Conservation Biology Masters : Overview and Curriculum

APLORI’s main purpose is capacity building for conservation in West Africa. We do this primarily by running a Masters in Conservation Biology. Although we grant degrees through the University of Jos we are an autonomous research institute answering directly to the Vice-Chancellor of the University. Our degree is European standard with teaching from invited international academics, exams set and run by staff of the St Andrews University, and external examiners from international universities such as Edinburgh, Ghent, Groningen and Oxford. We provide a proper Masters education without compromise to fully equip tomorrow’s conservationists.

We teach a small number of students every year, all on scholarship provided by our endowment from the Leventis Conservation Foundation. The course takes a year and involves 6 months taught and 6 months research. Our teaching is carried out by a team of academics who come from all over the world coordinated and supported by teaching fellows based at APLORI and the University of St Andrews. Typically an academic will come for a couple of weeks to teach a module at APLORI, and then the academic serves as a supervisor for one of the students during their research project. This gives a diverse and high level of teaching for the students as well as establishing strong international links for our graduates. Many of our graduates end up in PhD programs in international universities as a consequence.

The taught course consists of the principles of ecology and conservation biology with an underlying core of quantitative methods. In particular we teach scientific thinking, experimental design, and statistical analysis (in R) so that our students learn to be proper conservation scientists. They then carry out a 6 month research project to apply their skills and to give practical experience of solving the scientific problems they will encounter as practicing conservation biologists. We particularly emphasise field skills and teach a range of practical conservation skills from survey techniques to bird ringing.

Teaching is based at the A.P. Leventis Ornithological Research Institute on the outskirts of Jos. This is a well equiped field station providing a lecture theatre and seminar rooms, labs, a library, and student and guest accomodation within a small reserved natural area suitable for research and field classes. We also have a field station in the nearby Yankari National park which provides access to savannah habitats which still retain much of the large fauna of West Africa.

Course Outline

Evolution and molecular ecology

  1. Life on earth
    1. History of life on earth
    2. Review of major plant and animal groups
    3. Bird families and species as examples of evolutionary processes
  2. The theory of evolution
    1. History
    2. the concept of fitness
    3. Natural selection
    4. Sexual selection
    5. Genetic drift
  3. Variation in natural populations
    1. DNA and genes
    2. Types of variation
    3. Mutation
    4. Gene frequencies
      1. Hardy-Weinberg ratio
      2. Additive genetic model
      3. Quantitative variation and fitness
  4. Maintenance of variation
  5. Measuring genetic variation
  6. Quantitative genetics
  7. Molecular identification
    1. Defining species
    2. Hybridisation
    3. Identifying individuals
    4. Molecular identification methods
      Variation in natural populations
      1. Phylogeography
      2. Genetic variation in space
      3. Genetic variation in time
      4. Applied phylogeography
    1. Taxonomy
      1. Principles and cladistics
      2. Molecular phylogenies
      3. Comparative method

Principles of ecology: individuals to ecosystems

  1. Basic ecological processes4
    1. Definitions
    2. Abiotic components of ecosystems
    3. Energy flux through ecosystems
  2. Terrestrial ecosystems
    1. Review of major terrestrial ecosystems
    2. Role of history and geology
  3. Nutrients, soils & the decomposition cycle4
  4. Plant-herbivore interactions4
  5. Population dynamics4
    1. Abundance
    2. Measuring birth and death rates; life tables
    3. Demographic stochasticity
    4. Environmental stochasticity
  6. Intraspecific competition4
  7. Interspecific competition4
  8. Predation4
    1. Lotka-Volterra equations
  9. Parasitism
  10. Mutualism4,6
  11. The influence of population interactions4v
  12. Keystone species
    1. Functional groups
    2. Ecosystem engineering
  13. Behavioural ecology as a discipline and framework6
  14. Life history strategies6,3
  15. Solitary foraging behaviour6
  16. Group foraging behaviour and competition6
  17. Starvation/predation risk trade-off
    1. anti-predation behaviour6,5
  18. Choice of breeding habitat6
  19. Dispersal6,4
  20. Sexual selection6
  21. Mating systems and parental care6
  22. Cooperation and altruism6
  23. Communication6

Conservation biology

  1. What is conservation biology?
  2. Biodiversity theory and measures
  3. Extinctions
  4. Small and declining populations
  5. Metapopulations
  6. Habitat fragmentation
  7. Edge effects
  8. Island biogeography
  9. Theory of management of harvested populations
    1. Sustainable forestry uses
    2. Bushmeat and hunting
    3. Pest control
  10. Behavioural ecology and conservation
  11. Individual based population models
  12. The species approach to conservation
    1. Conservation genetics
    2. Captive breeding
    3. Prioritisation of conservation of genetic resources
    4. Reintroductions
  13. The habitat approach to conservation
    1. Habitat management
    2. Habitat creation
  14. The area or hotspot approach to conservation
    1. The protected area approach
    2. Nature reserve design
    3. Networks of protected areas
    4. Humans and protected areas
  15. The economics of nature conservation
    1. Direct economic values
    2. Indirect values
    3. Ecotourism
    4. Cost benefit analysis
  16. Conservation education
    1. Teaching and learning
    2. Changing behaviours
    3. Networking and marketing for conservation
  17. Conservation policy and politics
    1. Common land and resources
    2. Human needs other than conservation and conflicts
    3. Local people and conservation
    4. Global issues
  18. Sustainable development
    1. Ecosystem service
  19. Anthropogenic effects on ecosystems
    1. Pollution
    2. Introduced species
    3. Global warming
    4. Genetically modified crops
    5. Urban habitats
    6. Agricultural habitats
  20. Bird conservation in Africa: an overview case study Hazell Thompson

Biostatistics and experimental design

To be taught primarily within workshops using R, where the students tackle problems from real datasets, and often data sets they have collected as part of the Field Techniques course below.

  1. The scientific method
    1. Philosophy of science
    2. Why is statistics impotant?
    3. What is hypothesis testing?
    4. What is a null hypothesis?
      1. Type I and Type II error
      2. Power
      3. Stratified random sampling
      4. Pseudoreplication
      5. Bias
      6. Biological versus statistical significance
      7. Power and accuracy in estimating mean from samples
  2. Principles of experimental design
    1. How to design an experiment
    2. Statistics and experimental design
  3. Different types of data
    1. Continuous variables
    2. Factors
  4. Distribution and measures of central tendency
    1. Frequency and histograms
    2. The normal distribution
    3. Binomial and Poisson distributions
    4. Transformations
    5. Mean and standard deviation
    6. Confidence intervals
  5. General linear modelling
    1. Degrees of freedom
    2. Introduction to predictive equations – model building
    3. Residuals and normality (assumptions of parametric tests)
  6. Correlation and covariance
    1. Parametric correlation
    2. Spearman rank
  7. Data reduction
  8. Non-parametric statistics
    1. How do they differ from parametric tests
    2. Mann-whitney U tests
    3. Signs test
    4. Kruskall-Wallis 1-way ANOVA
  9. Frequency analysis
    1. chi square
    2. Exact probability tests
  10. Generalised linear mixed models
    1. Random factors
    2. Repeated measures
  11. Non-linear regression
    1. Curve fitting
  12. Binary logistic regression
  13. Poisson regression

Practical course 1: Field Techniques

To be taught primarily with the context of field exercises or min-projects where the students design a sampling program, and go out and collect the data.

  1. Basic field skills
    1. Field craft
    2. Observation techniques
    3. Binoculars and telescopes
    4. Recording data in the field
  2. Bird identification
    1. Bird topography
    2. Field marks
    3. Descriptions
    4. Use of field guides
    5. Use of bird calls and playback
  3. Sampling (in conjunction with Biostatistics and experimental design)
  4. Bird census techniques
    1. Species lists
    2. McKinnon lists
    3. Transects
    4. Point counts
    5. Distance sampling in the field
      1. Format of data for using DISTANCE
      2. Mayfield estimates
      3. Scale
      4. Vegetation density
      5. Vegetation characteristics
  5. Focal sampling
  6. Scan sampling
  7. Behavioural measures
  8. Life history traits
    1. Breeding parameters
    2. Nest survival
    3. Survival
  9. Habitat association
    1. Presence/absence and density
    2. Habitat classification
    3. Vegetation sampling
  10. Invertebrate sampling
  11. Measurement of abiotic factors
  12. Bird specific techniques
    1. Ringing and colour marking
    2. Biometrics
    3. Radio tracking
    4. Migration
    5. Diet estimation
    6. Foraging rates and energy intake
    7. Vigilance rates

Practical course 2: Computing skills

  1. PC file management
    1. Sharing files
    2. Viruses
    3. Backups
  2. Word processing
    1. Word
  3. Reference databases
    1. End note or Reference Manager
  4. Internet resources and search skills
    1. Internet etiquette
  5. Spreadsheets
    1. Excel
    2. Uses and limitations
    3. Formulas
    4. Efficient data entry
    5. Organising analysis
    6. File management
  6. Code driven statistical analysis: R (and as an integral part of the Biostatistics course)
    1. Programming in R
    2. Code files
    3. Data exploration
    4. Data synthesis
    5. Data manipulation (compute, if, select etc.)

Practical course 3: Writing and Presentation skills

  1. Scientific writing
    1. Structure
    2. Editing
    3. Preparation of figures and tables
  2. Graphing data
    1. Graphics packages
  3. PowerPoint
    1. Great features to use in Powerpoint
    2. Misuse of Powerpoint
  4. The process and requirements of scientific publishing
    1. Peer review
    2. Refereeing
  5. Writing for a non-scientific audience
    1. Popular journalism
    2. Press releases
    3. Report writing
  6. Seminar presentation
    1. Speed and delivery styles
    2. Dealing with questions

Course Textbooks

The course follows these text books:

  1. Evolutionary genetics John Maynard Smith
  2. An introduction to molecular ecology Trevor Beebe & Graham Rowe
  3. Evolutionary ecology of birds Peter Bennett and Ian Owens
  4. Ecology: From Individuals to Ecosystems Begon, Townsend & Harper
  5. Behavioural Ecology: An evolutionary approach 4th Edition John Krebs & Nick Davies
  6. Behavioural Ecology Danchin, Giraldeau & Cezilly
  7. Conservation Science & Action William Sutherland
  8. Essentials of conservation biology Richard Primack 4th Edition
  9. Conservation education and outreach techniques Jacobson, McDuff & Monroe
  10. Conservation: Linking ecology, economics and culture Borgerhoff Mulder & Coppolillo
  11. The conservation handbook: research, management and policy William Sutherland
  12. Ecological census techniques: A handbook William Sutherland
  13. Bird Census techniques Colin Bibby et al.
  14. Bird ecology and conservation William Sutherland, Ian Newton & Rhys Green
  15. Modern statistics for the life sciences Alan Grafen & Rosie Hails
  16. Statistics: An introduction using R Michael J. Crawley