EEB3899-007; Fall 2015, lab methods

A primer for phylogenetic data gathering

This seminar is offered to undergraduate students (mainly in their sophomore or junior year) interested in DNA sequencing and phylogenetic analysis as a tool to reconstruct evolutionary histories. It is specifically targeted to complement the activity of students who joined or plan to join a laboratory to work with DNA extraction and sequencing.

The seminar will allow the participants to understand and become independent in the complete process of phylogenetic data collection: the rationale of the lab techniques, (including DNA extraction, PCR, sequencing) and their troubleshooting; the manipulation and preliminary analysis of sequence alignments and the retrieval and upload of sequences to GenBank. Some basic theoretical background will be provided to understand broad evolutionary and cladistics concepts. Some of the sessions will require the student to bring a laptop to try and have some practice with different phylogenetic softwares. The seminar will be completed with paper discussions and a final invited talk.

Duration: 1 credit (13 sessions of 50 minutes)

Location and time: Wednesdays from 4.40 to 5.30PM. PBB (3rd floor conference room)

Prerequisites: BIOL1107 and BIOL1108/BIOL1110

Contact: If you have any question, email or


Date Instructor Subject
Sept 2 Medina Session 1. DNA extraction. PCR. Sequencing
Sept 9 Liu Session 2. Troubleshooting. Nested PCR. Primer design
Sept 16 Liu Session 3. Sequence manipulation. GenBank. Retrieving sequences (Laptop)
Sept 23 Medina Session 4. Sequence formats. Alignments. Ambiguities and indels (Laptop)
Sept 30 Liu Session 5. Uploading sequences to GenBank (Laptop)
Oct 7 Session 6. Paper discussion (TBA)
Oct 14 Medina Sessions 7. Evolution, phylogeny and classification. Homology and homoplasy
 Oct 21 Medina Session 8. Basic principles and terms of cladistics. Properties of phylogenetic trees
Oct 28 Session 9. Paper discussion (TBA)
Nov 4 Medina Session 10. Generating distance-based phylogenetic trees (Laptop)
Nov 11 Session 11. Paper discussion (TBA)
Nov 18 Liu Session 12: Introduction to Next Generation Sequencing and Genomics
Dec 2 Invited talk: (TBA)