9.8 years ago by
I have a list of orthologous genes and
a species tree, I would like to know
how to assign a dN/dS ratio for these
species for the ensembl of the
If you just want to know the global rate of protein sequence evolution you can choose between one of these methods:
- computing dN/dS individually and then computing the mean of those ratios (you should control their distribution first).
- concatenating the aligned sequences of all your genes and computing the dN/dS for this sequence.
You can check previously published papers using both techniques to know the pros/cons.
Of course this will only give you an overview of the selection occurring on your different branches but it still can be interesting to detect some differences in term of efficiency/pressure of selection between lineages.
For more fine-tuned analyses and to detect sites or branches whose patterns of selection might differ (typically to detect positive selection) you might perform more advanced analyses using different available PAML models.
Could this ratio be relative to a set
of genes not just one? If not is a
mean(dN/dS ratio) feasible to have an
idea on the speciation time depending
on a set of orthologous genes for each
As David said above this is not directly possible. dN/dS ratio will just allow you to assess the differences in terms of efficience/pressure of selection between your different branches.
The dS itself is an estimate of the neutral substitution rate but:
- it depends on the generation time
(along the whole branch), dN might be
higher if the generation time is
shorter in one branch.-
- you will need a molecular clock to know how many mutations occur per unit of time (this can be achieved using fossil data as previously mentioned).
modified 9.8 years ago
9.8 years ago by
Philippe • 1.9k