Phylogenetic Tree

Node

Represents averaged ancestral state, not single organisms.

Internal Node

Contains sub-nodes.

Represents a population common to two different branches.

Terminal

Outermost point.

Represents specific organisms.

Branch

Organisms of the same branch share the same feature or trait.

Ancestral Branch

Continuation of the last trait.

Derived Branch

New traits branch off.

Horizontal Gene Transfer

Organisms engulfing others and creating organelles -> genes swap between branches.

LUCA

Last Universal Common Ancestor

Rooted Tree

All organisms have a common ancestor, known as the out-group.

Un-Rooted Tree

No known common ancestor.

Relative measure of how closely related they are.

Protozoa Protists

Single-celled "microbial eukaryotes".

Clade

Ancestral population and all its descendant populations.

Every child node from an internal node (including all terminal species under those nodes).

Sister Clade

Most closely related clades.

Sister Species

Most closely related species.

Cladograms

Doesn't have a time reference.

Apomorphy Derived Trait

A novel character or character state that has evolved from its ancestral form.

Synapomorphy

Trait present in a common ancestor and shared exclusively by its descendants.

• Trait evidence of shared ancestry.

Sometimes a synapomorphy is lost during evolution

Snakes lost their 4 legs from ancestors.

Organism Classification

Law of Parsimony Law of Simplicity

The one that makes the fewest assumptions and simplest explanation, but not too simple, is the right one.

Data Sources

Morphology

Physical form & structure.

Development

Stages of development.

Fossil Record

Bone dating/traits.

Behavior

Personality

Molecular Data

Genetic Differences

Because of gene transfer, looking at multiple genes/traits is better.

Geography

Where something originated.

Groups

Paraphyletic

Not all descendants.

Polyphyletic

No common ancestor.

Monophyletic

Common ancestor and all descendants.

Features

Homologous Features Synapomorphies

Come from common ancestors.

Analogous Features

Look similar, but arose independently.

Study Guide

1. How is a phylogenetic tree useful?
   • They show how evolutionary traits evolved over time and the relationships between them.
   1. What is a synapomorphy?
      • Trait present in a common ancestor and shared exclusively by its descendants.
   2. What is a node? What happens at a node?
      • A node represents an average ancestral population, and a divergence of traits.
2. What is the difference between a phylogenetic tree and a cladogram?
   • Cladograms don't have a time reference, phylogenetic trees do.
3. In a phylogenetic tree (but not a cladogram) what does the length of a branch indicate?
   • Either percent genetic difference or how far back the evolutionary relationships go.
4. How does a node relate to a synapomorphy?
   • It represents a new synapomorphy arising and diverging from the ancestral population.
   1. Branches: What does ancestral mean? What does derived mean?
      • Ancestral means the last trait continues.
      • Derived means a new trait arose.
5. What is LUCA? Is it a specific species?
   • Last Universal Common Ancestor.
   • No, likely a group of similar organisms: an Ancestral Population.
6. What are the three main domains of life?
   • Archaea
   • Bacteria
   • Eukaryotes
7. Why are there so many different types of “Trees of Life?”
   • Because there are so many different traits and branches of traits.
8. Of the Prokaryotes: are Archaea or Bacteria more closely related to Eukaryotes?
   • Archaea
9. What is an ‘extant’ species?
   • A species that continues to exist.
10. what is an ‘extinct’ species?
    • A species that no longer exists.
11. What is a “rooted” phylogenetic tree?
    • Every species derives from a known LUCA.
    1. What is the root?
       • A common ancestral population.
    2. What is an ‘out-group’?
       • A common ancestral population.
12. What species do you use as the ‘out-group’ in an un-rooted tree?
    • None
13. What can happen at nodes, that makes phylogenetic trees or cladograms confusing?
    • They can swivel.
14. What is a clade? On any of the trees shown in the slides, circle a clade.
    • An ancestral population and all its descendant populations.
15. On a cladogram, be able to identify types of clades:
    1. Paraphyletic group
    2. Monophyletic group
    3. Polyphyletic group
16. Which of the three types of groups above is useful to classify organisms?
    • Monophyletic groups.
17. If two different types of animals have similar traits, what are the two ways that may have occurred?
    • Either passed down from parents, or arose independently.
18. What are two types of homologous features, give an example of each (think of synapomorphies!).
    • Analogous and homologous? wings and bones?
19. What drives the development of Analogous features in different animals?
    • Advantageous functions.
20. Scenario: two animals are in the same monophyletic clade, but one does not have a synapomorphy that is hallmark of the clade – how could that happen?
    • The trait was removed in a subsequent evolution after the clade was established (synapomorphy first arose).
21. How can snakes and lizards be classified closely together when snakes don’t have legs?
    • The lack of legs was a relatively recent reduction in features for snakes. a. Compare this to marine mammals: why is a whale classified with humans, bats, horses, etc.?
      • They went back into the water after evolving to live on land for a time.
22. Name the types of data we use to classify organisms?
    • Geography, molecular, behavior, morphology, fossils, development.
23. What is the Rule of Parsimony?
    • The simplest explanation that fits is often the correct one.