How to read a phylogenetic tree

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What's the point?

  1. To be able to interpret a phylogenetic tree in either phenogram or dendrogram fomat
  2. To be able to interconvert trees from one format to another

There is a Tree problem set that tests these skills.

A phylogenetic tree is a representation of the evolutionary/geneological relationships between a collection of organisms (or molecular sequences). There are many different ways to draw these trees, but they share a common set of features (please note that the trees that follow are generalized approximations used only for example and do not accurately represent the relationships between apes):

Example tree
Example phylogenetic tree
by Jim Brown, taken from vague memories from Anthropology classes taken as an undergrad in the 70's

  • Scale. This typically is either time or evolutionay divergence. Trees with a time scale are based on some form of physical data, such as a fossil record, that provide dating information. If the scale is time, all modern organisms should obviously be shown at the same part of the scale. More often, the scale is evolutionary divergence, some measure of change in the organisms (or molecules). Because the extent of divergence is usually different in various parts of the tree, this is usually depicted by varying the lengths of the branches and providing a scale bar.
  • Terminal nodes. These are the ends of the branches of the evolutionary tree - typically the modern organisms (or molecules) that are being compared, but in some cases the ends of evolutionary branches that became extinct.
  • Internal nodes. These represent the last common ancestors of all of the organisms (or molecules) bound by this node.
  • Root. This is the 'base' of the tree - the last common ancestor of all of the organisms (or molecules) in the tree. It is not always possible to identify the root of a tree - typically, this requires either physical data (e.g. a fossil record) or data about organisms outside of the part of the tree shown.
  • Branches. These are the connections between nodes in the tree. These represent to evolutionary pathway between common ancestors (internal nodes) and modern organisms (terminal nodes). The length of these branches is defined by the scale - each branch represents a certain amount of historical time, if time is the scale used in the tree, or a certain amount of evolutionary change, if evolutionary divergence is the scale used in the tree.

There are a variety of ways of drawing trees. Here are two other trees of the same organisms that also use time as the scale:

example tree
Example trees - Phenograms
Jim Brown - hypothetical, more-or-less from memory, for example only

The scales (time) in these two trees are horizontal rather than vertical, and the braches are simple diagonal lines connecting nodes, but the information in these trees is the same as in the previous tree. These trees are phenograms - the scale read by horizontal distance. Also notice that the order of the terminal nodes is irrelevant - only the topology of the tree and the lengths of the connections count. The positions of the branches and nodes can be switched around at will. as long as the nodes and their connections are not broken and remain true to the scale.

example trees
Example trees - Dendrograms
Jim Brown - hypothetical, more-or-less from memory, for example only

These trees use phylogenetic distance as the scale - measured by the extent of divergence of some sequence. Notice that the lengths of the branches are uneven, because the rates of evolutionary change in these sequences is not constant. The tree on the right is rootless - no root is shown. In order to root a tree (as in the tree to the left), you need data from the fossil record, or other physical information, or in a molecular-based tree, you need to use an outgroup in the tree to place the root. For example, in this tree of apes, you could root the tree using data from an Old World monkey.

These trees are dendrograms - the scale is measured along the branch lengths rather than horizontally or vertically. The evolutionary distance between any two organisms is the total of the lengths of all of the branhes that connect them. For example, the evolutionary distance between lowland gorillas and lowland chimps would be about 0.1:

example trees
Example trees - Dendrogram, showing how distance can be read
Jim Brown - hypothetical, more-or-less from memory, for example only

A phenogram can also be used with an evolutionary distance scale - in this case, remember that the scale (evolutionary distance) is measured only in horizontal (or vertical) distance:

example tree
Example phenogram showing how distance can be read
Jim Brown - hypothetical, more-or-less from memory, for example only

Because evolutionary rates are not constant, some organisms have changed more than others since their common ancestry. In the example above, the sequences of humans have changed more than those of lowland chimps since their last common ancestor. Lowland chimps, then are primitive relative to humans with respect to this sequence - humans are more highly derived than chimps, again with respect to this sequence. If the traits of an organism overall are more similar to the ancestor than in the other members of that group, that organism is thought of as a primitive organism. This is very useful information, but it can be dangerous - in most cases, the traits of an organism are not evolving at similar or constant rates, and so an organism might be primitive in most traits but highly derived in others. Sharks, for example, are primitive fish with respect to many traits (cartilaginous skeletons, dentat scales, &c) but are highly derived with respect to other (immunologically, and their electrosensory system). The danger is that there is a tendency to confuse generally primitive organisms with ancestors. For example, chimps are morphologically more primitive than humans, but chimps are not ancestors of humans - the common ancestor of humans and chimps was not a chimp. Chimps are modern organisms! They just share more morphological similarity to the common ancestor of humans and chimps than do humans.