1. Interpreting Cladograms Notes
Big Idea:
Phylogenies Depict ancestor and descendent relationships among organisms based on homology
These evolutionary relationships are represented by Diagrams called cladograms (branching diagrams that organize relationships)

2. Reading Cladograms
Read like a family tree: show patterns of shared ancestry between lineages.
When an ancestral lineage splits: speciation is indicated due to the “arrival” of some new trait.
Each lineage has unique traits to itself alone and traits that are shared with other lineages.
each lineage has ancestors that are unique to that lineage and ancestors that are shared with other lineages — common ancestors.

3. Quick Question #1 What is our definition of a clade?
A group that includes a common ancestor and all the descendants (living and extinct) of that ancestor.

4. Reading Cladogram: Identifying Clades
Using a cladogram, it is easy to tell if a group of lineages forms a clade.
Imagine clipping a single branch off the phylogeny
all of the organisms on that pruned branch make up a clade
So everything in the pink circle is a clade (common ancestor and all descendants)

5. Quick Question #2 Looking at the image to the right:
Is the green box a clade?
The blue?
The pink?
The orange?

6. Reading Cladograms: Clades
Clades are nested within one another
they form a nested hierarchy.
A clade may include many thousands of species or just a few.

7. Interpreting Cladograms
it's easy to misinterpret cladograms as implying that some organisms are more "advanced" than others
however, cladograms don't imply this at all.
when reading a cladogram, it is important to keep three things in mind

8. (mis)Interpreting Cladograms: One
Evolution produces a pattern of relationships among lineages that is tree-like, not ladder-like.

9. (mis)Interpreting Cladograms: Two
Just because we tend to read phylogenies from left to right, there is no correlation with level of "advancement."

10. (mis)Interpreting Cladograms: Three
For any speciation event on a phylogeny, the choice of which lineage goes to the right and which goes to the left is arbitrary. The following phylogenies are equivalent:

11. Interpreting Phylogenies: Human Example
The points described above cause the most problems when it comes to human evolution.
It is important to remember that:
Humans did not evolve from
chimpanzees. Humans and
chimpanzees are evolutionary cousins
and share a recent common ancestor
that was neither chimpanzee nor human.
Humans are not "higher" or "more evolved" than other living lineages. Since our lineages split, humans and chimpanzees have each evolved traits unique to their own lineages.

12. Quick Question #3 What is this called?
What do you think the red lines represent?

13. Creation of Cladograms
Given a set of observations, phylogenetic analysis seeks to find the simplest branching relationships between organisms to depict their evolution.
Heritable traits possessed by organisms, characters, are used to compare the organisms being studied.
Characters can be compared across organisms
physical traits
genetic sequences
behavioral traits.

14. BUT HOW DO WE CONSTRUCT A CLADOGRAM?

15. 3 Alternative, mutually exclusive Cladograms
How Do We Choose Between Them?

16. (Not an Ancestor, but a Stand-in to represent the Ancestral Condition)
INGROUP ORGANISMS PP RD PC
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
Primitive (ancestral) State
Derived States

17. Outgroup PP RD PC INGROUP ORGANISMS 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 organism separate them from other organisms
Horn
3 Steps (evolutionary transitions from ancestral  derived) to explain this tree
Wings
Fur/Mane
One Hoof
Ancestral characters shared by all taxa link organisms together
Eyes
Tail
Mouth

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

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

20. The preferred cladogram is the simplest! (Least number of assumptions)
3 Steps
The preferred cladogram is the simplest! (Least number of assumptions)
So, which cladogram is the best description of the evolution of these little ponies?
4 Steps
4 Steps