When visuliazing a phylogram is it preferable to show ticks on the x axis or a scale bar?
Given an example tree with branch lengths in newick format (A:0.01,(B:0.02,C:0.05):0.02);, the two options are illustrated in the plot below:
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Both will work. The convention is the scale-bar and the rationale is below (which is a bit complicated).
By convention:
- the right-hand tree where there is a scale-bar and is the traditional diagram for phylograms.
- the left-hand tree scale-bar ("x-axis") is used for molecular clock representations, i.e. not for phylograms, but dendrograms.
In terms of clarity the "x-axis" (or extended scale bar) appears clearer. However, firstly, for a seasoned phylogenecist it makes no difference and simplicity is preferred. Secondly, there's coalescent theory.
The left-hand tree ... the thing is in a molecular clock representation the scale is a reverse axes starting at the right-hand tips. Whether thats time or genetic diversity its a good representation (well for time its essential) because coalescent theory means that there is zero genetic diversity for that taxa at time 0 (the idea is you are extrapolating, or reconstructing, the common ancestor). The representation you presented confuses that convention because 0 starts at the assumed node in the outgroup.
Thus the scale-bar is better.
