Answers.Body: <p>What I suggest is the description sounds like a polytomy (star tree). In a phylogenetic tree, a polytomy is a node that has more than two immediate descending branches.</p>
  <p>A polytomy can have many branches originate from one node. In contrast, a bifurcating tree only two branches stem from one node.</p>
  <p>A polygomy simply means that the evolutionary relationships can not be fully resolved to dichotomies, i.e. bifurcations. There's nothing wrong with this result and it makes reading the tree much easier. The model you describe looks fine.</p>
  <p>The only thing to watch if you're not looking at a dendrogram, but are looking at the phylogram. I doubt thats the explanation in any case.</p>
  <hr />
  <p>From the update. The figure you presented is an asymmetry phylogeny and is perfectly normal, for example this is observed in molluscs, described in <a href="https://www.pnas.org/doi/10.1073/pnas.93.25.14279" rel="nofollow noreferrer">Palmer 1995</a>.  If a species is moving directionally e.g. east to west across a massive landmass and at uniform geographic intervals establishing an ecological niche and forming a new species this will result in an asymmetric tree and might form a &quot;cline&quot;.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-03-19T10:19:34.233Z
Answers.Text: Thanks but my tree is fully resolved so i don't have explicit polytomies. I tried to create an example figure to clearly show what i mean.
Answers.UserDisplayName: Mirk
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-03-17T18:25:12.407Z
Answers.LastActivityDate: 2024-03-19T12:14:38.350Z
Answers.LastEditDate: 2024-03-19T12:14:38.350Z
Answers.UserDisplayName: M__
Body: <p>I used RAxML software on about 300 species mtDNA region (COI gene).<br />
  Unfortunately I used a highly variable region so my tree only has highly support values for branches close to the leaves.</p>
  <p>But I also noticed that all the nodes split into one leaf and one other node... Why is this happening?<br />
  Isn't it common that a node will simply split into 2 other nodes?</p>
  <p>I am using the <code>GTRGAMMA</code> function in RAxML (I don't know if that may be the cause).</p>
  <p>Do you have any suggestions on this topic? Should I be suspicious of my tree if I don't see any node splitting into 2 other nodes?</p>
  <p><strong>More info</strong></p>
  <ul>
  <li>Alignment algorithm: MUSCLE</li>
  <li>Graphical example:  <a href="https://i.sstatic.net/cl91c.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/cl91c.png" alt="enter image description here" /></a><br />
  My tree looks like the one on the left. Every bifurcation links to a tip/leaf (terminal node) of the tree and a non-terminal node of the tree.  It sounds suspicious to me that I never observe a bifurcation that splits into 2 non-terminal nodes of the tree (figure on the right)</li>
  </ul>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-15T12:19:51.763Z
Comments.Text: What do you mean by "But I also noticed that all the nodes split into one leaf and one other node... Why is this happening?" ?
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-15T19:51:48.867Z
Comments.Text: Anyway if you can provide a clearer explanation I can probably answer your question @Mirk
Comments.UserDisplayName: M__
Tags: <phylogenetics><phylogeny>
Title: Why is my phylogenetic tree always splitting into one leaf and one node?
ThreadText: # Why is my phylogenetic tree always splitting into one leaf and one node?
  
  (Asked by: username_0 on 2024-03-14)
  
  I used RAxML software on about 300 species mtDNA region (COI gene).  
  Unfortunately I used a highly variable region so my tree only has highly support values for branches close to the leaves.
  
  But I also noticed that all the nodes split into one leaf and one other node... Why is this happening?  
  Isn't it common that a node will simply split into 2 other nodes?
  
  I am using the `GTRGAMMA` function in RAxML (I don't know if that may be the cause).
  
  Do you have any suggestions on this topic? Should I be suspicious of my tree if I don't see any node splitting into 2 other nodes?
  
  **More info**
  
  * Alignment algorithm: MUSCLE
  * Graphical example: [![enter image description here](https://i.sstatic.net/cl91c.png)](https://i.sstatic.net/cl91c.png)  
    My tree looks like the one on the left. Every bifurcation links to a tip/leaf (terminal node) of the tree and a non-terminal node of the tree. It sounds suspicious to me that I never observe a bifurcation that splits into 2 non-terminal nodes of the tree (figure on the right)
  
  **Tags:** phylogenetics, phylogeny
  
  > **Comments:**
  > **username_1**: What do you mean by "But I also noticed that all the nodes split into one leaf and one other node... Why is this happening?" ?  
  > **username_1**: Anyway if you can provide a clearer explanation I can probably answer your question @username_0  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2024-03-17. Score: 1 | Accepted answer
  
  What I suggest is the description sounds like a polytomy (star tree). In a phylogenetic tree, a polytomy is a node that has more than two immediate descending branches.
  
  A polytomy can have many branches originate from one node. In contrast, a bifurcating tree only two branches stem from one node.
  
  A polygomy simply means that the evolutionary relationships can not be fully resolved to dichotomies, i.e. bifurcations. There's nothing wrong with this result and it makes reading the tree much easier. The model you describe looks fine.
  
  The only thing to watch if you're not looking at a dendrogram, but are looking at the phylogram. I doubt thats the explanation in any case.
  
  ---
  
  From the update. The figure you presented is an asymmetry phylogeny and is perfectly normal, for example this is observed in molluscs, described in [Palmer 1995](https://www.pnas.org/doi/10.1073/pnas.93.25.14279). If a species is moving directionally e.g. east to west across a massive landmass and at uniform geographic intervals establishing an ecological niche and forming a new species this will result in an asymmetric tree and might form a "cline".
  
  > **Comments:**
  > **username_0**: Thanks but my tree is fully resolved so i don't have explicit polytomies. I tried to create an example figure to clearly show what i mean.  
  
  ---
  
  