Evolutionary biology can be distinguished by various fundamental dichotomies. One is between micro- and macroevolutionary processes, with speciation forming the dividing line between the two. A second dichotomy is the study of the evolutionary relationships between individuals versus the evolution of adaptations. Note that to a degree one can align issues of microevolution with the evolution of adaptation while macroevolution coincides instead with issues of evolutionary relatedness particularly over substantial phylogenetic distances. These associations are not perfect, however, since microevolution involves more than adaptation – that is, in addition to natural selection, there are the evolutionary forces of mutation, genetic drift, and migration, which also are important – whereas evolutionary relatedness can be viewed within as well as between species (microevolution versus macroevolution, respectively). To a degree, we can also distinguish evolutionary biology into more phenotypic aspects (e.g., adaptations) versus more genotypic aspects (e.g., organismal relatedness). In this section I introduce microevolutionary processes. In a subsequent section of this chapter I introduce evolutionary ecology, the study of organismal adaptation.

I leave for later chapters an introduction to phylogenetics, which is the study of evolutionary relationships. I also leave until later discussion of species and speciation. Each of these latter concepts are relevant to the study of macroevolution.

A standard way of introducing microevolution is in terms of what is known as Hardy-Weinberg equilibrium. In short, evolution represents those processes that result in populations violating Hardy-Weinberg equilibrium. Many students will panic when the names Hardy and Weinberg are brought up, and this is because Hardy-Weinberg equilibrium is very much complicated by sexual processes, i.e., both mating and the meiosis that generates the haploid gametes, or, at least, haploid gamete progenitors. Since a majority of microorganisms are neither obligately sexual nor diploid, however, we can mercifully set aside, at least initially, both mating and diploidy when considering microbial evolutionary biology. Microorganism haploidy and relative asexuality in fact is an advantage of the study of microbial evolution in comparison with the "macrobial" evolution of diploid, obligately sexual organisms (e.g., us). Thus, with microorganisms the key evolutionary processes, at least to a first approximation, are mutation, sampling error (a.k.a., genetic drift), selection (i.e., natural selection), and migration. Those are all processes that serve to violate the conditions necessary for the establishment of Hardy-Weinberg equilibrium.

By way of summarizing, make sure that you understand that mutation and migration put genetic variation into populations whereas selection and drift remove that variation from populations. More specifically, mutation is the ultimate source of genetic variation whereas migration can supply additional genetic variation to populations. This latter genetic variation, prior to migration, was present in other populations plus is found in these others populations as a consequence of a combination of mutation and migration. Drift impacts the existence of variation in a non-biased as well as random, i.e., stochastic manner, but has a greater impact on smaller rather than larger populations.

Selection, by contrast, impacts the existence of variation in a biased and non-random, i.e., deterministic manner, and impacts populations of any size, but can be lost in the noise of genetic drift given lower population sizes. Selection, in addition, over the longer term acts on allele frequencies rather than directly on genotype frequencies, though in more clonal organisms it can be difficult to differentiate allele from genotype frequencies. Furthermore, selection acts on allele frequencies through the filter of phenotype, whereas phenotype is not necessarily straightforwardly derived from genotype. Since the derivation of phenotype from genotype is simpler in haploid organisms, it is especially the haploid, not obligately sexual microorganisms, such as bacteria and viruses, for which evolutionary biology is most readily accessible (and particularly so since these organisms also are so readily sequenced due to their small genome sizes). Finally, though adaptation is the product of selection, whether or not an adaptation is indeed adaptive is dependent on the current conditions within the environment in which selection is operating. Therefore, adaptations are always tentative in terms of their potential to positively impact organism survival and reproduction over long time periods.

Complicating things, migration, among microorganisms, actually can take the place of many considerations of mating as seen among obligately sexual organisms. As I will get to subsequently, migration among many microorganism can occur via a process that is perhaps best described as introgression, though which is commonly referred to as horizontal or lateral gene flow or transfer. Alternatively, migration can occur between more closely related individuals. Within the context of this gene exchange, regardless of which descriptor is employed, what occurs is genetic recombination between genetic information sourced from different individuals. The result is a surprisingly dynamic and ongoing sexual process among microorganisms such as bacteria that seems to drive a substantial portion of their evolution, and which is highly accessible particularly given modern molecular approaches to organismal characterization, especially genome sequencing.