Re: Evolution in the laboratory

On 3/25/2025 5:29 AM, Ernest Major wrote:

An investigation of the response to regular but counteracting selection pressures.
 Out of 4 experimental populations, one went extinct, two reduced DNA repair/replication fidelity, and one evolved a hypermutable site at a particular locus.
 https://www.science.org/content/blog-post/evolving-ability-evolve
 

A type of switching sequence due to recombination has been known exist for decades.  I learned about yeast mating type switching as an undergraduate in the 1970's
https://pmc.ncbi.nlm.nih.gov/articles/PMC3338269/
This is a review of the system.
There is a directed genetic recombination event that alters the sequence of the yeast genome with respect to two loci.  Depending on which linear sequence exists the yeast is one of either two mating types.  Individual yeast can switch back and forth creating a different genomic sequence involving these two loci.
This is much more complicated than replication slipage resulting increasing or decreasing tandem duplicated sequences.
It is directed mutagenesis of the yeast genome that results in useful phenotypes needed for creating sexually reproducing yeast.  It would have evolved by natural mechanisms, and could have likely been adapted to creating hyper mutable loci that would allow survival in changing environmental conditions, but my guess is that this didn't happen because large diploid sexually reproducing populations that would exist with a huge amount of genetic variation in the population do not require this hypermutable system to retain genetic variation needed to survive in multiple environments.
The mutable system evolved in the bacteria isn't needed for diploid eukaryotes, and probably bacteria that survive with a lot of plasmid variation.
Another directed hyper mutable system is our adaptive immune response where single nucleotide changes are increased as well as recombining parts of the genome to create more sequence variation in the antibody binding regions of the immunoglobulins.  If just using this limited sequence alteration and differential recombination of variant sequences was not enough to evolve antibodies that can bind to specific antigens we would all likely be dead, and wouldn't survive for very long after birth.  This can be thought of directed mutation to achieve some unspecified goal, but selection is involved.  The single nucleotide changes and sequence recombinations are arbitrary relative to the antigen sequence, but the system selects for the sequences that have the best binding, more mutations are put into the binding regions, and selected again.  Mutation and selection are enough for our immune system to create highly specific antibodies and we can even create antibodies with new enzymatic functions that are produced during the successive iterations of mutation and selection.
Ron Okimoto