Phylogenetic analysis seeks to find the

simplest (i.e., most parsimonious) tree(s)

from a given set of observations

Observations are:

• The taxa we wish to study (the ingroup)

• The characters (traits, features) possessed by the taxa

We seek to find the most parsimonious tree possible to explain the distribution of traits observed in the taxa

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3 Alternative, Mutally-Exclusive Dichotomous Cladograms

How Do We Choose Between Them?

Outgroup

(Not an Ancestor, but a Stand-in to represent the Ancestral Condition)

PP RD CEFur/Mane No Yes Yes YesToes/Foot Many Toes One Hoof One Hoof One HoofWings No No Yes YesHorn No No No YesEyes Yes Yes Yes YesTail Yes Yes Yes YesMouth Yes Yes Yes Yes

Primitive (ancestral) State Derived (advanced) State

CharactersTaxa

Outgroup PP RD CEFur/Mane No Yes Yes YesToes/Foot Many Toes One Hoof One Hoof One HoofWings No No Yes YesHorn No No No YesEyes Yes Yes Yes YesTail Yes Yes Yes YesMouth Yes Yes Yes Yes

CharactersTaxa

Fur/ManeOne Hoof

Wings

Horn

EyesTailMouth

Primitive characters shared by all taxa are not informative

Derived character states found in only one taxon are not informative

3 Steps (evolutionary transitions from primitive advanced) to explain this tree

Outgroup PPRD CEFur/Mane No YesYes YesToes/Foot Many Toes One HoofOne Hoof One HoofWings No NoYes Yes

CharactersTaxa

Fur/ManeOne Hoof

Wings

Wings4 Steps (with wings developing convergently)

Wings

Loss of Wings

4 Steps (with wings developing in ancestral pony, and lost in PP)

OR

Outgroup PP RDCEFur/Mane No Yes YesYesToes/Foot Many Toes One Hoof One HoofOne HoofWings No No YesYes

CharactersTaxa

Fur/ManeOne Hoof

Wings

Wings4 Steps (with wings developing convergently)

Wings

Loss of Wings

4 Steps (with wings developing in ancestral pony, and lost in PP)

OR

3 Steps

4 Steps

4 Steps

Preferred Tree (Most Parsimonious)

1 origin of horns; wings either lost once or convergent)

1 origin of wings; horns either lost once or convergent)

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Polytomy (many branches)

A CONSENSUS TREE