Integrative Biology 200A
Syllabus and Handouts

Syllabus html pdf

Date Lecture Lab
Tuesday, Jan. 22 Introduction Discussion
Thursday, Jan. 24 Systematic Biology (same as 1/22) Museum Tour
Tuesday, Jan. 29 Hennig Principle Parsimony by hand
Thursday, Jan. 31 Character analysis Matrices in MacClade and Mesquite
Tuesday, Feb. 5 Intro to Morphological Data Intro to PHYLIP; Azolla DNA file
Thursday, Feb. 7 Morphological data - animals Project Topic Due
Tuesday, Feb. 12 Character Coding
Coding Exercise
GenBank
GenBank Step-by-Step
Thursday, Feb. 14 Morphological data - plants WinClada, Nona, TNT
Tuesday, Feb. 19 Molecular data POY and Clustal
Cephalopod sequences, text
Conus sequences, .fasta
Cephalopod matrix, .nex
Thursday, Feb. 21 Sequence alignment Alignment Assignment.pdf
Alignment Assignment.html
Conus sequences.fasta
Tuesday, Feb. 26 DNA Barcodes Intro to PAUP
Thursday, Feb. 28 Nomenclature, ICBN, ICZN Project Progress Reports
Tuesday, March 4 Biological Systematics Advanced PAUP
Thursday, March 6 Phylocode Discussion
Tuesday, March 11 Species concepts Matrix day: analyze your own matrix
Concatenating Data Sets
Thursday, March 13 Fossil classifications Discussion
Bring a paper from your group
Tuesday, March 18 Tree reconstruction Discussion
Bring a paper from your group
Thursday, March 20 Parsimony QUIZ 1
March 24 - 28: Spring Break
Tuesday, April 1 Distance-based algorithms Distance Methods in PAUP
Cephalopod matrix, .nex
Thursday, April 3 Maximum likelihood ML in PAUP
Cephalopod matrix, .nex
Tuesday, April 8 Bayesian methods Mr Bayes
Thursday, April 10 Support Support
primates.nex
anolis.nex
Tuesday, April 15 Consensus methods Tree comparisons
MrBayes Cephalopod Consensus.nex
MrBayes Cephalopod Tprobs.nex
Ray Matrix.nex
Thursday, April 17 Phylogeography Project Progress Reports
Tuesday, April 2 Morphometrics Morphometrics
Thursday, April 24 Dating Dating
Cephalapod.nex
CephTree.trees
baseml.ctl
CephSeq.nuc
baseml.exe
CEPHr8s.NEX
Tuesday, April 29 Historical Biogeography Treemap and DIVA
Thursday, May 1 Macroevolution Discussion
Tuesday, May 6 Comparative methods Advanced MacClade and Mesquite
Thursday, May 8 Conclusion QUIZ 2
May 12-20 Finals Week - Student Symposium will be May 14, 3-8 pm
Wednesday, May 21 Final projects due at 5:00 pm
Background image adapted from a phylogeny of all organisms with complete genome sequences.

Last update 1 May 2008
by Stephanie Stuart