About Collapsed Phylogenetic Tree
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8.8 years ago

I have a question about the statement "Branches corresponding to partitions that were reproduced in less than 50% of bootstrap replicates are collapsed". In the following paper, the author mentioned it whereas in the tree we can see nodes with bootstrap values lower than 50. I am confused by this. Could anyone lend me a hand? Thanks a lot!

Link: http://www.nature.com/nature/journal/v478/n7369/fig_tab/nature10464_F1.html [PAPER][1]

phylogenetics • 8.1k views
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Note that bootstrap values are associated with branches, not nodes. This is an important distinction - if you spend some time reading and thinking about how bootstrapping is used in the context of trees, and the role of bipartitions in this process, hopefully it will become clearer.

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8.8 years ago
qiyunzhu ▴ 430

"Collapsed" branches refer to those black or grey triangles you see in the figure. A triangle represents a branch, whose internal bootstrap values are lower than 50%. Therefore, drawing them out cannot convince readers. Therefore, the authors chose to hide them in an triangle. This is a common way of displaying trees.

You can try this by yourself: Open your tree in FigTree, select a branch, click "collapse". You will get a triangle.

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Thanks! Many branches are collapsed, however there are two nodes with bootstrap value lower than 50 which are not collapsed. I think this is not very rigorous if the authors have mentioned that "Branches corresponding to partitions that were reproduced in less than 50% of bootstrap replicates are collapsed"?

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I think you are right. I saw them in the figure. Also refer to 14134125465346445's answer.

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Thanks you very much!

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8.8 years ago

"Collapsed" means a group of branches are not shown, usually to make overall tree more visually clear.

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Thanks a lot. I got it!

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8.8 years ago

Hi, does anyone have any idea? I am waiting for any reply online.

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