Phylogenetic Analyses Of Sequences Containing Mixed Bases

Question

[Hugo D]

Dear all, I have a dataset of DNA sequences containing a large amount of mixed bases. Most phylogenetic programs I have used so far do not take into account positions where at least one sequence has a mixed-base (edit : or I failed to use the right setting for this utilization). This results in a heavy loss of information in my case.

Therefore, I am now searching for phylogenetic programs or tips to construct NJ, ML and Bayesian trees while considering mixed bases as informative characters.

Do you have any advices ?

hugo

[Whetting]

what do you mean by a mixed base? Do you mean IUPAC code (e.g. Y for pyrimidine?)?

[Hugo D]

My samples exhibit mtDNA heteroplasmy. This results in some individuals producing mixed signals with sanger sequencing at a few positions. I do use IUPAC code for these positions.

[Naren]

Have you tried MEGA5?

[Josh Herr]

This is my opinion, but I think MEGA is a horrible program. I am not aware of any phylogenetic analysis programs that DON'T accept ambiguous bases. Information in user manuals will explain how each respective program codes for ambiguous bases or unresolved sequencing calls.

[Hugo D]

Ok. Thanks. I will study this further.

[Hugo D]

I did. MEGA can handle sequences with ambiguous bases. However, it seems that it deletes positions with ambiguity for NJ and ML tree constructions. Maybe I do not set it properly ?

Answer 1

[David W]

Hugo,

Lots of software will handle ambiguous bases (RAxML, MrBayes,dnadist...) , but there are some things to think about.

1. Are you sure you are looking and mtDNA heteroplasmy, and not a nuclear pseudo-gene (NUMT) that is being co-amplified
2. If you really do have heteroplasmy you don't have ambiguity, you have two mitochondrial haplotypes. Munging that signal into a single consensus can (but won't necessarily) have unwanted consequences (see White et al, 2008 for some background on this).

[Hugo D]

Hi David, I am aware of these points. My organism seems to have complex mtDNA inheritance with frequent paternal leakage. Thanks for reminding me this review. hugo