Syllabus |
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Week 1
- September 8 |
Introduction |
Week 2 - September 13 & 15 | Character data and trees |
Week 3
- September 22 & 25 |
Molecular character data |
Week 4 - September 27 & 29 | Molecular sequence data and sequence alignment |
Week 5 - October 4 & 6 | Taxa & species concepts |
Week 6 - October 11 & 13 |
Phylogenetic analysis - Parsimony |
Week 7 - October 18 & 20 | Phylogenetic analysis - Distance methods |
Week 8 - October 25 & 27 | Phylogenetic analysis - Maximum likelihood |
Week 9
- November 1 & 3 |
Measures of support |
Week 10
- November 8 & 10 |
Comparison of trees |
Week 11 - November 15 & 17 | Using phylogenies - Comparative method |
Week 12 - November 22 & 24 | Using phylogenies - Coevolution |
Week 13 - November 29 & December 1 | Using phylogenies - Biogeography |
Week 14 - December 6 & 8 | Student Presentations |
Week 15 - December 13 | Independent work on final projects |
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Week 1 - September 8 |
Introduction |
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. |
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Week 2 - September 13 & 15 | Character data and trees |
Nature of data used in systematics. Characters and character
states. Homology and synapomorphy. Homoplasy and character conflict. Character
types: binary, multistate, additive binary. Character coding: transformation
series and ordering. Character state polarity: outgroup comparison, ontogenetic
criteria, fossil and stratigraphic data. Oher criteria. "Morphological"
vs. molecular characters. Combining or partitioning data. Sister groups
and ancestor-descendent relationships. Tree thinking. 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 |
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Week 3 - September 22 & 25 |
Molecular character data |
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. |
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Week 4 - September 27 & 29 | Molecular sequence data and sequence alignment |
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 |
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Week 5 - October 4 & 6 | Taxa & species concepts |
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. |
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Week 6 - October 11 & 13 |
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 |
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Week 7 - October 18 & 20 | Phylogenetic analysis - Distance methods |
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. |
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Week 8 - October 25 & 27 | Phylogenetic analysis - Maximum likelihood |
Models in evolutionary biology. Optimality criteria: distance and maximum
likelihood. Special considerations for molecular characters, controlling
for bias, estimating parameters. |
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Week 9 - November 1 & 3 |
Measures of support |
Reconstructions. Character optimization; delayed and accelerated transformation.
Reliability of trees. Bootstrap, jackknife, decay, randomization tests. |
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Week 10 - November 8 & 10 |
Comparison of trees |
Consensus (Strict, semistrict, Adams, majority rule, Nelson).
Data partitioning and combination. Comparison of trees. Tree to tree distances,
similarity. Readings: Kitching, Ch. 7 & 8 Computer lab: PAUP* Class notes |
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Week 11 - November 15 & 17 | Using phylogenies - Comparative method |
Comparative methods.Phylogenies, taxonomies, and classification. Relationships
among major groups of organisms. |
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Week 12 - November 22 & 24 | Using phylogenies - Coevolution |
Plant-insect interactions. Host-parasite interactions. Viral evolution. |
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Week 13 - November 29 & December 1 | Using phylogenies - Biogeography |
Ecological versus historical biogeography. Vicariance versus long distance
dispersal. Diffusion. Climates, plate tectonics. |
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Week 14 - December 6 & 8 | Student Presentations |
Week 15 - December 13 | Independent work on final projects |