What is a phylogenetic tree

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Information about What is a phylogenetic tree

Published on March 17, 2014

Author: islamnabi

Source: slideshare.net

What is a Phylogenetic Tree?What is a Phylogenetic Tree?

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

Where did the idea for a tree comeWhere did the idea for a tree come from?from?  Charles Darwin is credited with the earliestCharles Darwin is credited with the earliest representation of a phylogenetic treerepresentation of a phylogenetic tree published in his bookpublished in his book The Origin ofThe Origin of SpeciesSpecies..

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

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

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

The bifurcating treeThe bifurcating tree  A tree that bifurcates has a maximum of 2A tree that bifurcates has a maximum of 2 descendants arising from each of thedescendants arising from each of the interior nodes.interior nodes.

The multi-furcating treeThe multi-furcating tree  A tree that multi-furcates has multipleA tree that multi-furcates has multiple descendants arising from each of thedescendants arising from each of the interior nodes.interior nodes.

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

What criteria is important whenWhat criteria is important when building a tree?building a tree?  There are many different things that youThere are many different things that you should consider as you get set to buildshould consider as you get set to build your tree.your tree.  Some examples are;Some examples are;  EfficiencyEfficiency  PowerPower  Consistency/ReliabilityConsistency/Reliability  RobustnessRobustness  Are underlying assumptions ever violatedAre underlying assumptions ever violated

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

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