Syllabus
Phylogenetic analysis - Parsimony
Goals of systematics. Classification. Taxonomy vs. phylogeny. Special
versus general similarity; homology versus analogy. Relationships and
monophyly. Phenetics vs. cladistics. Optimality criteria. Tree thinking.
Philosophy of biology & systematics.
Readings: Page, Ch 1 & 2, Kitching, Ch 1; see also: Maddison, Ch
1-2; Wiley, Ch 1-2.
Computer lab: Introduction to specimen and taxonomy-based on-line
resources. MacClade (time permitting)
Class notes
Readings: Page, Ch 2. Kitching, Ch 2; see also: Maddison, Ch 3-5; Wiley, Ch 3; Hillis, Ch 1-2.
Computer lab: PAUP*, MacClade, file formats and conventions, character evaluation and coding, simple searches, tree formats.
Class notes
DNA to RNA to Proteins: Molecular and classical genetics. Information
lost and gained. Biochemical pathways: Integration of different genes.
Parallel evolution, control of expression. Developmental perspectives:
Connection back to morphological data. Number of genes needed for morphological
characters. Homology. Nucleus: size and structure in different organisms.
Polyploidy; gene duplications. Chloroplast: General structure, gene content,
variation, cyanobacterial origin. Mitochondria: Animal, fungal, plant,
protistian - origin of mitochondrion. Structure, gene content, variation.
Master molecule and subsets. Movement among genomes within a species and
between species. Protein based approaches: Isozymes and allozymes. Gene
duplications and gene families. Amino acid sequences. DNA-DNA hybridization.
Restriction site methods: nrDNA, mtDNA, cpDNA. Gene order data, duplications,
inversions, insertions and deletions. Fingerprinting approaches. Minisatellites,
microsatellites, RAPDs, AFLPs, SSCPs.
Readings: Page, Ch 3; Genetics textbook review (e.g., Griffiths);
see also: Hillis, Ch 4 (p51-67), Ch 6 (p169-178), Ch 8 (p249-282)
Computer lab: searching of databases; GenBank, NCBI, EMBL, etc.
Class notes
Sequence data (amino acid, RNA, and DNA): cpDNA genes, examples at different
levels. nrDNA genes, examples at different levels. Potential problems,
intercopy or interlocus variation. Protein coding nuclear genes. Orthology/paralogy,
gene duplication, silencing, conversion pseudogenes. Primary character
analysis of raw molecular data. Reviewing trace files, assembly of contigs,
survey for quality and problems, recognition of sites and motifs. DNA,
RNA, and protein sequences. Homology versus similarity in molecular data.
Alignment algorithms. Similarity significance testing, matrix plots. Pairwise
alignments versus multiple alignments. Gap versus mismatch penalties
Readings: Page ch 5; see also: Hillis, Ch. 9
Computer lab: molecular sequence editors, Clustal, TreeAlign, MALIGN.
Class notes
Species concepts: Traditional, typological, evolutionary, biological,
phylogenetic concepts. Phylogenetic (among species) versus Tokogenetic
(within species) relationships. Classical genetics, Mendelian genetics,
population genetics. Recombination, heterozygosity, polymorphism. Hybridization.
Lateral transfer. Phenetic analysis. Gene trees vs. species trees.
Readings: Page, Ch. 4; see also: Hillis, Ch 10.
Computer lab: Phenetic analysis software, Systat, GDA.
Class notes
Phylogenetic analysis - Parsimony
Gene trees vs. species trees. Tree building vs. tree-evaluation. Principle
of parsimony in biology. Optimality criteria: parsimony (Wagner, Fitch,
Dollo, Camin-Sokal, Polymorphism, Generalized). Weighting data. Tree building
techniques: heuristic versus exact methods. Compatibility and Clique analysis
Readings: Kitching, Ch. 3 & 4, Page, Ch. 6 (p 187-193); see also:
Hillis, Ch. 11 (p 407-425), Li, Ch. 5, Maddison, Ch.
Computer lab: PAUP*, MacClade.
Class notes
Concept of an evolutionary distance. Distance methods. Models in evolutionary
biology (geometric, graph & set theory, information theory). Optimility
criteria. Special considerations for molecular characters. Additive and
ultrametric distances. Four point condition. Transformations. Searching
for trees. Additive tree versis algorithmic methods.
Readings: Page Ch. 6 (pp. 172-186; see also: Hillis, Ch. 11 (pp.
426-477)
Computer lab: PAUP*
Class notes
Models in evolutionary biology. Optimality criteria: distance and maximum
likelihood. Special considerations for molecular characters, controlling
for bias, estimating parameters.
Readings: Kitching, Ch 5 & 6; Page, Ch 6 (p 209-227); see also:
Hillis, Ch. 11 (pp. 478-509).
Computer lab: PAUP*
Class notes
Reconstructions. Character optimization; delayed and accelerated transformation.
Reliability of trees. Bootstrap, jackknife, decay, randomization tests.
Readings: Kitching, Ch 5 & 6; Page, Ch 6 (p 209-227); see also:
Hillis, Ch. 11 (pp. 478-509).
Computer lab: PAUP*
Class notes
Readings: Kitching, Ch. 7 & 8
Computer lab: PAUP*
Class notes
Comparative methods.Phylogenies, taxonomies, and classification. Relationships
among major groups of organisms.
Readings: selected papers from Harvey, et al. 1996
Computer lab: Component, TreeMap, CAIC
Class notes
Plant-insect interactions. Host-parasite interactions. Viral evolution.
Readings: selected papers
Computer lab:
Class notes
Ecological versus historical biogeography. Vicariance versus long distance
dispersal. Diffusion. Climates, plate tectonics.
Readings: selected papers
Computer lab:
Class notes