2012 Molecular Phylogeny (NC21100) Homepage
2. The first assignment
Read "Classification" booklet and write a page of dafinition and description about Phenetics and Cladistics.
Due date: 9.21
3. The second assignment
Find "THREE" new "biological" or "phylogenetic" terminologies during the Dr. Ui Wook Whang's seminar and report their definition and meaning.
e. g., Tridigrada, bootstrap, sensu lato, ... and etc.
- Half page per an item (Total one and half pages; A4)
- Due date: Nov. 13
4. Final Exam: Dec. 14. 3:00PM Room C209
Note: a couple of midterm questions will be included in the final exam.
Week 1 (9.7) Course introduction
Week 2 (9.14~5) Field trip (official departmental break)
HOMEWORK: "Classification" BOOK <-- read this book and make one page of summary
Week 3 (9.21) Chap 1 PPT Chap 2 PPT The archaeology of the genome, Trees (chap. 1 and 2)
Week 4 (9.28) BOOK chapter PPT down Campbell General Biology Chap 26.
Week 5 ----------
Week 6 (10.12) Chap 3 PPT Genes: organization, function and evolution (chap 3.)
Week 6 (10.19) (Lab.) Lab basics and DNA extraction
Lab basics PPT UPDATED
DNA extraction @ general biology lab: CTAB method PPT
DNA extraction CTAB DNA extraction protocol I (Doyle and Doyle)
CTAB DNA extraction protocol II (Sangtae Kim)
GeneAll DNA extraction Kit (Commercial Kit)
FTA Card protocol
Samples and band test
Week 8 (10.26) Mid-term exam. UPDATED
Week 7 (11.2) (Lab.) PCR and sequencing
Book Chapter: PCR protocols
PCR and purification PPT UPDATED
Sequencing PPT UPDATED
Sequencing process, PCR condition, Primer information
Taq polymerase information sheet
PCR record form
OUR RESULT: extraction, PCR
Week 9 (11.9) (Lab.) Other methodologies: RFLP, RAPD, CAPS, and AFLP
Alignment, Sequence editing using SEQUENCHER
CAPS protocol Endonuclease information sheet
DNA purification protocol
TA cloning protocol
TOPO TA colning kit protocol
RFLP, CAPS, RAPD, ISSR, and AFLP PPT UPDATED
C.f. : P l a n t S y s t e m a t i c s C h a p . M o l e c u l a r P h y l o g e n y
Week 10 (11.16) Chap 5. PPT Measuring genetic change I (chap 5) UPDATED
Week 11 (11.23) Measuring genetic change II (chap 5)
Special seminar: Dr. Eu-wook Whang, Kyungbook Univ.
Week 12 (11.30) Chap. 6. PPT Inferring molecular phylogenyI I (chap 6) UPDATED
R a d f o r d et al Book Chapter
Week 13 (12.7) Reconstruct Phylogeny with RAPD and sequencing data using MEGA, PHYLIP (computer lab.)
PHYLIP web site TreeView web site
PHYLIP program TeeView Program
Phylogeny reconstruction using M E G A and P H Y L I P programs UPDATED
M E G A program M P sample data
Paper: Kim et al. 2001
Week 14 (12.14) Final exam.