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I would like to know the method of judging the distance between two nodes in the phylogenetic tree. For example, in the diagram below, is node 299 closer to node 151, or closer to node 201?enter image description here

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    – David
    Commented Nov 19, 2022 at 16:51

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It depends somewhat what you mean by "closer", but phylogenetic distances are usually judged by "branch length". By this logic, just eyeballing it, node299 is almost certainly closer to node151 than node201.

This means roughly "how far you have to travel up and down the tree to connect 2 nodes". From node299, it looks like you have to actually go back down the tree to pass through node151 to get to node201, so node151 is really in the middle here. Note that branches represent evolutionary time, so that the branch length distance between two descendants of the same ancestor can be expected to be around twice the evolutionary time experienced by each descendant relative to ancestor.

The arrangement of the tree in the left to right axis is arbitrary, for example for any subgroup you can flip it 180º and there is no change in the actual topology of the tree.

This is harder to see in a circular layout like this, but in a standard cladogram it is more obvious:

cladogram, source https://www.mymydiy.com/how-to-make-a-cladogram/

As one example, you can take the "Dinosauria" clade and flip it so that the chicken is closer to the the crocodile, and there is no difference.

In this specific case, you are noting the "root" of the tree as one of your nodes (node151). The placement of the root is generally the most uncertain/poorly estimated part of the tree, so making arguments based on it is non-ideal, but from the point of view of computation, the answer is unambiguous.

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  • $\begingroup$ Thanks a lot for your answer. But I have another problem. I want to know why the distance between two nodes evolved from the same ancestor is farther than the distance between the two nodes and the ancestor node. Is this situation caused by the introduction of genes from other species during the evolution of these two nodes? $\endgroup$
    – rona
    Commented Nov 20, 2022 at 6:31
  • $\begingroup$ @rona not sure that i understand. The distance (ancestor to descendant 1) or (ancestor to descendant 2) is always going to be shorter than the distance (ancestor to descendant 1) + (ancestor to descendant 2), if we're talking about the same ancestor. Negative branch lengths are technically possible but so rare they're not worth considering. Each of those lineages has experienced evolutionary time. Updated answer in bold to be explicit. $\endgroup$ Commented Nov 20, 2022 at 16:12

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