<p><a href="https://i.sstatic.net/XsQAC.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/XsQAC.png" alt="A figure comprising two subplots, on the left a phylogram with ticks on the x axis, on the right a phylogram with a scale bar" /></a></p>
<p>Both will work. The convention is the scale-bar and the rationale is below (which is a bit complicated).</p>
<p>By convention:</p>
<ul>
<li>the right-hand tree where there is a scale-bar and is the traditional diagram for phylograms.</li>
<li>the left-hand tree scale-bar (&quot;x-axis&quot;) is used for molecular clock representations, i.e. not for phylograms, but dendrograms.</li>
</ul>
<p>In terms of clarity the &quot;x-axis&quot; (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.</p>
<p>The left-hand tree ... the thing is in a molecular clock representation the scale is a <strong>reverse axes</strong> starting at the right-hand tips. Whether thats time or genetic diversity its a good representation (well for time its essential) <em>because</em> 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.</p>
<p>Thus the scale-bar is better.</p>

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2023-03-28T16:20:31.130Z
2023-03-28T16:27:00.613Z
2023-03-28T16:27:00.613Z
M__
<p>When visuliazing a <a href="https://en.wikipedia.org/wiki/Phylogenetic_tree#Phylogram" rel="nofollow noreferrer">phylogram</a> is it preferable to show ticks on the x axis or a scale bar?</p>
<p>Given an example tree with branch lengths in newick format <code>(A:0.01,(B:0.02,C:0.05):0.02);</code>, the two options are illustrated in the plot below:</p>
<p><a href="https://i.sstatic.net/XsQAC.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/XsQAC.png" alt="A figure comprising two subplots, on the left a phylogram with ticks on the x axis, on the right a phylogram with a scale bar" /></a></p>

<phylogenetics><phylogeny><visualization>
Using ticks on the x axis or a scale bar when visualisizing a phylogram?
# Using ticks on the x axis or a scale bar when visualisizing a phylogram?

(Asked by: username_0 on 2023-03-28)

When visuliazing a [phylogram](https://en.wikipedia.org/wiki/Phylogenetic_tree#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:

[![A figure comprising two subplots, on the left a phylogram with ticks on the x axis, on the right a phylogram with a scale bar](https://i.sstatic.net/XsQAC.png)](https://i.sstatic.net/XsQAC.png)

**Tags:** phylogenetics, phylogeny, visualization

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## 1 answers

### Answer by username_1 on 2023-03-28. Score: 1 | Accepted answer

[![A figure comprising two subplots, on the left a phylogram with ticks on the x axis, on the right a phylogram with a scale bar](https://i.sstatic.net/XsQAC.png)](https://i.sstatic.net/XsQAC.png)

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.


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