Question: How to know if the third codon position is evolving too fast
1
gravatar for qiyunzhu
4.8 years ago by
qiyunzhu130
United States
qiyunzhu130 wrote:

Dear all, I would like to know if there is any statistical test / program that allows me check whether the third codon position in my alignment is evolving too fast (too divergent) that it should not be included in a phylogenetic analysis. I googled around and didn't get any hits. I appreciate if you can share what you know on this topic.

ADD COMMENTlink modified 4.8 years ago by David W4.7k • written 4.8 years ago by qiyunzhu130

I don't get it, if the third codon is highly divergent that is information per se, why would you throw it out ?

ADD REPLYlink written 4.8 years ago by Gabriel R.2.6k

 

Because I fear (well, someone fears) that this could lead to bias in phylogenetic reconstruction.

ADD REPLYlink written 4.8 years ago by qiyunzhu130

Why are you studying nt seqs instead of aa seqs?

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by 5heikki8.4k

 

DNA provides more information, you know.

ADD REPLYlink written 4.8 years ago by qiyunzhu130

If you're studying really close lineages, like say strains of E. coli, then you're right. Otherwise, protein alignments almost certainly provide more information since things like saturation of the 3rd codon position can't happen there. For reference, see e.g. How To Tell If The Third Codon Position Is Saturated?.

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by 5heikki8.4k

You cannot just have "bias". Bias needs to be accompanied with a word like "it will bias towards [insert slant here]" 

 

ADD REPLYlink written 4.8 years ago by Gabriel R.2.6k

You may want to take a look at this post:

Question: How To Tell If The Third Codon Position Is Saturated?

How To Tell If The Third Codon Position Is Saturated?

ADD REPLYlink written 4.8 years ago by Biomonika (Noolean)3.0k
2
gravatar for David W
4.8 years ago by
David W4.7k
New Zealand
David W4.7k wrote:

There are a couple of tests for this, including Xia (2003, dx.doi.org/10.1016/S1055-7903(02)00326-3), which I gather is implemented in DAMBE. 

Probably the most common way to asses this though, is to plot the number of 3rd codon substitutions in a sequence against some corrected distance . If the curve "plateaus" you know you are hitting saturation.

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by David W4.7k

Thanks! I tried DAMBE. It works great!

ADD REPLYlink written 4.8 years ago by qiyunzhu130
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