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

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Visit the IU Geobiology Group



   

Geometric Morphometrics is the analysis of shape using Cartesian geometric coordinates rather than linear, areal, or volumetric variables. Geometric morphometric methods (GMM) include 2D and 3D points representing landmarks, curves, outlines, or surfaces. This course is a practical, applied introduction to GMM. Students learn to collect, analyze, and interpret geometric morphometric data. Shape theory and methods are covered, including Procrustes superimposition and its statistical implications, analysis of curves and outlines, and Monte Carlo modeling of shape.

[Course Syllabus 2014]


Lecture 1 - Introduction to Geometric Morphometrics

Lecture 1 - Introduction to Geometric Morphometrics

Overview of principles of geometric morphometric methods (GMM), including definitions of landmarks, outlines and surfaces, differentiation between traditional morphometrics and GMM, short history of morphometrics, components of a morphometric study, and examples of equipment needed for GMM studies.
[Download slides]

Lecture 2: Mathematica

Lecture 2 - Introduction to Mathematica

Learn basics of Mathematica, including basic operations, using cells and styles, writing short programs, defining functions, and making simple graphs.
[Download slides] [Assignment 1]
[Assignment 1 Example Answer]

Lecture 3 - First GMM Analysis

Basics of Procrustes analysis, principal components analysis of shape, and morphospace. Introduction to the morphometrics functions tpsImport[], Procrustes[], PrincipalComponentsOfShape[]. Analysis of faces.
[Download slides] [Assignment 2]

Lecture 4 - Procrustes , PCA, and Morphospace

Details of Procrustes, Procrustes distances, Principal Components Analysis, Eigenvalues, Eigenvectors, Scores, and shape modelling.
[Download slides] [Assignment 3]

Lecture 5 - Statistical Analysis of Shape

Review of PCA, introduction to statistical tests, introduction to R-squared values, univariate regression, multivariate regression, ANOVA, MANOVA.
[Download slides] [Assignment 4] [tarsal associated data]

 

Session 6 - Bootstrapping, Randomization, and Monte Carlo methods

This session is based on readings by Adams & Anthony (1996), Kowalewski & Novack-Gotshall (2010), and Efron & Tibshirani (1986). What are "statistics"? What is a statistical test? What is a statistical null hypothesis? How can resamppling and randomizations of real samples be used to construct customized statistical tests. Bootstrapping, jack-knifing, randomization, Monte Carlo.
[Assignment 5]

Lecture 7- Bootstrapping, Randomization, and Monte Carlo methods

Continues previous topic.
[Assignment 5 with tips]

Lecture 8 - Analysis of outlines and Euclidean DIstance Matrix Anlaysis (EDMA)

Intro to semilandmarks, Fourier analysis, semilandmark analysis, sliding semilandmarks, eigenshape, "Pinocchio effect", alternatives to Procrustes, EDMA.
[Download slides] [Assignment 6]

Lecture 9 - Phylogeny, trees, and morphospace

Phylogenetic signal in morphometric data, "factor thinking", tree building algorithms and terminology, building morphometric trees in Phylip, phylogenetic comparative statistics, trees in morphospace.
[Download slides] [Assignment 7]

Lecture 10 - Monte Carlo simulation of evolution of shape

Random walks, their properties and statistics, random walks in more than one dimension, random walks in morphospace, modeling random evolution.
[Download slides] [Assignment 8]



Mathematica Morphometrics Package

Download Geometric Morphometrics for Mathematica and other Mathematica packages here

Handouts

Mathematica Quick Guide
Manipulating Data In Mathematica
How to collect landmarks from photos
Collecting 3D landmarks with MicroScribe
Collecting outline points in ImageJ

Sample Data Files

Associated data from Caumul and Polly, 2005 [Excel format]
Onyx turtle images for outlines
Marmot molar TPS file
Mammal tree [Newick format]

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

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

PBDB Course 2013