Hello everyone, I hope y'all can answer a simple but problematic question.
I have been doing mutation accumulation experiment in 3 parallel lineages in bacteria and I now want to calculate the mutational rate after 300 generations of evolution.
I have been using this formula :
pooled number of mutations in all lineages / (genome size * number of generations * clones)
from Long et al. 2018
My problem is that I don't know how to account for the same mutations that occur in all 3 lineages: should I count them as 1 mutation overall, or should I count them independently ?
For instance my first lineage has 1 mutation, my second has 3 and my third has 5. But, one of the mutation (the only one in the 1st line) is also present in the 2nd and 3rd line.
Hence, in the formula, should my pooled number of mutations be 7 or 9?
I hope somebody can have an answer about that, that would greatly help me. As for most biologists, my maths skills aren't that good.....
Guillaume
You got 3 results from 3 experiments, so you should take the average of them which is 3 mutations per 300 generations. But how did you determine the "generations"? Is it 300 passages, taking a clone at the end of each passage? If you start with a single cell, after 300 binary splits (one cell divides into 2) you have 2 to the 299th power cells. which is quite a few. Did you sequence all of them and find that the entire population had 1 or 4 or 5 mutations? Obviously that is not the case.
The E. coli long term evolution project says it has now passed 50,000 "generations".
http://myxo.css.msu.edu/ecoli/
Many of the genomic changes are gene rearrangements, moving a block of genes from one region of the genome to another, which can greatly influence the expression level of the genes.
http://myxo.css.msu.edu/ecoli/genomicsdat.html
The best way to properly calculate mutation rates (even low) in bacteria or other microbes is to use the 'perfect order principle' elaborated by Khromov-Borisov et al., 2001 (Perfect order plating: principle and applications. Technical Tips Online, 2001. 6: 51-57).
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