Download Determining Evolutionary Relationships Using BLAST

BIG IDEA 1
3
EDVO-Kit: AP03
Determining Evolutionary
Relationships Using BLAST
See Page 3 for storage instructions.
EXPERIMENT OBJECTIVE:
The objective of the experiment is for students to become familiar
with databases that can be used to investigate gene sequences
and to construct cladograms that provide evidence for evolutionary
relatedness among species.
EVT AP03.120828
EX PERIMENT
AP03
Determining Evolutionary Relationships Using BLAST
Table of Contents
Page
Experiment Components
Experiment Requirements
Background Information
3
3
4
Experiment Procedures
Experiment Overview
Investigation I: Understanding a Cladogram
Investigation II: Building Simple Cladograms
Investigation III: Uncovering Fossil Specimen using BLAST
Investigation IV: BLAST Your Own Genes of Interest!
Study Questions, Expected Results and Selected Answers
7
8
9
11
18
19
Instructor’s Guidelines
Notes to the Instructor
25
The Advanced Placement (AP) Program is a registered trademark of the College Entrance Examination Board. These
laboratory materials have been prepared by EDVOTEK, Inc. which bears sole responsibility for their contents.
All components are intended for educational research only. They are not to be used for diagnostic or drug purposes, nor administered to or consumed by humans or animals.
THIS EXPERIMENT DOES NOT CONTAIN HUMAN DNA. None of the experiment components are derived
from human sources.
EDVOTEK and The Biotechnology Education Company are registered trademarks of EDVOTEK, Inc.
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
2
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
E XP E RIME N T
Determining Evolutionary Relationships Using BLAST
Experiment Components
•
Instructions
AP03
Store the entire
experiment at room
temperature.
This experiment is
designed for 10 lab
groups.
Requirements
•
Computer with internet access
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
3
EX PERIMENT
AP03
Determining Evolutionary Relationships Using BLAST
Background Information
Bioinformatics is a new field of biotechnology that is involved in the storage and manipulation of DNA sequence information from which one can obtain useful biological
information. Although DNA sequencing has existed since the early 1970's, it has not been
until the 1990's that the whole process has been automated. In particular, automated
DNA sequencers rapidly and efficiently analyze the reactions in a one-lane sequencing
process that uses four-dye fluorescent labeling methods and a real-time scanning detector. These machines automatically separate the labeled DNA molecules of varying sizes by
gel electrophoresis and also "call" the bases and record the data. In contrast to running
and reading the DNA sequencing gels manually, these automated sequencers can provide
much more information (up to several thousands of base pairs) per gel run.
DNA to be Sequenced - Shown is the “G” lane
CTCGGTCGCTCATT
3'
5'
3'
Primer
5'
Fragment Size
ddGTAA
21
3'
5'
3'
5'
3'
5'
3'
5'
3'
5'
ddGAGTAA
23
25
ddGCGAGTAA
ddGCCAGCGAGTAA
29
31
ddGAGCCAGCGAGTAA
The entire process of collecting and analyzing sequencing
data is automated. Robots perform the sequencing reactions, which are then loaded onto automated sequencers. After the automated sequencing run is complete, the
sequence information is transferred to computers, which
analyze the data. This highly efficient automated DNA
sequencing process has produced many large-scale DNA
sequencing efforts creating a new field of biology called
genomics. Genomics involves using DNA sequence information to understand the biological complexity of an organism. The Human Genome Project (HGP) will furnish a
complete human genetic blueprint by the year 2002. The
goal of the HGP is to determine the complete nucleotide
sequence of human DNA and thus localizing the estimated
80,000-100,000 genes within the human genome. Advances in DNA sequencing and bioinformatics will soon make
it possible to use information from the Human Genome
Project as a clinical diagnostic tool.
In addition to the human genome, some of the first
genomes to be sequenced are those of microbes. Information about genes in microbes represents new leads for
developing new therapeutic agents. It should be noted
that several smaller genomes such as that for Saccharomyces cerevisae and Helicobacter pylori have already been
completed. Additional efforts are ongoing for sequencing
the genomes of other organisms that are used extensively
in research laboratories as model systems (e.g. mice) or for
commercial reasons (e.g. corn).
The genetic revolution will continue to yield new discoveries. While scientists continue
to identify genes that cause disease or phenotypic differences (tall versus short), there is a
growing danger to see humans merely as a sum of their genes. Understanding the ethical,
legal, and social implications of genetic knowledge, and the development of policy options for public consideration are therefore yet another major component of the human
genome research effort. For example, one particular area of debate is that of psychiatric
disorders whereby researchers are trying to characterize traits such as schizophrenia, intelligence and criminal behavior purely in terms of genes. This simplistic view may create
situations in which genetic information has the potential to cause inconvenience or harm.
Additionally, ethical debate about prenatal screening of diseases in human embryos is
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
4
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
E XP E RIME N T
AP03
Determining Evolutionary Relationships Using BLAST
Background Information
also controversial. Thus in depth discussion is needed to balance improvements to human
health with the ethical implications of the genetic revolution.
Data from DNA sequencing is of limited use unless it can be converted to biologically useful information. Bioinformatics therefore is a critical component of DNA sequencing . It
evolved from the merging of computer technology and biotechnology. The widespread
use of the internet has made it possible to easily retrieve information from the various
genome projects. In a typical analysis, as a first step, after obtaining DNA sequencing data
a molecular biologist will search for DNA sequence similarities using various data banks
on the internet. Such a search may lead to the identification of the sequenced DNA or
identify its relationship to related genes. Protein coding regions can also be easily identified by the nucleotide composition. Likewise, noncoding regions can be identified by
interruptions due to stop codons. The functional significance of new DNA sequences will
continue to increase and become more important as sequence information is added and
more powerful search engines become readily accessible.
In order to gain experience in database searching, students will utilize the free service offered by the National Center for Biotechnology (NCBI) which can be accessed on the internet. At present there are several Databases of GenBank including the GenBank and EMBL
nucleotide sequences, the non-redundant GenBank CDS (protein sequences) translations,
and the EST (expressed sequence tags) database. Students can use any of these databases
as well as others available on the internet to perform the activities in this lab. For purposes of simplification, we have chosen to illustrate the database offered by the NCBI. These
exercises will involve using BLASTN, whereby a nucleotide sequence will be compared to
other sequences in the nucleotide database. BLASTP will also be used to compare the
amino acid sequence of a protein with other protein sequences in the databank.
Simple Cladogram
A simple cladogram is shown in Figure 1. A cladogram is a tree-like chart, with endpoints
of each branch representing a specific species. The closer two species are located to
each other, the more recently and closely they share a common ancestor. For example,
flowering plants and ferns share a more recent common ancestor than a spikemoss and a
clubmoss.
A properly scaled cladogram will show branches with lengths that are proportional to
length of time. The intersection between two branches represents the common ancestor the two species share.
Figure 1: Simple Cladogram Representing Different Plant Species
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
5
EX PERIMENT
AP03
Determining Evolutionary Relationships Using BLAST
Background Information
Complex Cladogram
Figure 2 includes additional information such as the evolution of particular physical
structures known as shared derived characters. The placement of the derived characters
corresponds with when that character evolved and that every species above the character
label possesses that structure. For example, lizard, tiger and gorilla have dry skin; however, lamprey, shark and salamander do not have dry skin according to the cladogram.
Figure 2: Cladogram of Several Animal Species with
shared derived characters.
In this laboratory investigation, you will use BLAST to analyze several genes and use the
information to construct a cladogram. A cladogram (also called a phylogenetic tree) is a
visualization of the evolutionary relatedness between species.
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
6
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
E XP E RIME N T
Determining Evolutionary Relationships Using BLAST
AP03
Experiment Overview and General Instructions
EXPERIMENT OBJECTIVE
In this investigation, students will:
1.
Create cladograms that depict evolutionary relationships among organisms.
2.
Analyze biological data with a sophisticated bioinformatics online tool.
3.
Connect and apply concepts pertaining to genetics and evolution.
1.
Wear gloves and goggles while working in the laboratory.
2.
Exercise caution when working in the laboratory. You will be using
equipment that can be dangerous if used incorrectly.
3.
Always wash hands thoroughly with soap and water after working in
the laboratory.
4.
If you are unsure of something, ASK YOUR INSTRUCTOR!
Experiment Procedure
LABORATORY SAFETY GUIDELINES
LABORATORY NOTEBOOKS
Scientists document everything that happens during an experiment, including experimental conditions, thoughts and observations while conducting the experiment, and, of
course, any data collected. Today, you’ll be documenting your experiment in a laboratory
notebook or on a separate worksheet.
BEFORE STARTING THE EXPERIMENT:
•
•
Carefully read the introduction and the protocol. Use this information to form a
hypothesis for this experiment.
Predict the results of your experiment.
DURING THE EXPERIMENT:
•
Record your observations.
AFTER THE EXPERIMENT:
•
•
Interpret the results - does your data support or contradict your hypothesis?
If you repeated this experiment, what would you change? Revise your hypothesis to
reflect this change.
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
7
EX PERIMENT
AP03
Determining Evolutionary Relationships Using BLAST
Investigation I: Understanding a Cladogram
EXERCISE 1
Chimpanzees and humans share 96% of their DNA which would place them closely on
a cladogram. Humans and fruit flies are placed farther apart on a cladogram since they
share only approximately 60% of their DNA.
Experiment Procedure
In the space provided, draw a cladogram that shows the evolutionary relationship between humans, chimpanzees, and fruit flies.
EXERCISE 2
Using Figure 2 illustrated in the background information as your sample cladogram,
answer the following questions:
Question 1: According to the cladogram, what organisms have hair?
Question 2: According to the cladogram, what four structures do tigers possess?
Question 3: According to the cladogram, which structure evolved first? Lungs or dry skin?
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
8
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
E XP E RIME N T
Determining Evolutionary Relationships Using BLAST
AP03
Investigation II: Building Simple Cladograms
EXERCISE 3
Use the following data to construct a cladogram of the major plant groups in the space
provided below.
Experiment Procedure
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
9
EX PERIMENT
AP03
Determining Evolutionary Relationships Using BLAST
Investigation II: Building Simple Cladograms
EXERCISE 4
Experiment Procedure
GAPDH (glyceraldehyde 3-phosphate dehydrogenase) is an enzyme that participates in glycolysis, an
important reaction in the process of cellular respiration. The following table shows the percentage of
similarity of this gene and the protein it expresses in humans versus other species.
a)
Why is the percentage of similarity in the protein always higher than the percentage
of similarity in the gene for each of the species?
b)
In the space below, draw a cladogram depicting the evolutionary relationships between all five species based on their percentage of similarity in the GAPDH gene.
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
10
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
E XP E RIME N T
Determining Evolutionary Relationships Using BLAST
AP03
Investigation III: Uncovering Fossil Specimen using BLAST
A. MORPHOLOGICAL OBSERVATION OF THE FOSSIL SPECIMEN AND
FORMING THE HYPOTHESIS
A team of scientists have uncovered the following fossil specimen near Hells Creek, Montana.
Make some general observations about the morphology (physical structure) of the
fossil and record your observations in the space provided.
Experiment Procedure
1.
________________________________________________________________________________
________________________________________________________________________________
________________________________________________________________________________
________________________________________________________________________________
________________________________________________________________________________
________________________________________________________________________________
2.
Little is known about the fossil other than it appears to be a new species. Upon
careful examination of the fossil, small amounts of soft tissue have been discovered.
The scientists were able to extract proteins 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 the following fossil cladogram:
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
11
EX PERIMENT
AP03
Determining Evolutionary Relationships Using BLAST
Experiment Procedure
Investigation III: Uncovering Fossil Specimen using BLAST
3.
Form an initial hypothesis as to where you believe the specimen should be placed on
the cladogram based on the morphological observations you made earlier.
________________________________________________________________________________
________________________________________________________________________________
________________________________________________________________________________
________________________________________________________________________________
________________________________________________________________________________
________________________________________________________________________________
4. Draw your hypothesis on the cladogram.
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
12
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
E XP E RIME N T
Determining Evolutionary Relationships Using BLAST
AP03
Investigation III: Uncovering Fossil Specimen using BLAST
B. USING BLAST TO ANALYZE GENES AND DETERMINE THE MOST LIKELY
PLACEMENT OF THE FOSSIL SPECIES
Step 1: Instruction for Downloading Gene Files
Before starting this investigation, students need to download four gene files (Gene 1- Gene 4)
to their flash drive or computer. These files are located at the following web address:
Gene 1 -- http://www.edvotek.com/site/img/AP_Biology_Lab3_Gene1.asn
Gene 3 -- http://www.edvotek.com/site/img/AP_Biology_Lab3_Gene3.asn
Gene 4 -- http://www.edvotek.com/site/img/AP_Biology_Lab3_Gene4.asn
Step 2: Instructions for BLAST Queries
Upload the gene sequences into BLAST by following the instructions below:
1.
Go to the BLAST homepage: http://blast.ncbi.nlm.nih.gov/Blast.cgi
2.
Click on “Saved Strategies” on the top of the page.
Experiment Procedure
Gene 2 -- http://www.edvotek.com/site/img/AP_Biology_Lab3_Gene2.asn
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
13
EX PERIMENT
AP03
Determining Evolutionary Relationships Using BLAST
Experiment Procedure
Investigation III: Uncovering Fossil Specimen using BLAST
3.
Under “Upload Search Strategy,” click on “Browse” and locate one of the gene files
you saved onto your computer.
4.
Click “View.”
//Users/Lab/Download
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
14
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
E XP E RIME N T
AP03
Determining Evolutionary Relationships Using BLAST
Investigation III: Uncovering Fossil Specimen using BLAST
5.
A screen will appear with
the parameters for your
query already configured.
NOTE: Do not alter any of
the parameters. Scroll down
the page and click on the
“BLAST” button at the bottom.
After collecting and analyzing all of the data for
that particular gene (see
instructions below), repeat
this procedure for the other
three gene sequences.
Step 3: Instructions for
Analyzing BLAST Queries
1.
Scroll down to the section
titled, “Sequences producing significant alignments.”
The list of organisms that
appear below this section
are those with sequences
identical to or most similar
to the gene of interest. The
most similar sequences are
listed first and as you move
down the list, the sequences
become less similar to your
gene of interest.
2.
Try clicking on a particular
species listed to get a full
report that includes the species’ classification scheme,
the research journal the
gene was first reported in,
and the sequence of bases
that appear to align with
your gene of interest.
Experiment Procedure
6.
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
15
EX PERIMENT
AP03
Determining Evolutionary Relationships Using BLAST
Investigation III: Uncovering Fossil Specimen using BLAST
Click “Distance tree of results.” A cladogram of the species with similar sequences
to your gene of interest placed on the cladogram will be shown according to how
closely their matched gene aligns with your gene of interest.
Experiment Procedure
3.
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
16
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
E XP E RIME N T
Determining Evolutionary Relationships Using BLAST
AP03
Investigation III: Uncovering Fossil Specimen using BLAST
Step 4: Analysis of Results
Species share similar genes because of common ancestry. The more similar genes two species have in common, the more recent their common ancestor. Thus, the two species will
be located closer on a cladogram.
As you collect information from BLAST for each of the gene files, explain whether the
data supports your original hypothesis and your original placement of the fossil species
on the cladogram.
1. What species has the most similar gene sequence as your gene of interest?
2. Where is that species located on the cladogram?
3. How similar is that gene sequence?
4. What species has the least similar gene sequence as your gene interest?
Experiment Procedure
For each BLAST query, consider the following:
Step 5: Drawing the Cladogram
Redraw the original cladogram and include your final placement of the fossil species.
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
17
EX PERIMENT
AP03
Determining Evolutionary Relationships Using BLAST
Investigation IV: BLAST Your Own Genes of Interest!
Now that the first part of the investigation is complete, the next step is to learn how to
find and BLAST your own genes of interest. To locate a gene, go to the Entrez Gene website (http://www.ncbi.nlm.nih.gov/gene) and search for the gene. Once you have found
the gene on the site, copy the gene sequence and input it into a BLAST query.
Experiment Procedure
Follow the instructions below to BLAST your own gene of interest:
1.
On the Entrez Gene website search the term “human actin.”
2.
Click on the first link that appears and scroll down to “NCBI Reference Sequences.”
3.
Click on the first file name “NM 001100.3” under “mRNA and Proteins.”
4.
Click on “FASTA” just below the gene title.
5.
The nucleotide sequence displayed is that of the actin gene in humans.
6.
Copy the gene sequence and go to the BLAST homepage (http://blast.ncbi.nlm.nih.
gov/Blast.cgi).
7.
Click on “nucleotide blast” under the Basic BLAST menu.
8.
Paste the sequence into the box “Enter Query Sequence.”
9.
Give the query a title in the box provided if you plan on saving it for later.
10. Under “Choose Search Set” select the type or genome you want to search (human
genome, mouse genome, or all genomes available).
11. Under “Program Selection” choose whether or not you want highly similar sequences
or somewhat similar sequences. Choosing somewhat similar sequences will provide
you with more results.
12. Click BLAST.
In humans, what is the importance of the gene you chose? Would you expect to find that
gene is all organisms? Why or why not?
Some gene suggestions you could try out:
Actin
Keratin
ATP synthase
Myosin Pax1
Catalase
Ubiquitin
GAPDH
Zinc finger
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
18
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
E XP E RIME N T
Determining Evolutionary Relationships Using BLAST
AP03
Study Questions, Expected Results and Selected Answers
Address and record the following in your laboratory notebook or on a separate worksheet.
Before starting the experiment:
• Write a hypothesis that reflects the experiment.
• Predict experimental outcomes.
During the Experiment:
• Record (draw) your observations, or save the results on your computer or flash drive.
INVESTIGATION I: UNDERSTANDING A CLADOGRAM
Exercise 1:
Cladogram showing evolutionary relationship between humans, chimpanzees, and fruit
flies.
Experiment Procedure
Following the Experiment:
• Formulate an explanation from the results.
• Determine what could be changed in the experiment if the experiment were repeated.
• Write a hypothesis that would reflect this change.
Exercise 2:
Question 1: According to the cladogram, what organisms have hair?
Answer: Tiger and gorilla
Question 2: According to the cladogram, what four structures do tigers possess?
Answer: Jaws, lungs, dry skin and hair
Question 3: According to the cladogram, which structure evolved first? Lungs or dry skin?
Answer: Lungs evolved before dry skin did.
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
19
EX PERIMENT
AP03
Determining Evolutionary Relationships Using BLAST
Study Questions, Expected Results and Selected Answers
INVESTIGATION II: BUILDING SIMPLE CLADOGRAMS
Exercise 3:
Cladogram showing evolutionary relationship among the major plant groups
Exercise 4:
Comparison of the Human GAPDH Gene & Protein With Other Species
a. Why is the % similarity in the protein always higher than the % similarity in the
gene for each of the species?
Answer: one gene can make several proteins.
b.
Cladogram depicting the evolutionary relationships between all five species according to their % similarity in the GAPDH gene.
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
20
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
E XP E RIME N T
Determining Evolutionary Relationships Using BLAST
AP03
Study Questions, Expected Results and Selected Answers
INVESTIGATION III: UNCOVERING FOSSIL SPECIMEN USING BLAST
A. Morphological Observation of the Fossil Specimen and Forming the Hypothesis
1.
Observations about the morphology (physical structure) of the fossil specimen near
Hells Creek, Montana
Thecodont, or teeth set in bony sockets, are found on the fossil specimen suggesting the
presence of some groups of reptiles including crocodilians and dinosaurs. Also found on
the fossil are traces of a feather-like material, suggesting the presence of bird-like creatures. Wing-like material was also recovered from the fossil, which indicated flying insects
might have been present.
2.
Construction of a cladogram based on the above morphological observations.
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
21
EX PERIMENT
AP03
Determining Evolutionary Relationships Using BLAST
Study Questions, Expected Results and Selected Answers
B. Using BLAST to Analyze Genes and Determine the Most Likely Placement of the Fossil Species
Gene Sequence # 1
1.
What species has the most similar gene sequence as the gene of interest?
Gallus gallus has the most similar gene sequence as gene sequence # 1.
2.
Where is that species located on the cladogram?
It evolved from the same branch Gallus gallus evolved from.
3.
How similar is that gene sequence?
They are 100% match.
4.
What species has the least similar gene sequence as the gene interest?
Danio rerio has the least similar gene sequence as the gene sequence # 1.
Gene Sequence # 2
1.
What species has the most similar gene sequence as the gene of interest?
Drosophila melanogaster has the most similar gene sequence as gene sequence # 2.
2.
Where is that species located on the cladogram?
It evolved from the same branch Drosophila melanogaster and other species of flies evolved from.
3.
How similar is that gene sequence?
They are 99% match.
4.
What species has the least similar gene sequence as the gene interest?
As predicted, Saccoglossus kowalevskii has the least similar gene sequence as the gene sequence #
2.
Gene Sequence # 3
1.
What species has the most similar gene sequence as the gene of interest?
Taeniopygia gutata has the most similar gene sequence as gene sequence # 3.
2.
Where is that species located on the cladogram?
It evolved from the same branch Taeniopygia gutata evolved from.
3.
How similar is that gene sequence?
They are 100% match.
4.
What species has the least similar gene sequence as the gene interest?
Bony fishes have the least similar gene sequence as the gene sequence # 3.
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
22
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
E XP E RIME N T
Determining Evolutionary Relationships Using BLAST
AP03
Study Questions, Expected Results and Selected Answers
Gene Sequence # 4
1.
What species has the most similar gene sequence as the gene of interest?
Alligator sinensis has the most similar gene sequence as gene sequence # 4.
2.
Where is that species located on the cladogram?
It evolved from the same branch Alligator sinensis evolved from.
3.
How similar is that gene sequence?
They are 100% match.
4.
What species has the least similar gene sequence as the gene interest?
Birds have the least similar gene sequence as the gene sequence # 4.
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
23
EX PERIMENT
AP03
Determining Evolutionary Relationships Using BLAST
Notes:
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
24
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
E XP E RIME N T
AP03
Determining Evolutionary Relationships Using BLAST
Instructor’s
Guide
Notes to the Instructor & Pre-Lab Preparations
OVERVIEW OF LABORATORY INVESTIGATIONS
The “hands-on” laboratory experience is a very important component of
science courses. Laboratory experiment activities allow students to identify
assumptions, use critical and logical thinking, and consider alternative explanations, as well as help apply themes and concepts to biological processes.
EDVOTEK experiments have been designed to provide students the opportunity
to learn very important concepts and techniques used by scientists in laboratories conducting biotechnology research. Some of the experimental procedures
may have been modified or adapted to minimize equipment requirements and
to emphasize safety in the classroom, but do not compromise the educational
experience for the student. The experiments have been tested repeatedly to
maximize a successful transition from the laboratory to the classroom setting.
Furthermore, the experiments allow teachers and students the flexibility to
further modify and adapt procedures for laboratory extensions or alternative
inquiry-based investigations.
Order
Online
Visit our web site for information
about EDVOTEK's complete line
of experiments for biotechnology
and biology education.
ED
VO
-
S E RV I C E
TECH
ORGANIZING AND IMPLEMENTING THE EXPERIMENT
Class size, length of laboratory sessions, and availability of equipment are factors, which must be considered in the planning and the implementation of this
experiment with your students. These guidelines can be adapted to fit your
specific set of circumstances.
Technical Service
Department
Mon - Fri
9:00 am to 6:00 pm ET
1-800-EDVOTEK
ET
(1-800-338-6835)
Mo
FAX: 202.370.1501
web: www.edvotek.com
email: [email protected]
m
6p
n - Fri 9 am Please have the following
information ready:
• Experiment number and title
• Kit lot number on box or tube
• Literature version number
(in lower right corner)
Investigations I, II and III can be completed in one class period
each. In addition, at least one additional class period should
be dedicated for students to explore Investigation IV.
If you do not find the answers to your questions in this section, a variety of resources are continuously being added to
the EDVOTEK web site.
www.edvotek.com
In addition, Technical Service is available from 9:00 am to
6:00 pm, Eastern time zone. Call for help from our knowledgeable technical staff at 1-800-EDVOTEK (1-800-338-6835).
PRE-LAB PREPARATION
No Preparation Needed.
• Approximate purchase date
Visit the EDVOTEK web site often for
updated information.
The Biotechnology Education Company® • 1-800-EDVOTEK • www.edvotek.com
Duplication of any part of this document is permitted for non-profit educational purposes only.
Copyright © 1989-2012 EDVOTEK, Inc., all rights reserved. EVT AP03.120828
25