Conservation Biology Masters: Curriculum

SDC10624

Course Outline

1. Evolution and molecular ecology

1. 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 processes3
  2. The theory of evolution1,6
    1. History
    2. the concept of fitness
    3. Natural selection
    4. Sexual selection
    5. Genetic drift
  3. Variation in natural populations 11
    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
  1. Maintenance of variation
  2. Measuring genetic variation
  3. Quantitative genetics
  1. Molecular identification2
    1. Defining species
    2. Hybridisation
    3. Identifying individuals
    4. Molecular identification methods
  2. Variation in natural populations 22
    1. Phylogeography
    2. Genetic variation in space
    3. Genetic variation in time
    4. Applied phylogeography
  3. Taxonomy
    1. Principles and cladistics
    2. Molecular phylogenies3
    3. Comparative method3, 6

2. Principles of ecology: individuals to ecosystems

2. 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. Parasitism4,6
  10. Mutualism4,6
  11. The influence of population interactions4
  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

3. Conservation biology

3. Conservation biology11

  1. What is conservation biology?8,10
  2. Biodiversity theory and measures4,7,8
  3. Extinctions7
  4. Small and declining populations7
  5. Metapopulations7
  6. Habitat fragmentation8
  7. Edge effects8
  8. Island biogeography8
  9. Theory of management of harvested populations4,14
    1. Sustainable forestry uses
    2. Bushmeat and hunting10,14
    3. Pest control4
  10. Behavioural ecology and conservation6
  11. Individual based population models5
  12. The species approach to conservation7
    1. Conservation genetics2
    2. Captive breeding8
    3. Prioritisation of conservation of genetic resources
    4. Reintroductions8
  13. The habitat approach to conservation7
    1. Habitat management14
    2. Habitat creation8
  14. The area or hotspot approach to conservation8
    1. The protected area approach
    2. Nature reserve design8
    3. Networks of protected areas
    4. Humans and protected areas10
  15. The economics of nature conservation7
    1. Direct economic values8
    2. Indirect values8
    3. Ecotourism
    4. Cost benefit analysis
  16. Conservation education7,9
    1. Teaching and learning9
    2. Changing behaviours9
    3. Networking and marketing for conservation9
  17. Conservation policy and politics7,8,10
    1. Common land and resources10
    2. Human needs other than conservation and conflicts10
    3. Local people and conservation10
    4. Global issues10
  18. Sustainable development8
    1. Ecosystem services
  19. Anthropogenic effects on ecosystems
    1. Pollution7
    2. Introduced species7
    3. Global warming
    4. Genetically modified crops2
    5. Urban habitats
    6. Agricultural habitats
  20. Bird conservation in Africa: an overview case study Hazell Thompson

4. Biostatistics and experimental design

4. Biostatistics and experimental design15, 16

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
  1. Principles of experimental design12
    1. How to design an experiment
    2. Statistics and experimental design
  1. Different types of data
    1. Continuous variables
    2. Factors
  2. 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
  3. General linear modelling
    1. Degrees of freedom
    2. Introduction to predictive equations – model building
    3. Residuals and normality (assumptions of parametric tests)
  4. Correlation and covariance
    1. Parametric correlation
    2. Spearman rank correlation
  5. Data reduction
  6. 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
  7. Frequency analysis
    1. chi square
    2. Exact probability tests
  8. Generalised linear mixed models
    1. Random factors
    2. Repeated measures
  9. Non-linear regression
    1. Curve fitting
  10. Binary logistic regression
  11. Poisson regression

Practical Course 1: Field Techniques

Practical course 1: Field Techniques12

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)14
  4. Bird census techniques13
    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 traits14
    1. Breeding parameters
    2. Nest survival
    3. Survival
  9. Habitat association12,14
    1. Presence/absence and density
    2. Habitat classification
    3. Vegetation sampling
  10. Invertebrate sampling
  11. Measurement of abiotic factors
  12. Bird specific techniques14
    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

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

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

Course Textbooks

Course Textbooks

The course follows these text books:

1Evolutionary genetics John Maynard Smith

2An introduction to molecular ecology Trevor Beebe & Graham Rowe

3Evolutionary ecology of birds Peter Bennett and Ian Owens

4Ecology: From Individuals to Ecosystems Begon, Townsend & Harper

5Behavioural Ecology: An evolutionary approach 4th Edition John Krebs & Nick Davies

6Behavioural Ecology Danchin, Giraldeau & Cezilly

7Conservation Science & Action William Sutherland

8Essentials of conservation biology Richard Primack 4th Edition

9Conservation education and outreach techniques Jacobson, McDuff & Monroe

10Conservation: Linking ecology, economics and culture Borgerhoff Mulder & Coppolillo

11The conservation handbook: research, management and policy William Sutherland

12Ecological census techniques: A handbook William Sutherland

13Bird Census techniques Colin Bibby et al.

14Bird ecology and conservation William Sutherland, Ian Newton & Rhys Green

15Modern statistics for the life sciences Alan Grafen & Rosie Hails

16Statistics: An introduction using R Michael J. Crawley