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BIO 370

EVOLUTION FALL 2017


TTH 9:30-11:00 (BUR 116) & TTH 11:00-12:30 (BUR 116)

Instructors: Dr. Thomas Juenger Office: PAT 637


tjuenger@austin.utexas.edu Hours: Mondays 9-10am; Wednesday 9-10am
or by appointment

Dr. Howard Ochman Office: NMS 4.114


howard.ochman@austin.utexas.edu Hours: Mondays 3-4 pm; Wednesday 2-3 pm
or by appointment

TAs: Alexandra Nishida Office: NMS 4.106


Hours: Tuesdays 12:30-1:30 pm
or by appointment

Serena Zhao Office: NMS 4.106


Hours: Wednesdays 12:30-1:30 pm
or by appointment

Discussions for TTH 9:30 AM lecture: 49550 Wed 11:0012:00 pm, WAG 208
49555 Wed 12:001:00 pm, MEZ 2.118
49560 Tue 2:003:00 pm, SZB 380
49565 Tue 3:304:30, GDC 1.406

Discussions for TTH 11:00 AM lecture: 49590 Wed 10:0011:00 pm, CLA 0.118
49595 Wed 11:0012:00 pm, GDC 5.304
49600 Tue 2:003:00 pm, JES A209A
49605 Tue 3:004:00 pm, GAR 3.116

Textbook : Freeman & Herron. Evolutionary Analysis 5th edition (2014).

Course Website: We will be using Canvas (canvas.utexas.edu) to make course announcements, post
lecture materials, distribute readings and assignments, etc. Access requires you to login with your EID
and Password, and you cannot login unless you are registered in the course. You can contact
the instructor via email or though CANVAS.

Course Description: This course is an introduction to biological evolution, including the history of the
field, mechanisms of evolution, and the historical record of evolution on Earth. Evolutionary biology is
currently a very active area of research, and the objective of this course is to provide the basis for
understanding the origins, evolution, diversity and relationships of organisms.
The prerequisite for this course is knowledge of basic genetic concepts. You are required to have taken
BIO 325 or its equivalent before taking this course. It will be necessary for you to know the
fundamentals of Mendelian and molecular genetics (e.g., gene inheritance, DNA replication,
transcription and translation, etc.), and you may need to review these concepts by reading an
introductory biology or genetics textbook.
Course Format: This course consists of two types of instruction: lectures that will present the course
material in what is hopefully an interesting and helpful-for-learning manner, and discussion sessions
that will allow you to refine your understanding of the material through supplemental readings, short
written assignments, problem sets, and interactions with your TA and fellow students.

Learning aids: To assist your learning, the instructors will assign the pages of the textbook
corresponding to a lecture and post a pdf containing slides presented in lecture (usually on the day
before the lecture). These slides are intended to supplement, not replace, the lectures and will allow
you to follow along with the material as it is being presented. Note that the posted materials do not
contain all of the information covered in lecture: they are intended to free you from taking copious
notes, and to allow you to direct your attention to the presentation and be more fully engaged with the
subject material.
The class policy is that computers may be used during class as long as their use is
limited to the materials (slides/outlines/handouts) distributed for lecture. TAs will
monitor the use of computers/electronic devices to assure that they are being used for class purposes. If
you violate this policy, the entire class will be banned from using electronic devices during class.

Grading: Your grade will be based on your performance on in-class exams, and on your attendance and
participation in discussion sections (and their associated assignments).
Lecture Exams: The four in-class exams are worth 80% of the course total (20% each). In addition,
there will be an optional fifth exam (of the value as the other four) given during the final exam period
(see below).
Optional fifth exam: Students who miss an exam for any reason and require a make-up can take the
fifth exam, which will be given during the final exam period. This fifth exam is comprehensive and
will test knowledge of all material covered over the entire semester. As such, the fifth exam need not
be of the same format as the in-class exams.
No other make-up exams will given, so if you do not take the optional fifth exam (due to scheduling or other
conflicts), your final grade will be based solely on the scores of the four in-class exams.
Students who are dissatisfied with a grade on an in-class exam may take the optional fifth exam. In
such cases, the score obtained on the fifth exam will replace the lowest score you received on an in-
class exam.
Discussion Section grades have two components attendance and participation worth 20% of the
course total (16% for assignments/attendance, and 4% for participation). During the semester, there
will be 13 discussions. We will drop your three lowest scores, and the other 10 will be worth 20% of the
course total.

Final Course Grade Standards and Cutoffs: We will apply a modified plus/minus grading system,
in that there are no minus grades. Please note that we do not round-up scores to the next full integer
(i.e., 89.99 receives a B+, not an A).
90.00 100% =A
87.00 89.99% = B+
80.00 86.99% =B
77.00 79.99% = C+
70.00 76.99% =C
67.00 69.99% = D+
60.00 66.99% =D
Less than 60% =F
Lecture Exam Policy: It is your responsibility to arrive at the exams on time. Exams will be held in our
regular classroom during regular class times (except for the optional fifth exam, see below). Students
who arrive late will not be given additional time, and anyone arriving after any other student has
completed the exam will not be permitted to take the exam. Failing to take a scheduled examination
will result in a score of 0.
Re-grades. If you believe a grading error was made on an exam, submit a typed appeal within a
week (7 days) from when exams were returned in class. Do not ask the instructors or the TAs about the
validity of your answer(s) or whether you should submit your exam for reconsideration and re-grading.
Your written appeal should be based on course materials and must stress the scientific validity of your
original response. Note that when submitting an appeal, the entire exam is subject to re-grading.
Please keep the following in mind when it comes to requesting a re-grade:
In the past, the vast majority of re-grade requests have been WITHOUT merit. Time and again
students have included in their appeals information that was NOT in their original answer on the
exam. We can only re-grade what is on the exam, NOT what was intended, meant, or in-mind.
If we feel that you received more credit for an answer than you deserved when the exam was originally
graded, we will deduct points from your exam.
We strive to be fair in our grading and re-grading of exams; a great deal of effort goes into this. If you
really feel that you did not receive the credit that you deserved for an answer, then you are certainly
welcome to submit a re-grade request. We only ask that you carefully consider the original answer you
gave to a question and the credit you received. Re-grade requests that are frivolous and without merit
will not be well-received, and you will lose all original credit (if any) assigned to the question.
Due to time constraints, there will be no re-grading of either the fourth or the optional fifth Exam.

Lecture Attendance Policy: Lecture attendance is not mandatory, but we strongly suggest that you
attend. Going to class is part of the educational process and the university experience.

Discussion Attendance Policy: Attendance at your assigned Discussion sections is required. BIO 370
has weekly meetings to discuss readings from the literature, questions from the book or from other
sources, and to participate in other assignments. The Discussion sections are an essential part of the
course as it is the place where you are asked to think like a scientist and have the opportunity to
critically discuss ideas and the evidence supporting them. Attendance and participation in the
discussions are required and will contribute to your discussion grade (see Grading above). All the
assigned readings should be read carefully before you attend your discussion section. Come prepared
to talk about the subject of the reading and the assigned review-questions. It is not required that you
fully understand the reading or each question before each discussion. Rather, through your
conversation with the other students in your section and with your TA, we expect you to develop a
better understanding of this material and of what they mean to science. If you find a reading or
review-question particularly difficult, you should feel comfortable using the discussion session to ask
questions for clarification. To help you formulate your thoughts on each paper, you will usually be
required to come up with one or two questions about the reading or to write a brief
answer to each review-question prior to each discussion section, and to bring these to
your discussion section on a sheet of paper with your name on it. Your questions/answers
must be handed to the TA at the beginning of the discussion session. The discussion section
readings will often cover material not covered in lecture; however, you are responsible
for the material covered in the discussion readings and this material will be tested in
the exams. Do not switch discussion sections without permission from your TA, or you will not
receive credit for the discussions into which you switched.
Religious Holidays and Excused Absences: Religious holy days sometimes conflict with class and
examination schedules. The University policy is that students who miss course work due to the
observance of a religious holy day must be given the opportunity to complete the work missed within a
reasonable time after the absence, provided that the instructor is notified in advance. The University
policy requires that students must notify the course instructor at least 14 days prior to the class or exam
that will be missed.

Incomplete Policy: Any incomplete grade given must be verified with a written agreement with the
student that specifies the work to be done and a timetable for completion. In accordance with
University policy, the grade of incomplete can only be awarded in cases of students whose
circumstances prevent them from finishing the required work for the course.

Special Needs and Accommodations: Any student with a documented disability (physical or
cognitive) who requires academic accommodations should contact Services for Students with
Disabilities (SSD) to request an official letter outlining authorized accommodations. We will do
everything in our power to accommodate students with special needs. The following is from the SSD
homepage:
At SSD, we determine eligibility and help implement reasonable accommodations for students with disabilities at the
University of Texas at Austin. More general resources for the UT community may be found on UTs Disability Resource
page. SSD is housed in the Office of the Dean of Students, located on the fourth floor of the Student Services Building.
Information on how to register, downloadable forms, including guidelines for documentation, accommodation request
letters, and releases of information are available online. Please do not hesitate to contact us at (512) 471-6259, VP: 1-
866-329-3986 or via e-mail if you have any questions. We look forward to making your experience at the university
more accessible!

Academic Integrity: Scholastic dishonesty in any form will not be tolerated. All of the work that you
submit for this course, on every assignment and examination, is to be entirely your own. Deviation
from this rule constitutes plagiarism (which is, using the work of another person and presenting or implying that
it is ones own). Any form of academic dishonesty, whether it be cheating on a test or an examination,
plagiarism, improper collaboration on assignments, lack of proper attribution, or the submission of the
same essay to two instructors without the explicit consent of both, will be reported to the Office of
the Dean of Students.
Under the University of Texas Code on Academic Integrity, students are allowed to study
together and to discuss information and concepts pertaining to the class; however, this cooperation can
not involve one student having possession of a copy of all or part of work done by someone else, or the
communication, verbally or in writing, of an answer to an assignment. In such situations, both the
donor and the recipient of the information or materials will be penalized. Penalty for violation of this
Code can be extended to include failure of the course and University disciplinary action. Additional
information pertaining to what constitutes academic dishonesty and the disciplinary process is
available at: http://deanofstudents.utexas.edu/sjs/scholdis_whatis.php

Confidentiality of Student Records: We strive to maintain the anonymity of individual students


taking this course relative to grades given on assignments or exams, or final grades at the completion of
the course.

Some final advice: If you have any problems, or if any course-related matters arise, please feel free to
contact one of the instructors, either by email or through the Canvas portal. If you send us an email,
we will acknowledge its receipt and try to answer your question or resolve the issue. If you do not
receive any response within 48 hours, please assume that we did not receive the original email and try
sending it again.
Some Important Dates for Fall Semester 2017:

September 5 Last day of the official add/drop period. After this date, changes in registration may
require the approval of the department chair and usually the students Dean. Last day undergraduate
students may register and pay tuition without the approval of the registrar.

September 15 Twelfth class day; this is the date the official enrollment count is taken. Payment for
added classes due by 5:00 pm. Last day an undergraduate student may add a class except for rare and
extenuating circumstances. Last day to drop a class for a possible refund. (If you want to drop a class
after the 12th class day, youll need to execute a Q drop.)

November 7 Last day that an undergraduate student may, with the deans approval, withdraw from
the University or drop a class except for urgent and substantiated, nonacademic reasons. Last day an
undergraduate student may change registration in a class to or from the pass/fail basis.

November 22-26 Thanksgiving holiday.

December 11 Last day of classes for the Fall 2017 Semester.

December 12-13 Reading period. No Class days.


BIO 370: EVOLUTION FALL 2017
SCHEDULE OF TOPICS, READINGS AND EXAMS

DATE TOPIC READINGS (CHAPTER OR PAGES IN


HERRON & FREEMAN, 5TH EDITION)
Aug 31 Course Information; Lecture 1 Scope of Evolution Chapter 2
Sept 5 Lecture 2 History, Scope, an Evidence Chapter 2
Sept 7 Lecture 3 Genetics Review Chapter 5
Sep 12 Lecture 4 Variation Chapter 9
Sep 14 Lecture 5 The Theory of Natural Selection Chapter 3
Sep 19 Lecture 6 Mendelian Genetics and Populations I Chapter 6
Sep 21 EXAM I During Regular Class Time in Regular Lecture Classroom
Sep 26 Lecture 7 Mendelian Genetics and Populations II Chapter 7
Sep 28 Lecture 8 Sexual Selection Chapter 11
Oct 3 Lecture 9 The Evolution of Sex Chapter 8, pp. 314-324
Oct 5 Lecture 10 Aging and Life History Evolution Chapter 13
Oct 10 Lecture 11 Units of Selection Chapter 12
Oct 12 Lecture 12 Applied Evolution and Review Chapter 14
Oct 17 EXAM II During Regular Class Time in Regular Lecture Classroom
Oct 19 Lecture 13 Molecular Evolution I: Mutation & Selection pp. 157-161; 169-171; 591-592
Oct 24 Lecture 14 Molecular Evolution II: Divergence & Rates pp. 246-248; 256-257; 260-272
Oct 26 Lecture 15 Phylogenetics I: Estimation & Inference pp. 109-123; 125-127; 130 (Box 4.2)
Oct 31 Lecture 16 Phylogenetics II: Problems & Applications pp. 19-23; 665-673; 132-133; 536;
744-747; 773-774
Nov 2 Lecture 17 Genome Evolution pp. 161, 164-166; 168; 581-586; 594-
596; 672-675
Nov 7 Lecture 18 Speciation pp. 609-614; 616-619; 629-631
Nov 9 EXAM III During Regular Class Time in Regular Lecture Classroom
Nov 14 Lecture 19 Social & Species Interactions pp. 456; 562-564; 748-749
Nov 16 Lecture 20 Origin & Diversification of Life pp. 62-66; 645-649; 652-654; 655-659
Nov 21 Lecture 21 Fossil Record & Extinctions pp. 51-53; 63; 663-665; 675-677; 691-
705; 709-719
Nov 23 Thanksgiving no lecture
Nov 28 Lecture 22 Human Evolution I: Fossil Evidence pp. 769-770; 776-778; 786-792; 802-
807; 138-139
Nov 30 Lecture 23 Human Evolution II: Molecular Evidence pp. 771-775; 793-794; 798-800
Dec 5 Lecture 24 Man & Mankind Adapting pp. 2-4; 15-17; 166; 180; 310-311;
737; 778-779
Dec 7 EXAM IV During Regular Class Time in Regular Lecture Classroom

There is NO mandatory Final Exam for this course. Instead, we are offering an optional,
comprehensive, hour-long exam (Exam V) during the final exam period that can serve as a make-up for
a missed exam or as a substitute for the lowest of your four in-class exams. The dates and times of this
optional fifth exam will be announced as soon as they are revealed by the Office of the Registrar.
BIO 370: EVOLUTION FALL 2017
SCHEDULE OF DISCUSSION SECTIONS

DATES DISCUSSION SESSION READINGS (OR END-OF-CHAPTER QUESTIONS


IN HERRON & FREEMAN, 5TH EDITION)

Aug 31 Week 1 No Discussion

Sept 5,6 Week 2 Discussion 1 Dobzhansky (1973) American Biology


Teacher, pp 125-129.

Sept 12, 13 Week 3 Discussion 2 Grant & Grant (2003) Biosciences 53: 965.
Lamichhaney et al. (2015) Nature 518: 371.

Sept 19, 20 Week 4 Discussion 3 Reznick et al. (1997) Science 275: 1943.

Sept 25, 26 Week 5 Discussion 4 Milano et al. (2016) Molecular Ecology 25: 5862.

Oct 3,4 Week 6 Discussion 5 Lumley et al. (2015) Nature 522: 470-473.

Oct 10, 11 Week 7 Discussion 6 Carroll et al. (2012) Science 346: 6207.

Oct 17, 18 Week 8 Discussion 7 Dawkins (1976) from The Selfish Gene
Foreword, Preface, pp. 13-21

Oct 24, 25 Week 9 Discussion 8 Chapter 5: Questions 12, 13


Chapter 7: Questions 7, 8
McDonald & Kreitman (1991) Nature 351:
652

Oct 31/Nov 1 Week 10 Discussion 9 Chapter 4: Questions 1, 2, 3, 4, 5, 6, 7, 8,


9, 12, 13, 14, 17
Chapter 17: Questions 4, 5
Hillis et al. (1992) Science 255: 5044

Nov 7, 8 Week 11 Discussion 10 This is included on Thursdays test


Chapter 15: Questions 1, 2, 4, 8, 11
Moran & Jarvik (2010) Science 328: 624

Nov 14, 15 Week 12 Discussion 11 Chapter 16: Questions 1, 2, 6, 13


Moeller et al. (2016) Science 353: 380

Nov 21, 22 Week 13 No Discussion (no readings this week)

Nov 28, 29 Week 14 Discussion 12 Chapter 17, Questions 2, 11, 12


Chapter 18: Questions 3, 4, 5, 6, 8, 9, 12,
14, 15, 16
Ceballos et al. (2015) Science Advances 1:
e1400253

Dec 5,6 Week 15 Discussion 13 Chapter 20, Questions 1, 2, 3, 4, 5, 9, 17


Chapter 7, Question 10
Chapter 1, Question 7 (for Discussion)
Sarich & Wilson (1967) Science 158: 1200