Learning paths

Learning paths

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Learning path

Full curriculum

Full curriculum
  1. Common ancestry, lineage divergence and phylogeny
  2. Homology, analogy and convergent evolution
  3. Sequence alignment as a hypothesis of positional homology
  4. Reading rooted phylogenetic trees by topology
  5. Molecular sequence evidence for phylogenetic inference
  6. Shared derived characters, outgroups and clade diagnosis
  7. Maximum parsimony for comparing phylogenetic tree hypotheses

Unit content

Reading rooted phylogenetic trees by topology

A rooted phylogenetic tree represents hypotheses about the order of lineage divergence from a common ancestor.

Important parts are:

  • the root, representing the ancestral lineage from which the displayed lineages descend;
  • branches, representing lineages through time;
  • nodes or branch points, representing lineage-splitting events;
  • tips, representing sampled species, populations or sequences.

Two tips are sister groups when they share an immediate common ancestor not shared with another sampled group.

For example,

        ┌─ B
    ┌───┤
────┤   └─ C
    └───── A

B and C are sisters because their most recent common ancestor is the upper internal node. A shares a deeper common ancestor with both.

Only the branching topology determines these relationships unless the figure explicitly assigns meaning to branch lengths. Rotating branches around a node changes the drawing but not the ancestry:

    ┌─ B                 ┌─ C
────┤          =      ───┤
    └─ C                 └─ B

Horizontal position, vertical order and visual proximity are therefore not reliable measures of relatedness.

A clade consists of an ancestor and all of its descendants. To identify a clade, choose a node and include every branch descending from it.

Phylogenetic trees should be read by asking which lineages share the most recent common ancestor?, not by reading the tips as a ladder from 'simple' to 'advanced'.