FAS 2024 Global and Regional Perspective in Fisheries. Spring. Credits: 3; No prerequisites. Fish biology, ecology and habitats relevant to fisheries on both a global and regional (Florida) scale. Follows the fisheries occurring from cold, mountain rivers to the depths of the oceans, with special topics (e.g., artificial reefs, fisheries bycatch, aquaculture). Intended for non-science and science majors.  Course Syllabus

FAS 4202C Biology of Fishes. Fall, odd years. Credits: 4. Prerequisite: BSC 2011-2011L. Course focuses on the general biology of fishes, with emphasis on trends in their evolution, integrative and sensory biology, physiology, feeding ecology, reproduction, growth, and population dynamics as they relate to fisheries.   Course Syllabus

FAS 4305C Introduction to Fishery Science. Spring. Credits: 3; Prerequisite: Junior standing Natural Resources and Conservation, Wildlife, or Forestry, or consent of the instructor.  Description: This course provides students with a basic understanding of fishery and limnological science. Knowledge will be gained through classroom lectures and hands-on experience with a broad array of methods used in fishery science. Research methods will include not only field and laboratory techniques, but also the procedures and formats for data analysis and formulation of management practices for aquatic resources. Fishery science encompasses a variety of scientific disciplines including physics, chemistry, and biology. Specific items that will be address in this course include: (1) structure and function of aquatic habitats, (2) limnological laboratory and field procedures, (3) fish sampling and study methods, (4) analysis and reporting of limnological and fishery data, and (5) an overview of some important Florida aquatic resource issues. Outcomes: When students complete this course, they will successfully be able to apply the scientific method and become proficient in analyzing, interpreting and presenting (oral and written) fish and limnological information. Students will also be able to prepare a manuscript for publication.  Course Syllabus / Past Student Papers and Data

FAS 4405 Aquariums, Water, and Aquaculture. Spring. Credits: 3; Prerequisite: BSC 2011-2011L or consent of instructor. Culture methods of fish and shellfish, species selection, biological and environmental principles, case histories and future trends. 

FAS 4905 Individual Study. Credits: 1 to 4. May be repeated with change of topic up to maximum of 8 credits. Prerequisite: Consent of Instructor. Individual study of a selected topic in fisheries and aquatic sciences as contracted with the instructor at the start of the term.

FAS 4932 Topics in Fishery Aquatic Sciences. Credits:1 to 4. May be repeated with change of topic up to a maximum of 8 credits; Prereq: Consent of instructor. Selected topics in fisheries biology, aquaculture and associated aquatic sciences not offered in other courses.

PLS 4613 Aquatic Weed Control. Fall, even years. Credits: 3. Prerequisites: PCB 3033 or BOT 3503C. Identification of Florida's aquatic weed problems and methods of chemical, biological, mechanical, and physical weed control. Specific topics will include plant biology/ecology, herbicide residue, lake reclamation, fish-plant interactions, and current laws regulating aquatic weed control. 

Graduate courses

FAS 5203C  Biology of Fishes [Fall, Odd Years, 4 Credits]
Description: Course focuses on the general biology of fishes, including general classification, zoogeography, trends in evolution, integrative and sensory biology, and physiology; as well as bioenergetics, feeding ecology, reproduction, age and growth, and population dynamics as they relate to fisheries. Weekly lab focuses on demonstrations and practical experience based on lecture topics.  Graduate students are also responsible for developing a research grant proposal.  This course is intended for first year graduate students and senior undergraduates. Outcomes: On completion of the course, all students should have: a working knowledge of all general aspects of fish biology; the ability to synthesize biological information spanning multiple areas; the ability to recognize and explain large-scale tradeoffs in fish feeding, growth, and reproduction; and practical laboratory experience in identification, external and internal morphology. Graduate students also should be able to draft, revise, and resubmit a grant proposal on a fish-related topic appropriate for a federal granting agency.

FAS 5255C Diseases of Warm Water Fish [Summer A, Every Year, 4 Credits, Prerequisite: instructor consent]
Description: Course is an intensive two-week class designed to provide instruction in the methodology of diagnosis and treatment of parasitic, bacterial, viral, nutritional, and environmental diseases of warm water food fish and aquarium species. Outcomes: Students who successfully complete this course will be able to assess fish disease problems through a thorough understanding of water quality analysis and life support systems, understand and be able to carry out the steps required to examine a fish for infectious disease. This includes being able to perform a basic examination, biopsy tissue from live and dead animals for parasite identification, and collect appropriate samples for microbiological and histological diagnostic tests. Finally, the student will be able to effectively calculate and administer basic chemical treatments used as part of aquaculture practice. This includes an understanding of legal constraints associated with drug and chemical use in an aquaculture setting.

FAS 5276C Field Ecology of Aquatic Organisms [Summer A, Odd Years, 4 Credits, No Prerequisite]
Description: The course provides an overview of the diverse aquatic ecosystems in Florida with an emphasis on freshwater systems. Extensive field trips are required. Predominant plants, invertebrates and fishes are identified from each field trip. An overview of ecological methodologies for field research is provided. This course is intended for upper-level undergraduates or entry-level graduate students.  Outcomes: Students who successfully complete this course will have knowledge regarding the physical, chemical and biological characteristics of Florida aquatic ecosystems and the skills to identify common flora and fauna, with a focus on fish, invertebrates and vascular plants. Students also will develop skills and knowledge related to field research on the systems visited during the course.  Course Description and General Information

FAS 5335C Applied Fisheries Statistics [Fall, Even Years, 4 Credits, Prerequisite FAS 5276C or instructor consent] Description: This course covers mathematical distributions, transforming data, outliers, significant figures, number of samples needed, effect of sampler size, sample design, mark-recapture and depletion methods of estimating abundance, length-frequency analysis, length-weight relationships (K, Wr, ANOCOVA), and basic statistical tests (e.g., t-tests, paired t-tests, tests of normality, correlations, simple ANOVAs, regression analysis).  Additional topics will include ratios, pseudo-replication, nonparametric statistics, repeated-measures ANOVA, multiple comparison testing, and variable selection techniques.  Handouts (computer printouts and primary literature) will be used extensively as supporting materials.  Students will learn the basics of SAS (Statistical Analysis System) programming for data management and analysis. Each student will conduct an independent "sampling" project on a fisheries or aquatic science topic of their choice, including review of the literature, proposal and budget preparation, completion of field and/or laboratory work, and preparation of paper and oral presentation based on their research. Outcomes: Students who successfully complete this course will be able to effectively organize data (past or future) apply appropriate parametric statistical tests, and have a critical understanding of methods of sampling and analysis.  Course Syllabus

FAS 5901 Scientific Thinking in Ecology [Fall, Every Year, 2 Credits, Prerequisite: One ecology course.]
Description: This course examines general philosophical foundations of science, the nature of scientific disputes, and relationships of science with society.  Assigned readings, class discussions and essays provide background, tools, opportunities and feedback designed to help students develop their own philosophy and ethics as guides for a professional career. Outcomes: Upon completion of this course, successful graduate students will be able to: distinguish science from other endeavors and better identify “good” science; formulate and deliver higher quality verbal and written arguments; demonstrate an ability to learn from other fields; and interact effectively as a part of a team exploring important issues. Syllabus and Readings  Class Materials

FAS 6154 Aquatic Invertebrate Ecological Physiology [Fall, Odd Years, 3 Credits, Prerequisite: instructor consent] Description: This course will focus on the biochemical, physiological, behavioral, and ecological adaptations of invertebrate animals. A comparative approach will be used to examine basic principles of adaptation, problems of size and scale, key mechanisms in physiology (excretion, thermal biology, respiration, etc.), and details of how organisms cope with particular aquatic environments (marine, estuarine and freshwater). This course will serve students in a variety of freshwater, marine, aquaculture, zoology and natural resource related disciplines. Students will develop an understanding of the underlying importance of physiology in the structure and function of communities and ecosystems. Outcomes: Upon successful completion of this course, students will: be able to apply interdisciplinary knowledge in the subject area of invertebrate ecological physiology; be familiar with the classical and contemporary literature of the discipline; apply critical thinking in evaluating the literature, engage in collegial discussion, and gain experience in verbal communication through oral presentations.

FAS 6171 Applied Phycology [Fall, Even Years, 3 Credits, Prerequisite: course in organic chemistry or biochemistry] Description: This provides an overview of the role algae play in the structure and function of freshwater and marine ecosystems, as well as in depth examinations of key issues related to the management of harmful algae and utilization of algae as a natural resource.  Topics will include: 1) The evolution and taxonomic classification of algae, 2) Algal structure and function, 3) Harmful algal blooms and their involvement in toxin production, anoxia and food web alteration, 4) Ecology of algae in freshwater and marine environments, 5) Control of algal blooms, management and ecosystem restoration, and 6) Utilization of algae in wastewater treatment, aquaculture, chemical production, energy production and the search for new medicines.  Students will be provided with basic principles and current literature dealing with contemporary issues.  A special topics assignment during the class will focus on the application of basic knowledge to a current issue. Outcomes: The course will provide students with sound and contemporary understanding of the organisms that represent the largest component of primary production in the biosphere.  The course will also provide students with an understanding of the basic knowledge and tools needed to address some of the emerging issues related to algae, such as the causes and consequences of toxic algae blooms and the relationships between algal population dynamics and ecosystem integrity and sustainability.  The core objective of the class is to promote the use of critical thinking in dealing with real world problems and challenges.

FAS 6337C Fish Population Dynamics [Spring, Odd Years, 4 Credits, Prerequisite: STA 6166 or higher, or consent of instructor] Description: Course demonstrates the analysis of fish population data for management purposes.  Methods for estimating fish population parameters (e.g., growth, recruitment, and mortality) will be demonstrated in lecture and conducted in the laboratory.  We will use a variety of computer models, SAS (Statistical Analysis Systems), and Microsoft Excel to assess fish populations.  You will predict yield and catch composition for recreational fisheries, and assess effects of harvest restrictions for fisheries management problems.  This course is intended for graduate students in FAS or other natural-resource departments. Outcomes: Students that take this class will become proficient in estimating fish population metrics needed for stock assessment.  After this course, you should be able to estimate and model fish growth, mortality, and stock-recruit relationships.   You should also be able to synthesize these estimates into practical age and size structured population models, and use these models to make predictions regarding optimal harvest regulations and management options for fisheries.  This course should prepare you for using common quantitative techniques by fisheries management agencies at the state and national levels.

FAS 6355C Fisheries Management [Fall, Odd Years, 4 Credits, Prerequisite: FAS 5276C or instructor consent]
Description:  Fisheries management requires an understanding of biological, social, political, economic and legal issues.  This course will provide students with an understanding of the methods and limits of fisheries management.  It will also demonstrate how political, social, economic, and legal factors affect which scientifically-based management programs can be implemented.  The course is intended for graduate students majoring in or studying fisheries science, aquaculture, ecology, limnology, zoology, or environmental engineering. Outcomes:  Students who successfully complete this course will, by integrating information from different disciplines, be able to address complex fishery issues from different stakeholder perspectives.

FAS 6905 Individual Study. Fall, spring and summer, variable credits (1 – 6), maximum 10. Students conduct independent study with mentoring by a faculty member and address a contemporary problem or topic.

FAS 6910 Supervised Research. Fall, spring and summer, variable credits (1 – 5), maximum 5, S/U. Students conduct independent research with mentoring by a faculty member.

FAS 6932 Stream Fish Biology [Spring, Even Years, 4 Credits, Prerequisite: instructor consent]
Description: In this course students will become familiar with stream and river ecosystems and the important roles of these ecosystems across the landscape.  They will examine the physical, biological, and ecological principles that structure lotic ecosystems with particular attention to assessing human impacts on stream and river ecosystems.  Outcomes: Students who successfully complete this course will be able to identify key ecosystem features of lotic ecosystems and develop a skill set to quantitatively assess river ecosystems. Course syllabus and general information

FAS 6932 Plankton Ecology [Spring, Even Years, 3 Credits, Prerequisite: instructor consent]
Description: This course provides a comprehensive overview of classical and contemporary aspects of the biology and ecology of freshwater plankton, with particular consideration of how zooplankton structure and function relates to fisheries and water quality. The course includes classroom, field and laboratory experiences, critical evaluation of methods used to collect and analyze zooplankton, and it examines current focus areas in plankton research. The emphasis is on freshwater plankton, however, selected marine literature will be examined and most of the principles covered apply across the freshwater – marine continuum. Students will participate in discussions regarding selected papers from the plankton ecology literature, and will conduct an independent analysis of an unpublished plankton / water chemistry data set from a Florida lake. Using knowledge acquired in the course, students will develop tables and figures to summarize major aspects of the data, draw conclusions about patterns observed in those data, cite the appropriate literature, establish hypotheses, and develop a research plan for hypothesis testing. The products of this exercise will include a written report and oral presentation to the class. Outcomes: Students who successfully complete the course will be able to independently develop and execute field and laboratory procedures for estimating zooplankton population density, biomass, productivity and grazing rates. They also will have a solid understanding of the major biotic and abiotic factors that control zooplankton dynamics in aquatic ecosystems and be able to critically analyze both published literature on the subject and raw data collected from observational or experimental studies. This course also will help students develop competencies in the following general areas: implementing projects efficiently and effectively; evaluating information and formulating high-quality arguments; and communicating effectively through oral and written materials. Course Syllabus   Plankton Web Site

FAS 6932 Marine Ecological Processes [Spring, Odd Years, 3 Credits, Prerequisite: instructor consent]
Description:  This course is intended to provide students with a broad overview of ecological processes operating in estuarine, near shore coastal and open ocean systems.  Initially, students are introduced to important primary producers and secondary consumers in each of these systems.  Insights into physiological and population levels of organization build on these basics.  Environmental factors that influence species-specific and population level interactions are discussed subsequently as a transition to the concepts of community organization.  The major chemical cycles in marine systems (e.g., carbon, nitrogen and phosphorus) are then discussed.  All of this material forms a foundation for explaining how the structure and function of communities are maintained over different scales in both time and space. Outcomes: Students who successfully complete this course will be able to recognize and appreciate the wide variety of biotic and abiotic factors that influence processes that occur across different levels of biological organization.  Students will be familiar with classical studies in ecology, as well as more recent works that challenges existing paradigms. Students will develop skills needed to critically evaluate and synthesize information and also be able communicate complex ideas in an effective manner.

FAS 6932 Fish and Limnology [Spring, Every Year, 3 Credits, No Prerequisite]
Description: This course provides students with a basic understanding of fishery and limnological science.  Knowledge will be gained through classroom lectures and hands-on experience with a broad array of methods used in fishery science. Research methods will include not only field and laboratory techniques, but also the procedures and formats for data analysis and formulation of management practices for aquatic resources. Fishery science encompasses a variety of scientific disciplines including physics, chemistry, and biology. Specific items that will be address in this course include:  (1) structure and function of aquatic habitats, (2) limnological laboratory and field procedures, (3) fish sampling and study methods, (4) analysis and reporting of limnological and fishery data, and (5) an overview of some important Florida aquatic resource issues. Outcomes: When students complete this course, they will successfully be able to apply the scientific method and become proficient in analyzing, interpreting and presenting (oral and written) fish and limnological information.  Students will also be able to prepare a manuscript for publication. Course Syllabus

FAS 6932 Fish and Water Chemistry [Fall, Odd Years, 3 Credits, Prerequisite: instructor consent]
Description: This course discusses International, Federal, and State of Florida water quality standards and how each standard affects fish. Students learn the facts behind the establishment of each standard, sources of the materials and the interactions between various water chemistry parameters that occur in a lake or body of water.  This course uses the Canadian Guide to Water Quality as the primary reference source and relates Canadian standards to USEPA and Florida standards and guidelines. The course is a discussion class graded on the S/U basis. Outcomes: When students complete this course, they can ascertain how water quality relates to fish production/community structure, fish health/kills, and fish contamination/human consumption issues.  Course Syllabus and Class Materials

FAS 6932 Introduction to Fish and Shellfish Histological Interpretation
Description: This class introduces graduate students to the basic histology of fish, bivalves, and shrimp, and demonstrates some common histopathology associated with these organisms.  We are using the hybrid striped bass, pinfish, and common carp as our fish models, but other species will be included as needed. Outcomes: Students who successfully complete this course will be able to understand basic routine histological processing; understand how to perform a thorough necropsy, how gross anatomy correlates with microscopic anatomy, and the relevance of histology for research and diagnostic work; identify normal micro-anatomical structures and their functions for a number of different aquatic vertebrate and invertebrate species; understand common physiological and patho-physiological processes and how they alter microanatomy; and learn how to approach the microanatomy of other species based on similarities and differences between those studied in class.  

FAS 6932 Conservation Genetics [Spring, Odd Years, 2 credits, Prerequisite: undergraduate  courses in genetics and evolution, cross-listed with WIS 6934] Description: This course provides students with a basic understanding of population genetic processes and focuses on the use and application of genetic methods in wildlife/fisheries management and species recovery. The course will be based in part on lectures, focusing on reviewing the basics of population genetics. Students will also present assigned papers and leading class discussions on particular topics. Major objectives are to: review aspects of population genetics as they apply to conservation/management; discuss the relative importance of genetics in conservation, with respect to the maintenance of evolutionary potential, avoidance of inbreeding; review methodologies for characterizing genetic diversity; and valuate the role of genetics in developing conservation strategies. Outcomes: This course will provide students with a comprehensive understanding of basic population genetic principles and an ability to create an informed opinion on the application of molecular genetics to management and conservation issues.

FAS 6932 Invasion Ecology of Aquatic Animals [Spring, Even Years, 3 Credits, Prerequisite: instructor consent] Description: This course will provide a comprehensive overview of the field of invasion ecology and will emphasize aspects related to aquatic animals. Through lectures, readings, discussions, and invited expert speakers, students will be presented the ecological concepts and debates underlying this developing field; the biology and life history of nonnative aquatic animals, including characteristics of successful invaders (emphasis on Florida); risk analysis methodology; and the conservation and regulatory implications of nonnative aquatic species. Outcomes: After taking this course, students will be expected to have a strong familiarity with the concepts associated with species invasions; to be able to use basic risk assessment methodology; to think critically to evaluate literature and arguments, especially when faced with uncertainty and scientific disagreement; to more effectively communicate orally in small groups of peers and in scientific writing; to develop an appreciation for the complex relationship between science, management, and regulation; and to work effectively with colleagues.

FAS 6932 Ecological Statistics and Design [Fall, Even Years, 3 Credits, Prerequisite: STA 6166 or FAS 5335C or instructor consent] Description: This course gives students experience in real-world sampling design and data analyses.  At its core, this is a statistics class and much of the focus is on specialized statistical design and analysis approaches that are frequently used in forestry, fisheries, and wildlife research.  Topics include applied regression, mixed models, ANCOVA, and repeated-measures analysis.  Additionally, analysis tools including a variety of resampling methods, non-linear modeling, indices assessment, and capture-recapture methods will be explored.  Each topic is complimented by both a lab exercise analyzing data sets and a weekly discussion focused on classic and contemporary analysis issues in ecological statistics.  This class is unique in that it is team taught by faculty from FAS, FOR, and IFAS-Stat with each faculty member bringing a unique perspective to the course. Outcomes:  Students completing this course will be capable of designing studies and analyzing a diverse array of data types that are common in ecological studies.

FAS 6932 Fisheries Ecology and Management [Fall, Even Years, 4 Credits, Prerequisite: FAS 6337C or instructor consent] Description:  This course is an advanced graduate course on fisheries stock assessment and management.  This course focuses on modern stock assessment models and why these methods work, why they sometimes fail, and how they can be improved and used in evaluating fisheries management decisions.  Students construct a variety of stock-assessment models and evaluate the performance of these models using both simulated and real data from a variety of global fisheries. Outcomes: Students completing this course will be experienced in the latest fisheries stock assessment and modeling methods. Students will be able to critically evaluate existing stock assessment programs and to identify data needs that will be informative in developing effective fisheries management policies.  Course Description and General Information

FAS 6932 Fisheries Ecology and Management II [Fall, 2007, 3 Credits] Description: The aim of this course is to provide students with concepts and methods needed to work effectively as a consultant or government scientist on common problems in applied fish biology. These problems range from analysis of fish habitat and population status in relation to conservation and environmental management issues, to fish stock and ecosystem assessment needed for sustainable harvest management. The course is organized as two meetings each week, a two-hour lecture on a broad topic then a one-hour tutorial or lab/field session to demonstrate specific methods of data gathering and analysis on the topic. Most of the tutorial sessions are computer-based “laboratories” where students will learn spreadsheet and other methods for data analysis. Course Description and General Information.

FAS 6933 Seminar. Credits: 1, maximum 3, S/U. Student seminar presentation associated with graduate degree requirements.

FAS 6935 Critical Readings in Fisheries and Aquatic Sciences [Fall, Spring, 2 Credits]
Description: Students critically read documents dealing with aquatic science and collegially debate their merits. Through practice, students will hone their critical thinking skills and their ability to handle verbal question-and-answer situations. Outcomes: Critical Reading in Aquatic Sciences primarily targets the competencies of project management (especially identifying “good” hypotheses and formulating valuable questions), application of the scientific process, critical thinking and effective communication. Achieving five objectives will foster these competencies: read broadly in the primary literature; demonstrate the value of drawing from diverse disciplines to design and implement scientific projects; exercise the skills needed to critically evaluate primary literature according to the scientific process; formulate well-reasoned arguments and defend them; and lead and engage in productive collegial discussions and debates with confidence.

FAS 6940 Supervised Teaching. Variable credits (1 - 5), maximum 5, S/U.

FAS 6971 Research for Master’s Thesis. Variable credits (1 – 15), S/U.

FAS 7979 Advanced Research. Variable credits (1 – 12), S/U.  This is research for doctoral students before admission to candidacy. It is designed for degree in the field of study or for students who have been accepted for a doctoral program. Not open to students who have been admitted to candidacy.

FAS 7980 Research for Doctoral Dissertation. Variable credits (1 – 15), S/U.

Supporting Courses: Courses taught in other departments which may be valuable for FAS students.