A phylogenetic tree is used to represent evolutionary relationships between organisms believed to have a common ancestry. Charles Darwin first represented evolutionary relationships as trees in his book On the Origin of Species. A phylogenetic tree connects organisms based on how closely related they are, with the distance between organisms on the tree indicating how long ago their common ancestor lived. While trees can provide insight, they have limitations and do not fully represent species histories due to factors like gene transfers.

1. What is a Phylogenetic Tree?What is a Phylogenetic Tree?

2. 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.

3. 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..

4. 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.

5. 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.

6. 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.

7. 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.

8. 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.

9. 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

10. 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

11. 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.