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 rafael.medina@uconn.edu or yang.liu@uconn.edu
Syllabus:
| 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) |