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«FW 401 Fishery Science: Ecology and Management LECTURE SCHEDULE - 2016 Homework DUE Date Topic 08/22 Course overview Citations 08/24 The Stock ...»

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FW 401 Fishery Science: Ecology and Management


Homework DUE

Date Topic

08/22 Course overview


08/24 The Stock Concept, ESUs

Crib notes: Metcalf

08/29 Abundance estimation I – Statistical underpinnings

08/31 Abundance estimation II – Study design

09/05 Labor Day – no class

09/07 Abundance estimation III – Examples Simple estimators 09/12 Age and growth: Ecological concepts 09/14 Ken Kehmeier: Glade Reservoir Crib notes: NCWCD, STP 09/19 Age and growth: Estimation techniques Crib notes: MacLean 09/21 Growth and production: Ecology and estimation 09/26 Catch up Growth calculations 09/28 FIRST MIDTERM EXAM 10/03 Mortality I: Ecological concepts and estimation 10/05 Mortality II: Estimation 10/10 Recruitment I: Ecological concepts Mortality calculations 10/12 Recruitment II: Mathematical models 10/17 Recruitment III: Maternal influence Crib notes: Shelton 10/19 Bioenergetics I: Eco-physiological underpinnings 10/24 Bioenergetics II: The energy budget and models 10/26 Bioenergetics III: Yellowstone Lake case study 10/31 SECOND MIDTERM EXAM 11/02 Fisheries management fundamentals, process 11/07 Evolutionary effects of fishing Crib notes: Belgrano 11/09 Fisheries management practices 11/14 Stocking and hatcheries 11/16 Regulating harvest: Demographic principles Crib notes: Rahel 11/21 Fall break – no class 11/23 Fall break – no class 11/28 Indirect effects of harvest regulations 11/30 Suppression of invasive fishes Crib notes: Hansen 12/05 Habitat rehabilitation 12/07 Fishery socioeconomics


12/15 Thursday 4:10-6:10 PM Dr. Brett Johnson CSU Department of Fish, Wildlife and Conservation Biology 1 FW 401 Fishery Science: Ecology and Management Syllabus - Lecture Instructors Dr. Brett Johnson, Professor, Department of Fish, Wildlife and Conservation Biology Office: 233 Wagar; Phone: 970-491-5002; Email: brett.johnson@colostate.edu Office hours: 10-11 am M, W or by appointment;

GTA: Tyler Swarr, Office: TBD Office hours: TBD or by appointment; Email:

tswarr@rams.colostate.edu The best way to contact us is by email to the addresses above with “FW401” in the subject line. Please do not send email from within Canvas.

Required Materials

• Calculator capable of computing basic statistics.

• There is no textbook required for this course

• FW401 slides (Canvas. These are copyrighted materials so you may not duplicate or distribute any of them, they are solely for your use in the course.

Prerequisites FW300, M141/155/160, ST301/ST307 or equivalent. Computer literacy is assumed.

Time and Place Lecture: M, W 9:00-9:50 am, 132 Wagar Lab: Tu 2:00-4:50, 107 Wagar, or CNR CLL (see Lab schedule) Credits and Instructional Methodology This is a 3 credit class, with lecture (2 credits) and laboratory (1 credit; computerintensive exercises and hands-on techniques).

Special Needs Please let me know as soon as possible if you have any special needs so that we can accommodate you.

Learning Objectives Fishery Science is a quantitative, ecological discipline that interfaces with human dimensions, particularly socioeconomics. The course requires students to draw on knowledge gained throughout the Fisheries and Aquatic Sciences curriculum (math, statistics, and fishery and wildlife biology, ecology, conservation biology, economics and human dimensions) to tackle complex concepts and apply that understanding to real world datasets and contemporary fisheries management issues.

Expected Competencies By the end of the course, students will have a firm grasp on the fundamentals of fish population dynamics, including basic concepts and stock assessment methods, and will learn how to apply demographic and ecological concepts to the management of sport and non-game fish populations and communities. Students will leave the laboratory section with essential practical and computer skills for gathering, analyzing and interpreting fishery data, and preparing reports in scientific format. Group projects allow students to hone their teamwork, critical thinking and communications skills.

–  –  –

My Expectations of You

• Attendance is very important- exams are largely based on material presented in class; if you miss a class you should get notes from a classmate.

• Students should come to class having read assigned readings, participate in exercises and discussions, and perform all homework and laboratory assignments.

• Students should expect to spend at least 8 hours per week outside of class reading, doing lab reports and homework for this class.

• Ask questions! If something is unclear to you it probably is to others also, and questions make the class more interesting for everyone.

• Respect your classmates and your instructor. This includes not chatting and turning off your cell phone during class periods.

Student Conduct No academic dishonesty will be tolerated. This course will adhere to the Academic Integrity Policy of the General Catalog and the Student Conduct Code. You may be asked to sign an Honor Pledge before taking each exam. I reserve the right to assign negative points for academic misconduct on exams or assignments.

Using personal electronic devices in the classroom can hinder instruction and learning, not only for the student using the device but also for other students in the class. Please turn off and do not use any personal electronic devices in class, including cell phones, laptops, tablets, and other similar devices. If you have a legitimate need to use a personal electronic device during class please see me for special consideration.

I do not allow students to record video of my lectures, or to post or distribute copies of course materials anywhere.

If you must miss an exam due to sickness or personal tragedy, Dr. Johnson must be consulted before the exam begins--call, and leave a message if necessary! Otherwise, you will receive a zero on the exam. I reserve the right to base grades on a subset of course scores instead of a makeup.

Attendance at Lab sessions is required, no matter what the topic. All lab sessions have points associated with them regardless of whether there is a write-up/report required.

Required Reading There is no textbook for this class. Readings will be available online. Papers should be read before coming to class- “crib notes” will be required for some readings.

Homework Assignments You will do better in the course if you do the homework. Late homework will not be accepted.

Grading Policies Course grades will use the +/- grading system; Pass/Fail is not an option. In general course grades will follow the conventional curve (below) but adjustments may be required based on class performance.

Letter grade A+ A A- B+ B B- C+ C D F Upper (%) 100 96.9 92.9 89.9 86.9 82.9 79.9 76.9 69.9 59.9 Lower (%) 97.0 93.0 90.0 87.0 83.0 80.0 77.0 70.0 60.0 0

–  –  –

Exams are cumulative and include lecture and laboratory material and readings. No electronic devices, except calculators, are allowed during exams.

Recommended References The following list of references is provided to supplement material presented in class, to give you some resources to dig more deeply into topics that interest you, and to allow you to review basic concepts covered in prerequisite courses (you may also wish to review course notes from prerequisite courses).

Ecology Gotelli, N. J. 2008. A primer of ecology, 4th edition. Sinauer Associates, Inc., Sunderland, MA.

Krebs, C. J. 1989. Ecological methodology. Harper Collins Publishing, New York, NY.

Smith, R.L. and T.M. Smith 2001. Ecology and field biology, 6th edition. Benjamin Cummings, New York, NY.

Fisheries Ecology and Management Guy, C. S. and M. L. Brown, editors. 2007. Analysis and interpretation of freshwater fisheries data. American Fisheries Society, Bethesda, MD.

Helfman, G. S., B. B. Collette, D. E. Facey, and B. W. Bowen. 2009. The diversity of fishes. Wiley-Blackwell, Oxford, UK.

Hilborn, R. and C. J. Walters. 1992. Quantitative fisheries stock assessment: choice, dynamics, and uncertainty. Chapman and Hall, London.

Hubert, W.A. and M. C. Quist (eds). 2010. Inland fisheries management in North America.

American Fisheries Society, Bethesda, Maryland.

King, M. 2007. Fisheries biology, assessment and management. Second edition.

Blackwell Publishing, Oxford, England.

Zale, A. V, D. L. Parrish, and T. M. Sutton, editors. 2012. Fisheries techniques, third edition. American Fisheries Society, Bethesda, Maryland.

Ricker, W. E. 1975. Computation and interpretation of biological statistics of fish populations. Fisheries Research Board of Canada Bulletin 191.

Mathematics and Statistics Dytham, C. 2011. Choosing and using statistics: A biologist's guide. John Wiley & Sons.

Gotelli, N.J. and A.M. Ellison. 2013. A primer of ecological statistics. Sinauer Associates, Inc., Sunderland, MA.

Samuals, M., J. Witmer, and A. Schaffner. 2011. Statistics for the life sciences, 4th edition.


–  –  –

Syllabus – Laboratory

Laboratory Objectives:

1. provide you with essential computer skills that employers and graduate schools will expect you to possess,

2. improve your ability to collect, analyze and interpret fish and fishery data, and

3. allow you to hone your technical writing and scientific graphics skills.

Grading of Lab Reports: Laboratory reports make up the single largest portion of your grade in this course. Thus, you would be wise to do your best on each lab. If you don’t understand how your report was graded, come see Dr. Johnson or the GTA. It is your responsibility to retain a copy of any assignments you turn in.

Grading of lab reports will be performed in accordance with laboratory objectives.

Thus, reports getting the highest grades will be those that a) demonstrate computer proficiency relative to the tasks in the lab exercise, b) are numerically correct, showing all work clearly and concisely (calculations need not be typed- write neatly on a separate sheet), and c) adhere to the Guidelines for the Preparation of Scientific Reports (below).

1. Completed laboratory assignments are due in on the date specified in the lab schedule, at the beginning of the lab period. Labs are late after 2:00 p.m. Tuesday.

Don't fall behind!

2. Late labs turned in by: Penalty Wednesday 5 p.m. - one day late 10% off For each day thereafter (8-5 p.m.) 10% additional

3. If there are field trips they will count toward your grade the same as one lab assignment.

4. You may drop 1 lab assignment/field trip. Use this option wisely, when you really need it.

Your work: I encourage students to discuss and help each other on lab assignments but each student must prepare their own lab report independently (see section on academic integrity) unless an assignment is specifically designated as a “team” assignment. You may not copy material from previous years’ students either.

–  –  –

Guidelines for the Preparation of Scientific Reports Lab reports should be prepared on a computer using word processing software. When a written answer is required use clear, complete sentences. Staple the pages- don’t

use a fancy binder. Reports should have the following sections in this order:

Introduction, Methods, Results and Discussion, Literature Cited, Tables, Figures, Appendices.

1. Introduction- Include some background information to set the stage for the topic, then describe the objectives of the laboratory exercise (in your own words) and why the exercise is relevant to the discipline. Cite other literature as necessary.

(~½ page)

2. Methods- Briefly describe the mathematical, statistical, sampling and other procedures used. Cite other literature as necessary. (1 page)

3. Results and Discussion- Describe what you found, refer to appropriate tables and figures (see below), answer any questions posed in the lab handout and discuss your conclusions and how these findings relate to published work on the topic (include citations). You may also include “Management Implications” if appropriate.

Hand written calculations should be included as an “Appendix” and referenced as such in the Results and Discussion section. (~ ¾ - 1.5 pages)

4. Literature Cited- your laboratory reports must have a “Literature Cited” section wherein you document any information sources used in your report. Each report must include at least three appropriate/relevant sources from the primary literature (peer-reviewed scientific journal articles) and you may also include books and book chapters, agency reports, contract reports, theses and dissertations, and internet web sites. You may not use references provided in the course- do your own literature search!

We will follow American Fisheries Society scientific journal style for bibliographic information in lab reports. Consult the TAFS “Guide for Authors” at http://fisheries.org/ or see a 2014 issue of the journal Transactions of The American Fisheries Society for examples of proper bibliographic format.

5. Tables- Tables come after the Literature Cited section and before figures. All tables should be numbered and include a descriptive table heading at the top of the table that completely describes the table, including symbol definitions, abbreviations used, and units of measure. The Table below (Rand et al. 1993) is a good one.

–  –  –

From: Rand, P. S., D. J. Stewart, P. W. Seelbach, M. L. Jones, and L. R. Wedge.

1993. Modeling steelhead population energetics in Lakes Michigan and Ontario.

Transactions of the American Fisheries Society 122:977-1001.

–  –  –

6. Figures- Figures come after the tables. Graphs should be computer-generated (in spreadsheet or graphics software) and imported into your word processing document.

Each graph must be numbered and must have the following features:

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