Overview

Course Goals: This course is an introduction to mathematical methods used in the-

oretical population biology. Population biology, here, refers to any area of the bio-
logical sciences focusing on population-level processes including areas in demog-
raphy, conservation biology, ecology, epidemiology, evolution, and population ge-
netics. The mathematical topics covered will include scalar and multivariate differ-
ence/differential equations, matrix and integral projection models, Markov chains,
random walks, and stochastic difference equations. As each of these topics, in and
of themselves, could take up the entire term, this course is meant as a gentle in-
troduction to each of these topics. Ideally, this introduction will allow you to delve
more easily into the theoretical population biology literature, and help you identify
Mathematical which of these topics warrant a deeper dive.

Methods in Pre-requisites: In order to focus on the main concepts for this course, I assume that

Population you have a basic familiarity with the following topics (OD refers to relevant pages in
the Otto and Day text, see next page):

Biology Calculus: Definition and interpretation of derivatives and partial derivatives, lin-
earization of single variable and multivariate functions, quadratic approxima-
ECL/PBG 231 tion of a single variable function (OD 89–106, 303–305)
Matrix Algebra: basic matrix algebra (i.e. addition, scalar multiplication, matrix
multiplication), solving systems of linear equations (OD 214–227, 236–236)
Statistics/Probability: Definitions of discrete and continuous random variables, ex-
Instructor Info pectation, variance, and independence (OD 513–518, 521–526, 536–538).
For those of you wanting a refresher or introduction to these topics, I will provide
g Sebastian Schreiber three optional review sessions on each of these topics during the quarter.
Pronouns: he, him, his
Course Structure, Grades, and Collaborative Learning: To achieve the goals of this
U Office Hrs: TBD course, we will have semiweekly Zoom lectures, semiweekly reading assignments,
weekly graded homework, and a take-home final. The lectures, for the most part,
½ Zoom Land will be self contained and the readings are meant to provide an alternative or com-
schreiber.faculty.ucdavis.edu plementary perspective on the topics. Homework assignments will be a mixture
of "pencil and paper" and computer-aided exercises to help you master the math-
@ [email protected] ematical methods and to apply them to different types of models from population
biology. The take-home final will be similar to the homework assignments and cover
topics from throughout the course.

Course Info The grade for the course will be determined by the homework scores (70% of grade)
and the take-home final (30% of the grade). Grades will follow the standard scale:
 Prereq: See description A = 90-100%; B = 80-89%; C = 70-79%; D = 60-69%; F <60%.

 Tues & Thurs Everyone is coming into this course from different fields and with different prior
knowledge of the material that will be covered in 231. I encourage you to work
U 10:30-11.50am together as you can teach each other far more than I can. That being said, it is
important that homeworks are written up individually, with your own words and
½ Zoom
calculations, and reflect your own understanding. This will allow me to asses your
level of understanding and provide more meaningful feedback.
Diversity and Inclusivity: I consider this virtual classroom to be a place where you
will be treated with respect, and I welcome individuals of all ages, backgrounds,
beliefs, ethnicities, genders, gender identities, gender expressions, national origins,
religious affiliations, sexual orientations, ability - and other visible and non-visible
differences. All members of this class are expected to contribute to a respectful,
welcoming and inclusive environment for every other member of the class.
Sickness/Care responsibilities/Absences: I realize that, especially during this global
pandemic, everyone has unique situations and responsibilities which are constantly
changing. My primary goal is to support you and your learning and that sometimes
requires flexibility. If you have illnesses, care responsibilities, or other scenarios
that require you to be absent from class or are affecting your learning, please con-
tact me so that I can work with you to develop a plan.
Learning Materials
Lectures and Lecture Notes: For this class, lectures and class activities will be held synchronously over Zoom. Please see the
syllabus for each section of the course for Zoom links and any additional information. I expect students to join and participate
in these synchronous sessions, but recognize there may be circumstances that may make attendance difficult, particularly
during the COVID-19 pandemic, so please be proactive about contacting me about these issues as they arise. I will record
these Zoom sessions and make them available on Canvas.
To facilitate engagement and discussion, it helps to have videos enabled during class, but I realize there are situations or
circumstances that make this difficult or impossible. Thus, I ask you to have your camera on if you can, particularly during
discussions. I also encourage you to ask questions during lecture and discussion, which can be done either by using the ‘raise
hand’ icon on Zoom or using the chat function
The most important resource for this course will be your notes from my lectures. Hence, take notes, actively work through the
in-class exercises, compare notes with fellow students if something doesn’t seem quite right, etc. To help you improve your
notes, my lectures will be recorded and posted on Canvas.

Reading Materials: The semiweekly required readings will come primarily from the following two books. For these reading
assignments, keep in mind the words of Paul Halmos “Don’t just read it” i.e. don’t be a passive reader but engage with the
reading – how did they do that calculation? why are they making that assumption? how does this idea relate to an earlier
idea? etc.
Otto, S. and Day, T. A Biologist’s Guide to Mathematical Modeling in Ecology and Evolution. Princeton University Press. This
book is available as a hardcover (used and new) and as a e-book on Amazon at https://www.amazon.com/dp/B005N8T8AM/
?tag=princetonuniv-20. You can rent or buy it there from $25.00 (ebook rental) to $61.65 (new hardback).

Edelstein-Keshet, L. Mathematical Models in Biology. Society for Industrial and Applied Mathematics. As part of UC Davis, you
can download this text for free at https://epubs.siam.org/doi/book/10.1137/1.9780898719147

Computational Resources: To explore the concepts visually and with more advanced applications, I will be posting R scripts and
links to Java scripts. To use the R scripts, you need to download R at https://cran.rstudio.com. In addition, I recommend
downloading the interface RStudio Desktop, available freely at https://rstudio.com/products/rstudio/download/. If you
haven’t used RStudio before, watch this 6 minute video at https://www.youtube.com/watch?v=5YmcEYTSN7k. To run the
java scripts, you will need to have Java installed on your machine. This is probably already the case, but if not then go to
http://www.java.com, from where you can both check whether you have Java (and whether your Java is up to date) and
download Java.

Homework Assignments and Final Exam

Homework Assignments: Associated with nearly every lecture, there will be a homework assignment. The assignments will
consist of a mixture of “pencil and paper” and computational problems. The homework problems for any given week need to
be turned in on the following Tuesday before lecture through Canvas. Late assignments will be accepted but with an increasing
penalty: −25% after 10:30am on Tuesday, −50% after 10:30am on Thursday, −100% after 5pm on Friday. Assignments need
to be submitted as PDFs with solutions to the problems presented in consecutive order. The submissions can be any legible
mixture of handwritten and hand drawn answers, “typed” (e.g. Word, LaTeX, etc) answers, and images (e.g. plots from R). I
encourage you to work together of the homeworks. However, the turned-in write-ups need to be written up individually, with
your own words and calculations, and reflect your own understanding.

Take Home Final: During the last week of instruction, I will provide you with a take home final that you need to turn in as PDF
on Canvas by 12:30pm on Wednesday, December 16. No late finals will be accepted. Unlike the homework assignment, you
are not allowed to work together on the take-home final problems and are not allowed to make use of external resources.
(Tentative) Class Schedule

MODULE 1: Scalar dynamics

Week 1 Linear difference & differential equations Reading: OD 191–195,198–202

Week 2 Nonlinear differential equations I: Reading: EK 164–171, OD 163–170

Phase lines & linearization

Nonlinear differential equations II: Reading: Handout

Bifurcations

Week 3 Nonlinear difference equations: Reading: EK 39–55

Periodic fluctuations and chaos

MODULE 2: Matrix models

Matrix algebra, eigenvalues & eigenvectors Reading: OD 214–228 (review), 228–230, 233, 237–239

Week 4 Discrete-time matrix models, I: Reading: OD 386–397

Non-negative matrices & Perron-Frobenius

Discrete-time matrix models, II: Reading: OD 347–361

Complex & distinct eigenvalues

Week 5 Continuous-time matrix models Reading: OD 254–273

Classification of 2d matrix models Review earlier readings in this module

& higher dimensional matrix models

MODULE 3: Multivariate nonlinear dynamics

Week 6 Nullcline analysis and vector fields Reading: EK 171–181

Linearization & Phase plane analysis Reading: EK 181-193

Week 7 Periodic solutions & chaos

Invasion analysis Reading: Handout

Week 8 Discrete-time models Reading: EK 55–59

MODULE 4: Markov chains and Random walks

Finite state Markov chains, I: Long-term behavior Reading: OD 608–611, 614–619

Week 9 Finite state Markov chains, II: Hitting times Reading: OD 612–614, 621–627

Thanksgiving EnJOY

Week 10 Random Walks, I: Law of Large Numbers Reading: Handout

Random Walks, II: Central Limit Theorem Reading: Handout

Week 11 the Diffusion equation Reading: EK 405 (the Box)

Invasion analysis for nonlinear random walks Reading: Handout