Iam doing research on the molecular phylogeography of the giant african snail in India. How can I calculate the mutation rate/time (time from which the change has occurred in the sequence)? Is there some specific software which could be used for that?
BEAST and other similar phylogenetic tools can do this, but you need some dated events in your tree such as knowing from the fossil record that one species split from another x million years ago.
If you don't have this in your won data, you may be able to find events in other snails sequenced by other people, perhaps the same species of snails that were separated when Japan split from the rest of Asia or something like that.
As an alternative you can try to use known mutation rates of closely related species (e.g. other terrestrial snails) to calculate the time since two alleles diverged. This may lead to wrong estimates if the number of mutations is very low. The calculation can be done in BEAST or as an estimate by hand (knowing the number of mutations and the rate of mutations/unit of time).
Just to add to Martin's comment -- use as many rates as you can find for similar species and calculate the mean.
The attached publication has an analysis of African/Asian snails, and they used 16S mitochondrial rRNA sequences. I aligned their sequences and built two trees myself, using PhyML and IQ-tree Maximum likelihood. I am sure my trees are not "better" or "worse" than the trees presented in the paper, but they illustrate that their may not be enough good information in this one gene to very accurately reconstruct the history of all these snails. But quite often even when a given gene cannot tell us about the deep history such as all of these snails or comparing all tetrapods, the gene can be quite accurate with recent history such as one of the clades of Gulella here, or the mammals within the tetrapods.
Dear, Keerthy
I advice you to set you a starting point from which you want to know this time of divergence. If you selected Africa, you need to have Reference sequences of this species from this region (Africa). The second thing is that the sequences compared must be from the same region of the genome. Counted the number of mutations between the two types of sequences (Africa and India) by bioinformatics SOFTWAR. It must be that these sequences is located at neutral genomic region and it is not highly repetitive region. Once the mutation estimated number between the two types of sequences you can estimate the divergence times since it is estimated that the mutation frequency of 10 -6 per generation
I assume you are looking for a rate of molecular evolution in terms of nucelotide substitution (NS). (This is not the same thing as a mutation rate). If you want to know how the rate for a lineage compares to another lineage, you should use multiple sequences for comparison, as has been said. If you want an NS rate over time, then you need fossils or another lineage NS rate based on fossils, as has been said. I would add that multiple fossils is a good idea, if possible. Here is an example of using multiple fossils for calibrating a molecular clock. Drovetski SV (2002) Molecular phylogeny of grouse: individual and combined performance of W-linked, autosomal, andmitochondrial loci. Systematic Biology, 51, 930 –945.
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