ECOL 8910: Quantifying Biodiversity (Spring 2014)

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

 

DateTopicReadingPresenter
6 Jan 14Introduction
13 Jan 14What 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 14No class (MLK Day)
27 Jan 14Software 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 14Collection 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 14Species 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 14Species 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 14Beta 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 14Phylogenetic diversity Morlon, H. 2014. Phylogenetic approaches for studying diversification. Ecology Letters. (In press)Vinson
10 Mar 14No class (spring break)
17 Mar 14Hill 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 14Checkerboard patterns Connor, E.F., M.D. Collins, D. Simberloff. 2013. The checkered history of checkerboard distributions. Ecology 94:2403–2414.Dallas
31 Mar 14Species 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 14Spatial 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 14Functional 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 14Ordination Legendre, P. and H.J.B. Birks. 2012. From classical to canonical ordination. Pp. 201-248 in Tracking Environmental Change Using Lake Sediments. SpringerVinson/Zokan
28 Apr 14Microbial 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