BioEE 1780

Introduction to Evolutionary Biology & Diversity

Fall 2014
Brian Lazzaro (Lead Professor)

When you have seen one ant, one bird, one tree, you have not seen them all.
biologist E. O. Wilson
Nothing in Biology makes sense except in the light of Evolution.
geneticist Theodosius Dobzhansky
Simply put, training in evolutionary thinking can help both biomedical researchers and clinicians ask
useful questions that they might not otherwise pose.
Nesse et al., editorial in Science 311: 1071 (2006)
This course is both a survey of the earths spectacular biodiversity and an introduction to the
fascinating processes of evolution that have produced the grand Tree of Life. The effects of evolution
span all of biology, from protein function to the most complex animal behaviors. And both evolution and
biodiversity are relevant to your personal life in ways you might not anticipate. For example, health
professionals deal with these topics every time they encounter a patient who harbors a community of
bacteria with antibiotic resistance and Cornell students experience elements of sexual selection
every time they flirt with potential partners.
Evolutionary theory is elegant and fascinating, and an understanding of how evolutionary
processes shape and maintain biological diversity is crucial for anyone interested in applied or basic
sciences. Active arenas of related research involve many disciplines, from lab projects on selection on
fruit-fly genomes to field biologists investigating why so many tree species
occur in a single patch of tropical rainforest. This course is designed as an
overview of the many evolutionary approaches to exploring, explaining,
and categorizing biological diversity.
We have three basic goals for the semester. First, we want you to
gain an understanding of the major evolutionary processes and an
appreciation for the ways that evolutionary biologists approach their work.
Second, we seek to arm you with the knowledge and tools needed to
understand the evolutionary issues you will encounter in the future, in both
academic and nonacademic settings. Finally, we will survey all major
groups of organisms, from bacteria to mammals, and learn how we are all
How does one ancestral
related via the evolutionary Tree of Life.
species
diversify into many
As professors and practicing scientists, we think that evolution and
descendent
species?
biodiversity are fun and fascinating topics. In this course, we get to explore
questions like: Why is sex so pervasive in the natural world? Why do we
age? How did life originate? Why are there 1000 times more species of
beetles than species of mammals? What factors determine whether a particular pest species will cause
heavy damage to a crop? Why do the sexes look so different in some species, but nearly identical in
others? What do we know about the relationships between humans and other primates? What
evolutionary challenges do medical professionals deal with every day?
You will see from the lecture schedule that the course is organized
into eight thematic modules, including modules on biological diversity and the
Tree of Life. The course includes a mandatory discussion section that
involves readings, laboratory exercises, and field trips that reinforce the
material presented in lecture.
All of us involved in teaching the course are excited about this
opportunity to share our intellectual passions with you, and we hope that you
come to share our sense of wonder at the processes that have enriched our
world with such an amazing diversity of
Why do many animals have ornaments
organisms and adaptations.
(like long tails) that are costly to their
survival?

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INSTRUCTORS
Lead Professor

Brian Lazzaro
Office Hours:

email: bplazzaro@cornell.edu
phone: 255-3254
Monday 9:30-10:30am and Wednesday 2:00-3:00
106 Stimson Hall

Additional Professors
Bob Reed
robertreed@cornell.edu
Willy Bemis
web24@cornell.edu
Cissy Ballen
mb2463@cornell.edu
Section Coordinator

Dr. Liz Balko

Head Teaching Assistant

Renee Petipas

email: eab74@cornell.edu

email: rp382@cornell.edu

Teaching Assistants
Renee Petipas (Head TA) rp382@cornell.edu
Amos Belmaker ab835@cornell.edu
Karin Van der Burg krv32@cornell.edu
Tessa Lessord tgl27@cornell.edu

Cait McDonald cam435@cornell.edu

Jacob Tyrel jat335@cornell.edu
Jake Berv (Track II WIM) jsb439@cornell.edu

Teaching Assistant Office Hours are posted on Blackboard and held in the Biology Study Center, 106
Stimson Hall.
COURSE WEB SITE AND E-MAIL ADDRESS
General course information, supplementary information, lecture outlines and slides, and section
assignments will be posted on the course web site. To access the web site you will need to sign up for
the course via the Blackboard Learning System, which can be accessed at:
http://blackboard.cornell.edu/
All emails about general course business, including questions about grades and discussion sections,
should be send to this address: bioee1780@cornell.edu. This address is constantly monitored.
Why do individual
organisms sometimes
cooperate with other
individuals of their species?

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Required: TEXTBOOKS and iCLICKER

Evolution: Making Sense of Life by Carl Zimmer and Douglas Emlen, 2013 (Roberts & Co.).
This is a brand-new and highly accessible survey of evolutionary biology. Zimmer is a science writer
and reporter for the New York Times; Emlen is a evolutionary biologist who also happens to be a
Cornell alumnus. Reading assignments from the textbook will complement and supplement the lecture
material.
Principles of Life: Diversity (Chapters 19-23) by Hillis et al., 2011 (Sinauer and Associates)
This is your Biodiversity text, covering the relationships among lineages in the Tree of Life. The text is
available in loose-leaf 3-hole punch format at the Cornell Bookstore.
If you prefer, you can buy an eBook version directly from the publisher [credit card required for
purchase]. To purchase the Biodiversity text as an eBook, follow these instructions:
1) go to http://ebooks.bfwpub.com/hillis1e.php
2) Click on PURCHASE this eBook
3) Select the third option: A custom version of the eBook
4) Include the Custom Version number: 5478385
5) Add the zip code for Cornell University: 14853
6) You will be prompted to create an account
7) Fill out the credit card information
8) You will be given a confirmation and password. You can then return to step 1, enter that information
and access your custom eBook.

iClickers and iClicker GO: Each student must have an iClicker remote or use the iClicker GO app.
iClicker remotes can be purchased from the campus bookstore.
To register your iClicker remote:
Login to Blackboard at http://blackboard.cornell.edu
Under your list of "My Courses" click on the name of the course using iClickers.
Click on the "Tools" button in your Course Menu.
Click on "iClicker Remote Registration".
Type in the iClicker Remote ID on the back of your clicker.
Click Submit.
Do not register iClickers at the iClicker.com site.
iClicker GO is a Web-based, virtual remote that students can use to respond to Clicker questions
using a standard Web browser or an app for iOS or Android phones.
Purchase an iClicker GO subscription from the Cornell Store. Please see the Campus Store
web site for pricing.
Register your subscription at: www.iclickerGO.com or download the app from the Apple Store or
Google Play Store on your smart phone. The app is free. IMPORTANT: For the Student ID field,
you MUST use your Cornell NetID (such as ewe2) and not your Cornell Student ID
Be sure to type in Cornells Zip Code: 14853 then clickLookup to find Cornell University
In class, login to www.iclickerGO.com or your app and answer the questions as they are
presented to you in class multiple choice (A-E choices) or short-answer (up to 16 alphanumeric characters)
YOU NEED AN iClicker OR A SUBSCRIPTION TO iClicker GO. YOU DO NOT NEED BOTH.

DISCUSSION SECTIONS
There are two tracks within BioEE1780. All students enter the course registered for Track 1. The
Track 2 Writing in the Majors option is available by application at the beginning of the semester.
STANDARD TRACK 1 SECTIONS (4 CREDITS)
Discussion Sections: Track 1 discussion sections will explore and further develop topics we cover in
lecture. Activities include field trips, reading and discussion of primary literature, in-class exercises,
online activities, and short quizzes and writing assignments. Material covered in discussion sections is
fair game for the prelims and final exam.
Discussion Section Scheduling: Track 1 discussion sections meet once a week; all activities and a
full schedule can be found on Blackboard. Although most of you have already signed up for sections,
some section enrollments will change as students move to the Track 2 option or modify their schedules
for other reasons. We might have to juggle a few students around in order to equilibrate the sizes of
individual sections. Section enrollments are always a bit chaotic for everyone at the beginning of the
semester, but dont panic: we have some time because section meetings do not start until September
2nd.
If you need to change your assigned section, please make every effort to use Student Center to move
yourself to a better time. Be patient, as spots open up steadily during the first week of classes as
students adjust their schedules. Additional section openings also become available when some
students move into the Writing in the Majors sections. If all else fails, email us at
bioee1780@cornell.edu and provide a brief description of your conflict and a list of which sections you
CAN attend. We will do our best to help all students get settled into sections that meet their needs.
Discussion Section Activities: Section activities will help you to synthesize and apply information
covered during lectures. Sections will also provide a forum for addressing questions that arise about
lecture material and assigned readings. Activities include field trips, online simulations, data collection
and interpretation, reading and discussion of primary literature, and in-class exercises.

A schedule listing section activities and assignment due dates is available through the Section
Activities link on Blackboard.
Section activity handouts will be made available on Blackboard by 5:00PM Friday the week
before the activity runs.
Pre-discussion talking points for Section Activity 5 must be submitted through the
appropriate link provided on Blackboard by 10:00 AM on Tuesday Sept 30th.
Take-home assignments (e.g., activity worksheets) are due by 5:00PM the Friday following the
week the activity was completed. Submit all section homework through the appropriate section
activity link on Blackboard.
Late assignments: In general late assignments will not be graded, however, to accommodate
short-term difficulties we will allow each student one late assignment per semester, with no
penalty. You are required to notify your TA that you will be handing in the assignment late before
it is due. The late assignment must be turned in electronically by 5:00PM Saturday (the day
after the activity was due).

Section Attendance and Grading: You must attend the section in which you are registered. Be sure
to select a section time for which you are sure you will not have conflicts (e.g., for athletic events or
other activities). Should extenuating circumstances lead you to seek one-time attendance in a section
other than your own, you must gain permission from the Head TA (email: bioee1780@cornell.edu) in
advance. Please note that if you miss more than four sections you will automatically fail the course.

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TRACK 2: WRITING IN THE MAJORS SECTIONS (5 CREDITS)

The ability to think about topics critically and the aptitude to communicate ideas effectively through
writing are essential skills for your everyday and professional lives. The BioEE 1780 Track 2 Writing in
the Majors (WIM) section is for motivated students who are particularly interested in using writing and
group discussions to integrate information from lectures, the textbook and popular and primary
literature. Students will explore concepts of evolutionary biology, learn how to think critically about
published literature, and gain experience in communicating to a diverse audience. Students will also
have the opportunity to learn from exercises outside the classroom, including visits to the Museum of
the Earth and at least one major specimen collection on campus. Evaluation is based primarily on
participation in section activities, written assignments, and interaction with peers; students take the
regular BioEE1780 exams, but they contribute only modestly to your semester point total (see below).
Track 2 students meet twice each week. Class sizes are slightly smaller than standard discussion
sections. The time and location of the section will be determined once the roster is complete.
If you are interested in Track 2, please find the application form and overview on the main BioEE1780
Blackboard site, complete the application, and e-mail it to the WIM TA, Jake Berv (jsb439@cornell.edu)
by the end of the day on Friday, August 29. Track 2 acceptances will be announced on Monday,
September 1. If you apply for Track 2 and do not hear anything on September 1, please attend your
regularly scheduled Track 2 section beginning September 2.
Grading
Grading for Track 2 differs substantially from Track 1. Please see a breakdown of grading below.
Short Assignments - 20%
Generally 1 single spaced page or less
Predominantly reading responses and select lab exercises
Longer Assignments - 30%
Generally 1-3 single spaced pages
Predominantly research driven essays
Attendance and Participation - 30%
Participation in section discussions and group exercises
Participation in Blackboard based message board assignments
Participation in field and lab exercises
Exams(5% each) 10%
You will take the first two prelims, and a written take home final exam to replace your
lowest scoring prelim.
iClicker questions 10%
Same policies as general lecture and section apply

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COURSE GRADING (Track 1 Only)

Discussion Section
iClicker Questions in Lecture
Prelim 1
Prelim 2
Prelim 3
Final Exam

Percentage of Grade
30%
10%
20%
20%
20%
20%

Total possible:
100%*
* As described below, we will automatically drop your lowest prelim score
DISCUSSION SECTIONS: Activity schedule and grading policies are posted on Blackboard and will be
covered during one of the first section meetings. In addition to weekly graded section assignments, we
will be using the Blackboard system to provide section handouts, diversity lesson modules, and
population genetics simulations to support active learning exercises taught in section. This material will
also be covered on the prelims and will be part of the comprehensive final exam. Please note that if you
miss more than four sections you will automatically fail the course.
iCLICKER QUESTIONS: We will be using the iClicker system in lecture starting on Wednesday,
September 3rd. Some iClicker responses earn you credit simply for answering, others will require you
to answer correctly. iClicker points make up 10% of the course grade, with points accumulated over the
semester up to the maximum allowable (10% of total course points = 50 points). There will be many
more opportunities to obtain iClicker points than are minimally required to reach the 50 point maximum,
so do not worry too much about individually missed points. Additional points scored over the maximum
50 will not be awarded. Our objective with the iClickers is to engage you in the class, not to shape your
grade. As the iClicker points from any one lecture session are a trivial component of your overall course
grade, we do not offer make-up or replacement points for lecture absences. It is very important to
register your iClicker at the beginning of the semester, as we do not give retroactive iClicker points.
PRE-LECTURE ASSIGNMENTS: You will be assigned a short pre-lecture reading assignment in
advance of most lectures this semester. We will often ask an easy question or two about these
assignments at the beginning of lecture using the iClicker system.
PRELIM EXAMS: The first two prelims will be held in the evenings of September 23rd and October
28th. The third prelim will be held during the first hour of the final exam period. Your lowest prelim score
will be automatically dropped before calculating your final point total for the semester. If you miss a
prelim exam, your missed score will automatically be the one that is dropped.
Dropping of the lowest prelim score is generally helpful because this procedure simultaneously rewards
students who perform consistently well in the course and provides a buffer for students who encounter
one-time emergencies and are forced to miss an exam. Make-up exams are offered only in very truly
exceptional circumstances. Illnesses, workload from other courses, and general stress are not typically
considered to be exceptional circumstances. The prelims and final may consist of a combination of
multiple choice, short answer, and short essay format questions.
Heed this word of advice that we know from experience: it is very unwise to strategically blow off the
first prelim on the assumption that you will do better on the later exams. Past experience strongly
shows that the key to success in this class is consistency, keeping up with lecture material and section
assignments, and putting forth your best effort for all exams and other assignments.

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THIRD PRELIM AND FINAL EXAM: The third prelim and final exam will be administered together on a
single date to be announced later in the semester. These are separate tests to allow the potential for
dropping the third prelim from your grade, and both exams will held during the final exam period. The
final exam will cover material from the entire semester. These exams will not be offered early or
rescheduled. Do not make end-of-semester travel plans that conflict with the final exam.
CALCULATORS AND OTHER DEVICES: Electronic devices are not allowed during exams. This
includes any and all calculators, phones, and/or tablet devices. Any devices you have in your
possession must be completely turned off during exams. If we find you in possession of a device that is
turned on during an exam, you may be subject to an Academic Integrity investigation.
POINT TOTALS AND LETTER GRADES: Your point total at the end of the semester will be used to
determine your letter grade for the course. We will use Blackboard to track your performance
throughout the semester. The course grading is not curved; end-of-semester point totals of 90% or
greater will earn a letter grade in the A range; point totals between 80-90% are in the B range; 70-80%
in the C range; 60-70% in the D range; and 60 and below a grade of F. Breakpoints for and + grades
are determined at the discretion of the instructor after the end of the semester, and A+ grades are
granted only to students with exceptional performance in all components of the course.
EXTRA CREDIT: Five points of extra credit (equivalent to 1% of the total points available for the class)
will be awarded for joining a Study Group organized by the Cornell Learning Strategies Center and
attending 75% of the group meetings. More information will be given in the first week of the semester.
Our experience is that these study group meetings are both fun and highly beneficial to performance in
the course.
ACADEMIC INTEGRITY AND RELATED SUBJECTS: Each student in BioEE1780 is expected to
abide by the Cornell University Code of Academic Integrity. Any work submitted by a student in
BioEE1780 for academic credit must be the students own work. Violations of academic integrity have
occurred (though rarely) in past semesters when students copied one anothers discussion section
assignments, cheated on exams, or plagiarized materials from outside sources such as Wikipedia. Any
such violation automatically initiates Cornells academic integrity hearing process, and the resulting
penalties are significant. Whatever the pressures and stresses of the moment, it is wiser to turn in an
assignment late (or not turn at all) than to plagiarize it.
All required written assignments may be subject to submission to Turnitin.com for the detection
of plagiarism. Submitted work may be included as source documents in the Turnitin.com reference
database to be used for the purpose of detecting plagiarism of such papers. Use of the Turnitin.com
service is subject to the Usage Policy posted on the Turnitin.com site.
THIRD PARTY NOTES: The lecture and written materials created by the faculty and staff of BioEE1780
are copyrighted by course staff. We provide all students in the course with detailed lecture outlines,
pdfs of lecture slides, and other resources for review. These materials make commercial sources of
notes (etc.) totally unnecessary. Commercial note takers, audio recorders, and video recorders are not
allowed in our lecture halls or discussion sections. You may be approached by commercial vendors
encouraging you to provide them with course materials, such as notes and papers, which are then
posted for distribution on third-party internet sites. Some of these vendors falsely convey that this
behavior is legal and/or sanctioned by the course faculty, but this is not true: we do not allow this kind of
activity and such unauthorized behavior violates copyright laws and could result in an Academic
Integrity violation. Do not provide any course information to third-party vendors and do not accept
course content from third-party vendors. We will provide you with all of the information you need, and
when you get the information from us, you will know that it is accurate and relevant to the course
offering this semester.

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BIOEE 1780 FALL 2014

PROVISIONAL LECTURE SCHEDULE
Precise reading assignments will be posted on Blackboard in the Handout for every lecture.
Lectures: M, W & F: 3:35 4:25 PM
Date
Module
Wed, Aug 27
Overview
Fri, Aug 29
Overview
Mon, Sep 01
LABOR DAY
Wed, Sep 03
Overview
Fri, Sep 05
Phylogenetics
Mon, Sep 08
Phylogenetics
Wed, Sep 10
Diversity
Fri, Sep 12
Diversity
Mon, Sep 15
Diversity
Wed, Sep 17
Diversity
Fri, Sep 19
Diversity
Mon, Sep 22
Phylogenetics and Diversity
EVENING EXAM TUES Sep 23
Wed, Sep 24
Adaptation
Fri, Sep 26
Adaptation
Mon, Sep 29
Adaptation
Wed, Oct 01
Adaptation
Fri, Oct 03
Adaptation
Mon, Oct 06
Speciation
Wed, Oct 08
Speciation
Fri, Oct 10
Speciation
Mon, Oct 13
FALL BREAK
Wed, Oct 15
Diversity
Fri, Oct 17
Diversity
Mon, Oct 20
Diversity
Wed, Oct 22
Diversity
Fri, Oct 24

Diversity

Mon, Oct 27

Diversity

Call Auditorium, KND 116

Lecture Topic
Welcome to Evolutionary Biology
Course Introduction and Pre-Course Assessment
NO LECTURE
History of Evolutionary Thinking
Tree Thinking I
Tree Thinking II
Biodiversity and the Origin of Life
Prokaryote Diversity
Endosymbiosis and the Rise of Eukaryotes
Light on Water: Algae and the Origin of pPlants
The Greening of the Land the Rise of Higher Plants
Diversity and Applications of Phylogeny

Chapter *

ZE 2
ZE 4
ZE 4,9
Life 19
Life 19
Life 20
Life 21
Life 21

Lazzaro
Reed
Reed
Reed
Reed
Reed
Reed
Reed
Hillis (Guest)

Natural selection I
Natural selection II
The Evolution of Life Histories
Kin Selection
Sexual Selection
Missed Connections: Different Paths to Isolation
Speciation in Time and Space
Linking Concepts in Phylogenetics and Adaptation
NO LECTURE
Fungi: Those Magical Molds and Mushrooms
Out of the Soup: Body Plans and the Hole that Matters
Protostomes I: Life with Cilia - Lophotrochozoa
Protostomes II: Living with Armor - Ecdysozoa
Deuterostomes I: Upside Down and Backwards Echinoderms to Chordates
Deuterostomes II: Jaws! Fishes to Tetrapods

ZE 8, 10
ZE 8, 10
ZE 12
ZE 16
ZE 10, 11
ZE 13
ZE 13

Lazzaro
Lazzaro
Lazzaro
Lazzaro
Lazzaro
Lazzaro
Lazzaro
Lazzaro / Ballen

Life 22
Life 23
Life 23
Life 23

Ballen
Ballen
Ballen
Ballen

Life 23
Life 23

Ballen
Bemis

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ZE 1

Lecturer
Lazzaro
Lazzaro

EVENING EXAM TUES Oct 28

Wed, Oct 29

Diversity

Deuterostomes III: Humans and our Ancestors

Fri, Oct 31
Mon, Nov 03
Wed, Nov 05
Fri, Nov 07
Mon, Nov 10
Wed, Nov 12
Fri, Nov 14
Mon, Nov 17
Wed, Nov 19
Fri, Nov 21
Mon, Nov 24
Wed, Nov 26
Fri, Nov 28
Mon, Dec 01
Wed, Dec 03
Fri, Dec 05

Diversity
Macroevolution
Macroevolution
Macroevolution
Macroevolution
Population Genetics
Population Genetics
Population Genetics
Population Genetics
Population Genetics
Population Genetics
THANKSGIVING
THANKSGIVING
Humans & Evolution
Humans & Evolution
Humans & Evolution

Linking Biodiversity and Phylogenetics

Deciphering History: Earth and Fossils
The Fossil Record: Unique Insights into Evolution I
The Fossil Record: Unique Insights into Evolution II
Origin of Novelty: Evolution and Development
The Raw Material of Evolution
Hardy-Weinberg Equilibrium: The Null Hypothesis
Genetic Drift: Evolution by Chance
The Genetics of Adaptation: Natural Selection I
The Genetics of Adaptation: Natural Selection II
Quantitative Genetics: Multiple Genes at Work

TBA

Final Exam

Prelim 3 (1 hour) followed by cumulative final exam

(1.5 hours)

What Have We Learned So Far?

Evolutionary Medicine and Post-Course Assessment
Humans as an Evolutionary Force, and Wrap-up

ZE17, Life
23
ZE 3
ZE 14
ZE 14
ZE 10
ZE 5
ZE 6
ZE 6
ZE 6
ZE 6
ZE 7

Bemis
Ballen / Bemis
Bemis
Bemis
Bemis
Bemis
Lazzaro
Lazzaro
Lazzaro
Lazzaro
Lazzaro
Lazzaro

ZE 18
ZE 8.7

Lazzaro / Ballen
Lazzaro
Lazzaro

* Assigned Readings refer to chapters in the Zimmer and Emlen Evolution: Making Sense of Life (ZE) or the Hillis et al. Principles of Life (Life)

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