Biology 53
General information & Syllabus
Biology 53 – Aquatic Ecology
GENERAL COURSE INFORMATION
Staff
Instructor:
TAs:
Brad Taylor
214 Gilman or 113B Centerra Bio Labs (7 Lucent Drive)
Gilman office hours – Tuesday and Wednesday 1-3, and by appointment.
Amy Dawson and Denise Steele
Office hours: Amy (TBA in lab) , Denise (Thurs 12-1).
Goals
To understand the physical, chemical, and biological properties of lakes and streams, and to be
familiar with the techniques used in limnological research. You will learn how concepts,
ecological theory, and methods can be integrated to address applied problems in aquatic
ecology. Also, I hope you learn that aquatic ecology isn’t rocket science; its much harder but
more fun!
Texts
The textbook we will be using is Freshwater Ecology by Walter Dodd’s. The chapters that
accompany the lectures each week are provided on the syllabus. Dodd’s book is neither the
magnum opus of freshwater aquatic ecology nor the das capital, but it is readable and
transportable compared to Wetzel’s Limnology text, which is an excellent reference that I
recommend purchasing if you think you will study aquatic ecology beyond this class. Copies
of Wetzel’s book are on reserve in Dana Library, along with Methods in Stream Ecology and
Limnological Methods.
Journal Articles
In addition to readings in the textbook, there will also be one journal article to read each week
(see Syllabus). You can find these articles in the library or online. This is a good way to get
exposed to the aquatic ecology literature and find information or ideas for your independent
projects, so I would encourage browsing other articles in the journals. I will be lecturing on the
assigned articles and we will discuss them informally as a group during the later portion of
some classes. Please do the readings ahead of time. Also, please read the handout, A guide to
critical thinking and evaluation of scientific literature.
Classes
Tuesday and Thursday 10:00-11:50 in 101 Gilman. The x-hour for this class is Wednesday
3:00-3:50. A few X-hours are already scheduled (see Key Dates), and it’s possible that more
will be used throughout the term – I’ll give you plenty of advance warning about any additional
ones.
Labs
Labs will begin next week, and meet Thursday or Friday 1:45-5:45 in 13 Gilman (see the Lab
Schedule for what you will be doing each week). You must attend all scheduled labs!
2/12/2016
Page 1 of 6
Biology 53
General information & Syllabus
Coursework and grading
Exam questions will cover material covered in the lectures, labs, articles, and textbook.
2 Problem sets
Midterm exam
Final exam (Dec. 5, 3:00 PM)
*Lake & stream gradient lab
Peer review (5%)
Paper (20%)
*Independent projects
Experimental design (10%)
Research/paper/presentation (15%)
10%
20%
20%
25%
25%
*There are two required papers. You will receive more detailed information about the papers
in the next few weeks. Both papers are based on integrating material learned in lecture and lab
to analyze, interpret, and synthesize field data from lakes and streams. The first paper is based
on data we will collect during the first two labs, and the second paper is based on an
independent project designed by you. The projects can be done in groups of 2-4 depending on
the size of the proposed project. We will discuss potential project ideas in the first X-hour, but
start thinking about what topics you are interested before next Wednesday. If your curious
about the length, ~15-17 pages double spaced, including text, tables, figures, and references (at
least 5-10). Please read the handout entitled Hints for how to write scientific papers. Please
plan ahead and do not turn papers in late, as you will lose one whole letter grade for each day
late.
Special needs
Students with learning, physical, or psychiatric disabilities enrolled in this course that may
need disability-related classroom accommodations are encouraged to make an office
appointment to see me before the end of the second week of the term. All discussions will
remain confidential, although the Student Disability Services office may be consulted to
discuss appropriate implementation of any accommodation requested.
2/12/2016
Page 2 of 6
Biology 53
General information & Syllabus
KEY DATES
September 28 (W) – X-HOUR (discuss independent project ideas)
October 5 (W) – X-HOUR (Problem set assigned)
October 6 (Th) – independent project: topic emailed to TA
October 12 (W) – independent project: experimental design due by 12 noon
October 13 (Th) – metabolism problem set due by 12 noon
October 17 (M) – independent project: bibliography due by 12 noon
October 19 (W) – X-HOUR (review session)
October 20 (Th) – MIDTERM EXAM in class
October 26 (W) – X-HOUR (invertebrate and algae taxonomy, and an optional graphing and data analysis
help session from 4-6pm)
November 7 (M) – lake/stream zonation lab write-up due by 12 noon
November 10 (Th) – peer review due by 12 noon
November 15 (T) – nutrient uptake problem set due by 12 noon
November 16 (W) – X-HOUR (PowerPoint instruction)
November 22 (T) – independent project: paper due by 12 noon
November 29 (T) – project presentations in class
November 30 (W) – X-HOUR (review session)
2/12/2016
Page 3 of 6
Biology 53
General information & Syllabus
SYLLABUS
Below is an outline of topics which will be covered in class, in the order in which we will cover them.
Especially in earlier classes, these topics may take longer than one class to complete. Unless I
specifically instruct you otherwise, assume that we will be getting to the next lecture topic in the
following class and do the readings. Some of the articles may change if a new and exciting one is
published during the quarter.
1. Introduction to aquatic ecology
Dodds: Chp 1&2.
Jackson, R.B. et al. 2001. Water in a changing world. Ecological Applications 11:1027-1045.
2. Physiography and water movements
Dodds: Chp 4-6
Kratz, T.K., K.E. Webster, C.J. Bowser, J.J. Magnuson, and B.J. Benson. 1997. The influence of
landscape position on lakes in northern Wisconsin. Freshwater Biology 37:209-217.
3. Light and heat
Dodds: Chp 3
Winder, M., and D. E. Schindler. 2004. Climatic effects on the phenology of lake processes. Global
Change Biology 10:1844-1856.
4. Oxygen, inorganic carbon, and pH
Dodds: Chp 11 & 12
Schindler, D. E., S. R. Carpenter, J. J. Cole, J. F. Kitchell, and M. L. Pace. 1997. Influence of food
web structure on carbon exchange between lakes and the atmosphere. Science 277:248-251.
5. Nutrients
Dodds: Chp 11, 13, 16
Peterson, B.J. et al. 2001. Control of nitrogen export from watersheds by headwater streams.
Science 292:86-90.
6. Primary producers and production
Dodds: Chp 7 & 8
Hutchinson, G. E. 1961. The paradox of the plankton. American Naturalist 95:137-146.
7. Detritus, fungi, and bacteria
Dodds: Chp 7 & 8
Pace, M. L., J. J. Cole, S. R. Carpenter, J. F. Kitchell, J. R. Hodgson, M. C. Van de Bogert, D. L.
Bade, E. S. Kritzberg, and D. Bastviken. 2004. Whole-lake carbon-13 additions reveal terrestrial
support of aquatic food webs. Nature 427:240-243.
8. Zooplankton
Dodds: Chp 9 & 10
Hairston, N. G., Jr., L. J. Perry, A. J. Bohonak, M. Q. Fellows, C. M. Kearns, and D. R. Enstgrom.
1999. Population biology of a failed invasion: Paleolimnology of Daphnia exilis in upstate New
York. Limnology and Oceanography 44:477-486.
9. Macroinvertebrates
Dodds: Chp 9 & 10
Strayer, D. L., N. Caraco, J. J. Cole, S. Findlay, and M. L. Pace. 1999. Transformation of freshwater
ecosystems by bivalves. Bioscience 49:19-27.
2/12/2016
Page 4 of 6
Biology 53
General information & Syllabus
10. Vertebrates
Dodds: Chp 21
Fittkau, E. J. 1970. Role of caimans in nutrient regime in mouth-lakes of the Amazon affluents (An
hypothesis). Biotropica 2:138-142.
11. Species interactions
Dodds: Chp 18, 19, 20
Peckarsky, B. L., A. R. McIntosh, B. W. Taylor, and J. Dahl. 2002. Predator chemicals induce
changes in mayfly life history traits: A whole-stream manipulation. Ecology 83:612-618.
12. Food webs and food chain length
Dodds: Chp 19
Baxter, C. V., K. D. Fausch, M. Murakami, and P. L. Chapman. 2004. Fish invasion restructures
stream and forest food webs by interrupting reciprocal prey subsidies. Ecology 85:2656-2663.
13. Eutrophication
Dodds: Chp 17
Carpenter, S.R., N.F. Caraco, D.L. Correll, R.W. Howarth, A.N. Sharpley, and V.H. Smith. 1998.
Nonpoint pollution of surface waters with phosphorus and nitrogen. Ecological Applications 8:559568.
14. Contaminants in aquatic systems
Dodds: Chp 14
Krümmel, E. M., R. W. Macdonald, L. E. Kimpe, I. Gregory-Eaves, M. J. Demers, J. P. Smol, B.
Finney, and J. M. Blais. 2003. Delivery of pollutants by spawning salmon. Nature 425:255-256.
14. Unusual aquatic environments
Dodds: Chp 15
Ellison, A. M., and N. J. Gotelli. 2002. Nitrogen availability alters the expression of carnivory in the
northern pitcher plant, Sarracenia purpurea. Proceedings of the National Academy of Sciences
99:4409-4412.
16. Dams and reservoirs
Dodds: Chp 22
Vinson, M. R. 2001. Long-term dynamics of an invertebrate assemblage downstream from a large
dam. Ecological Applications 11:711-730.
17. The future of aquatic resources
Dodds: Chp 23
Reading: TBA
2/12/2016
Page 5 of 6
Biology 53
General information & Syllabus
AQUATIC ECOLOGY LAB
Goals of the laboratory
1. Learn basic limnological field and lab methods.
2. Apply these methods to test hypotheses that you develop.
3. Understand the patterns and relationships between physical, chemical, and biological
properties in aquatic ecosystems.
Please map out well ahead of time when things are due and start early on them. I honestly tried to space
things out as evenly as possible, but some tight scheduling is inevitable.
The first two labs are devoted to sampling the dominant gradients in physical, chemical, and biological
properties of lakes and streams (i.e., vertical and longitudinal zonation). The third lab is to help you get
started early on your independent projects. This means you need to decide on a topic and have the
experimental design worked out and checked by your TA before the third week of lab. You will thank us
in the end for getting you started on the project early. During the 4th and 5th weeks, we will process and
analyze the stream and lake samples from the first two labs. After the 5th week, you will have all the data
you need to finish the stream/lake zonation paper. I have made suggestions on the lab syllabus of things
you can do as the data are gathered, so things don’t pile up at the end.
LAB SCHEDULE
Week
*Sept. 29-30
Topic
Lake lab (Field) Suggestion: Write the study site description and sampling methods sections of
the zonation paper following this lab.
*Oct. 6-7
Stream lab (Field) Suggestion: Write the study site description and sampling methods sections of
the zonation paper following this lab. Start writing the introduction.
*Oct. 13-14
Start independent projects (Field or Laboratory)
Oct. 20-21
Process lake and stream samples: water chemistry, chlorophyll, organic matter, etc. (Laboratory).
Suggestion: Make graphs and write the methods and results for these data.
Oct. 27-28
Process lake and stream invertebrate and algal samples (Laboratory). Suggestion: Make graphs
and write the methods and results for these data. Start writing discussion.
Nov 3- No scheduled labs for the rest of the quarter – work on independent projects. (This is subject to change)
*Remember to dress appropriately for field labs, we will go out regardless of the weather – and bring
water.
2/12/2016
Page 6 of 6