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Phylogenetic tree  [ Taxonomy  ]

Dictionary of botanic terminology - index of names

Synonyms: Cladogram,  Tree diagram
     
  Definition  
   
Phylogenetic Tree:

Look at the tree below and describe what sister relationships it depicts:

Phylogenetic Tree:

Look at the tree below and describe what sister relationships it depicts:

Tree 1:

Species 5 is the sister group to species 6

Species 3 is the sister group to species 4

The clade of species 3+4 is the sister group to the clade of species 5+6

The clade of species (3/4)+(5/6) is sister to species 2

Species 1 is sister to the clade containing all the other species

 

Remember, trees can be rotated at the nodes without changing the topology (i.e. without changing the relationships represented in the tree).

For example, look at the tree below.

Tree 2:

Although tree 2 looks superficially quite different from tree1, examine the relationships we deduced from tree 1 and see if they still apply.

Species 5 is the sister group to species 6. . . YES

Species 3 is the sister group to species 4. . . YES

The clade of species 3+4 is the sister group to the clade of species 5+6. . . YES

The clade of species (3/4)+(5/6) is sister to species 2. . . YES

Species 1 is sister to the clade containing all the other species. . . YES

 

THUS, Tree 1 and Tree 2 are identical trees that are simply drawn differently (rotated at the nodes).

 

 

Now examine tree #3 below in the same way

Tree 3:

Species 5 is the sister group to species 6. . .NO

Species 3 is the sister group to species 4. . .YES

The clade of species 3+4 is the sister group to the clade of species 5+6. . . NO

The clade of species (3/4)+(5/6) is sister to species 2. . . NO

Species 1 is sister to the clade containing all the other species. . . YES

 

Thus, although some branches in the tree are similar to tree 1 and tree 2, tree 3 is NOT the same tree!

 

 

 

Inferring Ancestral Characteristics on a Tree:

Look at the tree below and try to infer the character state (Blue or Red) of the ancestral node

 

Let's begin by guessing that the mystery ancestor was red

In this case, we would have to have the evolution of blue flowers twice in order to best explain the tree (i.e. 2 evolutionary steps).

 

Now let's see what happens if we guess blue to be the ancestral character.

In this case, the simplest explanation is that red flowers evolved once (one evolutionary step). Since it only calls for one change rather than two, assuming blue to be character at the ancestral node is the best and most likely explanation.

 

Monophyly vs. Paraphyly:

The tree below first shows an outgroup (family Outgroupaceae) to the left, and some other species labeled 2 - 6.

If we want to name these ingroup species as families, we want to be sure to only name Monophyletic groups. At first, a logical way to group these ingroup plants as families could be to segregate them by color into two families, Blueaceae (containing species 2, 5, and 6) and Redaceae (species 3 and 4).

 

First, we'll examine if Redaceae is a good monophyletic group. Follow the branches down to the node that would represent their common ancestor of species 3 and 4.

 

We can easily see that Redaceae would include that ancestor and all of its descendants (only species 3 and 4). Red color is a derived trait that is shared between those two species(a synapomorphy), and thus groups them together as a monophyletic group.

 

Now find the common ancestor of all of the blue species

 

Follow all the descendant branches from that common ancestor. The red species 3 and 4 are descendents of that ancestor too!

Grouping the blue species together based on the retention of an ancestral characer state makes it a paraphyletic group. Thus, naming species 2, 5, and 6 as the family Blueaceae is not acceptable.

 

So what are some monophyletic groups we could name as families? If we include species 3 and 4 in the Blueaceae (even though they're red!), it makes it a monophyletic family.

Taxonomists who combine formerly recognized families in order to make a larger monophyletic family are often called lumpers. Another way to create monophyletics is to be what is called a splitter. Splitters divide the larger monophyletic group into smaller monophyletic families, often with some families containing only one genus or species.

 

A splitter might divide the ingroup into three families in order to retain Redaceae as its own family. To do this, you must separate out species 2 as its own family. In this case, you could still call species 5 and 6 'Blueaceae' since they form a monophyletic clade. Species 2 would have its own family name (Neoblueaceae, perhaps?). And Redaceae would be a monophyletic family that is no longer included in a larger paraphyletic group.

Both splitting and lumping are equally correct and viable solutions, as long as the resulting groups are monophyletic. Sometimes lumping results in excessively huge groups or causes a popular, easily recognized taxon to be eliminated at the family level. Splitting can lead to a ridiculous number of families to be recognized and disintegration of natural groups at the family level. Both philosophies are widely applied. And both provide headaches to botanists who are constantly having to relearn plants under a new naming system.

 

Polytomy:

When a phylogenetic tree has more than two branches radiating from a node, it is called a polytomy. Polytomies arise when the relationships between a group of taxa are unresolved. For example, look at the polytomy in the tree below

The relationships between species 3 , 4, and 5 are unresolved. Species 4 and 5 could be a sister group, with species 3 as the sister group to their clade.

Alternatively, species 3 and 5 could be a sister group, or species 3 and 4 could be a sister group.

The polytomy shown in the original tree means that any one of the three trees that followed might be correct, but it is unresolved, and we just don't know the true relationships at that node..

 

     
 

 


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