery of DNA as the molecule of inheritance and the deciphering of the genetic code led to amazing elaborations of population-genetic theory, particularly the neutral theory of evolution (Kimura, 1983). Many subsequent theories were subjected to empirical tests only after recent advances in molecular biology and DNA sequencing technology. Hartl and Clark (2007) point to three major revolutionary advancements that have had profound effects on the study of population genetics. The first was the conceptual breakthrough of the theory of coalescence, based on thinking about populations and genes from the perspective of evolutionary or genealogical history. The coalescent model paved the way for a wealth of analytical tools for understanding evolution
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and demography. The second revolution was computational; many new and powerful computational methods are now available using maximum likelihood, Bayesian analyses, and Markov-chain Monte Carlo techniques. Many of these techniques are now commonplace in population genetics. The third revolution was technological, in which rapid methodological advancements in molecular biology have made the genomics era possible. Its simplest consequence, even for nonmodel organisms, is the availability of huge amounts of genetic data (Thomson et al., 2010). Today, it is feasible—and affordable—to obtain nucleotide sequences of entire genomes or to genotype tens of thousands of single-nucleotide polymorphisms (SNPs) from large samples. In the near future, genome sequences of multiple individuals will be the data expected for many types of studies in population biology. The massive amount of genetic data opens up opportunities for addressing questions that were impossible to conceive of a short while ago. An example of this is a genome-wide association study (GWAS), which can be used to discover the genes underlying ecologically relevant traits, particularly for discovering genes under selection for adaptation to different environments, for example, genes for adaptation of a pathogen to different hosts. This type of study has received relatively little attention in plant pathology so far but has been a strong motivation behind studies in human population genetics, particularly for finding genes associated with medically important traits (e.g., Nelson et al., 2008). As costs for acquiring genetic data continue to decline and bioinformatic methods for processing massive amounts of data continue to improve, these types of studies will become more common in plant pathology. The most serious bottleneck will no longer be acquisition and analysis of genetic data but phenotyping of samples large enough to find meaningful associations.
Introduction to Evolutionary Processes Most major questions in population genetics are rooted in understanding the effects of evolutionary processes. What is meant by evolution? At its simplest, evolution refers to changes in allele or genotype frequencies in populations over relatively short timescales. When evolution occurs over longer timescales, it may result in the evolution of genetically isolated species. Regardless of the timescale and magnitude of changes, evolution occurs by the same five processes: natural selection, mutation, random genetic drift, migration, and recombination. Each of
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