Course information
Class meetings: Mondays 9:05-9:55 (12 Ecology Building)
Instructor: Dr. John Drake (Office: 133 Ecology Building, email: jdrake@uga.edu)
Course description: Perspectives in Computational Ecology (ECOL 8910) is a course to introduce students to advanced topics in computational ecology, modeling, quantitative analysis, biostatistics, and visualization. The Spring 2014 semester concerns the quantitative measurement of biodiversity.
Course objectives: The student will be introduced to a range of techniques and scientific computing paradigms using the R statistical computing environment. The primary goal of this course is to develop new data analysis skills.
Assignments and grading policy: This course is graded on the S/U system. To receive a score of S you must satisfactorily complete all assignments. Class activities include
- Weekly class discussions led by students and occasional homework assignments
- Weekly outside reading from the peer-reviewed literature and one paragraph summary
- Independent or group research project using techniques studied in the class
Official university policy: The course syllabus is a general plan for the course; deviations announced to the class by the instructor may be necessary. All academic work must meet the standards contained in A Culture of Honesty. Students are responsible for informing themselves about those standards before performing any academic work.
Links
Bibliography
Three rules for leading a paper discussion
Class schedule
Date | Topic | Reading | Presenter |
6 Jan 14 | Introduction | | |
13 Jan 14 | What is diversity? | Patil, G.P. and C. Taillie. 1982. Diversity as a concept and its measurement. Journal of the American Statistical Association 33:548-567. | Drake |
20 Jan 14 | No class (MLK Day) | | |
27 Jan 14 | Software for estimating species richness | Wang, J.P. 2011. SPECIES: An R package for species richness estimation. Journal of Statistical Software 40(9):1-15. | Griffin |
3 Feb 14 | Collection curves | Gotelli, N.J., and R.K. Colwell. 2001. Quantifying biodiversity: Procedures and pitfalls in the measurement and comparison of species richness. Ecology Letters 4:379-391. | Vidal |
10 Feb 14 | Species abundance distributions | Fisher, R.A., A.S. Corbet, and C.B. Williams. 1943. The relation between the number of species and the number of individuals in a random sample of an animal population. Journal of Animal Ecology 12:42-58. | Kaul |
17 Feb 14 | Species description curves | Joppa, L.N. D.L. Roberts, S.L. Pimm. 2011. How many species of flowering plants are there? Proceedings of the Royal Society, Series B 278:554-559.
Costello, M.J., R.M. May, N.E. Stork. 2013. Can we name Earth's species before they go extinct. Science 339:413-416. | Fisher |
24 Feb 14 | Beta diversity | Anderson, M.J., Crist, T.O., Chase, J.M., Vellend, M., Inouye, B.D., Freestone, A.L., Sanders, N.J., Cornell, H.V., Comita, L.S., Davies, K.F., Harrison, S.P., Kraft, N.J.B., Stegen, J.C., and Swenson, N.G. 2011. Navigating the multiple meanings of β diversity: a roadmap for the practicing ecologist. Ecology Letters 14:19-28. | Zokan |
3 Mar 14 | Phylogenetic diversity | Morlon, H. 2014. Phylogenetic approaches for studying diversification. Ecology Letters. (In press) | Vinson |
10 Mar 14 | No class (spring break) | | |
17 Mar 14 | Hill numbers | Jost, L. 2006. Entropy and diversity. Oikos 113:363-375
Hill, M.O. 1973. Diversity and evenness: a unifying notations and its consequences. Ecology 54:427-432. | Kramer/Park |
24 Mar 14 | Checkerboard patterns | Connor, E.F., M.D. Collins, D. Simberloff. 2013. The checkered history of checkerboard distributions. Ecology 94:2403–2414. | Dallas |
31 Mar 14 | Species richness estimation | Chao, A. 2005. Species estimation and applications. Encyclopedia of Statistical Sciences, 2nd Edition, Vol. 12, 7907-7916, (N. Balakrishnan, C. B. Read and B. Vidakovic, eds) Wiley, New York. | Kaul |
7 Apr 14 | Spatial effects species composition | Dray, S. 2012. Community ecology in the age of multivariate multi-scale spatial analysis. Ecological Monographs 82:257-275. | Vidal |
14 Apr 14 | Functional diversity | Petchey, O.L. and K. J. Gaston. 2006. Functional diversity: back to basics and looking forward. Ecology Letters 9:741-758. | Griffin |
21 Apr 14 | Ordination | Legendre, P. and H.J.B. Birks. 2012. From classical to canonical ordination. Pp. 201-248 in Tracking Environmental Change Using Lake Sediments. Springer | Vinson/Zokan |
28 Apr 14 | Microbial diversity | Curtis, T.P. et al. 2006. What is the extent of prokaryotic diversity? Proceedings of the Royal Society, Series B 361:2023-2037. | Fisher/Dallas |