For a long time Biodiverse has allowed the user to visualise additional values on the phylogenetic tree in a spatial analysis tab. These include turnover of the branches in two neighbour sets, indices related to tree branched such as the weights used in a phylogenetic endemism calculation (another example is in this post).
This is very useful but before version 5 was limited to the set of lists in the spatial output being viewed.
From version 5 of Biodiverse you can plot lists results from any spatial output across all basedatas in your project. A big advantage of this is that you can run one analysis, for example a randomisation to generate a CANAPE output. Later you can run a calculation to see what the relative contribution of each clade in the tree is to each analysis window, without having to rerun the whole analysis to see the new list. This can be in a clone of the basedata so the randomisations won't be out of synch across a basedata's outputs (Biodiverse warns about this).
This is currently implemented as a menu option below the tree and map plots. Unfortunately this means it is not as obvious as it could be, and this is something still being worked on. There have also been minor changes since v5 was released, but only to how the selected list names are shown.
The screenshots below show it in operation for a very simple analysis that uses every cell in the basedata. This allows every cell in the tree to be coloured which works better as a demonstration.
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| The menu is at the lower right of the options below the map and tree plots. The exact location depends on your screen size. |
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| Users can select from any list across all spatial outputs across all basedatas in the project. In this case it is the PE weights in an analysis called Acacia_spatial0 in a basedata called Acacia1 (no, these are not informative names). |
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| And the tree branches are coloured as requested. |
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| The lists can also be categorical outputs. This is the results for a Range Weighted Branch Length Differences (RWiBaLD) analysis. More details for that are in Mishler et al. 2026. |
And that's pretty much it for the description. More of the theory is discussed in the posts linked to above.
Shawn Laffan
19-Jun-2026
For more details about Biodiverse, see http://shawnlaffan.github.io/biodiverse/
For a list of some of the analyses Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList
You can also join the Biodiverse-users mailing list at https://groups.google.com/group/Biodiverse-users or start a discussion at https://github.com/shawnlaffan/biodiverse/discussions
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