Academic Course Catalogs

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Master of Science in Marine Science

Ronald S. Kaufmann, PhD, Graduate Program Director, Associate Professor, Pelagic and Benthic Ecology
Michel A. Boudrias, PhD, Associate Professor, Locomotion, Benthic Ecology
Hugh I. Ellis, PhD, Professor, Avian Physiological Ecology, Waterbirds
Sarah C. Gray, PhD, Associate Professor, Paleoclimatology, Sedimentology
Mary Sue Lowery, PhD, Professor, Fish Biochemistry and Muscle Development
Bethany O’Shea, PhD, Assistant Professor, Environmental Geochemistry
Nathalie B. Reyns, PhD, Assistant Professor, Biophysical Dispersal of Larvae, Fisheries Oceanography
Drew M. Talley, PhD, Assistant Professor, Coastal Ecology, Habitat Connectivity
Zhi-Yong Yin, PhD, Professor, Hydroclimatology, GIS and Remote Sensing

Affiliated Faculty

Frederick I. Archer, PhD; Population Genetics and Delphinid Fisheries (Southwest Fisheries Science Center)
Lisa T. Ballance, PhD; Cetacean and Seabird Ecology (Southwest Fisheries Science Center)
Ann B. Bowles, PhD; Bioacoustics (Hubbs-SeaWorld Research Institute)
Mark Drawbridge, MS; Fish Hatcheries and Aquaculture (Hubbs-SeaWorld Research Institute)
Michael G. Hinton, PhD; Pelagic Ecology, Population Ecology, Statistics (Inter-American Tropical Tuna Commission)
Thomas G. Kretzschmar; Hydrogeology (Centro de Investigacion Cientificas y de Enseñanza Superior de Ensenada)
N. Chin Lai, PhD; Physiology of Fish (Veterans Administration; UC San Diego)
Russell D. Vetter, PhD; Ecology, Evolution, and Molecular Biology of Fishes (Southwest Fisheries Science Center)

USD’s Department of Marine Science and Environmental Studies offers graduate work leading to the degree of Master of Science in Marine Science. This degree is based largely on research and is intended to provide graduate students with an opportunity to design experiments or observations that test hypotheses; to contribute new information to a knowledge base; and to learn to write in a way that facilitates scientific exchange. The program, which combines coursework and research, culminates in a written thesis. The program utilizes not only the excellent facilities at the University of San Diego’s Shiley Center for Science and Technology, but those of some nearby institutions, such as the Southwest Fisheries Science Center (National Marine Fisheries, NOAA), Hubbs-SeaWorld Research Institute, and the Leon R. Hubbard Hatchery. Thesis committees may be headed by faculty listed on this page, as well as other scientists on and off campus. Committee members are drawn from the Marine Science faculty at USD, other science departments at USD, and senior research scientists at Southwest Fisheries Science Center, Hubbs-SeaWorld Research Institute, and several other institutions. Students are encouraged to have one outside member on their thesis committee in order to take advantage of San Diego’s rich community of ocean specialists.

USD faculty currently are involved in research in environmental geochemistry, climatology, paleoclimatology, hydrology, oceanography, marine biology, locomotion and fluid dynamics, physiology, ecology, and population genetics. Affiliated marine science faculty work in the areas of bioacoustics, fisheries, aquaculture, molecular genetics, hydrogeology, ecology, and physiology. Although there are opportunities for graduate students who are interested in biology to work with a variety of invertebrate and vertebrate animals, as well as a more limited number of plants, applicants should think carefully about the functional areas of biology they wish to work in. Whether in the life sciences or physical sciences, local research opportunities abound: from the coasts and estuaries of San Diego County to offshore and island environments. The deserts of southern California, which include inland water bodies and former ocean basins, offer additional research possibilities. In some instances, research may focus on more distant areas. More information about faculty interests, graduate student thesis titles, and facilities is available through our website.

The Master of Science in Marine Science degree can serve as a terminal graduate degree prior to entry into the work force, an enhancement of skills for an existing job in a technical area or in education, or a step toward a PhD.

Recommended Program of Study

First Year

Semester I Semester II
MARS 500 (2) MARS 501 (3)
MARS 510 or 511 (4) MARS 512 or 513 (4)
Elective (3) MARS 596 (2)

Second Year

Semester I Semester II
MARS 520 (3) MARS 512 or 513 (4)
MARS 596 (6) MARS 596 (4)
  MARS 597 (1)

Requirements for the Degree

I. Coursework (23 units)

MARS 500 Core Seminar I (2)
MARS 501 Core Seminar II (3)
MARS 520 Statistics (3)
Graduate Elective (3)

Three of:
MARS 510 Oceanography I (4)*
MARS 511 Oceanography II (4)*
MARS 512 Oceanography III (4)*
MARS 513 Oceanography IV (4)*
*Depending on student’s previous coursework, one or more of the MARS 510-513 series may be waived.

II. Thesis (minimum 9 units)

MARS 596 – Research (0.5*-6)
A maximum of 12 units may count toward degree
MARS 597 – Thesis (0.5*-1)
A minimum of 1 unit must be applied toward degree
*Students may take these courses for 0.5 unit only after they have completed 32 units in the graduate program.

III. Electives or Additional Research (4 units)

Four additional units, consisting of elective courses (approved by thesis chair), Research (MARS 596), or a combination

IV. Minimum Units

The minimum number of units required for graduation is 32; however, if three courses from the MARS 510-513 series are taken, the total units will add to 36.

A thesis committee of at least three members will be established during the second semester of enrollment. It will consist of at least one full-time USD faculty member and may include members from approved outside institutions. The entire thesis committee will meet with the student semi-annually to assess progress and give advice. Following approval of the thesis proposal by both the thesis chair and the graduate director, and satisfaction of any deficiencies noted at the time of admission to the program, the student will be recommended for candidacy by the thesis committee. Adequate progress will need to be made to maintain candidacy (see candidacy policy, available from the graduate director). Additional courses related to the student’s area may be required by the thesis chair (see also Thesis, page 68). All students must be enrolled for at least 1 unit to remain active in the program. Students who have completed all program requirements except MARS 597 (Thesis), including all required courses, may enroll in 0.5 unit to remain active in the program.

Courses and Seminars


An introduction to the infrastructure of the Marine Science graduate program and to those critical skills useful in graduate studies. Students will be exposed to a range of research areas through a series of seminars presented by the Marine Science faculty, allied university faculty in other departments, and scientists from other institutions. Students also will choose a thesis committee chair and develop a written preliminary plan for their own research in pursuit of the master’s degree.


During this seminar, students will learn how to develop questions that can be tested scientifically, design experiments that are amenable to statistical analysis, and collect data that are interpretable. Students will write a formal thesis proposal, which includes a review of pertinent literature, and present it orally to the assembled Marine Science faculty. They also will form their thesis committees. Successful completion of this seminar is a prerequisite for advancement to candidacy.


The origin and geologic history of the ocean basins, with a detailed investigation of the theory of plate tectonics, ocean sedimentation, and paleoceanography. Examination of how geological processes affect physical, chemical, and biological processes in the ocean will be emphasized. Students will present and discuss primary literature pertinent to the topics covered in the course. Three lectures and one laboratory per week. One cruise and one additional weekend field trip may be required. Prerequisites: a course in introductory geology, with laboratory, is recommended.


Biological oceanography is covered from an integrated, functional perspective. Unifying themes will be factors that affect marine ecosystems and the relationship between environmental characteristics and biological communities. Nearshore, open ocean, and deep sea environments will be covered. Ecological, behavioral, physiological, and biochemical adaptations of marine organisms also will be considered. Primary literature, scientific writing, and experimental design will be emphasized. Three lectures and one laboratory per week. One cruise and additional field work may be required. Prerequisites: one year of general biology, with laboratory.


Why are the oceans salty? This course begins by tracing the path of material sources to the ocean reservoir; from river, groundwater, atmospheric, and hydrothermal vent pathways. A significant emphasis is placed on chemical processes operating within the ocean reservoir, such as carbonate equilibrium, trace element distributions in sea water, and particulate matter reactivity. The course concludes with an analysis of geochemical processes occurring within material sinks in the oceans, which are largely controlled by sediment redox and diagenetic processes. Three lectures and one laboratory per week. Prerequisites: one year of general chemistry, with laboratory.


This course is intended to introduce students to the fundamentals of marine community ecology, provide students with field experiences so that they may become familiar with various ecological sampling designs and methods, and expose students to the diversity of coastal marine environments in the San Diego area. Students will read and discuss classic marine ecology papers, and conduct marine ecological studies in field and laboratory settings. Students will also be required to participate in a semester-long research project. Prerequisites: an undergraduate course in ecology or consent of instructor.


This course is intended to build on a basic understanding of statistical analysis gained at the undergraduate level. The course will review methods of hypothesis testing and the statistical tests most commonly used in oceanography. It will introduce multivariate techniques and modern non-parametric methods. The main emphasis will be experimental design and choosing the most appropriate methods of statistical analysis to answer specific questions. Students will learn how to use the statistical software package SPSS and will have the opportunity to work with their own data, if applicable. Three hours per week. Prerequisite: an undergraduate course in statistics or consent of instructor.


An introduction to the theory, development, and operation of the electron microscope with emphasis on development of knowledge of cellular fine structure. The laboratory portion of the course will focus on tissue preparation, microscope operation and evaluation, and presentation of electron microscopic data.


Course examines the various aspects of ichthyology encompassing the anatomy, physiology, ecology, evolution, ethology, and natural history of fishes. Lab includes techniques of identification and a general survey of fish systematics and zoogeography. Prerequisite: BIOL 300 or equivalent.


An examination of the biology of whales, pinnipeds, and other marine mammals. Topics will include general adaptations to a marine existence; systematics and biogeography; reproduction; diving physiology; communication and echolocation; feeding and migratory behavior; and marine mammal-human interactions. Some emphasis will be placed on species occurring in the North Pacific Ocean. Necropsies of a beach-stranded marine mammal may occur. Special projects will also be assigned. Three hours of lecture per week. Prerequisites: one year of introductory biology and at least two upper-division courses in zoology or ecology, or consent of instructor.


This course explores the biology of organisms inhabiting the deep ocean, especially as their biology is influenced by the environment in which they live. Topics will include the physical, chemical, and geological setting; instrumentation used in deep-sea research; the systematics and ecology of deep-sea fauna; physiological and biochemical adaptations to the conditions in the deep ocean; and impacts of humans on the deep-sea environment. Three hours of lecture per week. Prerequisites: one year of introductory biology and at least two upper-division courses in ecology or zoology, or consent of instructor.


A course to cover principles of climatology and methods of climatic data analysis. The fundamentals of climatology, methods and technologies used in acquiring and analyzing climatic data, and current issues such as human-induced climatic changes will be discussed. This course will cover the Earth’s energy budget and temperature, moisture in the atmosphere and precipitation, winds and the general circulation, and climates in different regions of the world. Three lectures and one laboratory per week. Prerequisites: a course in meteorology or earth science and a course in statistics, or consent of instructor.


A survey of the history of the earth system focusing on ocean-atmosphere-ice sheet dynamics and their interaction on past global climate change. Topics include geologic record of past climate cycles, causal mechanisms of past climate change, and the scientific basis of global warming. Three hours of lecture per week. Prerequisites: MARS 510 or 512, or consent of instructor.


A laboratory course designed to introduce students to methods and techniques used in historical geology and paleoclimatology including: a) identification of depositional environments; b) identification of invertebrate fossils and modes of fossilization; c) correlation and sequence stratigraphy; d) radiometric dating; and e) isotopic proxies of climate. The laboratory may include field trips. Prerequisites: MARS 510 or 512, or consent of instructor.


An introduction to remote sensing technology and its applications in earth science. This course will cover principles of remote sensing, aerial photography, photogrammetry, electronic multispectral imaging, and methods of digital imaging processing and analysis. Applications of remote sensing in marine and terrestrial environments and integration of remote sensing and geographic information systems also will be discussed. Three lectures and one laboratory per week and some field trips. Prerequisites: at least one course in GIS and at least one physical science course, or consent of instructor.


This course will provide an in-depth examination of the geological principles and issues pertinent to the environmental consulting industry. It will include a discussion of geologic hazards, including floods, mass wasting, earthquakes, and erosion. An examination of the geology of groundwater occurrence, groundwater flow, and groundwater development and management also will be addressed. Specific examples from the San Diego region will be emphasized. Three lectures and one laboratory per week. Prerequisites: a course in introductory geology, with laboratory, or consent of instructor.


A course to cover principles of surface water hydrology and methods to solve hydrologic problems related to urbanization, soil and water conservation, and water resources management. The components of the hydrologic cycle and the concept of water balance will be discussed in detail. This course also will cover various methods of hydrologic computation, the basics of watershed modeling, applications of GIS in hydrology, and issues especially relevant to Southern California. Three lectures and one laboratory per week and some field trips. Prerequisites: a course in introductory geology, with laboratory, or consent of instructor. An introductory course in statistics is recommended.


Topics of special interest or unique opportunity. Prerequisites may be listed for these offerings.


Specific sets of readings tailored to address particular needs of a student. Generally, this course would be related to the research interests of a student and would be under the guidance of a member of the student’s thesis committee. Typically, a maximum of 3 units may be used toward the degree requirements without consent of the director.

MARS 596 RESEARCH (0.5-6)

Research toward the master’s thesis. This research will be under the general supervision of a thesis advisor. No more than 3 units may be taken prior to candidacy. Pass/Fail only. A passing grade is contingent upon participation in the annual Graduate Student Colloquium during the same academic year. (Rules for taking 0.5 unit may be found on page 68.)

MARS 597 THESIS (0.5-1)

Independent writing of the thesis with consultation of the major advisor. Master’s candidates must be enrolled in this course to turn in a thesis. It may be taken more than once, but only 1 unit will be counted toward the degree requirements. Prerequisite: Consent of the major professor. Pass/Fail only. A passing grade is contingent upon participation in the annual Graduate Student Colloquium during the same academic year unless the student has successfully defended the thesis prior to the Colloquium. (Rules for taking 0.5 unit may be found on page 68.)

Undergraduate Courses

A maximum of six undergraduate units taken at the university may be applied to the graduate program. No course taken to fulfill an undergraduate deficiency may count toward the required units in the graduate program. The list below is not exhaustive; consult the graduate director. See the current Undergraduate Course Catalog for course descriptions.

BIOL 350 Invertebrate Zoology (4)
BIOL 364 Conservation Biology (4)
BIOL 416 Population Biology (4)
BIOL 460 Ecology (4)
BIOL 477 Invertebrate Physiology (3)
BIOL 478 Vertebrate Physiology (3)
BIOL 482 Molecular Biology (4)
CHEM 331 Biochemistry (3)
CHEM 355 Environmental Chemistry (3)
ENVI 315 Geographic Information Systems (3)

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