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Observations are:

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.

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Observations are:

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  1. 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

  2. ?

  3. 3 Alternative, Mutally-Exclusive Dichotomous Cladograms How Do We Choose Between Them?

  4. Taxa PP RD CE Characters Fur/Mane No Yes Yes Yes Toes/Foot Many Toes One Hoof One Hoof One Hoof Wings No No Yes Yes Horn No No No Yes (Not an Ancestor, but a Stand-in to represent the Ancestral Condition) Eyes Yes Yes Yes Yes Tail Yes Yes Yes Yes Mouth Yes Yes Yes Yes Outgroup Derived (advanced) State Primitive (ancestral) State

  5. Taxa Outgroup PP RD CE Characters Fur/Mane No Yes Yes Yes Toes/Foot Many Toes One Hoof One Hoof One Hoof Wings No No Yes Yes Horn No No No Yes Eyes Yes Yes Yes Yes Tail Yes Yes Yes Yes Mouth Yes Yes Yes Yes Derived character states found in only one taxon are not informative Horn 3 Steps (evolutionary transitions from primitive  advanced) to explain this tree Wings Fur/Mane One Hoof Primitive characters shared by all taxa are not informative Eyes Tail Mouth

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

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

  8. 3 Steps Preferred Tree (Most Parsimonious) 4 Steps 4 Steps

  9. ? 1 origin of horns; wings either lost once or convergent) 1 origin of wings; horns either lost once or convergent)

  10. Polytomy (many branches) A Consensus Tree

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