Microbial population biology considers the processes of selection, drift, mutation, and migration (as well as recombination) on alleles, genes, and genomes of microorganisms plus their parasites. This is as experienced on ecologically as well as evolutionarily relevant timescales. It exists as a discipline at the interface of (1) microbial ecology, which also studies more complex community-level interactions between microbes; (2) ecology and evolutionary biology, which consider a greater range of organisms and questions than those that are relevant to microbes; (3) epidemiology, which among other things is the study of medically relevant microbes; (4) molecular microbiology, which is much more mechanistic in focus; and (5) molecular evolution along with genomics, which both have more molecular emphases as well.
Microbial population biology encompasses questions of relevance not only to microbes. Microbial population biology also includes the testing of general principles of ecology and evolutionary biology, that is, by using microorganisms as models. The use of microbes as models of the behavior of other organisms, however, is not the emphasis of this text. Indeed, the text is intentionally more microorganism driven rather than so-called "question" driven, which here would be the use of microorganisms more for reasons of convenience than for the sake of understanding model microorganisms themselves as organisms. This is not to say that question-driven research cannot be informative of basic principles of microorganism functioning, since certainly it can. The goal here nevertheless is to understand microorganisms specifically rather than to exploit microorganisms as models for understanding the world beyond microbes. The exception to this latter point, however, is where the larger world is microbial in its functioning, that is, use of microbes to understand microbial processes which, in fact, are somewhat microbiological in their nature.
In this chapter I provide in particular an introduction to the disciplines of evolutionary biology, ecology, and, to a more limited extent, evolutionary ecology.
These topics I consider in greater detail below. First, though, are various terms and their definitions as useful to your understanding of the material presented in this chapter.
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Table: Important Terms and Concepts from Genetics and Evolutionary Biology.
Click Here for Online Practice Quiz Covering the Following Terms | |
| Term | Definition/Discussion |
| Adaptation | Morphological, physiological, biochemical, or behavioral aspects of organisms that contribute to their evolutionary fitness. |
| A change in organism phenotype that has the effect of increasing the fitness of possessing organisms. | |
| Allele | Variety of a gene, particularly as found at a single locus. |
| Variation on a gene. | |
| Artificial selection | Biased reproductive success as mediated by humans especially on non-human populations. |
| The consequence especially of breeding programs imposed by man on captive organisms, though can include inadvertent selection for certain traits such as greater fecundity in domesticated organisms. | |
| Balancing selection | Biases in reproductive success that serve to maintain polymorphisms within populations. |
| Selection that leads to the retention of multiple forms (i.e., alleles) within populations; results in polymorphisms. | |
| Bottleneck (genetic) | Reductions in populations to very few breeding individuals, potentially resulting in genetic drift. |
| A kind of genetic drift stemming from passage of populations through time in only small numbers, often for multiple generations. | |
| Darwinian fitness | The number of progeny produced by an organism, especially which survive to produce progeny of their own. |
| Discussion | |
| Determinism | What will happen in the absence of chance events. |
| Deterministic evolution is usually equated with that associated with natural selection. | |
| Directional selection | Motivation within populations towards the fixation of new adaptations. |
| Directional selection can also be described as positive selection. | |
| Disruptive selection | Biased reproductive success of more than one distinct genotype rather than of otherwise random mixtures of alleles. |
| Selection for extreme phenotypes within populations, especially selection against the mean. A form of balancing selection. | |
| Drift | Short for genetic drift. |
| Discussion | |
| Evolution | Change in allele frequencies within populations as a function of time. |
| Note that this is the population genetics definition of evolution. | |
| Fitness | Measure of the success of organisms in light of natural selection, typically determined in terms of reproductive success. |
| The strength of selection particularly as measured on a per allele or per genotype basis. | |
| Founder effect | Single round of bottlenecking that occurs when a new population is established, especially a relatively small population that has been derived from a relatively large population. |
| A kind of genetic drift stemming from passage of sub-population through single round of lower numbers, typically occurring as this sub-population founds a new population. | |
| Frequency-dependent selection | Difference in fitness of alleles or genotypes as a function of their prevalence within populations. |
| Situation in which the intensity of positive selection acting on an allele is a function of the frequency of that allele where positive selection can be stronger at lower frequencies (stabilizing frequency-dependent selection) or instead can be stronger given higher allele frequencies (disruptive frequency-dependent selection). | |
| Genetic drift | Changes in allele frequencies that occur within populations due to sampling error. |
| Unbiased, i.e., random changes in allele frequency other than as mediated by mutation or migration. Also can be described as sampling error. | |
| Genetic recombination | Mixing together of the genetic material coming from different sources and employing mechanisms particularly as seen during meiosis. |
| The endpoint of sexual processes. | |
| Genotype | An organism's hereditary information. |
| The sequence of nucleotides as associated with genes and other unidimensional structures encoded by DNA or, in certain viruses, RNA. | |
| Horizontal gene transfer | Movement of alleles between individual organisms but other than from parent to offspring. |
| Movement of alleles between individuals other than vertically and, as typically used, spanning larger phylogenetic distances. Contrast with vertical gene transfer/vertidal inheritance. | |
| Introgression | Low-level gene flow between species. |
| Movement of alleles between distinct species as mediated by sexual processes. | |
| Lateral gene transfer | Equivalent to horizontal gene transfer. |
| Discussion | |
| Lineage | Sequence of ancestors and descendants. |
| A lineage consists of all of the species spanning from a given species back in time to one or more ancestor species. | |
| Locus | Specific, physical location on a chromosome that a gene is found. |
| Location of a gene on a chromosome (or plasmid). | |
| Macroevolution | Divergence in the properties of two or more species following separation of their gene pools and in the course of speciation and extinction events. |
| Evolution as it occurs above the level of species, that is, in which lineages diverge plus display differing levels of success as measured in terms of lineage persistence or number of new species generated. | |
| Microevolution | Changes in allele frequencies as they occur within populations or species versus evolution as it occurs above the level of the species. |
| Evolution as it occurs within species, or between species as a consequence of introgression, as mediated by selection, drift, migration, and mutation (as well as genetic recombination and non-random mating). | |
| Migration | Movement of alleles into or out of populations. |
| Movement of alleles from one population to another, typically implying some kind of sexual process whereby alleles from more than one individual become present in one or more single individuals. | |
| Mutation | Replicable change in genotype. |
| Heritable change in nucleotide sequence making up genotype. | |
| Natural selection | Biased declines in the frequency of alleles within populations. |
| Selection as mediated by mechanisms other than those imposed directly by man. | |
| Polymorphism | Presence of more than one allele at a given locus within a gene pool. |
| The existence of multiple alleles per locus per population. | |
| Positive selection | Used here mostly equivalently to that of directional selection. |
| Selection during which a specific allele increases in frequency. In microbiology positive selection schemes result replication of the trait of interest, e.g.. such as to produce colonies. In evolutionary biology positive selection is that which gives rise to adaptation. | |
| Proximate causation | How things happen rather than why they do. |
| This generally is the anatomical or physiological explanation for how adaptations function. | |
| Selection | Biased choosing, biased survival, or biased propagation. |
| Generally within evolutionary biology used as shorthand for natural selection. | |
| Sex | Movement of genetic material from the cytoplasm, nucleus, or virion of one individual to that of another, where stable incorporation of that genetic material in the recipient can be viewed as a successful endpoint. |
| Any process that results in combining the genotype of two different organisms into one or more individual organisms. | |
| Speciation | Partitioning of one gene pool into two. |
| Process by which one species gives rise to a new species, with the concept of species defined variously. | |
| Stabilizing selection | Purging of detrimental alleles especially from well-adapted populations. |
| This is selection that leads to retention particularly of already frequent forms within populations. | |
| Stochastic | Random. |
| Stochastic processes in evolutionary biology include genetic drift, most mutations, and to a degree who migrates as well. | |
| Ultimate causation | The reason why things happen rather than how. |
| This generally is the evolutionary or evolutionary ecological explanation for especially adaptations. | |
| Vertical gene transfer (or Vertical inheritance) | Movement of genetic material from parent to offspring. |
| Vertical movement of genes is the predominant means by which genes move from one individual to another. Contrast, though, with horizontal gene transfer. | |