Notes on Phylogenetic Trees Lecture

Overview

• Phylogenetic or evolutionary trees are diagrams showing evolutionary relationships and diversification among organisms.
• Used in various fields: biology, conservation, epidemiology.
• Key questions: What are the parts? How are they constructed? How are they interpreted?

Parts of Phylogenetic Trees

• Tips: Ends of the branches.
• Root: Base of the tree.
• Branches or Clades: Lines representing lineages.
• Nodes: Points where branches diverge.
• Outgroup: A sister species used for comparison.
• Ingroup: Species that are the focus of the study.

Construction of Phylogenetic Trees

• Trees can be drawn in various orientations (sloped, angled, circular) but show the same relationships if the branching pattern is identical.
• Trees can be rotated around nodes without changing the relationships.

Interpretation of Phylogenetic Trees

• Time Component: Root represents the past; tips represent the present.
• Lineages: Represented by branches where new traits arose and were passed on.
• Gene Flow: Movement of genes among populations, part of lineage continuity.
• Speciation: New species form when populations become reproductively isolated.

Nodes and Lineages

• Nodes indicate the most recent common ancestor and speciation events.
• Monophyletic Group: Includes all descendants of a common ancestor.
• Paraphyletic Group: Excludes some descendants of a common ancestor.

Drawing Correct Phylogenetic Trees

• Trees are hypotheses of relationships among species.
• Traits data are used to test hypotheses (more parsimonious tree preferred).
• Character States: Ancestral traits coded with 0, derived traits with 1.

Tree Thinking

• Understanding evolutionary patterns through phylogenetic trees.
• Correct Interpretation: Focus on nodes, not proximity or node counting.
• Examples to practice tree thinking skills:
  • Example 1: C equally related to D and F.
  • Example 2: C more closely related to F than A.
  • Example 3: Fish more closely related to humans than snails.

Summary

• Tree thinking helps interpret evolutionary relationships.
• Identifying monophyletic groups using shared traits.
• Differentiating unique evolutionary traits and lineages through phylogenetic trees.