Answers.Body: <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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Body: <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>
  
Tags: <phylogenetics><phylogeny><visualization>
Title: Using ticks on the x axis or a scale bar when visualisizing a phylogram?
ThreadText: # 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
  
  
  ---
  
  ## 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.
  
  
  ---
  
  