Morgan, Katy

English

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University of New Orleans 
ScholarWorks@UNO 
University of New Orleans Syllabi 
Fall 2015 
BIOS 5534 
Katy Morgan 
University of New Orleans 
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This is an older syllabus and should not be used as a substitute for the syllabus for a current 
semester course. 
Recommended Citation 
Morgan, Katy, "BIOS 5534" (2015). University of New Orleans Syllabi. Paper 124. 
https://scholarworks.uno.edu/syllabi/124 
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Conservation Biology  
BIOS 5534 
Fall 2015 
 
 
Instructor: Dr. Katy Morgan 
Office: Biology Room 103 
Phone: 280-1365 
Email: nanthony@uno.edu 
Office hours: Tuesdays, Wednesdays and Thursdays 1.00 – 3.00 pm, or by appointment 
 
SECTION I: The Basics.  
 
This section will cover the general concepts of conservation biology and examine how the basic 
principles of genetics, ecology and evolutionary biology are applied to conservation practice.  
 
Week 1: General introduction to conservation biology (August 19, 21)     
 
a)   Scope of the course 
b)   What is conservation biology? 
 
Groom: Chapter 1; Chapter 2 pp. 27-39 
LAB: Critical analysis of a scientific paper. 
 
Week 2: Conservation genetics (August 24, 26, 28) 
       
a)   Questions that can be addressed with genetic tools 
b)   Quantifying genetic variation 
c)   Principles of population genetics 
d)   Bottlenecks and inbreeding 
 
Groom: Chapter 11 
LAB: Population genetics of small populations using POPULUS and calculation of inbreeding 
coefficients in a captive bat population [AMNH exercise] 
 
Week 3:  Taxonomy, phylogeny and conservation units (August 31, September 2, 4)  
     
a)   Taxonomy and classification 
b)   Phylogenetic systematics 
c)   Evolutionary significant units (ESUs) 
d)   Applications to conservation 
 
Futuyma: Chapter 5: pp. 87-98 
Ridley: Chapter 15: pp 423-449; Chapter 16: 471-474. 
LAB: Sequence alignment and phylogenetic analysis with MEGA  
 
LABOR DAY HOLIDAY September 7th 
** No class ** 
 
Week 4: Population biology and applied demography (Sept 9, 11)     
 
b)    Definition and study of populations 
c)    Estimation of animal densities 
d)    Basic demography 
e)    Models of population growth 
 
Krebs: Chapter 9: pp 116-132; Chapter 10: 133-149. 
LAB: Line transect census sampling methods at Lafitte National Park (field excursion) 
September 11th 
 
Week 5: Species biodiversity (Sept 14, 16, 18)        
 
d)    Species concepts 
e)    Measuring species diversity 
f)    Global patterns of species richness 
g)    Assigning conservation priority 
 
Groom: Chapter 2 pp 39-62; Chapter 6 pp 197-200 
LAB: Analysis of field data collected at Lafitte using DISTANCE 
 
Week 6: Community and ecosystem diversity (Sept 21, 23, 25) 
         
a)   Communities and ecosystems 
b)   Ecosystem functions and services 
c)   Species versus ecosystem approaches 
d)   Ecological consequences of extinction 
 
Groom: Chapter 13 
LAB: Canoe trip to Pass Manchac. Field excursion September 25th 
 
**** MID-TERM MONDAY September 28th**** 
 
SECTION II: Extinctions past and present.  
 
This section explores the problems inherent to small populations and examines factors contributing to 
the current biodiversity crisis. 
 
Week 7: Extinction (September 30, October 2)      
 
a)    Extinction as a historical process 
b)    The biodiversity crisis and major threats 
c)    The concept of rarity  
d)    Why some species are more susceptible to extinction 
 
Groom: Chapter 3 
LAB: Threat analysis using the IUCN red data book database 
 
 
Week 8: Population viability analysis (Oct 5, 7, 9)     
 
a)    Minimum viable populations 
b)    Genetic, demographic and environmental stochasticity 
c)    Vortex: modeling the probability of extinction 
d)    Case studies 
 
Groom: Chapter 12 pp. 419-435 
LAB: Population viability analysis using VORTEX 
 
Week 9: Ecosystem fragmentation and loss (October 12, 14)      
 
a)   Ecosystem degradation and loss 
b)   Environmental pollution  
c)   Fragmentation and its effects 
d)   Biological impacts of climate change 
 
Groom: Chapter 6 pp173-196; Chapter 7  
LAB: None 
 
***** FALL BREAK: OCTOBER 15-16 ****** 
 
SECTION III: Conservation management applications 
 
This section will explore several important applications to conservation theory and the major 
challenges that conservation managers face. Topics include population viability analysis, management 
of captive populations and species reintroductions, sustainable use of natural resources, invasive 
species management and reserve design.  
 
Week 10: Applied population management (October 19, 21, 23)      
 
c)    Management of captive populations 
d)    Re-introduction and translocation 
e)    Ex situ conservation strategies 
f)    Reproductive technologies 
 
Primack: Chapter 13, 14. 
LAB: Field trip to the Audubon Centre for Research on Endangered Species (ACRES) Field 
excursion October 23. 
 
Week 11: Sustainable management of natural resources (October 26, 28, 30)    
 
a)   Over-exploitation and the tragedy of the commons 
b)   Sustainable harvesting 
c)   The bushmeat crisis in central Africa  
d)   World fisheries  
 
Groom: Chapter 8 
LAB: VORTEX group work 
 
Week 12: Invasive species management and wildlife diseases (November 2, 4, 6)    
 
a)    What is an invasive species? 
b)    Ecology and management of invasive species 
b)    Emerging infectious diseases 
c)    Discussion of case studies 
 
Groom: Chapter 9 
LAB: Using MAXENT to model predicted species distributions  
 
Week 13: Protected area design and selection (November 9, 11, 13)    
    
c)    Habitat islands and island biogeography  
d)    Principles of reserve design 
e)    Protected area selection  
f)    Ecological restoration 
 
Groom: Chapter 14; Chapter 15 pp 553-565 
LAB: VORTEX group work  
 
SECTION IV: The bigger picture.  
 
This final section will address the economic and societal implications of conservation and examine 
species and ecosystem protection in the domestic and international arena.  
 
Week 14: Conservation law and policy (November 16, 18, 20)      
 
a)   U.S. Environmental Law 
b)   The Endangered Species Act 
c)   Habitat conservation planning 
d)   Major international treaties 
 
Van Dyke: Chapter 2: pp 28-52 
LAB: Negotiating an international treaty 
 
Week 15: Climate change (November 23, 25) 
 
a)   Inter-Governmental Panel on Climate Change 
b)   Current and projected change across the world 
c)   Implications for species and ecosystem conservation 
d)   The way forward 
 
THANKSGIVING BREAK NOVEMBER 26, 27 
 
Week 15: Presentation of group VORTEX projects (November 30, December 2, 4) 
LAB: Group presentations and wrap up 
 
*******************FINAL EXAM****************** 
Grading 
 
Mid-term exam:   15 % 
Final exam: 15 % 
Class participation/discussion: 10 %  
Lab exercises    20 % 
Group research project:  20 % 
Individual presentation: 10 % 
Conservation policy brief 10% 
 
Grading and course policies 
 
Your grade will be based on the seven items listed above. The following is an indication of how grades 
will be assigned: 
 
90% and above A 
80-89%  B 
70-79%  C 
60-69%  D 
Below 60%  F 
 
Assigned homework MUST be handed in on the appointed day or a grade will be docked off your score 
for each day past the due date. Exceptions will only be made in the case of an excused absence due to 
extenuating circumstances or illness.  
 
Assigned text book readings and exams  
 
The OPTIONAL text for this course is Principles of Conservation Biology by Martha Groome, Gary 
Meffe and Ronald Carroll (third edition). The text in these books is intended as a reference source and 
a copy will be made available through Moodle. Supplementary reading for weeks where there is no 
reference book chapter will be made available to the class a week in advance via Moodle. For both 
exams (mid-term, final) you will be tested on material covered in class and lab but you may also be 
tested on material from the assigned readings and articles discussed in class. 
 
Discussion of the primary literature 
 
You will also be required to read and discuss at least one article from the primary literature each week. 
The relevant pdf will be made available through the Moodle website a week in advance of the 
discussion period. Students are expected to have read the assigned article before class and should be 
able to demonstrate that they have read the assigned readings and are prepared with comments or 
questions. There will also be questions on these assigned readings in both the mid-term and final exam.  
 
Lab exercises and field trips 
 
A lab will be held once week to illustrate key concepts in lectures and to give students hands on 
experience in field work and working through modeling, data analysis and problem-solving exercises. 
Classroom exercises will either be based on: (i) database use and writing/discussion (ii) spread-sheet 
based exercises (iii) modeling exercises built around available software such as POPULUS, MEGA, 
VORTEX and MAXENT (iv) classroom exercises developed by the Center for Biodiversity and 
Conservation of the American Museum of Natural History (AMNH) or (v) field trips and analysis of 
data. The following two sources have also been used as inspiration for these exercises:  
 
Assignments will be handed out at the beginning of each lab and students will use the lab period to 
work through an assigned problem set or computer-based exercise. Students will be given a week to 
complete these exercises and hand them in for grading. This class will also involve some outdoor field 
work and class trips where a report of analysis of field collected data may be required, depending on 
the trip. If no analysis or report is required, an additional background reading relating to the field trip 
may be assigned.  
 
Group research projects and individual presentation 
 
Students will be asked to work together in small groups (3 students per group) on a research project 
that involves the use of simulation software (VORTEX) to conduct a Population and Habitat Viability 
Analysis (PHVA) of an endangered species of your choice. PHVAs are widely used by conservation 
professionals to predict extinction probabilities in endangered species. The software itself is very 
flexible and allows the user to model a wide range of realistic threat scenarios including natural 
catastrophes, habitat loss and hunting. Identification of focal species should be a group undertaking and 
group members are responsible for dividing up the necessary research and data analysis. Students will 
be encouraged to research the basic data for their model and draw from the available scientific 
literature resources.  
 
An outline of the group project and tasks of each member of the group must be submitted to me by the 
mid-term exam. Comments on this outline will then be given back to each research group as a guide for 
further research and data analysis. Assessment of group projects will be based on the final project 
report and the quality of each of the individual presentations. Grading for this project will be 20% for 
the final report and 10% for group presentations at the end of the semester. 
 
Conservation policy brief 
 
Everyone in the class will be required to give a five minute policy brief on a conservation issue you 
have read about in the local and national papers or in a magazine. In preparing your policy brief, you 
will also be expected to draw on information from one or two papers in the scientific literature that 
relate directly to this issue. You will then have a week to write up a one page presentation and provide 
evidence of your sources (e.g. citations). You can make your presentation anytime during the semester 
except the final week. In making your presentation, do NOT read what you plan to hand in but give an 
outline in your own words and make sure you keep your presentation to 5 minutes.  
 
Field trips 
 
Several field trips are planned for this semester. These trips may in some cases extend beyond the 
assigned lab time so please make sure you plan your return time accordingly. If you have problems 
please do consult me ahead of time. Equipment for these field trips will be provided although you 
should wear appropriate clothes for field work including sensible shoes, long pants, hat, sun screen and 
gloves. Detailed information for each field trip will be provided in class the week before.  
 
  
Additional assignments for graduate students enrolled in 5534 
 
Graduate students are expected to prepare a grant application within their area of study and prepare all 
of the elements required for a successful application. This grant application will include:  
 
(a)  Background and motivation for their proposed study 
(b)  Hypotheses and specific aims 
(c)  Methods and data analyses 
(d)  Description of expected results and the broader impacts of the study 
(e)  Budget and justification 
(f)   Time-line 
 
The instructor will work with the student on identifying suitable sources of funding and the format of 
the application. 
 
Learning goals: 
 
-   Understand the basic principles of conservation biology and evaluate how these principles are 
applied to problems in conservation  
-   Read the assigned literature and be able to critically assess the key concepts in a discussion and 
written format 
-   Demonstrate how to research data, work through spread-sheet exercises and manipulate software 
applicable to solving conservation problems 
-   Co-design an original research project and work effectively as a team member in a group 
environment 
-   Demonstrate an ability to effectively communicate research findings and key concepts through both 
oral and written presentations 
-   Be able to formulate testable hypotheses and outline the appropriate methods to test these 
hypotheses 
-   Demonstrate an ability to conduct independent research and synthesize key points from the primary 
literature 
-   Show that the proposed study could genuinely contribute to conservation efforts 
 
Attendance: 
 
Attendance is mandatory unless a leave of absence is granted in advance. Students that fail to attend 
more than three classes will drop a grade in their participation assessment. 
 
Academic dishonesty: 
 
In group research students are encouraged to consult with and work with their peers. However assessed 
work must be individually written and duplicate answers to assignments will not be accepted. 
Plagiarism is never tolerated and all points for a given question will be deducted from any lab 
assignments or exams if students are found to have copied their work from another source, published or 
otherwise.  
 
Students with certified disabilities: 
 
It is University policy to provide, on a flexible and individualized basis, reasonable accommodations to 
students who have disabilities that may affect their ability to participate in course activities or to meet 
course requirements.  Students with disabilities must arrange these accommodations with the Office of 
Disability Services (room 260 University Center, phone 280-6222) and with the instructor. 


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