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

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 CE Fur/Mane No Yes Toes/Foot Many Toes One Hoof Wings No Yes Horn No Yes Eyes Yes Tail Yes Mouth Yes Primitive (ancestral) State Derived (advanced) State Characters Taxa

OutgroupPPRDCE Fur/Mane No Yes Toes/Foot Many Toes One Hoof Wings No Yes Horn No Yes Eyes Yes Tail Yes MouthYes Characters Taxa Fur/Mane One Hoof Wings Horn Eyes Tail Mouth 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

OutgroupPPRDCE Fur/Mane No Yes Toes/Foot Many Toes One Hoof Wings No Yes Characters Taxa Fur/Mane One Hoof Wings 4 Steps (with wings developing convergently) Wings Loss of Wings 4 Steps (with wings developing in ancestral pony, and lost in PP) OR

OutgroupPPRDCE Fur/Mane No Yes Toes/Foot Many Toes One Hoof Wings No Yes Characters Taxa Fur/Mane One Hoof Wings 4 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 Preferred Tree (Most Parsimonious)

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

Polytomy (many branches)