PHYLOGENETICS

Lecture Schedule

Lecture

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Introduction to Phylogenetics

Traditional methods to discover "natural groups"
Modern phylogenetic methods

Phenetics

Concept of overall similarity
Definition of phenetics
Sokal and Sneath
Controversary over phenetics

Evolutionary phylogenetics

Evolutionary taxonomy

Cladistics [ = "phylogenetics" in the narrow sense]

Concept of shared derived characters and monophyletic lineages
Cladistics vs. overall similarities

Phenetic approach

Obtain data matrix

Character states for characters
Taxa (OTU=operational taxonomic unit)

Analyze data matrix

Cluster analysis

Derive phenogram

Principal Components Analysis (PCA)

Mutli-variate analysis
Principal components

Make taxonomic decisions
Case study example using UPGMA (unweighted pair-group method using arithmetic averages [cluster method])

 

Phylogenetic (cladistic) approach

Obtain data matrix as above [II.A.]
Order or polarize character states

Terms

Plesiomorph = primitive character state
b. Apomorph = advanced character state

Methods of deciding primitive vs. advanced

Outgroup analysis
Primitive = common
Other criteria (developmental, fossil record, biogeography, etc.)

Analyze data matrix

Concept of parsimony
Concept of synapomorph, symplesiomorph, autapomorph
Concept of convergence (=homoplasy)

Going from a phylogenetic tree to a classification

Evolutionary taxonomy vs. cladistics
Polyphyly, paraphyly, and monophyly