Lecture Notes: Phylogenetic Analysis and Synapomorphies

Key Concepts

• Primitive Character State: The original state of a character, often designated as T in this context.
• Derived Character State: A character state that has evolved from the primitive state, such as A found in the in-group.
• In-group vs. Out-group:
  • In-group: A clade previously defined, includes gibbons, great apes, and humans.
  • Out-group: Rhesus monkeys, used to infer relationships within the in-group.

Synapomorphies and Phylogenetic Trees

• Synapomorphy: A shared derived character state that provides evidence for common ancestry among groups.
  • Position 2, 7, and 25: Support a relationship between humans and two species of chimps.
  • Position 9 and 19: Show synapomorphies exclusive to the two species of chimps.
  • Position 16: Complex case with primitive states and multiple mutations; supports chimp clade.

Relationships and Clades

• Human and Chimp Clade: Positions supporting human and chimpanzee relationship.
• Human, Chimp, and Gorilla Clade:
  • Synapomorphies in positions 15 and 21.
• Human, Chimp, and Orangutan Clade:
  • Synapomorphies in positions 11, 17, and 24.

Homoplasy

• Homoplasy: Similar character states not due to a common ancestor but rather independent evolution.
  • Example: Position 10 shows a synapomorphy between humans and orangutans, most likely due to independent mutations.
• Parsimony in Phylogenetic Trees: Preferring the simplest tree with the fewest instances of homoplasy.

Data Analysis

• Large datasets required for reliable phylogenetic trees.
  • Example Positions: 3903 to 8474, demonstrating thousands of DNA positions analyzed.
• More DNA positions increase confidence in the phylogenetic conclusions.

Conclusion

• Synapomorphies are crucial for understanding evolutionary relationships.
• A large number of DNA positions provide robust evidence for constructing phylogenetic trees and understanding species relationships.