If, as it seems, the optimal state is phenotypic stability with a potential for modification, it is necessary to distinguish between variation and variability. Variation can be directly observed in nature as the occurrence of polymorphism, heterozygosity, and number of alleles in a population or as measures of the range in quantitative traits. Variability stands for an intrinsic capacity to change in response to environmental and genetic influences and is not so easily estimated. … In the long term, perspective of evolution, variability becomes evolvability, i.e. the ability of a population to produce adaptive variants without compromising past achievements and to prepare the population for disparity in the conditions that it has to cope with. Contrary to phenotypic plasticity, where the individual can meet fluctuating conditions within its lifetime, evolvability is assumed to meet longer periodicities of change, thus building up gene complexes that enable the organism to respond to novel situations, which may, but not necessarily must, alter its genetic constitution. … Evolvability, in this respect, may be seen as a flattening of the peaks and valleys which facilitates movements in the landscape and adaptation to a changing environment. — Marianne Rasmuson (2002) (p. 1)

Natural selection, which gives rise to what is known as Darwinian evolution, is a biased modification of allele frequency within populations. More specifically, natural selection is a large collection of factors, many of which are environmentally motivated, that can affect the survival as well as reproduction of organisms and which can have different effects on organisms displaying different phenotypes. To the extent that phenotypes are products of genotypes, then natural selection has a differential impact on the reproductive output of different genotypes. Usually, though, it is helpful to think of natural selection as acting on individual alleles along with individual loci. Another helpful means of conceptualizing natural selection is that mutation (as well as migration) places variation into a population (that is, different alleles) whereas natural selection is a deterministic mechanism that establishes which of those alleles will survive, will contribute to a polymorphisms, will become fixed, or will go extinct.


Table: Terms Relevant to Natural Selection, Including as among Microorganisms.

Absolute fitness

Number of successful offspring produced by a given entity, with entities often differentiation in terms of their genotypes.
Absolute fitness is the absolute reproductive output of an organism. More meaningful evolutionarily, however, is the absolute reproductive output of an organism per unit time, which takes into account not just number of offspring produced per individual but also how long it takes them to produce those offspring, i.e., fecundity and generation time, respectively. Those organisms that produce more offspring, whose offspring themselves are successful at reproducing, and which also produce those offspring sooner or faster will display a higher absolute fitness than those who don't, but also will display a higher fitness generally, a higher Darwinian fitness, and a higher relative fitness. The difference is that absolute fitness is an actual quantification of that output that can be referred to independently of an equivalent output displayed by other, comparative organisms. As such, however, this makes absolute fitness both more difficult to determine and even to interpret in an evolutionary sense, hence the utility of relying instead upon relative fitness measures instead, which are determinations solely of comparative reproductive outputs between different genotypes, populations, strains, etc.

Note that it can be all too easy to confuse absolute fitness with average fitness, presumably because the concepts are similar and both start with an "A". It is important, however, to avoid making this mistake. Absolute fitness is a property of genotypes, that is, the expected reproductive success of a given genotype under a given set of circumstances. Average fitness, by contrast, is literally the average of the Darwinian fitness as measured across a population. This could be measured in terms of the average of the absolute fitness of individuals found across a population or instead in terms of their relative fitness. Thus, one speaks of increases or declines in the average of fitness of a population (e.g., such as when referring to the impact of hard selection) rather than of increases or declines of the absolute fitness of a population.

Morphological, physiological, biochemical, or behavioral aspects of organisms that contribute to their evolutionary fitness.
Adaptation is an increase in the "fit" of an organism to its environment, i.e., such that survival potential or, especially, reproductive potential is enhanced. As an evolutionary mechanism it is a products of positive selection. Unfortunately, the term is complicated by additional connotations, such as the non-evolutionary adaptation of individual organisms by physiological, morphological, or behavioral means to their immediate environments. That connotation is somewhat different from evolutionary adaptation which instead involves the accumulation of alleles within populations, as well as the individuals making up those populations, that have the collective effect of increasing the Darwinian fitness of individual members of that population (as well as, potentially, the population as a whole). These concepts are further complicated by non-evolutionary adaptations generally being products of evolutionary adaptations. For the most part here, however, by adaptation we will mean the possession and expression of alleles that bestow upon an organisms some evolutionary fitness advantage, that is, an evolutionary adaptation such as, for example, an ability to digest the sugar lactose.
Adaptive evolution

Product of positive/directional selection.
Adaptive evolution is characterized by changes in allele frequencies that give rise to adaptation, and which typically but not always is a consequence of natural selection. Exceptions are rare cases where genetic drift dominates natural selection and happens to favor increases in frequency of otherwise beneficial alleles or increases in the frequency of genotypes that themselves are not beneficial but which can serve as precursors to beneficial genotypes. Adaptive evolution is what one expects to see when populations are responding evolutionarily to new environmental conditions. Adaptive evolution is the key product of positive selection, that is, selection for increases in the prevalence of otherwise less prevalent alleles.
Adaptive peak

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Illustration of those genotypes conferring the greatest fitness within a given environment.
An adaptive peak is a region within sequence space – all possible sequences that are somewhat evolutionarily available to an organism – in which fitness is greater as compared with other regions. Often adaptive peaks are depicted as "hills", found on a plane that coincides with this sequence space, where higher elevations correspond to higher evolutionary fitness. An important question is one of how organisms are able to "move" from one adaptive peak to another since selection should favor movement up adaptive peaks whereas movement between adaptive peaks often will involve reductions in fitness during transitions. Three answers to this question are genetic drift, environmental changes that modify the position of peaks on the sequence-space plane, and horizontal gene transfer, all of which are essentially stochastic rather than deterministic processes.
Artificial selection

Biased reproductive success as mediated by humans especially on non-human populations.
Artificial selection is selection imposed by man, including as inadvertently imposed, the latter particularly as seen in the domesticated species. Artificial selection, though not necessarily by that name, has and continues to play important roles in microbiology and microbial evolution. Whenever one purposefully adapts or otherwise modifies a microorganism genetically other than via genetic engineering, one is artificially manipulating the microorganism's evolution, and often this either implicitly or explicitly involves some form of subsequent selection whether intentionally or inadvertently imposed. So too, whenever an organism is introduced into novel conditions such as into the laboratory from the wild, that organism, if allowed to, will tend to evolve in the course of its "domestication" to its new environment. Consistently, numerous experimental evolution studies exist in which microorganisms are subject to various forms of selection in the laboratory. Thus, artificial selection can be a pervasive component of microbiology and microbial evolution even if the term itself is infrequently applied within these contexts.
Average fitness

Measure of potential for individuals in general across a population to survive and reproduce.
An increase in a population's average fitness means that the population has a greater potential to produce progeny, on a per capita basis, that as seen prior to that increase. Thus, a population displaying a greater average fitness is collectively more fit than an otherwise equivalent population that displays a lower average fitness. Note, though, that the greater average fitness could be a consequence of a group property, e.g., greater levels of cooperative behavior within the group, rather than a consequence of greater individual fitness as viewed independent of group properties, though such group-independent fitness typically will contribute to group fitness as well. Note also that a population's response to hard versus soft selection can be distinguished in terms of its impact on the population's average fitness with hard selection driving increases in average fitness but soft selection not.
Clonal interference

The blocking of fixation of a genotype among two or more competing genotypes possessing similar fitness within a population.
Clonal interference is seen as inefficiencies in periodic selection that result from competition between similarly fit genotypes. This interference typically will have the effect of preventing genotype fixation within clonal populations. Contrast with concept with that of selective sweeps or the somewhat equivalent clonal expansion where instead an allele or genotype is not blocked from rising to fixation within a population. Clonal interference explicitly has the effect of maintaining a balanced polymorphism within a population, though it is not the only mechanisms by which polymorphisms may be retained within a population.
Darwinian fitness

The number of progeny produced by an organism, especially which survive to produce progeny of their own.
Darwinian fitness is a measure of the impact of natural selection particularly measured as a function of genotype. Also known simply as fitness, Darwinian fitness importantly tends to vary depending on environmental context plus at what point in an organisms lifespan fitness is measured. Variations on the theme of Darwinian fitness, that differ chiefly in how fitness is quantified, are absolute fitness and relative fitness.

Reproductive output of an organism.
Or, if not the actual output then the potential output. Though similar to the idea of fitness, fecundity is more or an ecological term versus the use of fitness within evolutionary biology. In particular, fecundity is not necessarily conceptually linked with an organism's possession of specific alleles or genotypes whereas fitness usually is.

Measure of the success of organisms in light of natural selection, typically determined in terms of reproductive success.
"Fitness" is short for Darwinian fitness.
Frequency-dependent selection

Difference in fitness of alleles or genotypes as a function of their prevalence within populations.
Frequency-dependent selection is selection in which the fitness of alleles varies as a function of their frequency within a population, often (though not always) with lower allele frequencies giving rise to greater fitness. The latter can be described as a 'stabilizing frequency-dependent selection' whereas the converse, where fitness instead decreases with lower frequencies can be described as a 'disruptive frequency-dependent selection', where in both cases disruption or stabilization is with regard to polymorphisms. Stabilizing frequency-dependent selection is often seen in response to various forms of exploiter-victim relationships where being rare is advantageous either in effecting exploiting or in avoiding it. Disruptive frequency-dependent selection is also seen with antagonistic interactions, though here it is display of both the antagonistic action and protection against that antagonism that is selected for with greater fitness particularly at higher frequencies, e.g., such as may be seen with selection for bacteriocin production in bacteria.
Generation time

Interval spanning between birth or equivalent and reproductive formation by that organism of progeny.
Shorter generation times, all other factors held constant, typically will give rise to greater organism fitness. This, however, is less the case to the extent that shorter generation times conflicts with number of offspring produced by individuals, the survival and subsequent reproductive success of those offspring, or in the case of seasonality the potential to display appropriate states at appropriate times. For latter, e.g., it is not necessarily advantageous to be reproducing during times when displaying greater durable would be preferable, or indeed the converse. Note further that the time between "birth" of an individual and its reproductive output is a concept which is complicated by such things as iteroparity, i.e., an ability to display more than one reproductive episode per lifetime. Alternatively, many or most microorganisms instead are semelparous, that is, displaying only a single reproductive episode per lifetime.
Hard selection

Additional levels of mortality experienced by a population that can result in population extinction absent successful adaptation.
Hard selection results from environmental conditions that have the effect of reducing the absolute fitness of most or all of the individuals making up a population and where the result of such selection, assuming sufficient genetic variability within a population, is an increase in the average fitness of the so-exposed population. For example, the application of an antibiotic to a population of bacteria that is sensitive to that antibiotic is an example of hard selection, and the antibiotic-resistant bacteria that are selected in the course of these scenario will display a higher average population fitness than the population they replaced. It is important to appreciate, however, that it is explicitly within the antibiotic-containing environment that the higher average fitness is manifest. Thus, the hard selection imposed by the antibiotic had the effect of differentiating the average fitness of sensitive versus resistant populations, with the resistant populations displaying greater fitness and the sensitive population displaying greater mortality, and also, therefore, with the resistant population – so long as it is sympatric – coming to replace the sensitive population.
Historical contingency

Constraints on adaptation that stem from complications as well as limitations associated with an organism's current genotype or population's current genotypes.
Historical contingency is the idea that adaptation can occur via multiple steps whereby certain genotypes are better suited to the generation of subsequent, more fit genotypes than are other genotypes. The idea of multiple adaptive peaks that lineages can ascend embodies this idea where initiation of ascension of one peak means that an organism's genotype is more similar to genotypes found on that peak than genotypes associated with different peaks. Historical contingency thus is a description of a genotype's nearness to an appropriate adaptive peak, with the historical component of that statement a reflection of the fact that genotypes are generated over the course of evolutionary history and thus the genotype an organism possesses will be a function of the genotype of its ancestors, which in turn will reflect a long history of evolution. Contingency, on the other hand, refers to chance, that is, the potential that an organism has to respond evolutionarily to especially novel selective pressures will be a stochastic rather than deterministic function. Furthermore, historical contingency is not quite preadaptation but more closely what might be described as pre-preadaptation, not so much the possession of an adaptation that becomes useful as environments change as the possession of the potential to evolve a new adaptation.
Hitchhiking (Genetic hitchhiking)

Increase in the frequency of certain alleles based solely on their linkage to other alleles.
During periodic selection, alleles that are found within the same genome as the selected allele (or alleles) will similarly rise in frequency within a population, though only due to this association with the more fit allele. In hitchhiking down a highway it is the car's driver that is determining where the car goes and everything else in the car quite literally is going along for the ride. Thus, in genetic hitchhiking it is some beneficial allele that figuratively is the driver of the periodic selection (or instead more than one beneficial allele), it is the organism's lineage that is the car, and it is the everything else associated with the car including any passengers that are the hitchhiking alleles. Note that genetic hitchhiking is similar in its somewhat non-deterministic effects to the impact of genetic drift and this is so even though ultimately it is natural selection that is "driving" the process. This seeming contradiction is resolved, however, when one appreciates that only the impact of natural selection directly upon whatever is being selected, i.e., beneficial alleles, is potentially deterministic in its outcome whereas there can also be indirect consequences of natural selection that are not deterministic, and genetic hitchhiking is a prominent example of the latter.
Inclusive fitness

Description of the reproductive success of alleles as found in multiple individuals rather than just a single, otherwise unaffiliated, allele-carrying individual.
Inclusive fitness is associated with the concept of kin selection as well as the evolution of cooperation more generally. It is very much a gene- or allele-"eyed view" of evolution versus the more traditional individual organism as the unit of selection perspective. Inclusive fitness is not just fitness as measured across multiple individuals but fitness as reproductive success that is manifest other than just in terms of the single, unaffiliated individual otherwise living out its life alone. In other words, the interaction between individuals, particularly individuals carrying the allele that we care about, is key to appreciating what inclusive fitness is all about. Otherwise one is ignoring interactions between individuals and without those interactions there can be no inclusive fitness.
Kin selection

Evolutionary favoring of behaviors that especially benefit relatives.
Kin selection gives rise to that groups of related organisms have the potential to display a higher collective fitness, as a group, than the individuals making up the group are capable of achieving on their own. Note that many microorganisms, as clonal populations, can be especially closely related, but so too one can view the clonal collection of cells making up multicellular organism's bodies as also being especially closely related. See also the concept of inclusive fitness.

Close physical proximity especially of loci on chromosomes.
Linkage is a description of inefficiencies in the ability of recombination to separate the alleles found at specific loci. In obligately sexual organisms linkage typically is seen among more or less adjacent alleles found on the same chromosome, and this is true given sexual processes also among less sexual organisms such as bacteria. In asexual organisms, by contrast, all loci are fully linked.
Linkage disequilibrium

Tendencies for specific alleles to remain associated within genomes rather than separated via recombination.
Linkage disequilibrium is a consequence of inefficiencies in recombination to separate linked alleles. Clonal populations by definition display linkage disequilibrium resulting in greater representation of linkage relationships between specific alleles (their presence in the same genome) than would otherwise be the case were recombination more prevalent. Genetic hitchhiking too and for the same reason is a consequence of linkage disequilibrium.
Natural selection

Biased declines in the frequency of alleles within populations.
Natural selection is selection imposed by nature, that is, rather than by man. That statement is not quite as unambiguous as one might imagine, however, since what then is selection that is unintentionally imposed by man such as in the course of domestication? I would argue that unless a trait is explicitly under selection in the course of artificial selection then natural selection rather than artificial selection is, assuming selection is occurring, what in fact is deterministically impacting a population. Thus, selection imposed upon bacteria for their increased production of a metabolic product or utilization of some substrate can count as artificial selection whereas selection imposed in the course of experimental evolution studies in which organisms are simply exposed to new environmental conditions and challenged to evolve is more akin to natural selection.
Negative selection

Deterministic (non-random) loss of alleles from populations.
Negative selection is selection that has the effect of removing alleles from a population (a.k.a., purifying selection). Experimentally, in microbial genetics, this has the effect of removing alleles of interest so requires some form of replica plating to retain strains carrying those alleles once their inability to survive has been identified (a.k.a., indirect selection). Ecologically, negative selection has the effect of retaining or enriching for the equivalent to the wild-type genotype within a population. The conceptual difference between this and positive selection is that starting with alleles that are present at relatively low frequencies, while positive selection has the effect of increasing the frequency of those alleles, negative selection has the effect of decreasing that frequency (indeed, negative selection can be viewed as an imposition of hard selection against these certain alleles, dis-enriching them from the population). As noted, though, in the laboratory it is still possible, with often great tedium, nonetheless to retain cultures of these selected-against organisms so that they can subsequently be propagated under less selective conditions.
Periodic selection

Deterministic increases in the representation of certain genotypes within clonal populations.
Periodic selection is a kind of positive selection that can be imposed upon clonal populations of organisms. It is a manifestation of clonal expansions or selective sweeps within these populations. Periodic selection serves as a good, basal perspective on natural selection as it can occur within populations of microorganisms, particularly when those populations are purely clonal and existing within well-mixed environments. Alternatively, the presence of horizontal gene exchange (sex) interferes with periodic selection resulting in individual alleles rather than individual genotypes being selected within populations. Indeed, the greater the gene exchange then the greater that selection on individual alleles occurs rather than selection on individual genotypes. The impact of spatial structure, that is, impediments to organism movement or mixing, has the result of reducing the more global impact of periodic selection, with its consequence instead observed much more locally. Thus, the potential for periodic selection to contribute to the extinction of the alleles within extended populations is much lower – given both allele exchange and spatial structure – than a perspective purely on positive selection as it can occur in the laboratory might suggest. Still, as noted, periodic selection represents a good place to begin when considering natural selection as it can act on predominantly clonal microorganisms.
Positive selection

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Deterministic increases in the representation of certain alleles within populations.
Also known as directional selection, positive selection is selection that favors especially the allele of interest. Experimentally, in microbiology, this typically involves some form of enrichment including organism plating such that only the genotypes of interest are able to form, e.g., colonies. Positive selection thus can be viewed, at least in part, as a form of hard selection that enriches a population for those alleles that are beneficial under the selective conditions. Contrast with negative selection.
Purifying selection

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Deterministic (non-random) reductions in already rare alleles from populations.
Purifying selection is also known as stabilizing selection and is a form of negative selection. The connotation of "purifying" comes from the idea that "impure" detrimental alleles are actively being removed from populations via purifying selection. In fact, purifying selection is constantly going on, in all populations. It is the one form of natural selection that, when natural selection is operating at all, one can be fairly sure that purifying selection is operating. Indeed, purifying selection can't not operate since the loss of lethal alleles from populations is just one aspect of purifying selection and by definition lethal alleles are lost from populations (and also, though not exactly "by definition", are regularly mutationally gained by populations as well, that is, prior to their removal via purifying selection).
Relative fitness

Number of offspring that survive to reproduce as compared to the average for a population.
Relative fitness is the fitness of an organism relative to another organism, or genotype relative to another genotype. Rather than starting with absolute fitness measures and then comparing, instead relative fitness can be determined using a very straightforward but powerful methodology, that of simply comparing population sizes of competing groups at two or more points in time. That group whose population size becomes larger or which takes up a larger fraction of a total population size can be described as having a higher relative fitness. With microorganisms this is usually determined by employing what are known as selectably neutral markers, that is, alleles that have little impact on organism fitness during experiments but nonetheless which are relatively easily distinguished during subsequent quantification steps. Those organisms for which selectively neutral markers consistently increase in abundance can be said to display a higher relative fitness in comparison to competing organisms for which alternative selective neutral markers decline in abundance. Indeed these difference themselves can be quantified to determine that actual fitness difference between the two groups, which are presented as relative fitnesses. The more fit genotype, for example, may be described as having a relative fitness of 1.0 whereas the less fit genotype may be described instead as having a relative fitness of, e.g., 0.85.

Biased choosing, biased survival, or biased propagation.
Selection is the imposition of conditions that differentiate the reproductive output of different organisms. This differentiation can be at the point of reproduction or instead in terms of survival prior to reproductive, or indeed, to the extent that an organism has control over it, in terms of the survival of offspring so that they too can reproduce. Generally we can differentiate selection in an evolutionary biological sense into natural selection versus artificial selection, though where exactly the dividing line between the two should be placed is an open question. Natural selection further can be differentiated into a fairly large number of scenarios including directional (or positive), purifying (or negative), and various forms of frequency-dependent selection.
Selective sweep

Increase in frequency of an allele due to that allele's beneficial impact on the fitness of carriers.
Selective sweeps are an increase in the frequency of higher-fitness alleles within populations as equivalent to periodic selection if a population is clonal. Selective sweeps within clonal populations also can be described as clonal expansions with the "expansion" part referring to increases in frequency within a population. Within sexual populations, however, it is individual alleles that can sweep through populations rather than individual genotypes, i.e., as is instead the case with periodic selection/clonal expansion. Thus, am HIV clone (Human Immunodeficiency Virus) that is capable of evading its host's immune system may expand in frequency within the HIV population, sweeping aside, at least to a degree, competing alleles that are more readily immunologically recognized.
Selectively neutral marker

Especially alleles and associated phenotypes that allow a simple distinguishing among the genotypes of laboratory organisms but without otherwise substantively impacting especially experimental evolution procedures.
Selectively neutral markers are a means of distinguishing strains during relative fitness determinations. Ideally they are a genetic marker (an allele) that confers simple visualization or selection (particularly positive selection) of a strain during laboratory assessment but which does not otherwise impact fitness during competitions. Selectively neutral markers can include antibiotic-resistance genes, phage resistance, or detectable enzymes such as β galactosidase. They are not always perfectly selectively neutral under experimental conditions, but especially low levels of negative impact on the fitness of selectively beneficial genotypes can be compensated for, just so long as the marker does not synergistically or antagonistically interact with the non-marker alleles of interest.
Soft selection

Deterministic evolution that can result in increases in the relative fitness of certain individuals but not the absolute fitness of associated populations.
Selection resulting especially from interactions with conspecifics where improvement in fitness in the face of this type of selection has the effect of improving relative fitness but not absolute fitness. Basically, being better at doing something than other members of your own species does not necessarily mean that one is better at surviving or reproducing generally but instead might mean only that one is better at interspecific interactions. Contrast with hard selection.
Unit of selection

Entities possessing genetic variation in combination with differential reproductive success but not necessarily limited to individual organisms.
Units of selection can be alleles making up loci, genetic parasites such as plasmids, individual organisms, and even groups of organisms (i.e., group selection). Key to being a unit of selection is solely that natural selection is able to act upon these entities in terms of differential survival as well as differential reproductive success. Thus, the cells of your own body can individually be described as units of selection, which in fact is precisely the problem when it comes to the development of cancers. Natural selection can also be acting upon different units at the same time and not necessarily in the same direction for different, otherwise coexisting units. See too the concept of multilevel selection theory.