Chapter 4: Estimating Evolutionary Trees

• “Nothing in evolution makes sense, except in the light of phylogeny”

Tracing Evolutionary History

• Phylogeny: Pattern and timing of evolutionary branching events (“evolutionary tree”)
• Branching happened in the past so…
  • Common ancestors cannot be observed
  • Must infer from data

The Logic of Phylogenetic Inference

• A phylogeny (phylogenetic tree) is a hypothesis of the pattern of ancestor-descendent relationships
• Characters used in a phylogenetic tree must be…
  • Independent: change in one character does not induce change in another character
  • ie. they must be determined by different genes
  • Homologous: a trait shared because of inheritance format common ancestor
  • the similarity in limb structure among mammals

Evidence for Evolution

• Homology

Synapomorphy

• Synapomorphy: a shared, derived characteristic from a common ancestor
• Shared common ancestry → homology
• Ancestral vs. Derived → direction
• Synapomorphies identify evolutionary branch points.
• Synapomorphies are nested.

Cladogram

• Cladogram: a phylogenetic tree inferred clustering synapomorphies.

The Problem with Homoplasy

• Complications arise when traits are shared for other reasons, such as convergent evolution and reversal to the ancestral state.

Convergence

• Convergence: trait adapted to a similar function but with a different origin
  • Same solution, different problem

Reversal

• Mutations can create synapomorphies
• Reversals: (AKA back mutations) of a character state can remove synapomorphies

Homoplasy

• Homoplasy: similarity in the character found in different species that is due to convergent evolution and reversal
• NOT common descent

Parsimony

• Parsimony: a criterion for selecting among alternative patterns based on minimizing the total amount of evolutionary change
  • Frugal about changes
• Minimizes the amount of homoplasy because synapomorphies are theoretically more common than convergent evolution and reversals

What are phylogenies good for?

1. Classification

• Systematics: a scientific field devoted to the classification of organisms
• Phenetics: a classification scheme based on grouping populations according to similarities
• Cladistics: a classification scheme based on evolutionary relationships (phylogenies)
  • Monophyletic groups: including an ancestor and all of its descendants (“clade“)
  • Paraphyletic Group: a set of species that includes an ancestor but NOT all its descendants.

2. Detecting Coevolution

• Aphid-bacteria
  • Mutualistic and co-speciation
  • the branching patterns basically match

3. Origin of Pathogens

• Black plague
• Pathogen
  • Yersinia pestis
• 36 strains

4. Drawing the Tree of Life

• Phylogenies can help us draw the tree of life.
• Morphology trees
• RNA trees

Glossary

• Root: the base of the tree, the locations of the common ancestors
• Ancestral: the original character state in a group; opposite of “derived
• Derived: a newly-evolved character state; opposite of ancestral