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What is a Phylogenetic Tree?

What is a Phylogenetic Tree?. What is a phylogenetic tree used for?. A phylogenetic tree is used to help represent evolutionary relationships between organisms that are believed to have some common ancestry. The name “dendogram” is the broad term for trees.

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What is a Phylogenetic Tree?

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  1. What is a Phylogenetic Tree?

  2. What is a phylogenetic tree used for? • A phylogenetic tree is used to help represent evolutionary relationships between organisms that are believed to have some common ancestry. • The name “dendogram” is the broad term for trees.

  3. Where did the idea for a tree come from? • Charles Darwin is credited with the earliest representation of a phylogenetic tree published in his book The Origin of Species.

  4. What does this tree look like? • There are many different ways to represent the information found in a phylogenetic tree. • The basic format of a tree is generally in one of the two forms shown, although there are other ways to represent the data.

  5. What do the lines represent? • Each line on the tree represents one particular organism of interest. • The distance of the lines is used to determine how closely two organisms are related to one another or how long ago the may have had a common ancestor. • The line that connect all the other lines is the representation of the common ancestor that is being looked at to compare other organisms to.

  6. The “Rooted” vs. “Unrooted” tree • A rooted tree is used to make inferences about the most common ancestor of the leaves or branches of the tree. Most commonly the root is referred to as an “outgroup”. • An unrooted tree is used to make an illustration about the leaves or branches, but not make assumption regarding a common ancestor.

  7. The bifurcating tree • A tree that bifurcates has a maximum of 2 descendants arising from each of the interior nodes.

  8. The multi-furcating tree • A tree that multi-furcates has multiple descendants arising from each of the interior nodes.

  9. Where do I go to make a tree? • Many computational biology programs have dendogram programs. • An example of a free program that is available via the EMBL-EBI (European BioInformatics Institute) called ClutsalW or ClustalX. • You pick the program based on the format of your computer, i.e. command line verses graphical interface

  10. What criteria is important when building a tree? • There are many different things that you should consider as you get set to build your tree. • Some examples are; • Efficiency • Power • Consistency/Reliability • Robustness • Are underlying assumptions ever violated

  11. Limitations to the use of trees • It is important to remember that trees do have limitations. For example, trees are meant to provide insight into a research question and not intended to represent an entire species history. • Several factors, like gene transfers, may affect the output placed into a tree. • All knowledge of limitations related to DNA degradation over time must be considered, especially in the case of evolutionary trees aimed at ancient or extinct organisms.

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