Phylogenetics Notes

Phylogenetics Basics

  • Phylogenetic analysis aims to understand the evolutionary relationships between species.
  • Learning outcome: Understand the basics of phylogenetic analysis, including problems and solutions.

Darwin's Phylogenetic Tree

  • Darwin's notebook contained the very first phylogenetic tree, illustrating evolutionary relationships.
  • Darwin described patterns and relationships within the tree.

Tree Terminology

  • Root: The common ancestor from which all lineages diverge (e.g., node '1').
  • Outgroup: The most distantly related group to the taxa of interest (e.g., 'A').
  • Sister Species: Two species that are each other's closest relatives (e.g., 'B' and 'C').

Evolutionary Processes in Phylogeny

  • Anagenesis: Evolutionary change within a single lineage or species over time. Ancestral species A evolves through three different levels of evolutionary change, leading to the present-day species A.
  • Cladogenesis: The splitting of a single lineage into two distinct descendant lineages. Followed by anagenesis. Example: The common ancestor of species B and C splits, after which each lineage undergoes anagenesis.
  • Cladogenesis followed by anagenesis leads to evolutionary divergence.

Using Characters to Estimate Phylogenies

  • Phylogenies are estimated by looking and comparing traits.
  • Homologous Characters: Inherited from a common ancestor; phylogenetically informative.
    • Example: Limb structure in tetrapods. The same set of bones exists across different tetrapods (extant and extinct), but their form varies based on function (swimming, running, flying, etc.).
  • Phenotypic Characters: Wing color in butterflies, beak shape in birds.
  • DNA Characters: Nucleotide sequences (A, C, T, G) or amino acid sequences. Requires sequencing homologous genes.
  • Incorporating DNA sequences has greatly advanced phylogenetics.

Grouping Species

  • Species are grouped based on shared derived characters or synapomorphies.
    • Synapomorphies: Shared characters inherited from the most recent common ancestor.
      • Example: Single jawbone, milk, and hair are synapomorphies for all mammals.
  • Homoplasy (Homoplastic Characters): Characters that have evolved independently due to convergent evolution. Not phylogenetically informative.
    • Example: Bipedalism in humans and birds. Their common ancestor was not bipedal.
    • Homoplasy can disrupt phylogenetic patterns indicated by homologous characters.

Methods for Building Phylogenies

  • Two main groups of methods:
    • Distance-based methods (e.g., UPGMA, Neighbor Joining).
    • Character-based methods (tree-searching methods).

Basic Processes for Building a Phylogenetic Tree

  • Selecting a Homologous Character: Shared due to common ancestry. Example: A gene coding for a similar protein across different species, like the globin gene.
  • Aligning Characters: Comparing equivalent positions across sequences using multiple sequence alignment. Gaps may be inserted to account for gene duplication.
  • Building a Phylogenetic Tree: Using distance-based or character-based models.
  • Statistically Evaluating the Tree: Trees are hypotheses based on available data and may not reflect true evolutionary relationships.

Distance-Based Methods

  • Calculate pairwise distances between sequences. (e.g., genetic distance between X and Y, X and Z, and Y and Z).
  • Summarize pairwise distances in a distance matrix.
  • Create a distance tree by clustering closely related species first, then progressively adding distant relatives.
  • Fast and simple but explores limited tree configurations, yielding only a single tree.
  • Statistical clustering algorithms: UPGMA or neighbor joining.

Character-Based Methods (Tree-Searching Methods)

  • Examine all positions across alignments (all ATCG) to understand mutation patterns.
  • Explore the