This problem space gives students opportunity to practice thinking as scientists. Higher-level cognitive skills such as analysis, synthesis, and application are emphasized in this activity. Raw data, analysis tools (Biology Workbench), and guidelines are provided. For senior and graduate level courses, students can be encouraged to complete the problem space either in individuals or in groups. For introductory level courses, instructors should provide enough scaffolding in class, such as demonstrating how to analyze the data. Notice 1. The purposes of this problem space are listed under "Introduction". If students get lost or don't know how to generate research questions, there are a few general questions under "Introduction" for students to get started . 2. Students are encouraged to download and read the paper of Markham et al (1998) before they start the activity. The paper can be downloaded from this link: http://bioquest.org/bedrock/problem_spaces/hiv/Markham_1998.pdf 3. Instructors should explain the "Data Table README File (pdf) " under "HIV sequence data" before asking students to analyze the data. Terms such as "population subdivision", "population bottleneck", "diversifying selection" and "selective sweep" should be defined before the data analysis. 4. After downloading and opening the "Data Table (Excel file)", you may need to adjust the column width in order to view the data properly. I thought the data was incomplete at first, but after some adjustments in exel, every item described in the explanation sheet (pdf file) is shown in the data table (exel file).