Tropical Marine Ecology
SFS 3730
Syllabus, Spring 2016
Eliza N. Garfield, Ed.D.
Resident Lecturer in Marine Ecology
Office hours by appointment
The School for Field Studies (SFS)
Center for Marine Resource Studies (CMRS)
South Caicos, Turks & Caicos Islands
www.fieldstudies.org
© 2016 The School for Field Studies
Course Overview
Marine ecology is the study of how marine organisms interact with each other and with their
environment. In this course we will focus on the biogenic habitats that dominate tropical coastal areas,
i.e. mangrove forests, seagrass meadows and coral reefs, studying their biological and ecological
characteristics. We will also investigate the positive and negative anthropogenic impacts on the ecology
of marine organisms. Field exercises will be used to acquaint students with various marine organisms
and the techniques used to assess tropical marine habitats and biodiversity.
Learning Objectives
After completing this course, students should:
1. Understand the biological challenges of living in the marine environment.
2. Understand the ecological importance of mangrove, seagrass and coral reef habitats.
3. Be able to identify common marine macroalgae, seagrasses, mangroves, invertebrates and
vertebrates.
4. Understand the direct and indirect effects of Marine Protected Areas on marine communities.
5. Understand how pollution and climate change impact marine life.
6. Develop scientific skills in field work, data collection, analysis, and verbal and written presentation.
Case Study Foci
During the semester, the SFS program will use two case studies to frame our analysis and discussions,
each of which addresses specific issues:
Case Study I: The status of the marine resources that are currently considered important to the
ecological and socioeconomic well-being of the TCI. In the Marine Ecology course we will use Case Study
I to learn about marine organisms and the coastal habitats of the TCI.
Case Study II: Management strategies that assist in maintaining or improving the status of the marine
resources in the TCI and contribute to future economic development and diversification. In the Marine
Ecology course we will use Case Study II to learn about the potential value of Marine Protected Areas, as
well as the ecological threats associated with pollution and climate change.
Assessments
Assessment Item
Creature Feature Presentation (alone or in pairs)
Habitat Assessment Presentation and documentation
(group)
Marine Taxonomy ID exam (in 2 parts)
Case Study I final exam
Field Journal and Summaries (2)
Scientific Article Presentations (group)
AGRRA Research Proposal / Class Discussion
AGRRA Write Up
Case Study II final exam
TOTAL
2
Due Date
February 8, 9, 11, 12,15,18
February 15, 19, 23
Value (%)
10
15
February 25th
February 29th
February 29th, April 11
March 30, 31, April 1, 6, 7
March 31, April 7
April 11
April 11
15
10
15
15
5
5
10
100
Assessment Details
Students will be assessed in a variety ways during the Marine Ecology course. Rubrics, presentation
guidelines, and exam expectations will be clearly articulated.
In class presentations will be graded by the professor and your peers will be invited to give you and your
colleagues feedback. Field journal assessments will occur in journal workshops and at the mid-term. An
in-water taxonomy exam will give you feedback the next day, while the in-class portion will be graded as
quickly as possible. The written exams will be short answer and essays, requiring longer to read and give
you feedback on.
If at any time you feel you need more feedback on your performance or understanding the metrics you
are expected to achieve, please do not hesitate to come find me.
Lectures & field briefings are held at the Center. It is mandatory to attend all lectures and briefings.
PDFs of the lecture presentations will be provided to students via the Marine Ecology course folder on
the Student Drive; however, it is important to note that these slides only contain key points and
illustrations; it is essentially that students also take notes during lectures and background reading may
be necessary to support your learning.
Presentations
Students will be asked to make group presentations and lead discussions about throughout the
semester:
• Creature Feature
• Habitat Assessment
• Scientific Article
These presentations are designed to start with delivering simple facts (creature feature), progress to
presenting data and field work (Habitat Assessments), and finally to present experimental research and
findings from the scientific literature. In this process you are learning the elements of how scientists
present their work: in both spoken and written forms.
Creature Feature presentations (alone or in pairs) should include two things: factual taxonomic, habitat
and life history (life span, reproductive, predation etc.) information (posters around the center are just a
beginning) and be presented in the context of the habitats we are studying. Topics are in the syllabus as
“discussion” and should be the context and focus of all the creature feature presentations that day.
Active questioning and discussion by students not giving presentations are expected.
Habitat Assessment Presentations will be given by larger groups who will present their group’s findings
and then lead a whole class discussion. All groups of students should be ready to discuss their
assessments in the context of the one presented by the group that day. For example: Group A will be in
charge of presenting their Mangrove Assessment and leading the discussion that day. Groups B.C, and D
should have their data analyzed and in a document, from which they are ready to discuss any interesting
differences or similarities between their work and the presenting groups work. At the end of the
session: each group should hand in their data analysis and documents. Grades will be for the group.
Scientific article presentations and discussions will occur in the second half of the course. Groups will be
assigned to a collection of articles which they will need to then guide the class in discussing. Each
3
presenting group will meet with me before their assigned day to plan their presentations and
discussions. A variety of formats are possible - such as small group discussions, large group
presentations and workshop style.
Field Exercises
Marine Taxonomy exercise: In class, students will learn the taxonomic organization of life on earth,
along with the key characteristics of common marine taxa. During four field trips, students will observe
and document the macroalgae, flowering plants, invertebrate and vertebrate animals associated with
the marine habitats around South Caicos. Guide books and other resources will then be used to
scientifically identify these organisms and place them in their taxonomic hierarchy. Students will keep an
active field journal, prepare a final journal summary, and will be graded based on this report and an ID
exam. The knowledge gained during this exercise will be employed during subsequent Marine Ecology
and Resource Management field exercises, as well as during Directed Research.
Habitat Assessment exercices: Students will work in groups to collect data pertaining to the physical
and biological characteristics of mangrove, seagrass and coral reef habitats. We will employ well-known
techniques, which will provide students with field experience and know-how, which can be employed in
their Directed Research at SFS or during future opportunities elsewhere. Students are expected to keep
their field journals up to date thought the habitat assessment exercises and to prepare a final journal
summary of their work individually.
Marine Biodiversity exercises: Students will conduct one day biodiversity assessments in various marine
habitats, then analyze their data.
Coral Bleaching, Health and Phase-Shift exercises: Students will learn to collect data using the AGRRA
and Coral Watch protocols relating to the health of coral colonies. A class briefing will explain the field
protocols and the database used to store collected information, and this will be followed by the in-water
collection of data at both dive and snorkel sites.
Field Journals
The Marine Taxonomy exercise is comprised of exploratory field and desk exercises in which students
observe, document and determine the taxonomic status of the marine organisms inhabiting the waters
around South Caicos. Students will be assessed through the completion of a field journal and an ID
exam. A rubric for the journals will be provided on the Z drive.
The Marine Habitat Assessment exercises will introduce students to the field techniques commonly
employed to study mangrove, seagrass, coral reef habitats and the biodiversity therein. These exercises
will be the basis for presentations and discussions in class, and group reports will be handed in. Students
should include journal entries on their assessment work, data collected, observations and show
evidence of developing ecosystem understanding. For example - a mangrove assessment will include
lots of measurements (data) and the analysis of that data is substantial. In addition, students should
spend time observing: where were you, what was the weather, did you notice anything unusual or
surprising while there, did birds come or go? etc…. And lastly, how does your time doing assessment
alter how you had thought of mangroves previously or through your reading?
The several citizen science exercises provide students with the opportunity to participate in on-going
field assessments of coral health, birds, and fish populations around South Caicos, using protocols from
4
around the world (e.g. Coral Watch Health Charts). Students are expected to enter data into global data
bases and share their data with each other as part of the habitat assessment work they will be doing.
They should also include citizen science work in their journals.
Exams
The written exams at the end of Case Study I and Case Study II are academically rigorous and will require
students to display an in-depth understanding of the material covered in class. While an understanding
of ecological concepts and processes is the main goal of this course, Marine Ecology involves a lot of
factual information and students are expected to retain such information.
Exams are given after each Case Study and are based on the lectures and readings from that Case Study.
PLEASE BE AWARE THAT YOU NEED TO PREPARE FOR YOUR EXAMS AS YOU PROGRESS THROUGH THE
COURSE. Sometimes the days before exams can be busy with other course activities/assignments. This is
logistically unavoidable, so please ensure that you make full use of the time available earlier in the
semester. YOU HAVE BEEN WARNED!
AGRRA Research Proposal, Class Discussion and Write Up
The Atlantic and Gulf Rapid Reef Assessment (AGRRA) survey protocol was designed to allow for a quick,
effective transect-based visual surveys of structural and functional conditions of coral reefs over large
areas. As a class, we will have been working up to the skill level necessary to do a final large scale reef
assessment with a particular eye on the fact we are living through the third global bleaching event.
Together students will design, propose and then execute surveys to assess the bleaching and potential
phase shifts occurring in the South Caicos reef ecosystem. This is the culminating field project of the
marine ecology course, and will complement the work occurring in the Directed Research course.
Grading Scheme
A
95.00 - 100.00%
A- 90.00 - 94.99%
B+
86.00 - 89.99%
C+
76.00 - 79.99%
D
60.00 - 69.99%
B
83.00 - 85.99%
C
73.00 - 75.99%
F
0.00 - 59.99%
B-
80.00 - 82.99%
C-
70.00 - 72.99%
General Reminders
Readings: Assigned readings will be available on the student server. It is important that you read all
materials before class since the volume of the material in the class requires a brisk pace. You are
expected to have read all the assigned articles, and demonstrate that by answering quiz questions based
on them. Anything contained in the readings is fair game for the exams.
Textbook: Goldberg, W. M. (2013). The Biology of Reefs and Reef Organisms. Chicago, The University of
Chicago Press.
Plagiarism and Cheating: Using ideas and materials of others without giving due credit is cheating and
will not be tolerated. A grade of zero will be assigned to anyone caught cheating or aiding another
5
person to cheat, either actively or passively (e.g., allowing someone to look at your exam). Unless
specifically stated otherwise, all assignments should be individual pieces of work.
Appropriate use of technology: SFS has worked hard to provide internet access to all its staff and
students. Inappropriate uses include gaming or excessive video/music downloading. No screens
(laptops/tablets/phones) are permitted during lessons unless otherwise dictated by faculty.
Inappropriate use will result in the loss of this privilege.
Deadlines: Deadlines for written and oral assignments are instated for several reasons:
1. Deadlines are a part of working and academic life to which students need to become
accustomed.
2. Deadlines promote equity among students.
3. Deadlines allow faculty ample time to review and return assignments before others are due.
As such, deadlines are firm and extensions will only be considered under the most extreme
circumstances. Late assignments will incur a 10% penalty for every day that they are late. This means an
assignment that is five minutes late will have 10% removed, an assignment that is one day and five
minutes late will have 20% removed, and so on. Every effort will be made to hand assignments back to
students after a one-week grading period.
Naming assignments: ***** All documents should be handed in in the appropriate ME folder on the Z
drive. ****** Five points will be deducted from each paper incorrectly labeled!!!!!!
1. Word documents, Excel documents, and PDFs for all individual assignments, exams, and reports
should be saved as…
FirstName_LastName_Assignment
Example…
John_Smith_Literature Review
2. Group assignments should be named…
Group#_Assignment
Example… Group1_DataAnalysis
Participation: Participation in all components of the program is mandatory, as there will be no spare
time to catch up on any missed classes. Missing even one lecture or discussion can significantly affect
the experience you and your classmates have while at CMRS. Within our teaching environment, there is
no reason to miss classes. You will get as much out of this course as you put into it, so please dive in. In
all circumstances, we expect you to respect yourself and your fellow students. Dissent and discord are
expected, but disrespect will not be tolerated.
6
Lectures, Activities, Readings, Exams
Type- L: Lecture, FEX: Field Exercise, E: Exam, EX: Exercise, P: Presentations
No.
Title - Content
Readings
Course Introduction
• Course components
• Assessments and dates
• Expectations
• Research opportunities
Field Journal:
• Canfield, Michael R., Field Notes on
Science and Nature, Chapter 1: The
Pleasure of Observing, Chapter 2: Why
Keep a Field Notebook?
On becoming a scientist:
ME01
(L, 1.0 hr)
• Wilson, E.O., Letters to a Young
Scientist, Chapter 1 First Passion, Then
Training, Chapter 4 What is Science?,
Chapt. 5 The Creative Process, Chapt.
13. A Celebration of Audacity, Chapt.
14 Know your Subject, Thoroughly
The Marine Environment
• Ocean zonation
• Physical and chemical characteristics
• Tides
• Ocean life
ME02
(L, 1.0 hr)
• Online Research: Ocean Zonation
Read:http://russgeorge.net/2014/07/21
/sahara-dust-produces-massivebahama-carbon-sink/
• Swart, P. K., A. M. Oehlert, G. J.
Mackenzie, G. P. Eberli and J. J. G.
Reijmer (2014). "The fertilization of the
Bahamas by Saharan dust: A trigger for
carbonate precipitation?" Geology
42(8): 671-674.
• Goldberg, The Biology of Reefs and
Reef Organisms, Chapter 1 & 13
ME03
(L, 1.0 hr)
Primary Production
• What is primary production?
• How does it occur?
• What organisms are responsible for
primary production?
• How and why does primary production
vary in space/time?
• Nybakken (2001) Marine Biology,
Primary Production: 55-93
• Tsuda et al. (2003). A mesoscale iron
enrichment in the western subarctic
Pacific induces a large centric diatom
bloom. Science 300: 958 - 961
Review: ME06 Mangrove and Seagrass
Biology (pdf)
Creature Feature Presentations I:
Birds (Aves), Seagrasses (Angiospermae)
and Mangroves
Discussion: Mangrove Habitats
ME04
(L & P, 1.0 hr)
7
No.
Title - Content
Readings
ME05
(L, 1.0 hr)
Evening
Taxonomy Exercise: Briefing
Introduction to the Taxonomy Exercise
ID Session: Mangrove and Seagrass
Communities - Eva Ramey Presents
• Brusca x2, Invertebrates, Chapter 2 Classification, Systematics and
Phylogeny
• Hogarth (1999 or 2010) The Biology
of Mangroves (and Seagrasses)
Chapter 2 & 3
ME06
(L, 1.0 hr)
Mangrove Forests & Seagrass Meadows
• Distribution
• Environmental challenges
• Adaptations
• Reproduction
• Ecological importance
Discussion of Articles
• Mangrove and Seagrass ID - PDF
• Valiela et al. (2001). Mangrove
Forests: One of the world's most
threatened major tropical
environments. Bioscience 51: 807815.
• Orth et al. (2006). A global crisis for
seagrass ecosystems. Bioscience 56:
987-996.
ME07
Discussion: Algae and associated fauna in
Mangrove and Seagrass communities
Creature Feature Presentations II:
Chlorophyta, Phaeophyta, Rhodophyta,
Chordata, Chondrichthyes (3 examples),
and Echinodermata (4).
Taxonomy Field Exercise I & II:
• Field Survey of local marine macroalgae,
segrasses and mangroves
Taxonomy Field Exercise III:
• Briefing (I hour lecture)
• Field Survey of invertebrates found in
local mangrove, seagrass and coral
habitats
• Hogarth (1999 or 2010) The Biology
of Mangroves (and Seagrasses)
Chapter 7
(P, 1.0 hr)
ME08
(FEX, 2.0 hr)
Taxonomy ID Session: Invertebrates,
• Queen Conch & Spiny Lobster
ME09
(L. 1.0 hr)
Evening
o
Biology
o
Taxonomy
o
Distribution
o
Anatomy
o
Reproduction
o
Growth
• Castro (2003). Marine Biology:
Chapter 7. Marine Invertebrates
• Species Profile Queen Conch,
Strobes Gigas, Megan Davis
• Stoner, Allan, Winter mass migration
of juvenile conch…….
• Queen Conch and Lobster PPT
• Bos, et al. Preliminary Observations
on Habitat Use of Juvenile Caribbean
Spiny Lobster (Panulirus argus) in
South Caicos, Turks & Caicos Islands
• George, R.W. Evolution of life cycles,
including migration, in spiny lobsters
(Palinuridae)
8
No.
Title - Content
Readings
Discussion: Invertebrates
• Review Castro Chapter 7
• What is an invertebrate?
ME10
• What are the major invertebrate phyla?
(P,L, 1.0 hr) • What ecological roles do invertebrates
perform?
Mangrove Assessment Briefing
ME11
(FEX, 3.0 hr)
ME12
(L, 1.5 hr)
Evening
ME13
(P, 1.0 hr)
ME14
(FEX, 3.0 hr)
• Review ME10 Marine Invertebrates
Creature Feature Presentations III:
Invertebrata, Cnidaria, Porifera,
Annelida
Mangrove Habitat Assessment:
Field application of mangrove survey
techniques
English et al. (1997). Survey Manual for
Tropical Marine Resources: Chapter 3.
Turtle Research Presentation and Marine
Sponges/Inverts ID Session - Claire
Gonzales and Eva Ramey
• Goldberg, Chapter 5 Reef Sponges
• Review: ME12 Reef Invert ID PPT
Discussion: Coral Reef Community Members • Goldberg, Chapter 3 (Cyanobacteria),
- Keystone Species, Top Predators, Ecosystem 4 (Reef Algae), 12 (Fishes)
Engineers
• Lewis, S., The role of herbivorous
Briefing of Seagrass Assessment
fishes in the organization of a
Caribbean reef community
Creature Feature Presentations IV:
Elasmobranchii, Actinopterygii (reef
schools, and coralivores), Arthropoda
Seagrass Assessment Exercise:
Field application of seagrass survey
techniques
Discussion: Corals as Living Ecosystems
relates to neighboring habitats
English et al. (1997). Survey Manual for
Tropical Marine Resources: Chapter 5.
Read:
• Kopp et al (2007) Diel differences in
fish assemblages…..
• Huijbers et al (2008) Post-larval grunts
distinguish between seagrass,
mangroves ……
Creature Feature Presentations V:
ME15
(P, 1.0 hr)
Actinopterygii (reef dwellers, and sand
dwellers), Octocorallia and Hexacorallia
ME16
(L, 1.0 hr)
Coral Reefs
• Distribution
• Types of coral reef
• Corals
• Other reef builders
• Goldberg, Chapter 6 & 14
• Suggested: Chapters 7 (anneldia), 8
Mollusca, 10 Crustacea
9
No.
Title - Content
Readings
ME17
(EX, 2.0 hr)
Student Presentations of Mangrove and
Seagrass Assessments
Workshop on Ecosystem Assessments
ME18
(EX, 1.0 hr)
Journal Workshop
Coral Taxonomy Briefing: Desk III
Identification of the corals that were
surveyed in the field
Humann (2006). Reef Coral
Identification; Florida, Caribbean,
Bahamas.
Taxonomy Briefing and ID Session:
• Humann (1996). Reef Fish
Identification; Florida, Caribbean,
Bahamas.
ME19
(L, 1.5 hr)
Evening
ME20
(FEX, 3.0 hr)
ME21
(L, 1.5 hr)
Fish ID - Lily Zhao
• Claydon, 2004
Taxonomy Exercise: Field IV
Coral and Fish ID
Taxonomy Briefing and ID Session: Coral
Species - Chris Casaclang
Goldberg, Chapter 11
Creature Feature Presentations VI:
Hexacorallia, Acroporidae, and
Echinodermata
(P, 1.0 hr)
Discussion: Scleractinia and Diadema
antillarium, a relationship between two key
reef species, phase shifts introduced
ME23
(L, 1.0 hr)
Fish and Coral Community Ecology 2
Emphasizing our unique opportunity to
collect data during Global bleaching event
Goldberg: Chapter 15 &16
Review Goldberg 12: The effects of
Feeding by Reef Fishes on Corals and
Coral reefs
ME24
(FEX, 3.0 hr)
Taxonomy Field Exercise IV
Coral and Fish ID
Coral Health Assessment Exercise:
• Exercise briefing (1 hour lecture)
• Field collection of data
• Database entry
Siebeck et al. (2006). Monitoring coral
bleaching using a colour reference card.
Coral Reefs 25: 453 – 460.
ME25
(P, 1.0 hr)
Coral Health Assessments, Bleaching
building our observation databases
Assessment Presentations
ME26
(L and
Workshop,
2.0 hr)
Marine Biodiversity
TBD
• What is biodiversity?
• How is biodiversity assessed
• What are the spatial trends in biodiversity
• Biodiversity Exercise
• In-class biodiversity calculations using
various diversity indices
ME22
10
No.
Title - Content
ME27
(FEX, 3.0 hr)
ME28
(P, 1.0 hr)
ME29
Readings
Marine Biodiversity Field Exercise:
In groups students will collect data and
calculate biodiversity indices for 4-5
subjects (Birds, Invertebrates, Fish, Plants,
Corals)
Debriefing and Discussion
Review of species identified from field
surveys
Marine Biodiversity Presentations:
David Attenborough Film and Discussion:
(P, 1.5 hr)
Rise of the Animals: Triumph of the
Vertebrates
ME30
(E, 2.0 hrs)
Taxonomy Exercise: Exams
In-class ID exams on (1) macroalgae, (2)
corals, (3) other invertebrates, (4) fishes
Field Exams on (1) macroalgae, (2)
corals, (3) other invertebrates, (4) fishes
ME31
(L, 1.0 hr)
Case-Study I Final Exam
In class
Journals Due
ME32
(L, D 1.0 hr)
ME 33
All Day
Introduction to Case Study 2
Citizen Science Field Exercises:
Introduction
ME34
(L, 1.0 hr)
Ecological Effects of MPAs
• Direct effects
• Indirect effects
• Ecosystem functioning
• Lester et al. (2009). Biological effects
within no-take marine reserves: a
global synthesis. Marine Ecology
Progress Series 384: 33 – 46.
See Folder on Z drive for articles to be
discussed.
ME35
(L, 1.0 hr)
Fishery Effects of MPAs
• Spillover
• Egg and larval export
• Protecting vulnerable life stages
• Sale et al. (2005). Critical science gaps
impede use of no-take fisheries
reserves. Trends in Ecology and
Evolution 20: 74-80.
See Folder on Z drive for articles to be
discussed.
ME36
(L, 1.0 hr)
MPAs and Larval Ecology
• Indirect development
• Dispersal
• Currents
• Retention and connectivity
• Settlement
AGRRA research proposals due
See Folder on Z drive for articles to be
discussed.
11
No.
Title - Content
Readings
Phase Shift and Bleaching Assessments
Introduction of AGRRA protocols
Coral Reef Final Field Exercise I:
ME37
(FEX, 3.0 hr)
• Rogers & Miller (2006). Permanent
'phase shifts' or reversible declines in
coral cover? Lack of recovery of two
coral reefs in St. John, US Virgin
Islands. Marine Ecology Progress
Series 306: 103-114.
• Review: Goldberg Chapter 16
• English et al. (1997). Survey Manual
for Tropical Marine Resources:
Chapter 2.
• AGRRA Protocols
ME38
(L, 1.0 hr)
Human Impacts on the Marine
Environment
Pollution, Habitat alteration, Threatened
and endangered species
ME39
(L, 2.0 hr)
Climate Change and Marine Organisms
• Temperature effects
• Water circulation
• Climate change in the Caribbean region
Hoegh-Guldberg & Bruno (2010) The
impact of climate change on the world’s
marine ecosystems. Science 328: 15231528.
ME40
(L, 1.0 hr)
Ocean Acidification: What is ocean
acidification? How does ocean acidification
affect marine organisms?
See Folder on Z drive for articles to be
discussed.
ME41
(L, 1.0 hr)
Planning for the long term: Restoration,
Recovery and Recovery of Ecological
Originality
Discussion: Phase Shift and Endangered
ME42
Species
(L & D, 1.0 hr)
ME43
(FEX, 3.0 hr)
Coral Reef Final Field Exercise II:
Field application of AGRRA coral reef survey
techniques related to bleaching
ME44
(L, 1.0 hr)
Case-Study II Review
A review of the topics covered during CaseStudy II, Description of the Case-Study II final
exam
ME 45
64.0 hrs
See Folder on Z drive for articles to be
discussed.
Acropora Recovery Plan, NOAA
Students Discussion of Phase Shift
Assessments, AGRAA surveys of coral
health and bleaching
AGRRA Write Ups Due
Journal Summary Due
Final Exam Due
TOTAL CONTACT HOURS
12