General Ecology – BIOL 3700

Nature holds the key to our aesthetic, intellectual, cognitive and even spiritual satisfaction. – E. O. WilsonBIOL3700_top To do science is to search for general patterns, not simply to accumulate facts. – R. H. MacArthur
BIOL 3700-001, Summer/2014,
SB 132, TR 2:00-4:45 p.m.

Instructor:           Justin C. Bagley, Department of Biology, Utah Valley University; Office: SB 242-243; E-mail: justin.bagley@byu.edu; Website: http://www.justinbagley.org.

Office Hours:      Office hours will be held before class by appointment (e-mail me to set up a meeting or Skype conference call), initially for 4 h/week but modified according to student needs.

I. Course Description: Ecology is the scientific study of the relationships between organisms and their environment, including interactions that determine the distribution and abundance of organisms.  This course provides an introduction to the patterns and processes influencing variation across different biological levels, from individuals to populations, communities, and ecosystems.  Different timescales are also addressed, from brief behavioral processes, to historical processes operating over millions of years (e.g. evolutionary change, plate tectonics).  In this course, we investigate the principles that determine variation in 1) the growth, physiology, and reproduction of individual organisms (e.g. temperature regulation, life histories); 2) interactions between living organisms and the physical environment (ecosystems); 3) population fluctuations; 4) multispecies interactions; 5) community diversity and stability; and 6) global climate, biome structure and distribution, and earth history.  This course fulfills a 3.0 credit hour requirement for the BS degree in Biology.

 A. Course prerequisites: BIOL 1620 (or equivalent with instructor consent).  As we will discuss, ecology is not environmentalism; rather, it is a rigorous and interdisciplinary field of science in which natural history studies as well as rigorous statistical and mathematical models (e.g. of population dynamics and predator-prey relationships) are used to address important questions about the species distributions and abundances.  We will cover several of the key mathematical models developed in this field, so it is critical that students have good background knowledge of university algebra, and facility with basic calculus is also recommended.

II. Course Rationale and Learning Objectives: 

Ecology_Society_Economy_diagram_Earth_backgroundA. Rationale: why study ecology?  All human societies depend on the maintenance of healthy natural or semi-natural ecosystems, as well as the exploitation of natural resources.  The ever-ballooning human population faces an array of multiplying environmental and conservation issues, many linked to the ways that we alter ecosystems, even global climate and flows of energy.  Especially in this context, we each share a responsibility to one another, and to the many other species we share the planet with, to understand and protect the environment.  Here, ecology provides a basis for sustainable resource use, biodiversity conservation, and solving environmental challenges of today and of tomorrow.

All students, whether working towards careers in professional ecology/biology, the medical sciences, or another field in the life sciences, will benefit from the ability to view the world as an ecologist.  In fact, ecology is one of the biological disciplines of highest relevance to human populations and to our personal lives.  The foundation of ecological concepts developed in this course will provide a basis for students to understand how they interact with other organisms and the environment, ways that they may negatively impact ecological systems, and how to make personal decisions that improve the health and sustainability of the environment based on scientific principles.  Such objectives at the ecology-environmentalism interface will be accomplished through discussions and learning activities.  This new ecological understanding will help students make decisions about environmental issues that have the potential to directly affect their health, lifestyle, and economic and political decisions.

Students pursuing careers in health-related fields (e.g. dentistry, medicine, optometry) will benefit by understanding how human health is influenced by the degradation of healthy ecosystems.  Professional school entrance exams may include questions related to topics covered in this course, e.g. concepts in ecology and evolution sometimes show up in population genetics passages on the MCAT.  Moreover, future biological science educators will all be teaching many of the concepts and examples presented in General Ecology.

B. Specific learning outcomes*: I will instill in students an appreciation for the fascinating world of ecology and the historical and ecological processes responsible for biodiversity and distributions.  I will also instill in students an understanding of the scale and urgency of global environmental crises that ecologists study.  Moreover, by the end of this course, students will be able to:

    1. Identify the main areas of study in the field of ecology and relate these areas to other fields of study within biology.
    2. Describe the ecological and evolutionary influence of abiotic factors on organisms and how these factors affect the distribution and abundance of species.
    3. Describe, compare and contrast geometric, exponential, and logistic population growth and apply these models to natural populations (e.g. students will be able to estimate future population size).
    4. Explain how biotic interactions, including competition and predation, influence population growth and the likelihood of (local) extinction of the species involved (through extensions of models in #3 above).
    5. Relate life-history patterns to population parameters and to the extinction risk of populations of threatened/endangered species and introduced species.
    6. Explain how ecologists measure diversity, and how abiotic and biotic factors shape community diversity from local to regional scales.
    7. Describe basic models of energy flow through ecosystems, including the processes of photosynthesis (primary production) and decomposition, and list the factors controlling these processes.
    8. Describe the processes and components shaping natural nutrient cycles, and climate and oceanic circulation patterns, and illustrate how human impacts are disrupting these systems at a global scale.
    9. Describe the physical structure, biotic communities, natural disturbances, and human impacts on ecosystems.
    10. Describe at least 10 ways that they can make practical day-to-day decisions that promote sustainable use of natural resources, limiting human ecological footprint, and improved health and protection of natural ecosystems.

*Specific objectives for each lecture topic are given on the course website under “Lecture Objectives”.

III. Format and Procedures: This course represents a modification of traditional lecture course (“hear-read-talk”) format with strings of lecture presentations broken up by out-of-class student readings, midterm exams, and a final exam.  Class meetings are overall structured into (a) lectures broken up by (b) short (

By this point in their academic careers (5th semester or later), UVU students should have matured into active, lifelong learners fully capable of processing and surmounting the challenges of a 3.0-credit university course on their own.  This course will require that students meet academic standards of the institution of ≥3 h studying out of class for every 1 h of class time, and students should prepare accordingly.  Also, given that summer-term courses are by their very nature more intensive, students should expect to modify their study habits to master a similar amount of material as would be presented in a regular term course, only over a substantially shorter interval.  Because we are mature learners, all cell phones should be turned off throughout class time, and no ear buds or headphones are allowed.  Also don’t read the newspaper or magazines (I don’t really care if you sleep in my class though, although it is not recommended)!!!

Regarding course content, notes based on the text of PowerPoint slides and multimedia material used during lectures will be made fully available to students and can be used as notes or starter material for study guides.  Students will also have access to “pre-exam example questions” similar but not identical to the short-answer questions and math problems that will be on the exams.  However, allow me to make several caveats about the material.  Namely, our slides do not cover all of the material that we discuss in class.  Our PowerPoint slides do not include all of the material that you will be tested on.  Also, some concepts will not be presented using PowerPoint (but will be in the readings or written on the board), and this is where college note-taking skills come in handy (or, if lacking, must be developed).

IV.  My Assumptions & Biases
I am an ecologist and evolutionary biologist interested in using freshwater fishes as model systems to address questions in molecular ecology, biogeography, and evolution.  My organismal focus and training using fishes gives me a “fish-eyed” view of the world and the way I think about biology.  Despite my bias towards fishes and the aquatic environment, however, I will attempt to draw on examples from terrestrial and aquatic systems without preferential treatment for one or the other (though I’ll definitely talk about how awesome fishes are)!  Thankfully, my own mentors—who are mostly aquatic biologists—modeled a similar approach for me.

I will assume that students have a thorough understanding of basic biological science, imparted by meeting the prerequisite course BIOL 1620 (with lab).  In particular, I will assume that students have already gained an understanding of evolutionary theory.  This is critical, as evolution provides the key theoretical framework for interpreting ecological patterns and processes, and numerous evolutionary principles will be referred to during this course, including adaptation, fitness, selection, and genetic drift.

V. Course Requirements: 

A. Class attendance and participation policy:  Attendance is required for all lectures, activities, and exams.  The reasons for this are myriad; however, principal among them are that (a) many of the lecture topics/slides have been taken from the primary literature and are not presented in the text; (b) the material builds upon itself throughout the course; (c) students will receive participation grades; (d) you will fail exams that you miss; and (e) my experience and data from other courses confirms that students who attend class usually outperform students that do not.  Given the importance of attendance and that we will have fewer class periods than a regular term, students who miss >3 classes will automatically receive a failing grade for the course.

B. Course readings: 
Required text: Molles, M.C. Jr. (2013) Ecology: Concepts and Applications, 6th edition. McGraw-Hill, New York, NY.  To emphasize, the newest edition of this text is required.
Recommended text: Gotelli, N. (2008) A Primer of Ecology, 4th edition. Sinauer Associates, Sunderland, MA.  One copy is available from the instructor.
“Handout” readings: These are available and should be downloaded and read prior to the lectures/Discussion Sections specified on the course website.

VI. Grading Procedures: Please follow this link to find information about UVU’s grading guidelines, in the context of broader academic policies and standards.

A. Grading criteria: Student grades will be assigned based on performance on:

 Points PossiblePercentage
Total points possible405 points100%
i. Student evaluation (due May 29)5 points1.2%
ii. Participation grade*50 points ("Discussion participation" rubric)12.35%
iii. Utah Fish Project (due June 17)50 points (website with criteria)12.35%
iv. Midterm Exam I100 points27.4%
v. Midterm Exam II100 points27.4%
vi. Final Exam100 points27.4%
vii. Extra Credit: Discussion Section assignmentsNot required... but up to 15 points≤4%

*This grade consists of 25 points for in-class assessments (“Minute Papers”, “Personal Responses”, etc.) and 25 points for participation during discussions.

The focus of this course is not on grades but on learning ecology.  I do not grade “on a curve”.  Exams will not be conducted during precious lecture time.  Instead, I will schedule times for you to take exams outside of class at the Classroom Testing Center (CTC), the only exception being the final exam, which will be administered in the classroom on the last day of class.  The final exam will be non-comprehensive and will consist of questions related to information covered after the material on Exam II.  All letter grades will be assigned on the following (adjusted) 100 point grade scale: A = 94-100; A- = 89-93; B+ = 86-88; B = 82-85; B- = 79-81; C+ = 76-78; C = 72-75; C- = 69-71; D+ = 66-68; D = 62-65; D- = 59-61; E = 58 and below. 

I assess student learning using a variety of exam questions, including multiple choice, fill in the blank, matching, short answer, and problem solving (essay/math) questions; however, most exam questions will be short answer and problem solving questions.  Thus, you should be able to draw and label diagrams, graphs, and figures and explain them.  You will be expected to apply the quantitative skills and concepts learned in class to analyze novel situations.  Don’t worry; in class, we will work example problems similar to your actual exam questions to help you develop these skills.  By working the pre-exam example questions, you will have additional opportunities to work example problems similar to your actual exam questions.  The multiple choice and matching questions on the exams will come mainly from lecture material, but students should also be familiar with all readings.

Exams will be graded using keys, and established rubrics will be used for “direct assessment” of what I consider to be fair, quality, correct answers (in the case of assignments) or ratings for performance (in the case of participation).  A variety of rubrics may be used, including list, holistic, descriptive, and rating scale formats, and all reasonable care will be taken to ensure that rubric grading is free of scoring errors and potential biases (e.g. “halo effects”).  Ideally, keys will be made available to students following each exam.  Students may not retain copies of their exams or the exam keys.

B. Re-grading Policy: If you have a concern about a graded assignment, check the key first.  Please follow these procedures if you decide to request a re-grade:  (a)  Send an e-mail note to the instructor identifying the problem and why your answer is correct, providing documentation (such as specific page numbers in your text).  (b)  If you think you have a good reason for why your grade is incorrect, you must explain your logic.  Your explanation should be as concise as possible. If there is a flaw in your logic, please do not request a re-grade; that is, do not request a re-grade if you find that you have made a mistake (you would only be wasting your time).  (c)  Suggest how the grade should be changed.  For example, “Please increase my score by 2 points.”  If you do not suggest what should happen, no changes will be made.  Re-grade requests will not be honored after 5:00 pm 3 business days (during Mon.-Fri.) after the exam has been graded and returned to you.  There are no re-grades for Participation grades.

C. How to get an “A”: We are all unique individuals, with our own academic strengths and weaknesses, including experience and cognitive resources, etc.  There are also many learning styles, and I expect that each student is different and will learn best through different combinations of learning styles.  Nevertheless, students who get “A’s” in biology courses like this one tend toward a “success strategy” that I highly recommend.  Specifically, your best bet to get an “A” in this course is to do all of the following:

    • Study as a team while verbalizing your thoughts, and quiz one another.
    • Attend every class, be attentive, and listen.
    • Take careful notes.
    • Read the readings and notes every week for ~6 hours, at least.
    • Do all assignments and pre-exam example questions; this includes participation.
    • Come to pre-exam reviews (if available).

VII. Academic Honesty/Plagiarism Statement: Each student in this course is expected to abide by the Utah Valley University policies for academic integrity.  Any work submitted by a student in this course for academic credit will be the student’s own work. For this course, collaboration is allowed in all non-graded aspects of the course; this course is, in fact, a collaborative effort among us all; however, no collaboration is allowed on graded assignments.

Plagiarism, the use of others’ words or ideas without proper attribution, is an impediment to your education and to the educational mission of Utah Valley University (UVU).  According to UVU policy, work that has been plagiarized must receive a failing grade.  However, there is a difference between unintentionally plagiarized work, which must be corrected in order to be considered for a passing grade, and intentional plagiarism, which will be forwarded to the Office of the Dean of Student Life as a disciplinary matter in accordance with UVU’s statement on Student Rights and Responsibilities. Evidence of intentional plagiarism will result in a failing grade for BIOL 3700. For more information, please refer to www.uvu.edu/courseinfo/engl/plagiarism_policy.html to read a UVU resource on plagiarism.  Because plagiarism is not always a “black and white” issue, it is recommended that students speak to their instructor if they have questions about avoiding plagiarism.  Other external resources include http://www.plagiarism.org.

You are encouraged to study together in groups and to discuss information and concepts covered in lecture and the sections with other students.  You can give “consulting” help to or receive “consulting” help from such students.  However, this permissible cooperation should never involve one student having possession of a copy of all or part of work done by someone else, in the form of an e-mail, an e-mail attachment file, a hard disc, or a paper copy.  Should copying occur, both the student who copied work from another student and the student who gave material to be copied will both automatically receive a zero for the assignment.  Penalty for violation of this code can also be extended to include failure of the course and University disciplinary action.

During examinations, you must do your own work. Talking or discussion is not permitted during the examinations, nor may you compare papers, copy from others, or collaborate in any way. Any collaborative behavior during the examinations will result in failure of the exam, and may lead to failure of the course and University disciplinary action.

VIII. Accommodations for students with disabilities: In compliance with UVU policy and equal access laws, if you have any disability that may impair your ability to successfully complete this course, please contact the Accessibility Services Department (LC 213; 863-8747).  Academic accommodations are granted for all students who have qualified disabilities.  Services are coordinated with the student and instructor by the Accessibility Services Department, and I must have a letter from their office to give you accommodations.  I ask students to please make requests for academic accommodations within the first two weeks of class, if possible.

IX.  Inclusivity Statement
We understand that our members represent a rich variety of backgrounds and perspectives. The UVU Department of Biology is committed to providing an atmosphere for learning that respects diversity. While working together to build this community we ask all members to:

  • share their unique experiences, values and beliefs,
  • be open to the views of others,
  • honor the uniqueness of their colleagues,
  • appreciate the opportunity that we have to learn from each other in this community,
  • value each other’s opinions and communicate in a respectful manner,
  • keep confidential discussions that the community has of a personal (or professional) nature,
  • use this opportunity together to discuss ways in which we can create an inclusive environment in this course and across the UVU community.

X. Tentative Course Schedule:  (May change to accommodate guest speakers, new activities, or student needs; T=Tuesday, R=Thursday)

DateTopicsReadings (Key: M, Molles; G, Gotelli; Handout, reading; Nos. in parentheses, page nos.)
R June 26: *Last Day of Class**FINAL EXAM (Exam III, in SB 132)*
T May 13Lecture “0” – Introduction to BIOL 3700Syllabus
Lecture 1 – Introduction to EcologyM1, M2, Lecture notes
Lecture 2 – The Biodiversity CrisisM4, M9(214-216), Lecture notes
R May 15Lecture 3 – The Ecology of IndividualsM5, Handout #1
Part I. Thermodynamics & the NicheM5, M9(198-200), Lecture notes
Part II. Physiological EcologyM5, Lecture notes
T May 20Lecture 4 – Life History StrategiesM9(212-213), M12, Lecture notes, Handout #2
Lecture 5 - EcosystemsM18, M19(415-420), Lecture notes
R May 22 (Example questions set #1) Lecture 6 – Population Ecology and Growth in Single SpeciesM10(227-239), M11
Part I. Exponential GrowthM11, G(2-22), Lecture notes
T May 27 (Example questions set #2)Part II. Logistic GrowthM11, G(26-32), Lecture notes
Part III. Effect of Time Lags and Increasing r (Chaos)M11, G(33-47), Lecture notes, Handout #3
R May 29 (Example questions set #3)Lecture 7 – Community Ecology: Dynamics of Two or More SpeciesM13
Part I. Lotka-Volterra Competition ModelsM13, G(100-123), Lecture notes
F-T; May 30-June 2*EXAM I (in CTC)*
T June 3 (Example questions set #4) Part II. Lotka-Volterra Predation Models, and CoexistenceM14, G(126-152), Lecture notes
R June 5Part III. Community Ecology: Adding Many SpeciesM15(329-330, 340-342), M17, Lecture notes, Handout #4
A. Defining species diversityM16, G(204-210), Lecture notes
B. Scale and diversityM17, Lecture notes
C. Processes that determine the patterns of species diversityM22, Lecture notes, ETIB PowerPoint
W-F; June 11-13*EXAM II (in CTC)*
T June 10D. Diversity-stability relationshipM20(446-453), Lecture notes
E. SuccessionM20(431-446), G(180-182,191-201), Lecture notes
F. Community Assembly & MetacommunitiesM16, Lecture notes
R June 12Lecture 8 – The Biosphere: Biogeochemical Cycles & ClimateM2, M3, M10, M23
Part I. The Water CycleM2, M3, M23, Lecture notes
T June 17Part II. The Carbon CycleM2, M10(221-223), M23, Lecture notes, Handout #5
R June 19Part III. A Brief History of Life On EarthLecture notes, Handout #6
T June 24*The Field Trip*N/A
Field trip to Provo Canyon and Little Cottonwood CanyonN/A

XI. Additional Resource Readings on Ecology

Johnson, J.B., Bagley, J.C. (2011) Ecological drivers of life-history divergence. Pages 38–49 in J.P. Evans, A. Pilastro, and I. Schlupp, eds. Ecology and Evolution of Poeciliid Fishes. University of Chicago Press, Chicago, IL.

Lomolino, M., Riddle, B.R., Brown, J.H. (2013) Biogeography, 6th Edition. Sinauer Associates, Sunderland, MA.

MacArthur, R.H., Wilson, E.O. (1967) The Theory of Island Biogeography. Princeton University Press, Princeton, NJ.

Morin, P.J. (2011) Community Ecology, 2nd Edition. Wiley-Blackwell, New York, NY.

Real, L.A., Brown, J.H. (eds) (1991) Foundations of Ecology: Classic Papers with Commentaries, 1st Edition. University of Chicago Press, Chicago, IL.

Rockwell, L.L. (2006) Introduction to Population Ecology. Wiley-Blackwell, New York.  352 p.

Speth, J.G. (2004) Red Sky at Morning: America and the Crisis of the Global Environment. Yale University Press, New Haven, CT.

Sigler, W.F., Sigler, J.W. (1996) Fishes of Utah: A Natural History. University of Utah Press, Salt Lake City, UT.

Wilson, E.O. (1992) The Diversity of Life. Norton, New York, NY.

Wilson, E.O. (2006) The Creation: An Appeal to Save Life On Earth. Norton, New York, NY.