The concept of migration, from the perspective of microbial evolution, is unfortunately complicated. This complication stems from a combination of the standard meaning of migration, i.e., movement from one place to another, and migration as the term is used in conjunction with the Hardy-Weinberg theorem. According to the latter, migration is a mechanism that can affect allele frequencies. This clearly can occur as a consequence of movement of organisms from place to place, such as if population A which is located in place Y has members that migrate into population B, which is located in place Z. Migration as spatial movement, however, is less clear given otherwise distinct populations that are sympatric, that is, living in the same location, but where migration of alleles from population to population nonetheless can occur. In this section I elaborate on these latter considerations.


Part of the confusion indicated in the introductory paragraph to this section stems from Hardy-Weinberg equilibrium referring to intraspecific allele frequencies rather than interspecific frequencies. That is, for two distinct populations to exist sympatrically – that is, existing within the same space, meaning having overlapping ranges – it generally is helpful if not obligatory for those two populations to also represent different species. This is because species, especially within a Hardy-Weinberg context, are interbreeding populations of obligately sexual organisms. Consequently, the most reasonable scenario by which interbreeding may be avoided among obligately sexual species is via spatial separation. As a consequence, the allele migration postulated as violations of assumptions within the Hardy-Weinberg theorem is also a spatial migration.

Naturally, much changes when the organisms involved are not obligatorily sexual for their reproduction. Especially where sexual processes are also somewhat rare, then it is possible for two populations to exist sympatrically that also represent two different populations of the same species. For example, consider two clonal populations of the same bacterial species inhabiting the same environment, such as two strains of Escherichia coli inhabiting the same colon. In this case, there exist mechanisms by which bacterial DNA may be transported between the two populations, e.g., such as mediated by bacteriophage (transduction). This transferred DNA has the same impact on bacterial genetics as migration has on Hardy-Weinberg equilibrium, which is to say, either new alleles are introduced into a population or the frequency of existing alleles is modified by the addition of an allele to an already existing pool of the same allele. Spatial movement between populations, however, has not occurred but instead what has occurred instead is genetic movement within a single environment.


A term already exists that describes low-level genetic transfer between otherwise not interbreeding nor necessarily parapatric (i.e., sympatric) populations, and that is introgression. Specifically, introgression refers to the movement of alleles across a hybrid zone found at the interface of the ranges of otherwise distinct species, such as bird species or frog species. The DNA involved moves from one species into hybrid individuals formed between the two species and then into one of the other species that parented the hybrid. This latter mating is described as a backcross, i.e., hybrid mating with a member of one of its parent species. Hybrid formation is a rare event, occurring over a relatively small fraction of the total range of either species. Hybrids also may display low viability or fecundity, and backcrossing presumably is an even rarer event than hybrid formation itself. Thus, movement of alleles between the two populations occurs at only a low level, and in fact occurs despite opposing mechanisms that may serve as hybridization-preventing adaptations (i.e., during the process of speciation, it is the avoiding of hybridization that would is adaptive).

The word introgression is not (yet) widely employed to describe rare gene transfer events between microorganisms; see, however, (Cohan et al., 1991) (Campbell, 1994) (Lawrence and Ochman, 1997) (Brown et al., 2001) (Colegrave, 2002) (Johnson et al., 2004) . The terms horizontal gene transfer and lateral gene transfer are typically employed instead. The important thing to keep in mind, however, is that gene-transfer mechanisms can be viewed as counter to the conditions necessary to maintain Hardy-Weinberg equilibrium within affected populations. That is, they represent migration in the Hardy-Weinberg sense and, as a consequence, one of the four fundamental forces of evolution acting upon microorganisms. Indeed, as we will see, there may be no other mechanism more important to microbial evolution than genetic migration. Whether or not the newly introduced alleles prosper or even survive, however, will be a function, at least in part, of the impact of natural selection.

Clearly, despite the above arguments, migration for microorganisms also can be both spatial and genetic, and indeed spatial but not genetic. That is, two populations of the same species can exist in two (or more) different locations with movement of individuals occurring between locations. Again with E. coli, there exist both colonic and extracolonic populations with movement of individual bacteria between these various locations. Note that because these organisms are not obligately sexual, the spatial migration of an individual may or may not translate into introgression of its genes into the pre-existing population.


Darwin recognized three biogeographic patterns that he described in terms of "great facts" in On the Origin of Species. In summary, these are: (i) environmental conditions alone cannot account for the dissimilarity of flora and fauna among geographically distinct regions; (ii) barriers to dispersal significantly contribute to these differences; and (iii) although the spatial variability in community composition within regions is substantial, these communities remain evolutionarily related. … The prevailing view of Darwin and his contemporaries was that microorganisms are dispersed globally and able to proliferate in any habitat with suitable environmental conditions. On the Origin of Species proposes that "the lower any group of organisms is, the more widely it is apt to range," a notion that was crystallized by Lourens Baas-Becking in the 1930s by his widely referenced quote "everything is everywhere, but the environment selects." The small size and high abundance of microbes (as well as other aspects of their biology) were thought to increase the rate and geographic distance of dispersal to levels such that dispersal limitation is nonexistent… [though the authors goes on to suggest otherwise]. — Jessica Green (2012)

Population biology can also consider issues of organism location in environments or movement between environments, which of course can be greatly influenced by organism migration. Indeed, a great deal of microbial ecology is devoted to this task of determining organism location. Much closer to issues of microbial population biology is the study of biogeography, that is, exploration of what organisms are located where, and why. Such studies can include determinations of population variation across space as well as time or the determination of differences in community structure also as a function of location (and time). These studies are aided greatly by modern sequencing technologies. Migration in these instances can involve both the arrival of species into new locations along with changes in allele frequencies associated with existing populations. What moves where is greatly influenced by both organism and environment specifics.

From an evolutionary ecological perspective, the key question vis-à-vis biogeography is why organisms are located where they are. The answer to this question will have multiple components. First, can a given environment support a population? For example, can the population survive given the physical and chemical characteristics of the environment? Also, can the organism survive given the mix of other species that are also present, in terms of prey species, predator species, or competitor species? For individual alleles, or genotypes, one can add also the characteristics of the pre-existing conspecifics in that environment. We can also describe environments as sinks or sources where a source produces a net gain in individuals (of a given species) which may then migrate to other areas. By contrast, a sink is a location where a population experiences a net loss of individuals except for those gained via migration. It is possible, if source and sink environments are sufficiently close, for a sink environment to appear to hold sufficient population densities that it superficially resembles a source environment. Clarifying such distinctions is crucial to conservation biology, though conservation biology is not necessarily routinely applied to microorganisms. The same principles can be relevant to applied microbiology, where the presence of specific microorganisms in specific locations is desired, such as rhizobia presence along with characteristics in fields of cultivated legumes or the ingestion of acidophilus bacteria as a dietary supplement.

Many of the above points are relevant independent of issues of migration. What links biogeography, evolutionary ecology, and migration, therefore, are opportunities for migration, mechanisms of migration, and, of key importance, the appropriateness, from an adaptive perspective, for an organism to take advantage of migration opportunities. Thus, from the standpoint of either species or alleles, we can explore the degree to which different phenotypes can give rise to different likelihoods of movement or of migratory success. In this manner, migration, in fact, comes to represent another mechanism of natural selection. That is, there can exist biases in terms of migration that affect resulting allele frequencies, either in terms of loss of specific phenotypes (and thereby underlying alleles) or in terms of gain of specific phenotypes (ditto). Note that typically these phenotypic issues are missing from sequence-based studies. That is, there is a tendency in microbial biogeography studies to answer questions of what (is present) and how (organisms are distributed) but less emphasis, due particularly to the nature of the data obtained, on answering why questions: why an organism is located where it is, particularly from the perspective of the impact of phenotype on migration tendencies. These why questions, vis-à-vis migration will be covered, to a limited degree, in subsequent chapters under the more narrow headings of parasite transmission and progeny dissemination.