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BIOL 419

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Ecological and Environmental Problem Solving

Biology 419 - Spring 2016 – 3 credits


Instructor:         Dr. Katriona Shea

Teaching Assistant: Amalie McKee

Lectures and Labs:         M W 10:10 – 12:05 in 007 Life Sciences Building (LSB)

Office Hours:         F 10-11 in 415 Mueller Building


EEPS course goals and objectives

Course Goals

All students will learn a toolbox of modeling approaches to describe and solve ecological and environmental problems.


All students will demonstrate an ability to use modeling and simulation to solve ecological problems.

Course overview

The course will provide a general overview of the process involved in studying a variety of ecological and environmental problems. It will provide a toolbox of techniques for understanding ecological and environmental problems, and discuss how they can be used to address questions and generate testable predictions. It will examine connections between individuals and populations and communities as well as between theory and data. The focus will be on theoretical and computer modeling approaches, while maintaining a strong link to data and real systems.  After an introduction to modeling, students will learn to develop and use simple and stochastic optimization models for individual organisms, as well as applying basic game theory to interactions between individuals.  They will explore a sequence of population demographic models of increasing complexity, ranging from unlimited, unstructured population growth to density-dependent, structured population growth, in non-spatial and spatial contexts, culminating in individual-based models for population dynamics.  The students will then apply these models to interacting species, learning about mutualistic, competitive and host-natural enemy interactions.  Finally, we will explore theory for communities of species in space and time.  Applied problems will be drawn from all areas of conservation, harvesting, pest control and epidemiology throughout the semester.  No modeling experience is necessary as the course will start from basic principles.  


Prerequisites: BIOL 220W, any 1 semester Ecology course or permission of instructor.

Basic mathematical skills are also required (e.g. simple algebra).

For further information: contact Katriona Shea ( or 865-7910


Class material will be posted on ANGEL

Lecture Schedule 

Week 1

Introduction to modeling


Weeks 2-5



Optimality, dynamic programming, game theory


Weeks 6-11



Structured and unstructured population models, individual-based models, spatial models


Weeks 12-15



Competition, host-natural enemy interactions, multi-species models








Introduction to Modeling


12 Jan

Logistics and overview / Introduction to modeling I

Introduction to Excel

14 Jan

Introduction to modeling II

Introduction to Excel





19 Jan

Martin Luther King Day – no class

no lab

21 Jan

Simple optimality I: constraints and trade-offs

Optimal clutch size


26 Jan

Simple optimality II: Habitat selection and prey choice

Optimal foraging

28 Jan

State-dependent optimization and decision-making Other models for optimization

Stochastic dynamic programming (SDP) demonstration


2 Feb

Game theory I: symmetric games

Hawk / dove

4 Feb

Game theory II: asymmetric games

Parental care


9 Feb

Uncertainty and decision-making for management of natural systems





11 Feb

Unstructured populations, unbounded growth

Geometric and exponential growth


16 Feb

Midterm I (all material through 9 Feb)


18 Feb

Unstructured populations, density-dependent growth

Logistic growth


23 Feb

Structured populations: effect of life history on population dynamics

Structured difference equations

25 Feb

Matrix models

Matrix models


2 Mar

Equilibria, local stability and chaos

Bifurcation plots

4 Mar

Time series analyses

Time Series Presentation





16 Mar

Stochastic population models

Environmental stochasticity

18 Mar

Individual-based models

Demographic stochasticity and IBM’s


23 Mar

Pseudo-spatial models: metapopulations

Metapopulation models

25 Mar

Explicit spatial models: IBM's and cellular automata

Spatial Spread Presentation


30 Mar

Risk Assessment and Population Viability Analysis


1 Apr

Midterm II (all material through 30 Mar)






6 Apr

Interacting populations I: competition and collaboration

Logistic competition

8 Apr

Competition continued

Resource competition


13 Apr

Interacting populations II: hosts and natural enemies

Predator-prey models

15 Apr

Host-natural enemy models continued

Disease models


20 Apr

Multi-species models I: Island biogeography

Island biogeography

22 Apr

Multi-species models II: Succession



27 Apr

Multi-species models III: Diversity and disturbance

Disturbance demonstration

29 Apr

Multi-species models IV: Networks

Course review



FINAL in Finals week – date and time TBA


Academic Integrity

Unless specifically directed otherwise, all assignments must be completed without assistance from others, except for guidance from Dr. Shea, the class TA, and/or guest instructors, and must represent your own work. PSU's Academic Integrity Policy is posted HERE. PSU’s Code of Conduct addresses personal conduct issues for students and their interface with the law, including harassment, sexual misconduct, drugs, alcohol, forgery, and misrepresentations of person.  See THIS LINK for more information (see point 10 for academic integrity). 

Our College, the Eberly College of Science (ECoS) has also adopted a “Code of Mutual Respect and Cooperation”. Students will be required to follow the guidelines concerning academic integrity as described in the Biology Department’s Policy and the Senate Policy 49-20

Weather delay policy

In years past, weather events have caused delays in the start of activities and classes at University Park campus. If a delay is announced at University Park, classes and activities that begin before the announced time are canceled.
Those classes or activities beginning at or after the conclusion of the announced delay time will be held as originally scheduled. For example, a two-hour delay until 10 a.m. due to snow or ice would mean that all classes that begin before 10 a.m. are canceled and will not be held. Classes beginning at 10 a.m. or later will continue on their regular schedule.
As this class runs across multiple periods, please note that CLASS WILL BE HELD if the delay only affects part of the class session.  So, class will start at the end of the announced delay time and continue through the end of the normal class period. For example, if a 3-hour delay is announced, class will start at 11 a.m.