Zero length branches on a phylogram

Question

[nancydong20]

Hello everyone!

I am currently comparing the orthologs of a single protein, doing multiple alignments and constructing a phylogram using MEGA7. I am seeing several zero-length branches (three out of seven branches). I search around online and see that this is assumed to be because the "descendants" have the same characteristics as the immediate ancestor. This makes sense as both human and mouse "branches" on my phylogram are zero-length, and they are 99.7% identical in sequence. However, there are other zero-length branches. It seems that this is frowned upon? I tried to use other models to construct the tree, and still see the same result.

Is a phylogram like this not usable? I have used MEGA7 quite a lot before to make phylogenetic trees from comparative genomic analyses, and this is the first time that I am seeing this.

Any input will be greatly appreciated!

[Cacau]

Presumably your sequences have too many identical nucleotides. Try to use data with more divergence.

[nancydong20]

Thank you very much for the quick reply!

I am comparing the sequences of a single protein across species, so unfortunately I don't know how I can use data with more divergence?

[Cacau]

You can add more taxa/sequences with potentially more divergence. The branches with 0 lengths are fine because they may reflect the fact that there is no difference between these species in the protein you analyze.

Answer 1

[Sergey Naumenko]

Hi Nancy!

1. Try to exclude mouse branch from the analysis - maybe your method is sensitive to the case with 2 almost identical sequences?

2. Are you aligning amino acids sequences or DNA? With DNA you will have larger divergence, because synonymous substitutions will be counted (however, depending of the model you are using to build a tree). If you are using amino acid alignments, try DNA.

3. Try to add an outgroup (a species which lies outside of your group of species).

4. Have you tried jmodeltest + raxml? Raxml should handle short branches well.

Best! SN

[nancydong20]

Thank you very much!