The evolution of microorganisms, at its most basic, can be viewed as a consequence of mutation, genetic drift, and migration – especially migration in terms of the movement of genes between populations or organisms – plus of natural selection. All but natural selection may be described as mechanisms of non-Darwinian evolution, whereas natural selection we describe instead as Darwinian (Darwinian evolution will be addressed in the following chapter, "Natural Selection"). In addition, and associated especially with migration, we can consider various recombination mechanisms. Here I present overviews of these non-Darwinian phenomena, mutation, genetic drift, and migration, where appropriate providing a microbial context.

Note that in this and subsequent chapters I will distinguish background material from more microbial evolution-pertinent information, and will do this by employing a different font. Thus, anything that looks like this, "This font", is background while everything that looks like this, "This font", i.e., the font that most of this paragraph is written in, is material which should be considered to be pertinent, that is, potential exam material. By contrast, the immediately following paragraph is in "This font" font. This "non-essential" material can viewed as a hybrid between "boxes" or asides and regular text, with the prose intended to be read but nonetheless it is not essential to the course.

In this chapter, note that I view evolution as a change, over time, of the frequency of alleles within populations. That is, the genomes of organisms consist of a series of gene or genetic locations called loci (sing., locus). At these loci, nucleotide sequences may vary going from individual organism to individual organism within a population or species. If so, then two or more individuals can be said to possess different genetic alleles, that is, gene variants as found at specific genetic locations within genomes. The population at that locus, as a consequence, is said to be polymorphic and more generally can be described as possessing genetic variation. Over time, within a population, the frequency of a given allele may change as a consequence events that are either deterministic (non-chance) or stochastic (chance). These events are evolutionary processes while the products of these processes, from the perspective of a population geneticist – which is the perspective we are considering right now – are changes in allele frequencies. Populations that are in Hardy-Weinberg equilibrium experience display no change in allele frequencies over time and therefore are not evolving whereas populations that are not in Hardy-Weinberg equilibrium do experience changes in allele frequencies over time and therefore are evolving.


Table: Terms Associated with Non-Darwinian Evolution.

Allele frequency

Proportion of a specific genetic variant as found at a given locus within a population.
In haploid organisms, allele frequency and genotype frequency, as considered at a specific locus and both as across a population, are generally the same thing. This is because genotype is based on only a single copy of a gene per individual so therefore whatever allele an individual possesses is also its genotype (for that locus). Contrast with diploid organisms where genotype is a function of whatever alleles are found at two genes such that genotype for a given gene can be a function of two identical alleles (of various types) or instead two different alleles (also of various types). As a result of this distinction, the population genetics of haploid organisms becomes relatively uncomplicated and comparatively easy to grasp, as too and more specifically are issues of allele frequency. Yet another way of considering this point is that there is little concern with recessive-dominance relationships between alleles, or other within-locus genotype-phenotype complications, because in haploid organisms there will not be more than one copy of gene so therefore different alleles of the same gene cannot directly interact.
Antagonistic pleiotropy

Improvement in the utility of one aspect of phenotype in one context that results also in a decline in utility in a different context.
Differences in phenotype, especially the fitness impact of a single allele, can vary as a function of circumstances, often where benefits are provided under one or more circumstances and negative impacts (detriments) are seen under other circumstances. This is often seen in symbiotic organisms where improvement in the fitness of these organisms as they are associated with one host, e.g., as a consequence of mutation, results in decreases in the fitness of these same organisms when they are found in association instead with a different host. Particularly, in these instances, these are different hosts possessing different genotypes as a consequence different phenotypes/physiologies as well. In other words, colloquially, you can't get something for nothing and improvements in one area, including in terms of an organism's genotype/phenotype, typically will be associated with decreases in abilities in other areas. These conflicts when they are genetically based can be described as antagonistic pleiotropies.
Beneficial mutation

Change in the base sequence of a genome that has the effect of increasing the fitness of the so-affected organism.
That is, beneficial mutations results in increases in an organism's potential to survive and, especially, to replicate successfully. Contrast most obviously with detrimental/deleterious mutation, but contrast as well with neutral mutation. In addition, note that the consequence of a beneficial mutation often is a beneficial allele. That is, new alleles ultimately are products of mutations (though recombination can be important as well) and if a mutation provides a benefit in many cases that benefit, from a genetic perspective, is a consequence of the formation of a beneficial allele.
Compensatory mutation

Mutation that reduces the negative consequences of another mutation.
A mutation that reduces the negative fitness consequences of another mutation. If the compensatory mutation is found in a different gene, then this represents a form of epistasis. Compensatory mutations are a specific/special kind of beneficial mutations, specifically where the associated benefit is seen in some genetic backgrounds – ones where the allele being compensated for is present – but not others. Compensatory mutations can exist only following the acquisition/presence of detrimental mutation within an organism' genome.
Convergent evolution

Appearance of similar but not identical adaptations that are a response to similar selective pressures.
Here our interest particularly is on the appearance of similar if not identical nucleotide or amino acid changes in similar if not identical positions within genes or polypeptides, particularly given genes or polypeptides that are not identical nor nearly so to begin with. Thus, when two divergent but not necessarily highly divergent lineages are subject to the same selective pressures they may respond by fixing similar mutations. It is the resulting increasing similarity especially at the molecular level, as that is driven particularly by natural selection, that represents convergent evolution within the microbial evolution literature. In other words, if two similar but not too similar alleles within two separate, that is, not genetically interacting lineages are evolving over time such that they are becoming more similar – particularly though not exclusively in terms of their amino acid sequences – then that increasing similarity can be viewed as a convergence of genes and therefore as convergent evolution. Contrast divergent evolution.
Deleterious mutation

Change in the base sequence of a genome that has the effect of decreasing the fitness of the so-affected organism.
That is, deleterious mutations results in decreases in an organism's potential to survive and, especially, to replicate successfully. Contrast most obviously with beneficial mutation, but contrast as well with neutral mutation. In addition, note that the consequence of a deleterious mutation often is a deleterious allele. That is, new alleles ultimately are products of mutations (though recombination can be important as well) and if a mutation is deleterious in many cases that detriment, from a genetic perspective, is a consequence of the formation of a deleterious allele. Equivalent to detrimental mutation.
Divergent evolution

Descent with modification resulting in increasing dissimilarity between two or more species.
Divergent evolution is the accumulation of genotypic and phenotypic differences between lineages due to mutation, drift, selection, or migration. Divergent evolution is the typical, default expectation for the separate evolution of distinct populations and is what occurs, for example, following speciation events. A lack of divergence between lineages typically is a consequence of natural selection for the retention of similarities, due to horizontal gene transfer (that is, where divergence is lacking because of a temporal lack of opportunity for such divergence in certain regions of genomes), or, in extreme cases, is associated with convergent evolution.

Strength of natural selection relative to genetic drift as measured particularly in terms of fixed mutations in populations.
Ratios of nonsynonymous to synonymous substitutions often as observed in related but nonetheless distinctly evolving lineages. Higher ratios (e.g., dN > dS) are seen as an indication of the impact of positive selection whereas. Lower ratios (e.g., dN < dS) are seen as an indication of genetic drift. What is going on is that nonsynonymous substitutions (N) are more likely to represent changes in phenotype than synonymous substitutions (S) and the evolutionary fixation of changes in phenotypes is more likely as consequence of natural selection than genetic drift whereas the evolutionary fixation of changes in genotype that are not associated with changes in phenotype are generally a consequence of genetic drift rather than of natural selection.

Change in allele frequencies within populations as a function of time.
This is the population genetics definition of what otherwise can be a highly complex as well as ecologically based phenomenon. For means by which evolution occurs, consider the allele-frequency modifying violations of Hardy-Weinberg equilibrium assumptions (i.e., mutation, genetic drift, genetic migration, and natural selection).

Process by which an allele becomes the only allele found at a given locus within a gene pool.
Fixation is the loss of the polymorphism found at a specific locus, i.e., the extinction of all but one allele that previously had been found, within a population, at that locus. This equivalently is creation of an allele prevalence of one where previously allele frequency had been less than one. An allele thus can be said to have been fixed. Note that this definition generally is operational, i.e., an allele is considered to be fixed at the point where genetic variation at that locus can no longer be detected, though in principle it is always possible that genetic variation could still be detected given sampling of a greater number of individuals.
Fixed allele

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Sole genetic variant found at a specific locus within a population.
Fixed alleles are the products of fixation and as such the presence of a single allele within a population at a specific locus does not mean that this allele was always the only allele present nor that it can never be replaced. Indeed, in practice it is not even necessarily the only allele but rather the only allele that tends to be readily detected within a population, again as found at a specific locus. The likelihood of fixation of an allele is greater to the extent that an allele is beneficial and lesser to the extent that an allele is detrimental. Natural selection tends to drive the fixation of beneficial alleles whereas genetic drift drives, though much less efficiently, the fixation of detrimental/deleterious alleles.
General mutator

Organism that displays a substantially reduced replication fidelity in comparison to parental or otherwise equivalent strains.
Also described simply as mutators, general mutator strains can display mutation rates that are on the order of one-hundred to one-thousand times higher than those of parental or equivalent strains. Mutator strains form via mutations that affect proofreading, DNA repair, or other replication-fidelity enhancing functions. Organisms, particularly microorganisms, are able to mutate to general mutator status as well as mutate back again. The reversion mutation, that is, back to wild type in terms of replication fidelity, can occur with relatively high likelihood given the already high mutation rates associated with these strains. In principle, therefore, lineages can become more prone to generating, acquiring, and even fixing mutations and then switch back to becoming less prone, but without losing the previously accumulated mutations.
Genetic drift

Changes in allele frequencies that occur within populations due to sampling error.
Sampling error is a consequence of sampling less than an entire population where sampling represents movement of populations through time such as from one generation to the next. The smaller a sample then the larger the error expected and therefore the more powerful drift can act as an evolutionary force. Genetic drift is typically described simply as 'drift'. In sufficiently small populations drift can be as a strong a motivator of changes in allelic frequency as natural selection.

Low-level gene flow between species.
Also known as horizontal or lateral gene transfer, introgression is the low-level movement of alleles between populations. This can be as equivalent to genetic migration, though populations in terms of introgression explicitly can represent different species rather than different populations found within the same species.
Migration (genetic)

Movement of alleles into or out of populations.
Genetic migration is the movement of alleles from one population to another. This like genetic drift is also stochastic to the extent that such movement is limited, i.e., less than infinite. Without question, however, various alleles are more likely to move between different individuals under different circumstances than others. Note that genetic migration typically is described, in a Hardy-Weinberg sense, simply as migration. As occurs between species genetic migration can be described instead as introgression. As occurs through mechanisms other than meiosis-associated sex, migration can be described instead as horizontal- or lateral-gene transfer.
Muller's ratchet

Manifestation of genetic drift where, in small, non-sexual populations, there will be a tendency for the wild-type genotype to be lost.
Note though that Muller’s ratchet does not imply nor necessarily is even consistent with the loss of specific alleles from a population. Instead it is associated with the loss of specific alleles from specific individuals most notably such that the wild-type genotype within a population is lost, often irretrievably so.

Replicable change in genotype.
Mutations are heritable changes in nucleic acid sequence as well as the mechanism of creation of new alleles and therefore serve as the 'ultimate source of genetic variation' within populations. Defined broadly, mutations can include any change in nucleotide sequence including the consequences of especially molecular recombination. Such recombination as a driving force of change, however, typically is considered separately from mutation and particularly so to the extent that recombination occurs in associated with genetic migration. Thus, mutation might be viewed as an endogenously (solely within the same organism) change in nucleotide sequence and particularly where that change is relatively discrete, e.g., such as confined to individual genes.
Neutral mutation

Change in the base sequence of a genome that has little effect on fitness of the so-affected organism as compared with the parental sequence.
Neutral mutations do not impact the Darwinian fitness of their carriers, though do not necessarily do so also without impacting phenotype. In addition, the neutrality of mutations is not necessarily observed across all possible environments. Contrast with beneficial mutations as well as with detrimental/deleterious alleles. Note that neural mutations give rise to neutral alleles and that the fixation of neutral alleles generally is a consequence of stochastic processes such as genetic drift.
Nonsynonymous substitution

Mutational change in a codon that results in a change in the specified amino acid.
A nonsynonymous substitution is a missense mutation and particularly one that has become fixed within a population. Nonsynonymous substitutions are amino acid changes at specific locations within polypeptides. These contrast with missense mutations that do not result in amino acid changes (synonymous substitutions). Changes in polypeptide sequence are more likely to give rise to changes in organism phenotype than mutations that do not impact polypeptide sequence. Nonsynonymous substitutions therefore are more likely to become fixed within populations as a consequence of natural selection than are synonymous substitutions (since natural selection requires at a minimum genetically based phenotypic differences between related organisms).
Parallel evolution

Changes in phenotype or genotype that are similar or even identical within closely related but nonetheless independently evolving lineages.
Such changes can be seen in individual genes and can be taken as evidence for the occurrence of positive selection. That is, the chance of identical mutations becoming fixed within a population due to stochastic forces alone – stochastic mutation in combination with the ever stochastic genetic drift – is high unlikely, leaving stochastic mutation in combination with non-stochastic natural selection as a fairly likely explanation. An alternative non-stochastic, i.e., deterministic force, however, can also give rise to what can appear to be parallel evolution, and that is genetic migration. That is, two genes, or genetic segments, retain highly similar sequences as a consequence of horizontal gene transfer, though note that in this case what is violated is the important assumption of that two lineages are independently evolving. Products of horizontal gene transfer by definition are not evolving independently from the source organism.

One locus impacting a diversity of characters.
The characters can vary across an organism, across time within a single organism, or across environments such that an individual existing in one place may display a different trait in comparison to an individual living in a different location, despite possessing the same genotype (essentially a variation on the concept of phenotypic plasticity). Traditionally, however, the concept of pleiotropy is applied particularly to the first situation, that is, where one locus impacts multiple phenotypic characteristics of an organism. In the Aging literature can be found the second connotation, that of traits varying over time within an individual organism, particularly as the organism ages. Lastly, we will be considering especially the latter of these concepts – variation between environments – and as in the Aging literature we will be considering particularly a variation on the concept of pleiotropy, that of antagonistic pleiotropy.

Presence of more than one allele at a given locus within a gene pool.
That is, if you examine the nucleotide sequence at a particular spot in the genome of more than individual within a population, you will be able to observe more than one mutational difference. Indeed, in heterozygous, diploid individuals, you by definition will observe more than one allele at the heterozygous locus, thereby implying a polymorphism within a population without even requiring further examination of the population. Nonetheless, for a polymorphism "more than one" is typically taken to mean two or more alleles having absolute prevalences of somewhat greater than one, that is, where more than one allele found at a given locus is actually detectable within a population. Note that polymorphisms must exist for natural selection to differentiate among individuals within a population. That is, polymorphisms are an essential underlying component of Darwinian evolution, and not implicitly but instead explicitly so. That is, when one states that natural selection must have variation upon which to act, variation by definition is seen as polymorphisms.

Mixing together of the genetic material coming from different sources.
Recombination is the shuffling within individuals of pre-existing alleles or, more precisely, pre-existing nucleotide sequences. We can differentiate this recombination into a number of different types including what I like to describe as molecular recombination, i.e., crossing over such as one observes during meiosis, though site-specific recombination also can be described as molecular. Such recombination often is homologous, but also can be dependent on much less similarity between recombining genetic material than is typically thought to be required for homologous recombination (i.e., so-called illegitimate recombination). Alternatively, independent assortment, as during meiosis, or reassortment as one sees with certain viruses, also is a form of recombination. Particularly when the two difference sources of genetic material that are coming together ultimately are from two different individual organisms then we can described recombination as representing genetic recombination, again the shuffling of genetic material. Alternatively, genetic recombination as it occurs between distinctly different aspects of the same genome we can describe essentially as a form of mutation, e.g., multiple-nucleotide insertion mutations. Recombination also is a key component of horizontal gene transfer.

Mutation, recombination, and drift are stochastic, the first two on a per-individual basis. Infinite populations by contrast will experience on a per-population basis all possible mutations as well as recombination events. Natural selection, by contrast, is non-stochastic, also known as deterministic. Stochastic processes play key roles in evolution and particularly non-Darwinian evolution. Adaptations, however, ultimate are associated at least in part (often a large part) with non-stochastic evolution.

Overlapping of geographical ranges.
A prerequisite for gene exchange between organisms is sympatry. Sympatry, however, is not sufficient for the occurrence of such gene exchange and two purely clonal populations therefore can exist within the same environment and simply not exchange genes. It is possible for lineages to acquire genetic material from even clonal lineages, and this can occur particularly under circumstances where the DNA from these otherwise clonal organisms can gain access to a recipient organism's cytoplasm via various processes (e.g., conjugation, transformation, transduction). Purely clonal organisms thus can participate in sexual processes even if they themselves cannot serve as recipients of foreign DNA.
Synonymous substitution

Mutational change in a codon that does not result in a change in the specified amino acid.
A synonymous substitution is a point mutation that does not modify the sense of a codon, i.e., what amino acid is encoded. This is possible due to the redundancy of the genetic code, that is, the fact that many amino acids are specified by more than one codon. In addition, in many cases these more than one codons are interchangeable as a consequence of a single nucleotide change. The existence of synonymous substitutions means that mutations and therefore evolution can be more conservative than would otherwise be the case. In addition, the fixation of synonymous substitutions is generally viewed as being more likely to be a consequence of genetic drift (stochastic forces) rather than natural selection (deterministic forces). The latter is because it often is more difficult for natural selection to distinguish among alleles that specify otherwise identical polypeptide products than it is to distinguish among non-identical polypeptide products.

Phenotypic variation on a character.
A trait is a specific, often genetically variable variation on a character, such as 20 min versus 30 min generation times under otherwise constant environmental conditions (or in terms of eye color, blue eyes would be a trait). Note nonetheless that genetic differences between individuals are not necessarily associated with trait differences between individuals. On the other hand, the phenotypic variation specifying different traits can be subtle between individuals, i.e., difficult for us to detect though not necessarily impossible for natural selection to detect (in very small populations, alternative, even obvious trait differences that could give rise to differences in reproductive success may not be readily distinguished via natural selection due to the high levels of genetic drift that will tend to operate under those conditions.
Wild type

Form of an allele or genotype that is predominantly associated with organisms upon isolation from nature.
The concept of "Wild type" is not unambiguous, except to the extent that it represents that genotype that is present upon isolation of a microorganism. That is, "Wild type" alleles are not necessarily the highest fitness alleles that are either present within a population nor which are possible, though to the extent that the population from which an isolation took place is in fact dominated by more-fit alleles, then wild type likely represents an at least more fit genotype within the isolation environment, and probably most fit (at least assuming that it is the product of deterministic evolution, i.e., of natural selection rather than of genetic drift). If the population is clonal, though, then less-fit alleles nevertheless may still be associated even with wild-type organisms.