Course Objectives for Students:

  • To be able to describe the evidence for evolution.
  • To understand how populations, species, and biotas change through micro- and macro-evolutionary time-scales.
  • To be able to “think like a mutation.”
  • To be able to describe the major approaches to the study of evolution, including observational, experimental and comparative approaches, and their strengths and weaknesses
  • To relate evolutionary biology to pertinent conservation, medical, and social issues.
  • To improve their writing in general, and gain expertise in formal scientific writing in particular.
  • To be able to read and critically evaluate primary literature in the field of evolution.
  • To gain experience posing and testing hypotheses.


Course Objectives for Instructors:

  • To promote active learning.
  • To create learning environments in which all students feel welcome to participate.
  • To provide timely, constructive, and fair feedback.


Prerequisites: Biol 20A, Bioe 20B, Bioe 20C, and Biol 105 (Genetics)

Text (not required): Evolutionary Analysis, 5th Edition by Scott Freeman and Jon C. Herron,

(will be on reserve in Science Library)

Required course materials: none but you might consider getting the textbook if you like to have a written support

Professor: Giacomo Bernardi, bernardi (at)

Office Hours: by appointment, my office is at the Long Marine Lab

Class web site: you found it, congratulations!

TAs: David Fryxell and Katie Kobayashi


Overview of Grading System: 

Discussion sections    25% (section is worth 10%; SimBio 15%)

Midterm   35%

Final           40%


Disciplinary Communication Assignments

  • Our goal is to help students improve their writing without the anxiety of having the writing assignments contribute quantitatively to the course grade. We seek to provide constructive and useful feedback.
  • Disciplinary Communication (DC) assignments will be assessed on a pass/no-pass basis, and you cannot pass the class without receiving an overall passing grade on the DC assignments.
  • Writing assignments will involve writing, reviewing, or rewriting scientific papers. They will be described in detail in class and/or section and will be posted on the course website under “Assignments”.
  • Turning in writing assignments late or exceeding the page/margin/font size limits will contribute to a “no-pass” grade for a writing assignment.
  • Students receiving a “no-pass” grade on their first assignment are required to meet with a TA about their writing at some point during the quarter in order to achieve an overall passing grade on the DC assignments.
  • In order to achieve an overall passing grade on the DC assignments, students must complete every writing assignment, receive passing scores on all but the first assignment, and meet with a TA about their writing (if required, see above).
  • Detailed grading rubrics will be available for each assignment prior to the due date.


Midterm (35% of grade) and Final exams (40% of grade)

  • Midterm exam  will account for 35% of final grade
  • Final exam will account for 40% of grade.
  • Final will not be cumulative, but may have a few bonus questions about early lectures.
  • Make-up exams are not offered except under extraordinary (and documented) circumstances, and may be in a different format (oral or essay) than standard exams.
  • The format of both exams will be multiple choice. Material from the SimBio labs and the discussion section readings is fair game for testing on the exams.


Discussion Sections (10% of grade)

  • There is assigned reading from the primary literature for each discussion section. Readings are posted on the course website under “Resources”, and the schedule is detailed below.
  • You are expected to complete the readings before coming to section.
  • at the beginning of each section, there will be a quiz pertaining to the lectures and readings.


There is a computer lab assignment (Sim Bio) and also a research proposal to be written:


SimBio (5% of grade)

Lab Information: Understanding experimental design

You will be doing a computer lab that reviews experimental design.  The material covered in this lab will be helpful for this class in general and for your writing assignment (a research proposal) coming later in the class.  The lab is due by Wednesday February 21st at 5 p.m.  Details on how to register for and gain access to the lab are below.  The cost is $6 and you will need access to a computer.  There is a way to use a USB drive and download the software to use on a shared computer, and there are instructions on the site if you wish to do this.  For software issues, please contact SimBio directly.  Details on how to do this are below.  If you have problems that can’t be readily resolved by them please let us know. You will submit your answers through SimBio directly and the grades will be available to us.  The SimBio lab represents 5% of your final grade.


It is important that you review the information below before you subscribe to the SimUText for Evolution at University of California – Santa CruzTo avoid possible problems, do not wait until the last minute.

Should you encounter problems, you may need your course-specific Access Key. It is:  UhN2-fqSL-YuZ4-mwTs-y78M


Problems or questions? Visit SimUText Support (



Research proposal (10% of grade)

You will need to write a research proposal based on the SimBio material and review two of your classmates’ research proposals. First, write a research proposal that is no more than two pages, double-spaced. Print two copies of your research proposal (double spaced) and swap with two classmates on Monday February 12th. You should have two people reviewing your proposal and you should review two students’ proposals. Return your reviews to one another no later than Wednesday February 21st so that you will be able to make edits to your work before the final deadline on Wednesday February 28th. Please let me know if you do not receive reviews back on time. Incorporate the reviewers’ comments into your work and print this final draft. Return to us the final version (wit your name) and the two reviews (with reviewers names). Your grade for this assignment will include the quality and thoroughness of your peer reviews. The paper will account for 10% of your course grade.




Discussion Section Readings (starting with # 1 but no section on first week of class)

The  schedule of the readings can be found here (Schedule)

The readings themselves can be found here (Readings)

Academic Integrity

Please don’t cheat, it is not cool, and puts me in a situation I don’t like at all.

Academic misconduct includes but is not limited to cheating, fabrication, plagiarism, or facilitating academic dishonesty. Everything you turn in must be your own expression of your understanding of the material. Academic misconduct in any part of the course may lead to failing the particular assignment and the course, and may result in disciplinary sanctions.

Please see:

You are welcome and encouraged to discuss papers and assignments with each other, but copying or paraphrasing of someone else’s work is not acceptable. Borrowing from work from previous years is not okay. Also, copying directly from, or cutting and pasting from, published work, including the internet, even if you cite the author, is considered plagiarism. Always put it in your own words. The consequences of cheating and academic dishonesty —including no credit for the work done, a formal discipline file, possible loss of future internship, scholarship, employment opportunities, or admission to graduate school—are simply not worth it. I always report students caught plagiarizing to their college for disciplinary sanctions, even if it was an accident, a small amount of plagiarism, or the first time they have been caught.


DRC Accommodation

If you qualify for classroom accommodations because of a disability, please submit your Accommodation Authorization from the Disability Resource Center (DRC) to me after class or during my office hours in a timely manner, preferably within the first two weeks of the quarter. Contact DRC at 831-459-2089 or by email at