The basis of evolution is change as a function of time, specifically change in genotype rather than physiological or morphological adaptation. Since time is inevitable, and genetic material is both mutable and subject to the various additional evolutionary forces, evolution simply happens. The one exception to this point is stabilizing selection, where the frequencies of more prevalent alleles in fact don't change through time, or when fixed alleles remain fixed. But here too evolution is occurring; it is just that it is less visible because it involves loss of already minor players (rare alleles) rather than more qualitative changes in allele frequencies. Alternatively, these rarer alleles can become more common, giving rise to polymorphisms within populations, or common alleles can become rare, for example in the course of previously rarer alleles become fixed (which inevitably means that what had been more common alleles become lost from populations). Thus, mutation, drift, migration, selection, polymorphism, fixation, and a host of additional concepts considered in the previous chapters are part and parcel of how populations evolve, including how populations of microorganisms evolve. These processes all occur as populations progress through time and in populations that are small enough, in terms of their volumes, that they can be manipulated in whole, we can describe them as being passaged in a microbiological sense through time.

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Part II:

Vocabulary

Table: Important Terms and Concepts Considering Experimental Evolution
Term	Definition/Discussion
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.
	In serial passage experiments this is seen in conflicts between life stages, particularly potential to replicate versus potential to be transferred (that is, passaged or transmitted). More generally, antagonistic pleiotropy essentially is the specialization of a population for one situation versus another, rather than the retention of more generalist strategies, and specialization inevitably involves tradeoffs. This specialization involves improvement in the ability to do one thing (e.g., exploit one host organisms for a parasite) results in a reduced potential to do another thing (such as exploit other types of host organisms).
Attenuation	Reductions in especially a symbiotic organism's growth potential or virulence.
	Attenuation can occur following mutation and such mutations can be selected for via serial passage within alternative environments, thus resulting in antagonistic pleiotropies. That is, virulence or growth rates can be enhanced in one environment, such as one host type, with this enhancement occurring in association with reductions in virulence or growth rates – that is, attenuation – in another environment or environments, such as in another host. See for example the concept of live-attenuated vaccine.
Batch culture	Production of especially microorganisms within a single vessel particularly from which media is not removed nor additional media added.
	Batch culture is the most common broth-based means of growth of microorganisms, e.g., such as bacterial growth within a test tube or flask. Often in batch culture populations are allowed to grow to relatively high densities such as stationary phase, resulting in display of the standard bacterial growth curve, or equivalent (that is, lag phase, log phase, stationary phase, and decline phase, in that order). Note that serial transfer/passage experiments are often based on batch culture. Contrast with continuous culture.
Bottleneck (genetic)	Reductions in populations to very few breeding individuals, potentially resulting in genetic drift.
	Typically it is bottlenecking that is avoided during experimental evolution procedures, that is, unless genetic drift, through bottlenecking, is intentionally being imposed upon a population. The latter can be seen by transferring only small volumes of cultures in serial transfer experiments or indeed transferring from isolated colonies or plaques.
Bottom-up control	Determinants of population densities, especially in predator-prey situations, that are based on prey access to resources.
	With bottom-up control the population densities of organisms tend to remain relatively stable, at least so long as limiting resource densities also remain relatively stable. In addition, with bottom-up control of organism population densities, the concentrations of limiting resources tend to be somewhat low. As a result, prey densities tend not to become so high that predator densities can subsequently become sufficiently high, resulting in prey densities that are substantially impacted by predator densities. In other words, with bottom-up control, low resource densities can sustain only low prey densities which in turn can sustain only low, relatively un-impacting, predator densities. Contrast with top-down control.
Carrying capacity	Maximum population size that can persist indefinitely within an environment.
	Experimentally, this is seen with microorganisms particularly within chemostats, in fact helping to define the "stat" of chemostat. Less strictly defined, carrying capacity can also refer to the population density observed at stationary phase in batch culture but note that such a population, since it is no longer replicating, cannot strictly be described as being carried by an environment. Alternatively, a population that exists at high, stationary phase-like densities and which is being sustained by low-level nutrient additions to that environment, i.e., as equivalent to what one sees in terms of resource addition in continuous cultures, in fact can be described as existing at that environment's carrying capacity.
Chemostat	Means of culturing microorganisms under constant physiological conditions over long time frames that involves a constant-rate of input of fresh medium.
	Chemostats represent the most common means by which continuous culturing is achieved in the laboratory. Not only is fresh media continuously added but the same volume is continuously lost from the growth chamber of chemostats. Chemostats in addition are subjected in their growth chambers to substantial mixing so as to retain an approximation of homogeneity in terms of resource densities, waste densities, and organism densities. Technically a chemostat retains relatively stable organism populations sizes though this can be less the case when chemostats contain either evolving populations or instead communities of organisms which are competing, or indeed which display predator-prey interactions. Chemostats also can be described as continuously stirred tank reactors, and variations on the general chemostat concept exist such as turbidostats in which culture turbidity is maintained at a constant level rather than resource input and washout rates being maintained at a constant level.
Competitive exclusion	Two sympatric species occupying the same niche cannot exploit the same array of resources, especially a single limiting resource, without one or the other being driven extinct.
	Key to competitive exclusion is the simplicity of niches since not only must two species be competing directly over the extent of their ranges, but also those species by-and-large must be competing at their carrying capacities such that insufficient limiting resource is present to sustain one of the competing populations. This competition can be seen with either serial passage or continuous culture experiments, though it is easier to illustrate in terms of continuous culture experiments.
Competitors	Sympatric organisms that exploit the same limiting resources within environments.
	Competitors often are visualized in terms of interspecific competition though certainly conspecifics compete as well. Indeed, the concept of species itself can be defined in terms of this competition, where the most intense competition occurs between competitors that make up the same species due to their essentially complete niche overlap, i.e., see the ecological species concept, whereas members of different species compete less intensely. Competition can result in the extinction of one of the competitors, i.e., competitive exclusion, but also can result specialization. The ladder involves a reduction in competition due to reductions in niche overlap, i.e., as one sees with resource partitioning.
Continuous culture	An approach to propagating microorganisms that involves an ongoing supply of fresh media and as well as ongoing removal of cultured media, resulting in potentially indefinite propagation of a population of organisms.
	Continuous culture is achieved in the microbiology laboratory primarily via the use of chemostats where fresh media continuously flows into a growth chamber while spent media continuously flows out. Continuous culture allows for long-term as well as convenient culture propagation, ecological experiments, and experimental evolution. It is in many ways the simplest method of microorganism passage through time though also is limited in terms of the complexity of manipulations that can be imposed on population during that passage, i.e., contrasting serial passage. Chemostats basically select for organisms that are able to more effectively retain their presence within chemostat growth chambers, whether in terms of growth rates, efficiency of resource utilization, suppression of the growth of competitor organisms, or due to physical attachment to chemostat surfaces.
Experimental evolution	Especially laboratory-based culturing of microorganisms that involves serial transfer, serial passage, or, in certain instances, substantial population bottlenecking.
	Basically experimental evolution involves either the adaptation of organisms to specific, generally relatively simple, laboratory-defined conditions, or instead the imposition of severe bottlenecking especially on organisms displaying high mutation rates. Experimental evolution also can explore the impact of other evolutionary forces, besides natural selection and genetic drift, such as mutation rates and genetic migration, etc. Experimental evolution typically will involve allowing a population explore sequence space on it is own, with genotype thus not under direct experimental control, but also can involve competition between better defined genotypes, such as following the mixing of more one otherwise isogenic genotype. Competition between different species, on the other hand, though it can involve evolutionary change in one or both species (i.e., change in allele frequencies), nonetheless is not strictly an example of experimental evolution since evolution occurs within populations rather than in terms of one species outcompeting another species.
Exploitative competition	Antagonism between organisms that is both indirect and over resources.
	Exploitative competition typically involves other than direct contact between organisms and nevertheless can result in competitive exclusion. The competition that one observes during serial passage or continuous culture experiments is equivalent to exploitative competition in that it is primarily over resources that such competition is being conducted, though the caveat that in experimental evolution experiments this competition is occurring within populations (intraspecific) rather than between populations (interspecific). The distinction between these two cases is less clear, however, when such competition is occurring within a clonal population since the individuals within those populations are no more exchanging alleles than members of different species.
Half-maximal resource density (alt link)	Amount of required substances that are sufficient to sustain a specific, intermediate level of organism population growth.
	This constant is the equivalent of the Michaelis-Menten constant and which can also be described as the Monod constant. It is the resource density, such as of limiting nutrients, that supports especially microorganism population growth rates that are one-half those that are possible when the same nutrients are not limiting within the organism's growth environment. Keep in mind that the units of this constant are ones of resource density and further that this constant is used to help to define organism growth rates, during modeling, as they can change as a function of resource densities such as within chemostats.
Intrinsic population growth rate	Description of ability of organisms to replicate within environments that are lacking in resource limitations.
	Intrinsic population growth rates, abbreviated as r, are an ideal that normally is approximated only given small population sizes and no competition from other organisms for the same, limiting resources. Intrinsic population growth rates nonetheless help to define logistic growth and particularly so the lower below carrying capacity a population's density. Population growth rates thus are reduced from these intrinsic rates as environmental resources become limiting and one way of modeling these reductions involves use of the half-maximal resource density, i.e., Monod constant.
K (alt link)	Abbreviation for carrying capacity.
	The variable K is seen particularly in the logistic growth equation where it contrasts with the variable, r. Note that populations do not necessarily sustain themselves at their carrying capacity since population sizes are impacted by environmental issues other than resource densities such as interspecific competition or exploitation. In addition, species vary in their ability to avoid exceeding environmental carrying capacities, e.g., such as one sees with microorganisms during their growth in batch cultures. Chemostats, by contrast, are essentially defined by their ability to retain organism populations at their carrying capacity, i.e., that population density and associated replication rate at which resources are used at the same rate that the resources flow into the chemostat growth chamber.
Life stages	Specific variations in organism characteristics during maturation as that occurs during progression from birth through natural death.
	Life stages often include an immature, prior to reproductive maturity stage, a reproductive stage, and often a dissemination or transmission stage as well. Importantly, optimization of functionality or effectiveness at any one stage can have the effect of reducing functionality or effectiveness at a different life stage (i.e., see the concept of antagonistic pleiotropy). See also life cycle.
Live-attenuated vaccine (alt link)	Microorganism variant displaying reduced replication competence that is administered to stimulate protective immune responses against that microorganism.
	Traditionally, live-attenuated vaccines have been generated by selecting for antagonistic pleiotropies. This is achieved via especially serial passage of organisms through non-standard environments, such as either different host organisms or instead external to the host organisms entirely, that is, within tissue culture. Particularly it is virus pathogens that have been subject to attenuation in the course of vaccine development. See equivalently attenuated whole agent vaccine.
Logistic growth	Increase in population size that at first is unconstrained but subsequently is limited by resource availability.
	Logistic growth is typified by exponential growth, that is, population growth as it can occur in the absence of limitations on such growth, but that is followed by constraints on that growth. Rates of growth without constraints are defined by the growth rate or intrinsic growth rate constant, r. With constraints on population growth fully effected, then populations display no net growth in size, and thus are said to have attained a population density that conforms to their environmental carrying capacity, or K. Logistic growth is a default assumption as to the population growth dynamics of most organisms given finite resources densities as well as environmental volumes. Nevertheless, not all populations are "well behaved" as they approach carrying capacities and thus instead can exceed their carrying capacities, resulting in sufficient environmental modification that population crashes occur. Alternatively, organisms may modify their environments in such a way that they become less effective competitors within those same environments, i.e., as one sees with ecological succession. Organisms additionally can be subject to exploitation by other organisms resulting either in population that are maintained below carrying capacity or instead such that populations are particularly vulnerable to such exploitation once they approach or indeed exceed an environment's carrying capacity.
Monod equation	Means of incorporating saturation kinetics into models of organism population growth.
	The Monod equation is equivalent to the enzyme kinetics described by Michaelis-Menten kinetics. Specifically, there is an asymptotic increase in rates as resource (or substrate) densities are increased. This occurs because at sufficiently high densities these resources are no longer limiting to organism replication rates (or substrates limiting to enzyme activities) such that replication rates instead are defined by intrinsic organism characteristics. At sufficiently low densities of resources (or substrates), however, increases in these quantities can result in an approximately linear impact of resource densities on population growth rates. Thus, at sufficiently low densities a doubling in resource concentration can result in approximately a doubling in rates of organism replication. Note that the Monod equation is often employed to model microorganism division rates as seen during chemostat growth.
Pure culture technique (alt link)	Means of propagation of especially microorganisms that involves periodic bottlenecking of populations to a single organism.
	Not to be confused with aseptic technique, which is important as well, pure culture technique is both how one reduces microorganism communities to a single strain and then limits the evolution of that strain over time. The latter, the limitations on evolution, are handled today usually via freezing rather than ongoing organism propagation. Nevertheless, pure culture technique is relevant to experimental evolution especially because violations of this approach are precisely what can give rise to organism evolution during laboratory propagation. In other words, serial passage/transfer/propagation or instead continuous passage are both circumstances in which pure culture technique is explicitly not being adhered to over time (though in most cases nonetheless does tend to be adhered to at the start of such propagation, i.e., with to-be-propagated cultures initiated as pure cultures.
r	Abbreviation for intrinsic population growth rate.
	The variable r is seen particularly in the logistic growth equation where it contrasts with the variable, K. Note that populations do not necessarily replicate at their intrinsic growth rate since rates of population growth are impacted by environmental issues as well, such as in terms of nutrient densities.
Saturation kinetics	The idea that the relative impact of increasing something within a system will be greater the lower the starting concentration.
	Saturation is seen particularly in terms of the impact of limiting nutrients or other resources on organism growth. The result, for example, is that a doubling of concentrations of resources will tend to double growth rates at low resource concentrations and population densities but a doubling will much less than double growth rates when resource concentrations are already high. Thus, instead of a straight line increase in population growth rates as resource densities increase, instead the resulting curve is asymptotic, bending over to a growth rate maximum as defined by a population's intrinsic growth rate. See in particular the Monod equation as well as Michaelis-Menten kinetics, both of which describe saturation kinetics.
Serial passage	Movement especially of subpopulations of individual symbiotic organisms from environment to environment.
	This is movement particularly from host to host or, instead, artificial environment such as cell culture to cell culture. Serial passage is a kind of serial transfer. It is used in the development of live, attenuated vaccines.
Serial transfer	Movement especially from vessel to vessel of a subpopulation of individual organisms.
	Serial transfer contrasts particularly with propagation of microorganisms using pure culture technique. Serial passage is a kind of serial transfer, or vice versa, as the two terms often are or at least can be used interchangeably. Note regardless that transfer is from equivalent environment to equivalent environment. In principle one could also change the environment to something novel, e.g., a different temperature, with each transfer, but that explicitly is not what what's happening with serial transfer/passage experiments.
Stationary phase	Period during the batch growth of cellular organisms, such as bacteria, where growth rate equals death rate.
	With batch culture this is the familiar physiological state where population growth has ceased due to a running out of nutrients or build-up of wastes. With continuous culture, as seen in chemostats, this instead is still the point where population growth has ceased but organism replication nonetheless continues, with replication balanced by losses particularly due to washout from the growth chamber. The defining feature of stationary phase thus is that microorganism population sizes are stationary, that is not changing particularly in terms of viable counts, whether this lack of change is due to a complete lack of growth or instead where growth is ongoing but with "births" balanced by organism losses ("deaths").
Sympatric	Overlapping of geographical ranges.
	Two populations competing within the same environment are sympatric (though so too are two populations that are cooperating or indeed simply existing within the same environment). Basically, one cannot have interspecific interactions unless two (or more) species are sympatric. An exception to this statement is where products of organisms are able to flow between environments but not the organisms themselves, i.e., such that "downstream" organisms can interact with the products of "upstream" organisms, weather these products are feces, dead bodies, or indeed genetic material, resulting in horizontal gene exchange.
Top-down control	Determinants of population densities, especially in predator-prey situations, that are based on predator access to prey.
	Given top-down control then prey densities will be determined particularly by what is eating or otherwise exploiting them rather than prey access to resources such as nutrients. Predator-prey interactions often cycle in association with top-down control due to the potential for predator densities to overshoot their prey-density defined environmental carrying capacity, resulting in prey-density "crashes" that are followed by predator-density crashes, which in turn are followed by prey-density recovery, and then predator-density recovery, and so on.
Transmission	Movement of especially symbiotic organisms from one host organism to another.
	A if not the primary source of selection on obligately symbiotic organisms is on their transmission, with transmission an essential component of life cycles given that no current host is immortal. Thus, to survive, an obligate symbiont must possess some ability to be transmitted to a new host. See also transmission of disease. Note, however, that symbiotic are not necessarily disease causing but can include commensalistic and mutualistic symbiosis as well as parasitic ones.
Trophic level (alt link)	Degree to which an organism is 'removed' nutritively from primary producers in ecological food chains.
	Trophic levels include those primary producers (which are carbon fixers), primary consumers (which eat primary producers), secondary consumers (which eat primary consumers), and tertiary consumers. Also relevant are organisms that eat the dead remains of other organisms, the decomposers. Among the latter are heterotrophic organisms that consume already partially or fully digested carbon-containing molecules, including many bacteria such as Escherichia coli. In this case, the carbon-source represents a lower trophic level, the heterotrophic bacterium the next level up, and consumers of the heterotrophic bacteria, including protists and phages, a further trophic level up. See also the related concepts of trophic interactions and trophic ecology as well as trophic efficiency.
Virulence	The capacity for a parasite/pathogen to cause disease.
	Serial passage has the potential to result in the evolution of increased levels of symbiont virulence. This often occurs within the context of an antagonistic pleiotropy where increased virulence in association with the passage environment is associated with decreased virulence in other environments. This decreased virulence can be described as an attenuation, and such passage within environments that are other than that of the normal host is the traditional means by which live-attenuated vaccines have been generated. Note that modification of how transmission is effected during serial passage also can have the effect of selectively modifying a symbiont's associated virulence.
Washout	Movement out of an environment via flow.
	Equivalent to outflow. Washout is seen, for example, in chemostats where random movement of broth media (usually somewhat spent, that is, used by the associated organisms), nutrients (that have not yet been used by associated organisms), and organisms flow out of growth chambers, with this outflow occurring at a rate that is equal to the rate of inflow of fresh media into the same growth chamber. Inflow ideally is well mixed into the chemostat growth chamber's volume prior to washout. Washout gives rise to one form of microorganism "deaths" during chemostat propagation, and indeed for most chemostats outflow is either the predominant or effectively only form of "death" that these organisms experience. In turn, for a stable population sizes, these "death" is what balances "births" that are a consequence of organism reproduction, particularly as via binary fission.