1. STEPHANIE HINTZEN BIOL 471 SIV and HIV: Differences in Diversity and Divergence

2. Markham HIV paper Island SIV paper Divergence  Rapid progressor had a significantly higher rate of increase over non  Rapid had a greater rate of increase but not significant over moderate  Moderate significant over nonprogressors Diversity  The differences in slope were significant between the rapid progressors and nonprogressors  Between nonprogressors and moderate progressors was significant  Moderate and rapid had a trend toward significant Divergence  Unknown! Diversity  Unknown! Background

3. The Question My thoughts Are the measurements of diversity and divergence of mutation less than, the same or greater in SIV than in HIV. There will be equal amounts of diversity and divergence between HIV and SIV Consider

4. Methods Use NCBI and genBank (FASTA) to retrieve sequences of SIV Use of Biology Workbench and ClustalW to align all sequences MEGA for diversity and divergence Weblogo

5. Methods

6. Results: ClustalW Phylogenetic tree  Rooted tree (generated by Phylip's Drawgram)

7. Results: Weblogo

8. Discussion Diversity  Coefficient of Differentiation  0.035 Divergence  Overall Distance/Divergence  0.551  HM363427.1 and HM363426.1  89.3% identity  HM363412.1 and HM363426.1  47.6% identity

9. References Markham R., et al. 1998. Patterns of HIV -1 evolution in individuals with differing rates of CD4 T cell decline. Proc. Natl. Acad. Sci. USA:95, p 12568- 12573. Worobey M., et al. 2010. Island Biogeography Reveals the Deep History of SIV. Science:329, 5998, p 1487