Indiana University Bloomington
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G562 Geometric Morphometrics

P. David Polly
Department of Geological Sciences
Indiana University
1001 E. 10th Street
Bloomington, IN 47405 USA
http://www.indiana.edu/~geosci

Email the instructor | Instructor's website
Visit the IU Geobiology Group



   

Analytical Paleontology Short Course
Macquarie University, June 2013


Lecture Slides

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

Image sets

Shrew and Marmot Mandibles (1 Mb) [Tree in NEXUS format]
Dog skulls
(91 Mb)
Trilobites (9 Mb)

Data

cope.txt (TXT)
Carnivore Tarsal Figure (JPG) Associated Data (CSV)
3D Coordinates of Mammal Skulls (TPS file)
Within-population shape data set - shrews from Poland (TPS file)


Readings

Day 1:

Holland, S. M. 2006. A short R tutorial.

Day 2:

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.

Day 3:

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 troglodytesEvolution and Development, 7: 244-258.

Day 4:

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

Day 5:

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.

 

 



Handouts

How to collect landmarks from photos
Collecting 3D landmarks with MicroScribe

Morphometrics Resources

Jim Rohlf's morphometrics site
MorphoJ software from Klingenberg
GMM tools for Mathematica and R
EVAN toolbox

Online Morphometric, Image, and Scan Data

Digital Morphology Site (DigiMorph)
MorphoBrowser
Virtual Zooarchaeology of the Arctic

Mathematica Morphometrics Package

Download Geometric Morphometrics for Mathematica and other Mathematica packages here

IU Natural History Collections

IU Paleontology Collection
Adams Zooarchaeological Collection
Glenn Black Lab of Archaeology
IU Herbarium

IU Paleo Collection on
FaceBook
IU PaleoCollection on FB

Online Phylogenetic Data

CladeStore
TreeBase
MorphoBank
NCBI Taxonomy
Molecular Data from Extinct Species