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I am wondering what the proven mechanisms of micro-evolution are. For instance, in the case of bacteria, when a strain evolves that is resistant to antibiotics

1) Is the genetic combination that enables the bacteria to resist the antibiotics present the entire time and only made prevalent by the environment through natural selection, or do mutations occur to the DNA that change the organism so that it can then survive?

2) With the antibiotics removed, is the evolved strain generally more resilient in a normal environment or weaker?

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    $\begingroup$ A good answer would require writing a whole introduction to evolutionary biology which is way too broad. You should have a look at a very introductory course to evolutionary biology such as Understanding Evolution by UC Berkeley for example. $\endgroup$ – Remi.b Oct 8 '16 at 0:37
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    $\begingroup$ In short, (1) No, mutations do not occur strategically in order to adapt. They just occur, their effect on the phenotype is random but sometimes such random effect is beneficial and it then gets selected for. (2) A priori we would think there is a trade-off and evolving defense against an antibiotic would come at a cost which makes this antibiotic-resistent strain less competitive in an environment without antibiotic. However, this prediction might well fail in many cases where such trade-off do not exist or are negligible $\endgroup$ – Remi.b Oct 8 '16 at 2:05
  • $\begingroup$ I agree with remi.b that the question suggests some misconception about evolution. The question could be refined to asking about the relative importance/contribution, to the process of adaptation, made by standing and novel genetic variation which is an important topic in evolutionary biology. $\endgroup$ – rg255 Oct 8 '16 at 3:15
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    $\begingroup$ Please note that, to biologists, there is no such thing as "microevolution" or "macroevolution" - there is just evolution. $\endgroup$ – MattDMo Oct 9 '16 at 0:11
  • $\begingroup$ @MattDMo - Remi. b notes in one of his answers that it was microbiologists themselves who invented the term macro/micro evolution (biology.stackexchange.com/questions/39711/…). If this terminology is unacceptable then what terms are used to draw distinctions between evolutionary behavior observed in a lab vs. that which is inferred from fossil records and theory? I would think that this is a useful distinction. $\endgroup$ – Ian Oct 10 '16 at 20:39
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There are several mechanisms through which a bacteria can evolve antibiotic resistance.

One way is by acquiring an already-existing gene from another bacteria or virus by what is called horizontal gene transfer. In this case, there is no requirement for any mutation to occur although the new gene can be integrated into the host genome and so, in a sense, the genome itself is mutated since it now contains a new gene but the gene itself is not.

Another way of acquiring resistance is indeed by genetic mutations. One beautiful example of this is the resistance acquired toward some aminoglycoside antibiotics. This class of antibiotics interferes with the ribosome assembly by binding to a specific site of it. In some cases, a simple point mutation of the aminoglycoside-binding-site is enough to acquire resistance. Some strains of bacteria exhibit aminoglycoside resistance due to a transport defect (mutation of a channel for example) or membrane impermeabilization (mutation of a pump), acquired by other mutations. Others use specific enzymes to digest the antibiotic, different variants (mutants) of such enzymes broaden the spectrum of resistance. There are many other different cases in which a simple mutation is enough to acquire resistance.

Here some references:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC182597/

http://www.uphs.upenn.edu/bugdrug/antibiotic_manual/aminoglycosideresistance.htm

http://www.antibioresistance.be/aminoglycosides.html

https://www.ncbi.nlm.nih.gov/pubmed/27690121

https://www.ncbi.nlm.nih.gov/pubmed/27651364

https://www.ncbi.nlm.nih.gov/pubmed/27699821

With the antibiotics removed, is the evolved strain generally more resilient in a normal environment or weaker? No, in general, there is no extra advantage in being resistant to an antibiotic if the antibiotic is not present.

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