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The Scope and Basic Premises of Population Genetics

Population genetics is concerned with the origin, amount, and distribution of genetic variation present in populations of organisms and the fate of this variation through space and time. The kinds of populations that will be the primary focus of this book are populations of sexually reproducing diploid organisms, and the fate of genetic variation in such populations will be examined at or below the species level. Variation in genes through space and time constitutes the fundamental basis of evolutionary change; indeed, in its most basic sense, evolution is the genetic transformation of reproducing populations over space and time. Population genetics is, therefore, at the very heart of evolutionary biology and can be thought of as the science of the mechanisms responsible for microevolution, evolution within species. Many of these mechanisms have a great impact on the origin of new species and on evolution above the species level (macroevolution). A few of the impacts of population genetics upon species and speciation will be discussed, but this is not the main focus of this book.

Basic Premises of Population Genetics

Microevolutionary mechanisms work upon genetic variability, so it is not surprising that the fundamental premises that underlie population genetic theory and practice all deal with various properties of DNA, the molecule that encodes genetic information in most organisms. (A few organisms use RNA as their genetic material, and the same properties apply to RNA in those cases.) Indeed, the theory of microevolutionary change stems from just three premises:

• DNA can replicate
• DNA can mutate and recombine
• Phenotypes emerge from the interaction of DNA and environment

The implications of each of these premises will now be examined.

DNA Can Replicate

Because DNA can replicate, a particular kind of gene (specific set of nucleotides) can be passed on from one generation to the next and can also come to exist as multiple copies in different individuals. Genes, therefore, have an existence in time and space that transcends the individuals that temporarily bear them. The biological existence of genes over space and time is the physical basis of evolution.

The physical manifestation of a gene's continuity over time and through space is a reproducing population of individuals. Individuals have no continuity over space or time; individuals are unique events that live and then die and cannot evolve. But the genes that an individual bears are potentially immortal through DNA replication. For this potential to be realized, the individuals must reproduce. Therefore, to observe evolution, it is essential to study a population of reproducing individuals. A reproducing population does have continuity over time as one generation of individuals is replaced by the next. A reproducing population generally consists of many individuals, and these individuals collectively have a distribution over space. Hence, a reproducing population has continuity over time and space and constitutes the physical reality of a genes' continuity over time and space. Evolution is therefore possible only at the level of a reproducing population and not at the level of the individuals contained within the population.

The focus of population genetics must be upon reproducing populations to study microevolution. However, the exact meaning of what is meant by a population is not fixed, but rather can vary depending upon the questions being addressed. The population could be a local breeding group of individuals found in close geographic proximity, or it could be a collection of local breeding groups distributed over a landscape such that most individuals only have contact with other members of their local group but that, on occasion, there is some reproductive interchange among local groups. Alternatively, a population could be a group of individuals continuously distributed over a broad geographical area such that individuals at the extremes of the range are unlikely to ever come into contact. Sometimes, the population includes the entire species. Within this hierarchy of populations found within species, much of population genetics focuses upon the local population or deme, a collection of interbreeding individuals of the same species that live in sufficient proximity that they share a system of mating. Systems of mating will be discussed in more detail in subsequent chapters, but, for now, the system of mating refers to the rules by which individuals pair for sexual reproduction. The individuals within a deme share a common system of mating. Because a deme is a breeding population, individuals are continually turning over as births and deaths occur, but the local population is a dynamic entity that can persist through time far longer than the individuals that temporarily comprise it. The local population, therefore, has the attributes that allow the physical manifestation of the genetic continuity over space and time that follows from the premise that DNA can replicate.

Because our primary interest is on genetic continuity, we will make a useful abstraction from the deme. Associated with every population of individuals is a corresponding population of genes called the gene pool, the set of genes collectively shared by the individuals of the population. An alternative, and often more useful, way of defining the gene pool is that the gene pool is the population of potential gametes produced by all the individuals of the population. Gametes are the bridges between the generations, so defining a gene pool as a population of potential gametes emphasizes the genetic continuity over time that provides the physical basis for evolution. For empirical studies, the first definition is primarily used; for theory, the second definition is preferred.

The gene pool associated with a population is described by measuring the numbers and frequencies of the various types of genes or gene combinations in the pool. Evolution is defined as a change through time of the frequencies of various types of genes or gene combinations in the gene pool. This definition is not intended to be an all-encompassing definition of evolution. Rather, it is a narrow and focused definition of evolution that is useful in much of population genetics precisely because of its narrowness. This will therefore be our primary definition of evolution in this book.

Since only a local population at the minimum can have a gene pool, only populations can evolve under this definition of evolution, not individuals. Therefore, evolution is an emergent property of reproducing populations of individuals that is not manifested in the individuals themselves. However, there can be higher order assemblages of local populations that can evolve. In many cases, we will consider collections of several local populations that are interconnected by dispersal and reproduction, up to and including the entire species. However, an entire species in some cases could be just a single deme or it could be a collection of many demes with limited reproductive interchange. A species is therefore not a convenient unit of study in population genetics because species status itself does not define the reproductive status that is so critical in population genetic theory. We will always need to specify the type and level of reproducing population that is relevant for the questions being addressed.

DNA Can Mutate and Recombine

Evolution requires change, and change can only occur when alternatives exist. If DNA replication were always 100% accurate, there would be no evolution. A necessary prerequisite for evolution is genetic diversity. The ultimate source of this genetic diversity is mutation. There are many forms of mutation, such as single nucleotide substitutions, insertions, deletions, transpositions, and duplications. For now, our only concern is that these mutational processes create diversity in the population of genes present in a gene pool. Because of mutation, alternative copies of the same homologous region of DNA in a gene pool will show different states.

Mutation occurs at the molecular level. Although many environmental agents can influence the rate and type of mutation, one of the central tenets of Darwinian evolution is that mutations are random with respect to the needs of the organism in coping with its environment. There have been many experiments addressing this tenet, but one of the more elegant and convincing is replica plating, first used by Joshua and Esther Lederberg (1952) (Figure 1.1). Replica plating and other experiments provide empirical proof that mutation, occurring on DNA at the molecular level, is not being directed to produce a particular phenotypic consequence at the level of an individual interacting with its environment. Therefore, we will regard mutations as being random with respect to the organism's needs in coping with its environment (although, as we will see soon, mutation is highly nonrandom in other respects at the molecular level).

Mutation creates allelic diversity. Alleles are alternative forms of a gene. In some cases, genetic surveys focus on a region of DNA that may not be a gene in a classical sense; it may be a DNA region much larger or smaller than a gene, or a noncoding region. We will use the term haplotype to refer to an alternative form (specific nucleotide sequence) among the homologous copies of a defined DNA region, whether a gene or not. The allelic...