Evolution (Bio.

205/405), Spring 2015

Instructor: James D. Fry, Ph.D.
Office: 318 Hutchison Hall
Phone: 275-7835
Email: james.fry@rochester.edu
Office hours: By appointment; please email me one day in advance (slots usually available M-F).
T.A.'s: Shagun Kaul (skaul@u.rochester.edu) and Madeleine Keefe (mkeefe@u.rochester.edu).
Lectures: MW 2:00-3:15, Goergen 108
Recitations (mandatory): times TBA. In so far as possible, we will schedule recitation sections
so that everyone should be able to attend at least one.
Required textbook: Herron and Freeman, Evolutionary Analysis, 5th ed. (2013).
Highly recommended book: Coyne, J. Why Evolution is True. (2009). An easy read,
entertaining and informative. Available as paperback or e-book.
A few additional readings will be assigned and made available on Blackboard.
Point breakdown:
Problem Sets (9)
Species Identification Project
In class exercises
Test 1
Test 2
Final exam (cumulative)
Total

18%
12%
10%
16%
18%
26%
100%

Course policies and other important information:

1) Once your recitation time is determined, you should attend that recitation each week. Do not
switch back and forth. (If your schedule changes so that it becomes necessary for you to change
sections, let us know).
2) Problem sets should be handed to your T.A., in recitation.
3) Much useful information will be posted on Blackboard (last years exams, problem sets, etc.);
make use of these resources!
4) Important announcements will sometimes be made by email; you are responsible for checking
your university email account daily.
5) Exam regrade requests should be made in writing and given to your T.A. no later than the
fourth class meeting after the exam was given.

Schedule of Topics

Bio. 205

Spring 2015

J. Fry

(subject to revision check Blackboard for latest version!)

#

Date

Topic

Reading in H & F

W 1/14

Introduction/course organization

W 1/21

Evidence for common descent

Ch. 2 (Coyne Ch. 1, 3, 4)

M 1/26 R

Natural selection

Ch. 3 (Coyne Ch. 5)

W 1/28

Phylogenetic reconstruction

Ch. 4

M 2/2*

Applications of phylogenetic reconstruction

W 2/4

Population Genetics 1: Microbial evolution example

M 2/9*

Pop. Gen. 2: Hardy-Weinberg Law

pp. 162-163; 6.1

W 2/11

Pop. Gen. 3: Selection

6.2-6.3

M 2/16*

Pop. Gen. 4: Selection, cont.

10

W 2/18

Pop. Gen. 5: mutation; mut.-sel. balance

5.2, 6.4

11

M 2/23

Pop. Gen. 6: Random drift

Ch. 7 (except 7.3)

12

W 2/25

Exam 1 (in class, 20 points)

13

M 3/2*

Pop. Gen. 7: Inbreeding and conservation genetics

14

W 3/4

TBA

Ch. 7 (except 7.3)

Spring Break
15

M 3/16*

Early history of earth and origin of life

2.5; 17.1-17.2

16

W 3/18

Tree of life

17.3-17.4

17

M 3/23*

The fossil record

Ch. 18 (Coyne Ch. 2)

18

W 3/25

Fossil record, cont.

19

M 3/30

Evolution of species interactions

20

W 4/1

Exam 2 (in class, 20 points)

21

M 4/6*

Sexual selection and mate choice

Ch. 11 (Coyne Ch. 6)

22

W 4/8

Social behavior and altruism

Ch. 12

23

M 4/13*

Quantitative Genetics 1: Variance and heritability

5.1; 9.1-9.3

24

W 4/15

Quantitative Genetics 2: Response to selection

9.4-9.6; 3.4

25

M 4/20*

Quantitative Genetics 3: Human variation

9.7; 14.5

26

W 4/22

Species and speciation

Ch. 16 (Coyne Ch. 7)

10.1; 394-397; 14.3, 14.6

Friday 4/24: Species identification project due to your T.A.

27

M 4/27

Human Evolution

28

W 4/29

TBA
Tuesday May 5, 4 P.M.

Ch. 20 (Coyne Ch. 8)

Final Exam (cumulative, 30 points).

Recitations start this week *homeworks due (in recitation )

last day to withdraw or declare S/F

Assignments, Exams and Grading

Bio. 205

Spring 2015

J. Fry

Exams will consist of a mixture of problems, multiple choice, true-false, and short-answer
questions (up to a few sentences). Some questions will test straight factual recall, but
others will be integrative and require you to think hard. Graph interpretation will be an
important skill.
Homeworks (problem sets) will be essential practice for the exams. Each will be worth
two points.
Species identification project: This is described in a separate handout.
In-class exercises: On many days, about 10-15 minutes will be devoted to in-class
exercises, to be done in small groups. You will be given a problem or question to ponder
and expected to write a short answer after consulting with the other students in your group.
Each student should turn in their own answer. If you are stumped, rather than taking a wild
guess, you should explain what it is that you dont understand. All serious attempts to
answer the question will receive full credit ( 1 point). However, we will sometimes
call on students to explain their answer, so do not come to class expecting to snooze or
trade text messages with your friends!
Grading Scale
If you get the percent of points indicated, you are guaranteed to get at least the grade
shown. If necessary, the cutoffs will be dropped so that the median grade is near the B/B
cutoff. This will be done at the end of the course only, based on final averages. Individual
exams will not be curved.
It is assumed that everyone will make a strong effort. No points are awarded for effort.
Percent

Minimum grade

Percent

Minimum grade

93-100

73-76.99

90-92.99

70-72.99

87-89.99

B+

67-69.99

D+

83-86.99

63-66.99

80-82.99

60-62.99

77-77.99

C+

<60

Academic Honesty: Cheating is frowned upon. Please review the College academic honesty
policy (http://www.rochester.edu/college/honesty/ ).

Bio. 205

Spring 2015

J. Fry

Course Goals
Overview: Students should gain an appreciation of how the diversity and complexity of living
things is the result of three core processes operating over vast amounts of time: undirected
mutation, natural selection, and chance. Depending on what phenomenon one is interested in,
determining how these processes can explain the phenomenon ranges from being relatively
straightforward to virtually impossible. Nonetheless this basic explanation of lifes diversity has
withstood the test of time.
Specific goals:
1) Become familiar with the multiple types of evidence that all organisms descended from a
common ancestor.
2) Develop an understanding of the process of natural selection, including an understanding of
why it can lead to what at first seem like counterintuitive outcomes.
3) Become familiar with the forces that can alter the genetic composition of populations,
including how they can be modeled mathematically, and how their contributions can be inferred
from molecular and other types of data.
4) Appreciate the practical significance of rapid evolutionary change in organisms (e.g.,
evolution of antibiotic and pesticide resistance).
5) Understand how data from extant (living) species can be used to infer their evolutionary
relationships.
6) Become familiar with how traits influenced by many genes evolve in response to natural and
artificial selection, in theory and practice.
7) Explore the deep history of life on earth, including theories and evidence on how life
originated, and the origin of the eukaryotic cell.
8) Learn the major events in the history of macroscopic life on earth, as inferred from the fossil
record.
9) Develop a basic understanding of the role of natural selection in shaping interactions among
species (host-parasite, predator-prey, competition, mutualism), and interactions between
individuals within species (parental care, altruism, mate choice, competition for mates and
resources).
10) Learn theories and supporting evidence for how speciation, the splitting of one species into
two, occurs. Become familiar with the species concept by learning to identify several species of
trees and vertebrate animals that occur in the Rochester region.
11) Learn the key events in the evolution and world-wide spread of Homo sapiens, as inferred
from fossil and molecular evidence.