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 |