Evolutionary Genetics Honors
Homework Assignments
October 3, 2011 – November 4, 2011
(The homework is for the night assigned and due the next day unless otherwise noted)
Day/Date
Cycle
Period 4
Plant many strains of maize for our Intron
Polymorphism Experiment. Go over tests.
Read Chapter 6 in The Making of the Fittest, and
answer the following questions which will be due
by 4:00 pm on Friday.
CHAPTER 6:
27. What is convergent evolution? Give at least two
examples of animals that represent this
phenomenon.
28. Why does it just make sense, practically, for
evolution to repeat itself?
29. What role does gene duplication seem to play in
an organism’s ability to evolve?
10/3/2011
Day 2
10/4/2011
Day 3
DROP DAY
10/5/2011
Day 4
10/6/2011
Day 5
Volleyball: 1st Round of Area Tournament
Read Chapter 2: Intro to Bioinformatics,
Genome Browsers & Genetic Analysis and
define the bold terms. Also, we will be going
over pages 16-21 (through the top of the page –
stop at DNA sequencing for now)..
Read pages 76-87, as we will do this as a class
exercise tomorrow in class. Also, your Chapter
6 Making of the Fittest Questions are due
tomorrow.
You guys enjoyed a wonderful, open air book
discussion with Dr. Scott today!
Cross Country: 4:00 Home Meet
Volleyball: 2nd Round of Area Tournament
Starting looking at NCBI in class today and using
BLAST to look at Hemoglobin Gene (pages 7681). We also looked at phylogenetic trees and
similar hemoglobin genes found among close
relatives of homo sapiens.
Your take home test is due Tuesday in class.
10/7/2011
Day 1
Football: 7:30 Spartans vs. Social Circle
Volleyball: 10/8 Area Tournament Finals
Day/Date
Cycle
Period 4
10/10/2011
Faculty Work
Day
Student Holiday . . . Enjoy! 
10/11/2011
Day 4
10/12/2011
Day 5
Introduced our Intron Polymorphism experiment,
downloaded different intron sequences (4996,
169020, 161335) and broke into groups. Used
BLAST function on NCBI to learn a little about
our unknown intron sequence and find out which
plant species it originates from.
Introduce another genome browser, Phytozome,
and begin using this Plant Genome Browser to
annotate our intron sequence and do some gene
predictions. We went through the actin example
together as a class, and then each group did
their specific genetic sequences.
Cross Country: 4:00 Home Meet
Finished up with Phytozome and set up DNA
Subway Accounts
Nicholas turns THREE!!
Extract DNA from various maize strains
10/13/2011
Day 1
10/14/2011
Day 2
Football: 7:30 Spartans @ Commerce
Day/Date
Cycle
Period 4
10/17/2011
Day 4
Start DNA Subway Projects today.
Continue work on DNA Subway. Also, start
google document to electronically record gene
annotation for your mite. Electronic google
document should contain the following
information (some of which should have already
been captured in your notebook):
1. On which chromosome can your sequence
be found? (information gained from Phytozome)
2. About where within the chromosome is the
hit? (information gained from Phytozome)
3. Is your sequence on the +/- strand of the
DNA?
4. Is there cDNA/EST evidence to support your
gene predictions?
5. Draw a sketch of the gene predictions (and in
particular, the applicable region surrounding
your intron of interest). Make sure to identify the
# of exons/introns within your predicted gene
and make notes about where you will design
primers.
Compare your notes with your other group
members to make sure everyone is on the
same page. You can also take screen shots
using the “snipping tool” and add them to
your google document, if you like!
Share your google document with me and
entitle it with your intron # and name, please.
10/18/2011
Day 5
Cross Country: 4:00 Clarke/Oconee Meet (HOME)
Volleyball – 2nd Round of State vs. Providence
Christian – 6:00 pm
Extract Sequence from DNA Subway, get all the
information ready to go for Primer 3 Plus and
design primers!
Read Chapter 7 in Carroll’s The Making of the
Fittest, pages 164-187 and answer the
following questions before Tuesday:
30. What is a coevolutionary arms race? Give an
example of such a race. Why is this race
important in terms of life and death for the
existence of the species?
31. Who is William Charles Wlls and why is he
significant? (page 168) American born
physician, articulated principles of natural
selection 40 years prior to Darwin,
unbenknownst to Darwin and attributed it to
human diversity.
32. Why has selection prevented variations found
in the MC1R gene in Africans from being
anything but synonymous while in nonAfricans there are many non-synonymous
variations that can be found? (172-173)
33. Who is Anthony Allison? What is known
about diseases such as sickle cell anemia,
malaria and others that arise as a result of a
single base pair change? (174-177)
34. What is meant by a heterozygote advantage?
As it relates to sickle cell, for instance.
35. On page 179, Carroll states that the HarvardOxford Malaria Genome Diversity Project
concluded that the Plasmodium falciparum
caused the most virulent form of malaria and
that it was also the form of the disease of the
most recent origin. Does this make sense
from an evolutionary standpoint? Why or
why not?
36. Why has combination drug therapy become
an ever increasing method to combat the war
on pathogens? (181)
37. Do you find some irony in the fact that we are
spending billions of dollars and so much
intellectual power to fight an organism as
simple and what we would label “brainless”
as a bacterium? Explain.
Play close attention to the closing
paragraphs on pages 186-187, as we will
have a discuss these closing paragraphs in
the coming days!
10/19/2011
Day 1
10/20/2011
Day 2
Finish Primer Design today in class
10/21/2011
Day 3
Football: 7:30 Spartans @ ACS
10/22 Cross Country @ Carrolton Last Chance Meet
Day/Date
Cycle
Period 4
10/24/2011
Day 5
schedule)
10/25/2011
Day 1
10/26/2011
Day 2
Bonfire tonight – Finish DNA Extraction and
Isolation
Light Homework Night
Book Discussion on Chapter 7
Liquid Nitrogen ICE CREAM Party
10/27/2011
Day 3
Cross Country: 4:00 Region Meet @ ACS
Drop Day
Drop Day (no class today due to homecoming
Drop Day
Run Genomic DNA on Gel to ensure we have
good DNA before setting up PCR
10/28/2011
Special
Schedule
Day/Date
Cycle
10/31/2011
Day 1
11/1/2011
Day 2
HOMECOMING!
Football: 7:30 Spartans vs. Riverside MA
Period 4
Finish up Experimental Design, complete DNA
Dilutions, Organization of Lab Set-up and Group
Coordination et al in preparation for PCR set up
tomorrow! For homework, you need to make
sure that your lab notebook, both electronically
and your paper notebook, have all your
protocols updated and that you are organized as
we get back to the wet bench. Your google
document needs to be updated by tomorrow as
well!
Set up PCR for your respective introns. Read
Chapter 8. Questions will be due on Friday.
38. What is meant by the terms microevolution
and macroevolution, and how would you
describe your personal belief in both
processes?
39. 10. When Carroll talks about tool kit genes
producing tool kit proteins such as Pax-6, the
implication is that these ancient proteins are
the foundation upon which the great
anatomical diversity of animal eyes (some 4065 different types) has been built. What do
you think about this evolutionary explanation
for the complexity of vision and moreover,
the complexity of life?
40. Use the stickleback fish as an example to
explain how a tool-kit gene, Pitx1, has
affected the pelvis development of the
stickleback based on the selection pressure
determined by the fish’s varying environment.
11/2/2011
Day 3
Drop Day
Run our gel today and hope for results
tomorrow!!!
Finish up your question set for tomorrow.
Senior Night @ Football Game
11/3/2011
Day 4
11/4/2011
Day 5
Football: 7:30 Spartans vs. Region 8AA 9th place team
11/5 – Cross Country: State Meet
Day/Date
Cycle
Period 4
11/7/2011
Day 2
11/8/2011
Day 3
11/9/2011
Day 4
11/10/2011
Day 5
11/11/2011
Day 1
Date
Cycle
11/14/2011
Day 3
11/15/2011
Day 4
11/16/2011
Day 5
11/17/2011
Day 1
11/18/2011
Day 2
US SERVICE DAY
Date
Cycle
Period 4
11/21/2011
Day 4
11/22/2011
Day 5
11/23/2011
Day 1
11/24/2011
Day 2
11/25/2011
Day 3
Date
Cycle
11/28/2011
Day 5
Period 4
Drop Day
Enjoy the
Thanksgiving
Break!! 
Period 4
11/29/2011
Day 1
11/30/2011
Day 2
12/1/2011
Day 3
12/2/2011
Day 4
Date
Cycle
12/5/2011
Day 1
12/6/2011
Day 2
12/7/2011
Day 3
12/8/2011
12/9/2011
Day 4
US Review
Day
Date
Cycle
12/12/2011
US Review
Day
12/13/2011
US EXAMS
12/14/2011
US EXAMS
12/15/2011
US EXAMS
12/16/2011
US EXAMS
Drop Day
Period 4
Drop Day
Period 4
ENJOY THE HOLIDAY BREAK!