In this section I provide what essentially are essays that consider microbiologically relevant non-Darwinian evolution. So that this is not simply a rehash of previous chapters, I use this opportunity to look for further commonalities between concepts.

Mutation, General Mutators, and Mutational Meltdown

A mutation, broadly defined, is a change in nucleotide sequence. Such changes can come about via local changes, losses, or gains in nucleotides. Deletion mutations (losses) and insertion mutations (gains) can profoundly disrupt gene reading frames, resulting in what are known as frameshift mutations. Note that the five principle means by which mutations can occur include occasional base-incorporation errors, chemical modification of bases, local as well as more general reductions in base-incorporation fidelity, slippage of polymerases (resulting in small losses or gains in numbers of bases), and recombination. The latter, in particular, involves movement of multiple bases from one place to another, including from the genome of one organism to the genome of another. All of these changes have the effect of modifying genotype with some potential of modifying phenotype as well. Mutation is the ultimate source of genetic variation in organisms.

Some strains of microorganisms possess higher mutation rates than related strains and these lower-fidelity strains can be described as general mutators. The higher mutations rates often result from errors in base incorporation that are due to polymerase infidelities (i.e., polymerases that don't work as well in making sure that base incorporation occurs properly in the course of genome replication). Strains of microorganisms also exist that display higher rather than lower levels of replication fidelity. Indeed, it is possible to posit an ideal level of replication fidelity that balances the metabolic costs of higher fidelity replication, the requirements by organisms for genomic stability, and the needs by populations for genetic variation upon which natural selection can act. Generally the less stable an environment then the greater the utility of the higher mutation rates that one sees with general mutator strains.

The basic underlying mechanisms for the selection of these higher mutation rates is one of linkage between mutation-generating adaptations and the occasional beneficial mutation that might be generated. If higher rates of beneficial-mutation generation has utility, particularly if new beneficial mutations are greatly needed (such as in a new or fluctuating environment), then higher mutation rates may be selected for. It is important to keep in mind, however, that most of the mutations a general mutator strain experiences will not be beneficial but instead can (often) be detrimental to the carrying organism. As this point is mostly independent of mutation rates, it is actually true for any organism, though general mutator strains are more affected simply because they experience more mutations.

An extreme of detrimentality, when it comes to mutations, is seen in a process known as mutational meltdown, a.k.a., lethal mutagenesis or error catastrophe. The limits of how many mutations an organism can handle, per generation, is a consequence of most mutations being detrimental. Even below that limit, a mutation rate in the range of one per organism can lead to declines in fitness of populations that is a consequence simply of accumulating detrimental mutations at too rapid a rate. Even if mutations are to some degree beneficial, however, when two mutations occur per genome per round of replication then even if a beneficial mutation should occur it can be too likely paired with a detrimental mutation (i.e., as found in the same genome) to provide a net selective benefit to the holder. More generally, the accumulation of detrimental mutations with a population to the point that overall population viability is compromised is what mutational meltdown, etc., refers to. Such states can be created in organisms by inducing mutagenesis via the application of chemicals or radiation. It is important, however, to distinguish declines that are due to the detrimentality of mutations from physical damage to genomes that more directly blocks nucleic acid polymerization.

The following quote, in addition to pointing to potentially relevant references, speaks to issues of mutational meltdown and pathogen evolution in the face of antimicrobial treatment.

Interference among mutations can also play a relevant role in the extinction of viruses through lethal mutagenesis, a new antiviral strategy that derives from theoretical considerations and that consists in the treatment of virus infections through the artificial increase of the virus error rate . Our results show that virus replication under mutagenic conditions can lead to the simultaneous presence in the mutant spectrum of multiple mutations conferring different advantages in the presence of the mutagen. The fixation of these mutations in particular individuals upon transmission of the virus through population bottlenecks… can lead to the co-circulation of viruses differing in their adaptive properties, jeopardizing in this way the efficacy of further treatments. — Cabanillas et al. (2013)

Substitutions, Polymorphisms, Fixation, and Clonal Interference

A mutation that involves a change to a different nucleotide can be described as a substitution. There are only three substitutions that are possible for a single nucleotide, one transition (i.e., to the other purine or other pyrimidine) and two transversions (from pyrimidine to purine or vice versa). At the level of codons, substitutions can be synonymous or non-synonymous. A synonymous substitution results in no change in the sequence of amino acids making up a protein, and potentially no change in an organism's (or cell's) phenotype. That is, one codon synonym, in this case, is swapped for another, keeping in mind that multiple codons can encode for the same amino acid, a phenomenon described as the degeneracy of the genetic code. One source of selectively neutral mutations is this degeneracy and associated synonymous substitutions. Again, it is important to keep in mind that not all synonymous substitutions are selectively neutral, though as a rule of thumb often they are considered to be. Furthermore, keep in mind the dual meaning of "substitution", which in this paragraph is being used as equivalent to mutation whereas elsewhere refers instead to mutations that have become fixed within populations.

A polymorphism is the presence of non-trivial amounts of genotypic variation within a population as found at a single locus. Mutations or migration is what gives rise to this variation. At first novel variation is found within populations at low frequencies, e.g., as low as one incidence of an allele per population. Consequently, newly arising variation tends to be highly prone to extinction as a consequence of genetic drift and otherwise is not considered to contribute to a polymorphism. If, however, these mutations both survive and increase somewhat in frequency within a population then they can be described as contributing to a polymorphism. The basic progression for new genetic variation within populations thus is either extinction or contribution to a polymorphism. It is more likely that a selectively beneficial allele will avoid extinction though drift can allow for the retention within populations, at least over shorter time spans, of selectively detrimental alleles as well as the extinction of beneficial ones.

An allele that contributes to a polymorphism has three possible fates: subsequent extinction, continued contribution to a polymorphism, or fixation. Fixation is associated with extinction, more or less, of all of the other alleles associated with a specific locus. Especially highly beneficial new alleles thus progress from initial presence to their contribution to a polymorphism to their extinction. That is only a deterministic progression, however, and stochasticity or indeed competition with other alleles can impact any of those steps.

Note that a genetic locus in which alleles are not fixed, one that remains stable in this state over relatively long periods, can be described as experiencing a balanced polymorphism. Contributors to balanced polymorphisms include a process known as clonal interference as well as what can be described as stabilizing frequency dependent selection. These are a failure of one allele to outcompete another allele (or more alleles) due to similarities in overall genotype fitnesses or, instead, actual declines in allele fitness at higher versus lower frequencies, respectively. Both have the effect of interfering with the ability of one allele to out compete another such that allele fixation becomes deterministically unlikely.

To reiterate, clonal interference is what occurs, particularly within clonal populations, when selectively beneficial alleles cannot rise to fixation because they are found within genotypes that are not sufficiently beneficial to outcompete other genotypes found within the same population. The reason that clonality is important stems from linkage disequilibrium, which is to say that without sex then alleles tend to be highly linked to whatever other alleles are found in the same genome that they are in. Thus, it is the fitness of entire genotypes that is hugely important given competition within clonal populations, or communities of clones, more so than the fitness of individual alleles which, by contrast, are the typical emphasis of animal or plant population genetics.

Pleiotropy, Phenotypic Plasticity, and Specialization

A pleiotropy represents multiple phenotypes associated with a single locus. These can be different aspects of phenotype within a single individual at a single point in time or instead different phenotypic manifestations over time or across different environments. As such, there is some overlap between the idea of pleiotropy and that of phenotypic plasticity, which is variation of phenotype across environments. The basic difference between the two ideas is that pleiotropies, by definition, are a function of a single locus whereas phenotypic plasticities can involve multiple loci. At least in terms of temporal or environmental pleiotropic variation, it is possible to thus view pleiotropies as single-locus phenotypic plasticity.

In microbial population biology pleiotropies are often ascertained solely in terms of fitness effects. Thus, a phenotype expressed at one time and/or in one environment may supply fitness benefits whereas the same allele might give rise to fitness costs in a different time or place. These ideas are codified in terms of what is known as antagonistic pleiotropies, a concept that also can be seen as a kind of specialization where improvement in fitness under one set of circumstances is associated with declines in fitness under other circumstances. Obviously, though, these fitness differences have mechanistic underpinnings which, in principle, may be more thoroughly characterized such as molecularly. In practice from a microbial evolution perspective they often aren't so characterized, however, but instead it is the relative reproductive capacity of different genotypes under different circumstances that is the principle means by which antagonistic pleiotropies are identified.

Epistasis and Compensatory Mutations

In addition to one locus or even one allele having multiple phenotypic effects, it is also possible for individual loci to impact other loci found within the same genome. This idea is a relatively basic genetic principle known as epistasis. A simple means of visualizing epistasis is that adaptations often involve the contribution of more than one gene, so can be altered by the action of more than one gene, or altered in different ways or phenotypic "directions" by different genes. Furthermore, gene products such as proteins often interact. As a consequence, changes in one locus often can affect phenotypes that are associated with other loci.

Like pleiotropy, epistasis is a description of phenotypic characteristics rather than strictly genotypic ones. As such, it is possible to view epistasis purely from the perspective of the impact of these interactions between genetic loci on organism fitness. For reasons of ease of experiential characterization, often such epistatic interactions are observed as what are known as compensatory mutations. Here an original or primary mutation provides some detrimental impact on organism fitness. The secondary or compensatory mutation reduces the fitness decline associated with the primary mutation, which is to say that an organism that possesses both the primary mutation and the compensatory mutation will display a higher fitness than those that display the primary mutation alone.

Note that it is possible for compensatory mutations to build upon one another, incrementally returning fitness towards the pre-primary mutation level. Note also that compensating mutations may not compensate under all circumstances or all conditions. Indeed, they may provide no selective benefit or even selective costs in the absence of the primary mutation. As such, compensatory mutations can be viewed as another form of specialization, which here is to internal idiosyncrasies of an organism rather than to external ones. Note, again as with pleiotropies, that it is certainly possible to characterize epistatic interactions molecularly. Such molecular characterization, however, are not something that is necessarily attempted within the context of evolutionary investigations.

Drift and Muller's Ratchet

Genetic drift, as a stochastic evolutionary processes, basically consists of sampling error in combination with blind luck, with the latter particularly as within the context of environmental catastrophe (big, medium, or small). Thus, even beneficial alleles or genotypes can be driven to extinction by pure chance. That chance is more likely, however, given smaller versus larger population sizes as well as smaller versus larger population ranges.

One consequence of genetic drift is a process known as Muller's ratchet. What happens with Muller's ratchet is slightly different from the idea of allele extinction due to stochastic processes. Indeed, Muller's ratchet by definition does not so much involve allele extinction as instead genotype extinction. As with considerations of clonal interference, Muller's ratchet is a phenomenon particularly of clonal populations, though is based on drift rather than natural selection. What happens is the chance extinction of more-fit genotypes.

Typically, more- or most-fit of genotypes are those associated with "wild type". Random mutation can occur that produces detrimental alleles. If different genotypes come to exist, each of which possesses a detrimental mutation in a different allele, then it is possible for the wild-type genotype to be lost due to genetic drift while all of the wild-type alleles are nonetheless retained within the population, just not all in a single individual. Without sex, that original, wild-type genotype cannot be restored except through very rare reversion mutations that convert mutated alleles back to wild-type alleles.

Keep in mind the distinction between loss of wild-type genotypes from populations versus loss of wild-type alleles. If all of a population's wild-type alleles remain, but not the wild-type genotype, then Muller's ratchet may be operating. Alternatively, if wild-type alleles have been lost in addition to the wild-type genotype, then this is simply the typical consequence of genetic drift, i.e., something that could operate in sexual as well as asexual populations.

Horizontal Gene Transfer and Introgression

Sex is the movement of genetic material from one individual to another. In eukaryotes, this movement is usually reciprocal, meaning that two parental cells contribute more or less equally to the formation of a new cell, the product of fertilization (such as between a sperm and an egg). Note that the formation of the sperm and egg, or at least their haploid progenitors, involves meiosis, the reduction division from the diploid to the haploid state. These various ideas are applicable to some microorganisms but not to most. That is, neither bacteria nor viruses nor asexual eukaryotes display either meiosis or fertilization. These organisms nonetheless can still participate in sexual processes.

Eukaryote sex can be abstracted to two basic components. One is the sequestration of whatever genetic material is going to be transferred from one individual to another (meiosis or gamete production) and the other is reception of that genetic material by the other individual (fertilization). In non-meiotic sexual processes it is typical for the to-be-transferred genetic material to consist of much less than an entire genome, and indeed meiosis itself involves the generation of to-be-transferred genetic material that consists of only about one-half of the original genetic complement. In non-meiotic sexual processes, furthermore, the genetic material is typically received by an individual that is fully genetically intact. This latter detail substantially differs from that of fertilization and indeed the very idea of having a "donor" and a "recipient" of genetic material (which are fragmented and fully genetically intact, respectively) differs from meiotic sex where instead there are both two not fully intact donors (e.g., sperm and egg) and two not fully intact recipients (again, e.g., sperm and egg). Sex between intact viruses, contrasting further, typically is between two fully intact genomes. The sex you see particularly in bacteria, by contrast, is a very unequal undertaking and typically only relatively small pieces of DNA are received by the recipient bacterium.

Bacterial sex also varies from especially eukaryotic sexual processes in its rarity. The result – as a consequence of movement of genetic material among bacteria, or between bacteria and other types of organisms – is similar to the movement of genetic material that can go on between distinct species within the eukaryotic world. This movement is often described as a horizontal gene transfer or lateral gene transfer, contrasting the vertical transfer of mother-to-daughter inheritance and even the within-species mixing of genetic material one sees with fertilization. One can also consider bacterial sex and associated horizontal gene transfer as equivalent to the macroorganism concept of introgression, where movement between species can happen, such through ordinary matings, but is rare in occurrence.

Macroorganisms are also subject to horizontal gene transfer events that do not involve fertilization, e.g., such as movement between individuals of genetic material associated with viruses. Note that the Hardy-Weinberg concept of migration also can be co-opted to describe the movement of genetic material into a population, even if this movement is occurring between distinctly different species. Thus, sexual processes among bacteria, though different in some ways from those that occur among eukaryotes are, at the same time, not altogether different from eukaryotic gene transfer mechanisms.