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I am looking for help (and possibly references) regarding the correct mapping of time in a cladogram. As far as I know, it is considered incorrect to draw a time axis diagonally in a cladogram as shown below:

enter image description here

This setting would lead to conclusions like: Species B and ancestor b lived at the same time, because they would both fall upon the same place on the time axis. But we know this is incorrect. Or is this an acceptable positioning for a time axis?

The image below correctly represents the time axis, if I'm not wrong, using a vertical axis.

Cladogram with vertical time axis

This positioning makes it clear that species B and b are not living at the same time. In this case, species B is alive and b is an extinct ancestor.

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    $\begingroup$ I think it really depends what you're trying to show. The folks in our lab that do these sort of diagrams make scaled cladograms for time (calculated by rates of mutation). $\endgroup$ – James Sep 26 '16 at 4:19
  • $\begingroup$ @James does your comment imply that the first diagram could make sense in some circumstance? Following, the OP's description I don't understand how the first diagram could make any sense. $\endgroup$ – Remi.b Sep 26 '16 at 17:38
  • $\begingroup$ Why did the question receive two close votes? $\endgroup$ – Remi.b Sep 26 '16 at 17:39
  • $\begingroup$ @James I am sorry, but I don't really understand your comment. I don't think it makes any difference what one is trying to show with the cladogram. A correct time axis shouldn't depend on the information being presented. The branch lenghts would matter in a phylogram, but that's not the case here. $\endgroup$ – JuanGrt Sep 26 '16 at 19:21
  • $\begingroup$ @Remi.b I voted to close because OP introduced a cladogram I have never seen before that is wrong and tells us why it's wrong. My comment was trying to explain that even the figure 2 axis has problems. For example is A as genetically distinct from a as D is from a, or is it just reflecting time passed? I'm not entirely sure what the question is... Figure 2 is better than Figure 1, but it's still arguably incorrect depending on what you want to show. $\endgroup$ – James Sep 27 '16 at 3:15
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In your first example, each species becomes "frozen in time" once it evolves implying there is no further change. A slightly more complex cladogram will help. enter image description here

Imagine the species A ancestor, after branching off the remote ancestor, serves as the ancestor to species E. You need to draw that line in some direction other than along A. Most popularily, that line would extend upward to the right. With the temporal axis as you first show, how did species E even evolve since A is frozen in time? Furthermore, the advantage of a vertical time axis allows us to see that species E appeared after species B and a bit before species C (horizontal dashed line).

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  • $\begingroup$ Thanks for your answer. That's precisely my line of thought as to why the first setting is wrong. I guess the person I'm trying to convince is connecting the nodes and ancestors to the time axis horizontally, instead of using a line perpendicular/normal to the axis. That's why this person said the first option is not wrong. $\endgroup$ – JuanGrt Sep 26 '16 at 19:29

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