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Reading Phylogenetic Trees

Gloria Rendon

NCSANovember, 2008

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Tips, Internal Nodes, Edges

The tips of the phylogenetic tree represent groups ofdescendent taxa (often species) The internal nodes of the tree represent the common

ancestors of those descendents. The tips are the present and the internal nodes are the

past. The edge lengths in some trees correspond to time

estimates evolutionary time.

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Sister Groups and a common ancestor

Two descendents that split from the same node are calledsister groups. In the trees above, species A & B are sister groups

they are each other's closest relatives; which means that: i) they have a lot of evolutionary history in common and very little

evolutionary history that is unique to either one of the two sisterspecies and ii) that they have a common ancestor that is unique to them.

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Equivalent trees

For any speciation event on a phylogeny, the choice ofwhich lineage goes to the right and which one goes to theleft is arbitrary. These three phylogenies are therefore equivalent.

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Outgroup

Many phylogenies also include an outgroup a taxonoutside the group of interest. All the members of the group of interest are more closely

related to each other than they are to the outgroup.Hence, the outgroup stems from the base of the tree. An outgroup can give you a sense of where on the bigger

tree of life the main group of organisms falls. It is alsouseful when constructing evolutionary trees.

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Branches and clades

Evolutionary trees depict

clades. A clade is a group of

organisms that are alldescendent from acommon ancestor; thus a

clade includes an ancestorand all descendents of thatancestor. You can think of a clade as

a branch on the tree of life.

Some examples of cladesand non-clades in aphylogenetic tree areshown here

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More on clades. Nested clades

Clades are nested within one another they form anested hierarchy. A clade may include many thousands of species or just a

few.

Some examples of clades at different levels are markedon the phylogenies above. Notice how clades can be nested within larger clades.

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Types of trees: unrooted vs rooted

A rooted phylogenetic tree is a tree with a unique rootnode corresponding to the (usually imputed) most recentcommon ancestor of all the entities at the leaves (akatips) of the tree. A rooted tree is a binary tree.

Unrooted trees illustrate the relatedness of the leafnodes without making assumptions about commonancestry. An unrooted tree has a node with three edges;the rest of the nodes have up to two edges.

http://en.wikipedia.org/wiki/Imputation_%28statistics%29http://en.wikipedia.org/wiki/Imputation_%28statistics%29

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Phylogenetic Trees and classification

Phylogenetic trees classify organisms into clades. By contrast, theLinnaean system of classification assigns every organism a kingdom,phylum, class, order, family, genus, and species. The phylogenetictree depicted here identifies four clades

To build a phylogenetic tree biologists collect data about the characters of

each organism they are interested in. Characters are heritable traits that canbe compared across organisms, such as physical characteristics(morphology), genetic sequences, and behavioral traits.

Some molecular biologists (like C. Woese) build phylogenetic trees fromgenetic sequences alone.

http://evolution.berkeley.edu/evolibrary/glossary/glossary_popup.php?word=Linnaean+classificationhttp://evolution.berkeley.edu/evolibrary/glossary/glossary_popup.php?word=characterhttp://evolution.berkeley.edu/evolibrary/glossary/glossary_popup.php?word=characterhttp://evolution.berkeley.edu/evolibrary/glossary/glossary_popup.php?word=Linnaean+classification