Comparing DNA sequences to understand evolutionary relationships with Blast (AP Bio Lab #3)

How can bioinformatics be used as a tool to determine evolutionary relationships and to better understand genetic diseases?

BACKGROUND
Between 1990–2003, scientists working on an international research project known as the Human Genome Project were able to identify and map the 20,000–25,000 genes that define a human being. The project also successfully mapped the genomes of other species, including the fruit fly, mouse, and Escherichia coli. The location and complete sequence of the genes in each of these species are available for anyone in the world to access via the Internet.
Why is this information important? Being able to identify the precise location and sequence of human genes will allow us to better understand genetic diseases. In addition, learning about the sequence of genes in other species helps us understand evolutionary relationships among organisms. Many of our genes are identical or similar to those found in other species.
Suppose you identify a single gene that is responsible for a particular disease in fruit flies. Is that same gene found in humans? Does it cause a similar disease? It would take you nearly 10 years to read through the entire human genome to try to locate the same 
sequence of bases as that in fruit flies. This definitely isn’t practical, so a sophisticated technological method is needed.
Bioinformatics is a field that combines statistics, mathematical modeling, and computer science to analyze biological data. Using bioinformatics methods, entire genomes can be quickly compared in order to detect genetic similarities and differences. 
An extremely powerful bioinformatics tool is BLAST, which stands for Basic Local Alignment Search Tool. Using BLAST, you can input a gene sequence of interest and search entire genomic libraries for identical or similar sequences in a matter of seconds.
In this laboratory investigation, you will use BLAST to compare several genes, and then use the information to construct a cladogram. A cladogram (also called a phylogenetic tree) is a visualization of the evolutionary relatedness of species.

We are going to borrow the directions from another website that already has the entire thing listed.  Click here to go there!
When you open the pre-lab questions, use the information and answer the questions on pg 69. Once you collect the data, analyze your results on pgs 70-71.
Your own design goes on pgs 72-73 (can go onto pgs 74-75 if needed)
This lab should take all week.  On Friday, we will come together and discuss what was learned and 

Walking with Cavemen

Moving onto Human evolution.
Watching "Walking with Cavemen"
The website has some very interesting additional information -- click here!

Evolution review, Founder effect, population bottleneck, & genetic drift

Founder effect pg 66
Population bottleneck pg 67
Genetic drift pg 68

We went back over some basics of evolution.  Below is the "take home messages" from the PowerPoint.  Remember to go to the textbook website for additional information



Here is another slideshow of information about evolution. Thought it was helpful!

Mammals episode from Life

Watching the"Mammals" episode from Life.  
Think about what we have learned about evolution when watching.  Why might certain species have specific adaptations?

Adaptive Curriculum & lab reports

Work on Adaptive curriculum, lab reports, or anything else that needs to be completed 
Remember for Adaptive Curriculum your log-on is 
puhsmt-ID#
Students, you should remember your password ;)

Guppy Simulation & notebook check

Agenda for the block day

• Continue working on "Sex and the Single Guppy"

• Finish up anything in your notebook that isn't finished

• Notebook check

Sex and the Single Guppy

Check your plants and record data, then . . . 


Sex and the single guppy is a simulation on the pbs.org evolution website

See below for instructions, or click here for a PDF