Hi all,
I would like to estimate the relative rates of evolution of a bacterial gene locus (protein-coding) across time. The length of the locus ranges between 10000bp and 25000bp. I have performed multiple sequence alignment using CLUSTALW in MEGA6 using 90 sequences corresponding to the locus. I would like to create a model to estimate the relative rates of evolution of each locus - how rapidly a sequence can change into any other 89 sequences. I would like to check rates of recombination and base substitutions among the sequences. Please tell me any method or protocol for estimating the evolutionary rates.
Thank you.
Hi,
In my opinion, this may not be an very straightforward approach for inferring evolution of the locus of interest because
1) the locus length is highy variable (10K to 25k) and hence there will be many long regions missing in many sequences. These needs to handled carefully using multiple parameters and if needed algorithms
2) see how the gaps are placed in MSA and whether they needs to be edited and how they are handled in the alignment program. if needed use another program also
3) indel regions may not allow to see how the site has evolved in all sequences...you need to use different approach for different regions
4) inferrring molecular evolution is also based on shared and evolved characters...if there are too many differences (indels) between too sequences it may be difficult to infer their divergence correctly...Better would be to use similar length sequences for evolution
5) The evolution of a locus can be studied but it may not be useful for inferring evolution of the organisms
See the concerns related to MSA and then move forward to evoltionary inferences. A wrong MSA file will yield incorrect infromation later
10,000 to 25,000 bases sounds like more than a single bacterial gene. Are you looking at a complete operon or something even larger? To measure rate of change vs time, you need many dated events in the phylogeny (evolutionary history) and for most bacteria we do not have a real solid fossil record for example for telling us when Eshcerichia coli last shared a common ancestor with Salmonella typhi. As you note, recombination is rampant within most genomic regions of that size over timescales far shorter than many other evolutionary processes. And the more similar the bacterial "species" or "strains" are to each other the more often they recombine and the less easy it is to detect the recombination events. Escherichia coli exchange plasmids and phages much more often with other Escherichia coli, than they do with Listeria or other more distantly related bacteria.
Thank you for your replies. I would like to mention the assumptions I would like to make. Please tell me whether I am correct in the assumptions or not.
After constructing a phylogentic tree by maximum parsimony using a boot strap of 1000, I observed the sequences cluster into two major clades. Now I would like to assess the rates of divergence among two closely related sequences, which will be grouped in a clade. That way I can eliminate the presence of large indels. Sequences with large indels must have evolved by recombination rather than substitution. So I would like to calculate the rates of substitution among closely related sequences and rates of recombination among distantly related sequences.
To do the following calculations, please tell me any protocol or methods to follow in MEGA or any other software.
Thank you.
Unless you have a dated event, or good estimate, of at least one node in the tree, there is no way to estimate the rates. Do you know how many years ago the main clades shared a common ancestor? Are there two closely related sequences that you know shared an ancestor x years ago?
Insertions and deletions can happen by a variety of mechanisms other than recombination. And recombination will create strains with mosaic gene regions, with some of the gene region derived from one lineage while the rest of the gene region is derived from a different history. In those cases, a phylogeny is a misrepresentation of the history.
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