FUNDAMENTALS OF EVOLUTION
ECOL 600A
Spring 2012
3 units
Instructor
Meeting times
Dr Regis Ferriere
regisf@email.arizona.edu
Lectures:
BioSciences West 302
Mon 9 - 10:15 AM
Tue 9 - 10:15 AM
Office hours:
LSS 233
Fri 2 - 3 PM
Course goals
This course represents half of the EEB graduate core sequence in ecology and evolution, and
serves a broader audience interested in a graduate-level, conceptually oriented course in the
science of evolution.
All of biology is concerned by evolution, and the field of evolutionary research borrows from an
incredible array of scientific notions and techniques. The course will present the fundamental
facts and theories that students need to know in order to apprehend the current science of life
evolution i.e. ‘descent with modification’. This is not a course on the history of the science of
evolution or a mere review of classics; rather, selected historical elements, basic concepts,
important models and major empirical findings will be reviewed as they provide critical insights
to understand the contemporary science—its achievements, frontiers and perspectives.
Some concrete “metrics” by which success of the course may be measured include: giving
students enrolled in the Ecology and Evolution Biology graduate program a solid background
and strong confidence to take their comprehensive exams; making students able to understand
fully the abstract (at least!) of any important current publication on a topic related to evolution;
making them comfortable attending conference talks in evolution; and helping all students in
their doctoral research.
Course content and structure
Most class time is used for lectures. I teach a majority of the lectures myself, in order to ensure
homogeneity in teaching style, coherence, extent of coverage, and to maintain continuous
feedback between the students’ expectations and progress and the course’s content. The course
material is organized as follows; however, the lecture outline and schedule may evolve during
the semester, so that the course’s flow can be adjusted in response to the learning dynamics of
the class and feedback from the students.

Our starting point is the reality that the theory of evolution is meant to explain: the history of
life on Earth, of its diversification and complexification in relation with the geophysical
history of the Earth itself, as we can portray them from geological and fossil records.

We will then show how the key principles of evolutionary theory emerged from Darwin’s
revolutionary thinking and from the work of the giants who came after him, brought genetics
in, and thus forged the Modern Synthesis.

We will review our current understanding of the biology of phenotypic variation and
inheritance.

We will explain how population genetics theory is developed and used to model
(1) molecular diversity across species, thus establishing the means for phylogenetic analysis
and reconstruction of the history of life diversity;
(2) natural selection acting on heritable variation within species;
(3) the interaction between mutation, selection, and migration, depending on population size.

We will show how evolution works when ecological interactions between individuals,
between sexes, or between different species are considered explicitely—thus raising the
topics of kin selection, sexual selection, and co-evolution.

Equipped with this broad conceptual and empirical platform, we will tackle the most
fundamental issues of conflict, cooperation, and major transitions; species, speciation, and
the evolution of species diversity; the evolution of genetic systems; the evolution of
developmental programs and phenotypic novelty; and human evolution.
Mandatory or supplementary readings will be posted as PDF files on the D2L course website,
and announced as needed.
Students presentations
In addition to my lectures focusing on the fundamentals, a number of time slots are reserved for
students of the course to elaborate on the fundamentals and present recent advances and
emerging research directions in major areas of evolutionary biology: paleontology, molecular
genetics and phylogenetics, natural selection, phenotypic evolution and adaptation, major
evolutionary transitions, coevolution, and human evolution. Presentations will be 45 minutes,
leaving 30 minutes for discussion with the whole class.
Depeding on the size of the class, each presentation will be prepared and given by one or two
students. Each student will take part in one presentation during the semester. Presentations are
aimed at offering a synthesis of recent work, explaining how recent work goes beyond the
fundamentals (and sometimes brings them into question), raises new questions and challenges,
and thus opens new perspectives for future research. The presentation should highlight the
technical details that are needed to understand the novelty and importance of an approach or
result—but no more than strictly necessary: the main general ideas and perspectives should not
be lost in technicality.
Presentations will be assigned to students and scheduled at the beginning of the semester.
Adjustments of schedule and topics are possible during the semester, e.g. to accomodate changes
in the lecture schedule.
Homework assignments
These will be short essays either in preparation or following up specific lectures, or problem sets
to get hands-on experience with particular techniques discussed in class. Frequency will vary.
Students will turn their homework in as PDF files on the due date, using D2L dropbox.
Final exam
It will be take-home open-book. The main (possibly only) part will be an essay, in the style of
doctoral prelim written questions, involving background research, original ideas, careful writing
style and organization. This essay will be 8-10 pages double-spaced (Times or Times New
Roman 12 font), not including the references. If necessary, I will give additional writing
instructions in class. By reading your essay I should be able to tell that you took this course! In
other words, you should use extensively what you have learned in the course. This includes the
content of my lectures but also what you took from the students’ presentations and informal
discussions happening in class.
Class participation
Presence in class is mandatory (except by prior arrangement). The class should be as interactive
as possible. Collective discussion is expected to take place during oral presentation sessions.
Participation also means doing the assigned readings and showing up to class on time (except by
prior arrangement). A maximum score for class participation will be granted to each student at
the beginning of the semester, and degraded should these basic rules be broken.
Prerequisites
A solid background in general biology is expected. Students who suspect they are insufficiently
prepared (e.g. with little knowledge of basic molecular and cellular biology) should discuss
preparatory reading with the instructor as soon as possible.
Calculus as used in introductory physics or chemistry (e.g. derivatives, simple formalism of
differential equations, notion of equilibrium) and basic linear algebra (notion of vector and
matrix) will be needed. If this might be a problem, I strongly encourage you to seek an
appointment with me before the start of the semester so that we can discuss the issue.
Access to and fluency with the University of Arizona D2L system is required. Course material
and information updates on the class will be posted on D2L, and you will use the dropbox for
assignments.
Books and reading
No specific textbook is assigned mandatorily for the course this year (2012) but I recommend
Evolution by Nick Barton et al. as our key reference. Other textbooks that offer broad, up-to-date
overviews of evolutionary biology include Evolution by Doug Futuyma (2nd ed.), Evolution by
Steve Stearns and Rolph Hoekstra (2nd ed.), Evolution by Mark Ridley (3rd ed.), Evolutionary
Analysis by Scott Freeman and Jon Herron (4th ed.), The Tangled Bank by Carl Zimmer. Mark
Ridley’s Evolution edited volume provide a valuable source of classical papers.
Readings (research articles, chapters from books) may be assigned in preparation for specific
lectures or student presentation. Readings will usually be posted on the course’s D2L website as
PDF files.
Grading
The following break-up is given as an example, assuming two graded homework assignments
besides the final exam.
 Oral presentation
250 points
 Homework assignments
300 (150 points each)
 Final take-home, open-book exam
350
 Class participation
100
Note that homework submitted late will have points deducted from it.
Absence policy
On-time class attendance and participation in class is required. Absences may be approved in
advance, e.g. to accommodate research-related travel. All holidays or special events observed by
organized religions will be honored for those students who show affiliation with that particular
religion. Absences pre-approved by the UA Dean of Students (or Dean's designee) will be
honored.
Ethics
University of Arizona policy regarding ethical conduct and plagiarism will be enforced. Consult
Student Code of Academic Integrity at http://dos.web.arizona.edu/uapolicies
Grade appeals
If you think that an error was made in the grading of an assignment or exam, you must appeal in
writing (no email) within two days of posting explaining in detail where the mistake was made.
Regis Ferriere
Last revised: 13 March 2012.