Experimental evolution studies are a means of testing
evolution
Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...
ary theory under carefully designed, reproducible experiments. Given enough time, space, and money, any organism could be used for experimental evolution studies. However, those with rapid
generation times, high
mutation rate
In genetics, the mutation rate is the frequency of new mutations in a single gene or organism over time. Mutation rates are not constant and are not limited to a single type of mutation; there are many different types of mutations. Mutation rates ...
s, large
population sizes, and small sizes increase the feasibility of experimental studies in a laboratory context. For these reasons,
bacteriophage
A bacteriophage (), also known informally as a ''phage'' (), is a duplodnaviria virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν ('), meaning "to devour". Bact ...
s (i.e.
virus
A virus is a wikt:submicroscopic, submicroscopic infectious agent that replicates only inside the living Cell (biology), cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and ...
es that infect
bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...
) are especially favored by experimental evolutionary biologists. Bacteriophages, and microbial organisms, can be frozen in stasis, facilitating comparison of evolved strains to ancestors. Additionally, microbes are especially labile from a molecular biologic perspective. Many
molecular tools have been developed to manipulate the
genetic material
Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main clas ...
of microbial organisms, and because of their small
genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ...
sizes,
sequencing
In genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succi ...
the full genomes of evolved strains is trivial. Therefore, comparisons can be made for the exact molecular changes in evolved strains during
adaptation to novel conditions.
Experimental studies, by category
Laboratory
phylogenetics
In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups ...
Phylogenetics is the study of the evolutionary relatedness of organisms. Laboratory phylogenetics is the study of the evolutionary relatedness of laboratory-evolved organisms. An advantage of laboratory phylogenetics is the exact evolutionary history of an organism is known, rather than estimated as is the case for most organisms.
Epistasis
Epistasis is a phenomenon in genetics in which the effect of a gene mutation is dependent on the presence or absence of mutations in one or more other genes, respectively termed modifier genes. In other words, the effect of the mutation is dep ...
Epistasis is the dependence of the effect of one
gene
In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...
or
mutation
In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, m ...
on the presence of another gene or mutation. Theoretically epistasis can be of three forms: no epistasis (additive inheritance), synergistic (or positive) epistasis and antagonistic (or negative) epistasis. In synergistic epistasis, each additional mutation has increasing negative impact on
fitness. In antagonistic epistasis, the effect of each mutation declines with increasing numbers of mutation. Understanding whether the majority of genetic interactions are synergistic or antagonistic will help solve such problems as the
evolution of sex.
The phage literature provides many examples of epistasis which are not studied under the context of experimental evolution nor necessarily described as examples of epistasis.
Experimental adaptation
Experimental adaptation involves
selection
Selection may refer to:
Science
* Selection (biology), also called natural selection, selection in evolution
** Sex selection, in genetics
** Mate selection, in mating
** Sexual selection in humans, in human sexuality
** Human mating strat ...
of
organisms
In biology, an organism () is any living system that functions as an individual entity. All organisms are composed of cells ( cell theory). Organisms are classified by taxonomy into groups such as multicellular animals, plants, and f ...
either for specific
traits or under specific conditions. For example, strains could be evolved under conditions of high temperatures to observe the molecular changes that facilitate survival and
reproduction
Reproduction (or procreation or breeding) is the biological process by which new individual organisms – " offspring" – are produced from their "parent" or parents. Reproduction is a fundamental feature of all known life; each individual o ...
under those conditions.
The reader should be aware that numerous phage experimental adaptations were performed in the early decades of phage study.
Adaptation to usual hosts.
Adaptation to new or modified hosts.
The older phage literature, e.g., pre-1950s, contains numerous examples of phage adaptations to different hosts.
Adaptation to modified conditions
The older phage literature, e.g., pre-1950s, also contains examples of phage adaptations to different
culture conditions, such as
phage T2 adaptation to low salt conditions.
Adaptation to high temperatures.
Adaptation as compensation for deleterious mutations.
There are many examples in early phage literature of bacteriophages adapting and compensating for deleterious mutations.
Adaptation as toward change in phage
virulence
Virulence is a pathogen's or microorganism's ability to cause damage to a host.
In most, especially in animal systems, virulence refers to the degree of damage caused by a microbe to its host. The pathogenicity of an organism—its ability to ...
Virulence is the negative impact that a
pathogen
In biology, a pathogen ( el, πάθος, "suffering", "passion" and , "producer of") in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a ger ...
(or
parasite
Parasitism is a Symbiosis, close relationship between species, where one organism, the parasite, lives on or inside another organism, the Host (biology), host, causing it some harm, and is Adaptation, adapted structurally to this way of lif ...
) has on the
Darwinian fitness
Fitness (often denoted w or ω in population genetics models) is the quantitative representation of individual reproductive success. It is also equal to the average contribution to the gene pool of the next generation, made by the same individ ...
of a harboring organism (host). For phage, virulence results either in reduction of bacterial division rates or, more typically, in the death (via
lysis
Lysis ( ) is the breaking down of the membrane of a cell, often by viral, enzymic, or osmotic (that is, "lytic" ) mechanisms that compromise its integrity. A fluid containing the contents of lysed cells is called a ''lysate''. In molecular bio ...
) of individual bacteria. A number of theory papers exist on this subject, especially as it applies to the evolution of phage
latent period.
The older phage literature contains numerous references to phage virulence, and phage virulence evolution. However, the reader should be warned that virulence is often used as a synonym for "not temperature", a usage which is neither employed here nor to be encouraged generally.
Impact of sex/
coinfection
Coinfection is the simultaneous infection of a host by multiple pathogen species. In virology, coinfection includes simultaneous infection of a single cell by two or more virus particles. An example is the coinfection of liver cells with h ...
More than one phage can
coinfect the same bacterial cell. When this happens, the phage can exchange genes, which is equivalent to "sex." Note that a number of the immediately following studies employ sex to overcome
Muller's ratchet while papers that demonstrate Muller's ratchet (i.e., without employing sex to overcome the result) are instead presented under that heading.
Muller’s ratchet
Muller’s ratchet is the gradual, but irreversible accumulation of deleterious mutations in
asexual organisms. Asexual organisms do not undergo gene exchange and therefore cannot recreate mutation-free genomes. Chao, 1997, provides a phage-emphasizing review of the subject.
Prisoner’s dilemma
The Prisoner's Dilemma is an example of a game analyzed in game theory. It is also a thought experiment that challenges two completely rational agents to a dilemma: cooperate with their partner for mutual reward, or betray their partner ("def ...
Prisoner's dilemma is a part of
game theory which involves two individuals choosing to
cooperate or
defect, reaping differential rewards. During phage coinfection, it pertains to viruses which produce more
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...
products than they use (cooperators) and viruses which use more
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...
products than they produce (defectors).
Coevolution
Coevolution
In biology, coevolution occurs when two or more species reciprocally affect each other's evolution through the process of natural selection. The term sometimes is used for two traits in the same species affecting each other's evolution, as well ...
is the study of the evolutionary influence that two
species
In biology, a species is the basic unit of Taxonomy (biology), classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of ...
have upon each other. Phage-bacterial coevolution is typically studied within the context of
phage community ecology.
References
Breitbart, M., F. Rohwer, and S. T. Abedon. 2005. Phage ecology and bacterial pathogenesis, p. 66-91. In M. K. Waldor, D. I. Friedman, and S. L. Adhya (eds.), Phages: Their Role in Bacterial Pathogenesis and Biotechnology. ASM Press, Washington DC.
d'Hérelle, F., and G. H. Smith. 1924. Immunity in Natural Infectious Disease. Williams & Wilkins Co., Baltimore.
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http://en.citizendium.org/wiki/Bacteriophage_experimental_evolution/Bibliography -
Laboratory
phylogenetics
In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups ...
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Experimental adaptation
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Adaptation to modified conditions
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phage T2 adaptation to low salt conditions.
Adaptation to high temperatures.
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Adaptation as compensation for deleterious mutations.
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Adaptation as toward change in phage
virulence
Virulence is a pathogen's or microorganism's ability to cause damage to a host.
In most, especially in animal systems, virulence refers to the degree of damage caused by a microbe to its host. The pathogenicity of an organism—its ability to ...
*Betts A., Vasse M., Kaltz O. & Hochberg M.E. (2013). Back to the future: evolving bacteriophages to increase their effectiveness against the pathogen Pseudomonas aeruginosa PAO1. Evol App
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*Bull, J. J., I. J. Molineux, and W. R. Rice. 1991. Selection for benevolence in a host-parasite system. Evolution 45:875-882.
The older phage literature contains numerous references to phage virulence, and phage virulence evolution. However, the reader should be warned that virulence is often used as a synonym for "not temperate", a usage which is neither employed here nor to be encouraged generally.
Impact of sex/
coinfection
Coinfection is the simultaneous infection of a host by multiple pathogen species. In virology, coinfection includes simultaneous infection of a single cell by two or more virus particles. An example is the coinfection of liver cells with h ...
*Froissart, R., C. O. Wilke, R. Montville, S. K. Remold, L. Chao, and P. E. Turner. 2004. Co-infection weakens selection against epistatic mutations in RNA viruses. Genetics
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Muller’s ratchet
*de la Peña, M., S. F. Elena, and A. Moya. 2000. Effect of deleterious mutation-accumulation on the fitness of RNA bacteriophage MS2. Evolution 54:686-691.
*L. Chao. 1990. Fitness of RNA virus decreased by Muller's ratchet. Nature 348:454-455.
Prisoner’s dilemma
The Prisoner's Dilemma is an example of a game analyzed in game theory. It is also a thought experiment that challenges two completely rational agents to a dilemma: cooperate with their partner for mutual reward, or betray their partner ("def ...
*Turner, P. E., and L. Chao. 2003. Escape from Prisoner's Dilemma in RNA phage _phi6. Am. Nat. 161:497-505.
*Turner, P. E., and L. Chao. 1999. Prisoner's dilemma in an RNA virus. Nature 398:441-443.
Coevolution
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*Buckling, A., and P. B. Rainey. 2002. Antagonistic coevolution between a bacterium and a bacteriophage. Proc. R. Soc. Lond. B Biol. Sci. 269:931-936.
*Buckling, A., and P. B. Rainey. 2002. The role of parasites in sympatric and allopatric host diversification. Nature 420:496-499.
*Lenski, R.E. and B.R. Levin. 1985. Constraints on the coevolution of bacteria and virulent phage – a model, some experiments and predictions for natural communities. Am. Nat. 125:585-602.
*Chao, L., B.R. Levin, and F.M. Stewart. 1977. A complex community in a simple habitat: an experimental study with bacteria and phage. Ecology. 58:369-378.
{{DEFAULTSORT:Bacteriophage Experimental Evolution
Evolutionary biology