Not an evolutionary biologist, but thought someone here might have insights. A Google search mostly returns "the oldest bacterial genome/DNA we have recovered." However, my question is which bacterial genes evolved earliest, and are thus the oldest?
The idea came from a past project I worked on, in addition to a paper I read today. "The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota" discusses that SOD (superoxide dismutase, a radical scavenging gene), a gene I studied in my first research project, is conserved enough to be similar in bacterial metabarcoding performance to the genes 16S and rpoB (both ribosomal genes). The reason I mention a specific project I studied, is that I learned the SOD gene and other genes in the heavy metal detoxification system evolved prior to an oxygen rich atmosphere, making it extremely old (not sure an actual number for age).
How difficult is it to determine an actual evolutionary age of a given gene? And what tools would you use?
The short answer is that it's very difficult, if not borderline impossible, without ancestral sequences.
The field of ancient DNA has grown a lot recently, so we're beginning to get better calibrated molecular clocks, but i don't know if we could really say with any certainty which gene was truly the oldest, and it likely doesn't make much sense to ask that question, since things co-evolve.
BEAST is generally used for this, but horizontal gene transfer in bacteria makes it incredibly difficult to be certain.
really complicated question. Molecular clocks on very old and divergent genes would probably be quite wrong (correct me if I am wrong but I think that one of the assumptions of molecular clocks is that mutation rate has not changed in the history of that gene). Maybe you could start by listing all genes shared by most bacterias (and maybe present in eukaryotes and archaea)
Thank you. What would be a good tool recommendation to determine which genes are shared between all bacteria, then bacteria and archaea? Basically a MSA tool? Are there tools designed for metagenomes that get shotgun sequenced?
There are core/pan-genome tools out there, but I don't know if there are any which would scale to all bacteria/archaea etc. as there are simply too many genomes.
Most of them will use a sequence homology approach, and thus they will begin to breakdown once sequence homology becomes low. It would probably be better to use a HMM-based approach in this case - but again - slow.
For instance,
roaryis a widely used one, however it is only recommended for comparisons out to about the species level.