PHYLOGENETICS I

  • Outline of Important Topics:

    • Anatomy of phylogenetic trees

    • Terminology and tree thinking

    • Connection between phylogenetics and taxonomy

    • Forming and testing evolutionary hypotheses using phylogenies

    • Inferring evolution trees

Page 2: Introduction to Phylogenetics

  • Definition: Phylogenetics is the study of evolutionary relationships among species and forms the basis of modern systematics and taxonomy.

  • Importance of Phylogenies: Critical for forming and testing evolutionary hypotheses, echoing T. Dobzhansky’s quote: “Nothing in biology makes sense except in the light of evolution.”

  • Phylogenetic Corollary: “Nothing in evolution makes sense except in light of phylogeny.”

  • Anatomy of a Phylogenetic Tree:

    • Represents the pattern of evolutionary branching

    • Can be "rooted" (includes time) or "unrooted" (excludes time)

Page 3: Understanding Phylogenetic Trees

  • Tree Examples:

    • All four illustrated trees are identical and depict relationships among species.

    • Closest relative of ‘orange’ is ‘purple’; closest to ‘orange+purple’ is ‘blue’ and then ‘gray.’

  • Drawing Variations: Different ways of drawing trees, such as using circles for space efficiency.

  • Subtree Concepts:

    • Extracting and collapsing subtrees enhances tree clarity.

Page 4: Analyzing Ambiguity in Relationships

  • Polytomies: Instances where relationships are ambiguous with multiple possible trees.

  • Mapping Information:

    • Tracks the evolution of traits and taxonomy.

    • Example question: "Which came first, the chicken or the egg?"

  • Branch Length Significance:

    • Genetic Change: Indicates which lineage has undergone the most genetic changes since divergence from the Drosophila outgroup.

    • Chronological Time: Helps determine the timing of divergences, such as when humans diverged from frogs.

Page 5: Linnaean Taxonomy and Its Connection to Phylogeny

  • Modern Taxonomy:

    • Based on phylogenetic trees, focusing only on monophyletic groups.

  • Taxonomic Definitions:

    • Monophyletic: Contains an ancestor and all its descendants.

    • Paraphyletic: Contains an ancestor and some, but not all, of its descendants.

    • Polyphyletic: Includes distantly related species without an immediate ancestor.

  • Scientific Validity: Many traditional names are not scientifically valid as they do not represent monophyletic groups and reflect pre-evolutionary thinking.

  • Example Fields of Study:

    • Herpetology and Ichthyology study paraphyletic and polyphyletic parts of the tree, respectively.