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.
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.