AP Biology: BLAST Lab

Just your Basic Local Alignment Search Tool: BLAST Today we'll review cladogram information and then use an open world-wide resource to help us analyze how everything is connected. Use the cladogram to answer the following questions: The cladogram above can be used to answer several questions. What features do the salamander, lizard, tiger, and gorilla share? jaws and lungsWhat three structures do all lizards possess? dry skin, lungs, and jawsWhich evolved first - dry skin or hair? dry skinWhat features do tigers and gorillas share? hair Draw a cladogram Humans and fruit flies share approximately 60% of their DNA, which would place them farther apart on a cladogram than a chimpanzee which shares more of its DNA with humans. Can you draw a cladogram that depicts the evolutionary relationships among humans, chimpanzees, fruit flies, and mosses? Match the Enduring Understanding to the example 1A2: Natural selection acts on phenotypic variations in populations Traits can give differential survival and reproductive success which allows for change in populations over time. 1A4: Biological evolution is supported by scientific evidence from many disciplines, including mathematics Hardy Weinberg, the fossil record, our knowledge of DNA, and morphological similarities provide evidence for evolution. 1B2: Phylogenetic trees and cladograms are graphical representations (models) of evolutionary history that can be tested. We can see how closely related (or not) to other organisms by organizing them by similarity and DNA percentage. 3A1: DNA, and in some cases RNA, is the primary source of heritable information. The central dogma of biology is that DNA makes RNA makes protein. We get the DNA from our ancestors which creates the proteins for the phenotypes we possess. Imagine I give you the following sticky note: Your job is to go to the library, look for every book that has this phrase, and write down the exact page number and name of every book you find. Next, search for every book that has your three letters, even if the spelling is not perfect. Last, put all the names and page numbers of the books you find in order from most to least similar to the original phrase. This is what BLAST does for you. Let's organize the data Take a look at the sequences below. Determine which is most closely related and least closely related to the original strand. Then calculate how similar they are to the original. Original Strand 1: ATGATCCAGT Is the strand given more or less closely related? What is the percentage similarity? Organism 2: ACGACTCAGT less 70% Organism 3: TTGATCCAGT more 10% Practice drawing the cladogram based on data: Here's another cladogram :) Draw the cladogram depicting the evolutionary relationships among all five species (including humans) according to their percentage similarity in the GAPDH gene. DNA vs. Protein Why is the percent similarity in the gene always lower than the percentage similarity in the protein for each species? Archaepteryx A team of scientists has uncovered the fossil specimen above near Liaoning Province, China. MAke some general observations about the morphology (physical structure) of the fossil below.Little is known about the fossil. It appears to be a new species. Upon careful examination of the fossil, small amounts of soft tissue have been discovered. Normally, soft tissue does not survive fossilization; however, rare situations of such preservations do occur. Scientists were able to extract DNA nucleotides from the tissue and use the information to sequence several genes. Your task is to use BLAST to analyze these genes and determine the most likely placement of the fossil species on a given cladogram. Cladogram Place an asterisk (*) where you think this fossil belongs based on your observations above Attached in google classroom are three sample strands of DNA taken from this actual fossil. You will want to save them to your desktop as gene 1, gene 2 and gene 3. Don't try to open them since they are formatted already to use in the BLAST program so the computer won't know what to do with it. Instructions: Go to the BLAST website(attached here). Click on saved strategies from the top tab.Under Upload File upload one of the gene files you saved to your computer and click view. Do not alter any parameters, just scroll down and click BLASTbutton at bottom.Record the information in the chart below and repeat for the other two genes. Information about Genes Info to know -the higher the score the closer the alignment -the lower the e value, the closer the alignment -sequences with e values less than 1x10-4 can be considered related with an error rate of less than 0.01%. Genes What species in the BLAST results was most similar to the gene of interest? Where would that species be located on the cladogram (ex: near the great apes) How similar is the gene sequence? What species has the next most similar gene sequence to the gene of interest? Gene 1 Gene 2 Gene 3 Reflect on the information from the table... Now that you know about the DNA information where would you place the species on the cladogram from earlier (where you put the asterisk)? Place an exclamation point in the area you believe it's most likely located now (it's okay if your spots are similar). Why is it important to consider morphological AND biochemical information when determining relatedness? When this lab was first introduced in the AP Biology curriculum there were under 30 organisms DNA in the BLAST website. The following year there were nearly 100. How many total organisms are in BLAST now (this may be difficult to find... use whatever means necessary to locate an approximate number) and how does the number of included organisms in BLAST help scientists find accurate relationships between organisms? Choose ONE gene from the following list to explore and utilize BLAST to find answers. Choices: ATP synthase, catalase, GAPDH, keratin, myosin, Pax1, ubiquitin Chosen Gene: What is the function of the gene? Would you expect to find the same protein in other organisms? If so, which ones? Is it possible to find the same gene in two different kinds of organisms but not find the protein that is produced from that gene? If you found the same gene in all organisms that you test what does this suggest about the evolution of this gene in the history of life on earth? Does the use of DNA sequences in the study of evolutionary relationships mean that other characteristics are unimportant in such studies? Explain your answer. Practice Free Response Question: Discuss two different types of evidence we have for evolution and explain one positive and one negative for each. Make an argument for what are strongest evidence is and why.