*Topics in Marine Ecology: Systematics of marine organisms

Course Overview: This course introduces students to the fundamental basics of systematics by allowing each student to develop an original systematics project and write it up for submission to a peer review journal. The student will learn the steps by which one goes about writing a systematic paper that will be submitted for publication in a peer-reviewed journal. The first third of the class is focused on identifying and developing a project, learning the basics of determining the identity of a species, how to use library and museum resources to verify the status of a species, and the steps to go about writing up a description. The latter two-thirds of the class concentrate on writing the paper with weekly discussions on the progress of the individual projects. Students are also required to make periodic presentations and participate in discussions of problems that may arise as they proceed through the various stages of writing their research paper. A final 20-minute presentation on their project will be given near the end of the semester and by the last day of class each student will submit their paper to a recognized peer review journal for publication.

Depending on their project topic, students may have the opportunity to name and describe a new species. In addition, each student should get a publication out of this course and may have the opportunity to present their findings at a professional society meeting such as Western Society of Naturalists, American Society of Ichthyologists and Herpetologists, American Elasmobranch Society.

Objectives: Students will learn the basics of alpha taxonomy and systematics, but as importantly will learn valuable skills in researching and writing up a project for peer review publication. Students will also learn important skills for communicating with editors, curators from major museum collections, interacting with established professionals, and others as they analyze and research their respective projects. Each student will have to develop a presentation that would be suitable for presenting at a professional conference.

Outcome from previous class: This course was last taught in the fall 2005. Each of the students submitted a manuscript with six of seven students having their papers published. Four of the papers were descriptions of new species. Five students have presented their papers at professional conferences with one winning an award at the 2006 Western Society of Naturalists meetings. Two students turned their projects into Masters Thesis projects.

Barnett, L.A.K., Didier, D.A., Long, D.J., & Ebert, D.A. 2006. Hydrolagus mccoskeri sp. nov., a new species of chimaeroid fish from the Galapagos Islands (Holocephali: Chimaeriformes: Chimaeridae). Zootaxa, 1328: 27-38.

Haas, D.L. & Ebert, D.A. 2006. Torpedo formosa sp. nov., a new species of electric ray (Chondrichthyes: Torpediniformes: Torpedinidae) from Taiwan. Zootaxa, 1320: 1-14.

Quaranta, K.L., Didier, D.A., Long, D.J., & Ebert, D.A. 2006. A new species of chimaeroid, Hydrolagus alphus sp. nov. (Chimaeriformes: Chimaeridae) from the Galapagos Islands. Zootaxa, 1377: 33-45.

Schaaf-DaSilva, J.A. & Ebert, D.A. 2006. A new species of lanternshark, Etmopterus burgessi sp. nov., (Squaliformes, Etmopteridae) from Taiwan. Zootaxa, 1373: 53-64.

Walsh, J.H. & Ebert, D.A. 2007. A review of the systematics of western North Pacific angel shark, genus Squatina, with redescriptions of Squatina formosa, S. japonica, and S. nebulosa (Chondrichthyes: Squatiniformes, Squatinidae). Zootaxa, 1551: 31-47.

*Chondrichthyan Biology

Course Overview: This 2-unit graduate seminar will entail ~2 hours in class per week for the 16 week semester.  After an introductory session, we will organize the seminar into weekly topics, some of which will involve visiting lecturers from other academic institutions. We will attempt to discuss as many aspects of chondrichthyan fishes (sharks, skates, rays, and chimaeras) as possible.  Subjects will include taxonomy, zoogeography, phylogeny, morphology, ecology/life history (feeding habits, age, growth, and demography), reproduction, habitat utilization, physiology, sensory biology, behavior, and genetics.

Students will be required to complete the assigned reading each week. Each student will also lead one or more discussion sessions on the topic for a given week, including a review of the reading material for that week (papers or text chapters).  The number of sessions run by a given student will depend upon the total number of students enrolled (estimates range from 6-10). To help the rest of the class more completely understand the topic under consideration, each student will be responsible to choose one or more representative articles for the entire class to read prior to the talk, some of which may already be on the suggested reading list for that topic. Each student discussion leader will make copies of their chosen paper(s) for every student in the class in sufficient time to allow them to read the paper (i.e. at least one week prior to the talk).

*Large Marine Ecosystems of the World: an integrated approach to understanding marine ecosystems

Course Overview: The popular approach being taken by regulatory agencies attempting to protect ocean resources is what has been termed an “Ecosystem Approach” to management.  Since 1984, the NOAA Fisheries Large Marine Ecosystems (LME) Program has been engaged in the development and implementation of an ecosystem-based approach to support assessment and management of marine resources and habitats. Governmental agencies and other grant funding sources are now requesting proposals to be in the context of an ecosystem perspective. Similarly, scholarly journals are also suggesting that authors present their research findings in the context of a broader ecosystem perspective.

The primary goal of this course is for you, the students, to be able to define an ecosystem-based approach, and be able to apply this concept to your own research.  Each student will be required to gain a level of familiarity with this concept through an independent class project.  In this project you will choose a “Large Marine Ecosystem” about which you 1) attempt to characterize and parameterize the individual biological and oceanographic components of the system paying particular attention to how these may define the boundaries of the ecosystem, 2) illustrate how the components act and interact with one another in the system, particularly if there are unique areas of biological/oceanographic significance that serve to characterize this region and its inhabitants as a “Large Marine Ecosystem”. It should be noted here that ecosystems could, and likely should, be ignorant of popular geopolitical boundaries that tend to define most studies due either to convenience or necessity.

*Topics in Marine Vertebrates: Advanced ichthyology

Course overview: The course will cover additional topics that could not be covered in Ichthyology, due to time limits, as well as some subjects in greater detail.  The actual subjects covered may be tailored to student interests, based upon conversations with students, and our own sense of what is needed by these same students in order to progress toward their various career goals.  Subjects we anticipate including are: muscle function (in conjunction with electromyography lab session; ventilation and respiration; energetics and activity (in conjunction with respirometry lab session; trophic analyses and feeding ecology, migration and movements, vision and communication (in conjunction with Pt. Sur field trip to use deep-sea animals to teach this system; reproduction and development; natal/nursery grounds (how are they defined? Plus determination by otolith/vertebral microchemistry – led in conjunction with Elkhorn slough field trip in late spring; recruitment; Ecosystem-based fisheries management; systematics.

Course format will be a lecture combined with readings from the primary literature.  Each week, the instructor(s) will lecture for 1 – 2 hours in preparation for the readings to be done that week.  The readings will be 3 – 4 topical or controversial, often opposing, papers from the recent peer-reviewed literature.  The following week, the papers will be discussed for 1 – 2 hours for the first half of class.  This will be followed by a lecture by the instructors, during the second half of class, preparing students for the following week’s readings.  Students will be asked to guide discussions of the papers on the various topics.  In this role, it is their job to be very familiar with the papers for that week, and likely additional background reading that they will need to locate themselves, and have a set of ideas for potential discussion at the ready.  It will be the role of the student to keep the discussion going and directed in a productive manner for the full 1 – 2 hours.  Students will be graded on their ability to do this, as well as their participation in all discussions.  In lieu of an examination students will be asked to write a paper about one of the subjects covered in class.  This may or may not be the same subject as that for the guided discussion.  Lectures by the instructors may be replaced by guest speakers if there is available expertise that can be utilized.  This will be accompanied by demonstration labs or field trips, as noted in the list of topics, but we do not anticipate a complete laboratory compliment to this course at this time as we could not hope to perform some of the techniques we plan to investigate.

Learning Outcomes will include an in-depth understanding of their own area of research.  This is, perhaps, the most important learning outcome. As part of this students will also gain additional experience with ichthyological topics outside their specific area of research from week to week.  However, we have also built in to the course opportunity to critically read and evaluate scientific literature, form and verbalize opinions about said literature, guide discussion, improve scientific writing skills, and prepare a scientific paper as though for publication.