Analytical Paleontology Short Course
Macquarie University, June 2013
Day 1: Introduction and R Boot Camp
Day 1A - Module Overivew
Day 1B - Introduction to R (by Gene Hunt)
Day 1C - Answers to Exercises (by Gene Hunt)
Day 2: Introduction to Geometric Morphometric Methods (GMM)
Day 2A - General intro to GMM
Day 2B - GMM in R
Day 3: Procrustes, shape space, and statistical tests
Day 3A - Procrustes
Day 3B - PCA and shape space
Day 3C - Statistical tests (regression and MANOVA)
Day 3D - Exercise on mammal tarsals
Day 4: Shape modeling
Day 4A - Shape modeling
Day 4B - Brownian motion evolution
Day 4C - Multivariate statistical tests and shape modeling
Day 5: Evolution, trees, triangles, etc.
Day 5A - Evolution, trees, etc.
Day 5B - Extra stuff about triangles and curvature of shape space and graphics tips
Morphometric R Functions
Shrew and Marmot Mandibles (1 Mb) [Tree in NEXUS format]
Dog skulls (91 Mb)
Trilobites (9 Mb)
Carnivore Tarsal Figure (JPG) Associated Data (CSV)
3D Coordinates of Mammal Skulls (TPS file)
Within-population shape data set - shrews from Poland (TPS file)
Holland, S. M. 2006. A short R tutorial.
Adams, D. C. and E. Otárola-Castillo. 2013. Geomorph: an R package for the collection and analysis of geometric morphometric shape data. Methods in Ecology and Evolution, 4: 393-399.
Mitteroecker, P. and P. Gunz. 2009. Advances in geometric morphometrics. Evolutionary Biology, 36:235-247.
Rohlf, F. J. 1993. Relative Warp analysis and an example of its application to mosquito wings. Pp. 131-159 in L.F. Marcus and E. Garcia-Valdecasas (eds.), Contributions to Morphometrics. Museu Nacional de Ciencias Naturales: Madrid, Spain.
Mitteroecker, P., P. Gunz, and F.L. Bookstein. 2005. Heterochrony and geometric morphometrics: a comparison of cranial growth in Pan paniscus versus Pan troglodytes. Evolution and Development, 7: 244-258.
Polly, P. D. 2004. On the simulation of the evolution of morphological shape: multivariate shape under selection and drift. Palaeontologia Electronica, 7.2.7A: 28 pp. http://palaeo-electronica.org/2004_2/evo/issue2_04.htm
Caumul, R. and P. D. Polly. 2005. Phylogenetic and environmental components of morphological variation: skull, mandible and molar shape in marmots (Marmota, Rodentia). Evolution, 59: 2460-2472.
Rohlf, F. J. 2002. Geometric morphometrics and phylogeny. In N. MacLeod and P. Forey (eds), Morphology, shape and phylogeny, pp. 175–193.