Phylogenetic Tree Inference and Construction

Phylogenetic Relationships and Tree Construction

Phylogenetic trees are constructed using data to infer evolutionary relationships between organisms. While different data collection methods can lead to variations in the trees, even with the same taxa, the underlying relationships depicted remain constant.

Displaying Phylogenetic Trees

  • There are various ways to display phylogenetic trees.
  • Traditional layouts: Often seen at the bottom left of diagrams, these are the most common and familiar.
  • Circular layouts: Increasingly used in modern scientific papers. This format efficiently accommodates a large amount of information within the visual representation. Despite different appearances, all display types convey the same relationships.

Terminology of Phylogenetic Trees

  • Branches: These represent lineages within the phylogenetic tree.
  • Basal branches: Located towards the bottom or origin of the tree, these branches signify older evolutionary successes.
  • Common ancestor: The point where branches connect, representing a shared ancestor. For example, in a given tree, species 'b' and 'c' share a common ancestor at their connecting point.
  • Traits on branches: Traits can be written alongside branches. A trait placed at a specific point on a branch indicates its presence in all organisms that evolved past that point in the lineage. For instance, a trait marked on the branch leading to 'b' and 'c' (but after 'a' diverged) would be present in 'b' and 'c' but not in 'a'.
  • Taxa on trees: Trees can represent different taxonomic levels, such as species, strains, or broader groups.
  • Branch direction: The visual direction of two branches can be flipped without altering the information conveyed by the tree. For example, if 'b' appears closer to 'a' than 'c' does visually, it does not imply 'b' is more closely related to 'a' than 'c'. The true evolutionary distance is determined by the length and connections of the branches, not merely their visual proximity in a two-dimensional layout.

Constructing Phylogenetic Trees: The Process

Phylogenetic trees are built to infer how organisms are related to one another.

  1. Pick Differentiating Traits:

    • Select traits that are present in some organisms within the group but not all.
    • Consider both ancestral traits (found in many organisms, appearing earlier in evolution) and derived traits (appearing later, found in fewer organisms).
    • The goal is to choose traits that effectively differentiate between the organisms being studied.

  2. Fill Out a Data Matrix:

    • Create a matrix where rows represent organisms and columns represent selected traits.
    • For each organism and trait, assign a numerical value:
      • 00: If the organism does not possess the trait.
      • 11: If the organism does possess the trait.

  3. Calculate Total Scores:

    • Sum the '11's for each organism to get a total score indicating the number of traits it possesses.
    • Organisms with higher total scores (meaning more traits in common) tend to be placed towards the