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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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 2016]


Lecture 1 - Introduction to Geometric Morphometrics

Lecture 1 - Introduction to Mathematica

Overview of Wolfram's Mathematica.
[Download slides] [Assignment 1 (PDF) (NB)]

Lecture 2

Lecture 2 - Introduction to Programming

Basics of programming using Mathematica.
[Download slides] [Assignment 2 (PDF) (NB)]

Lecture 3

Lecture 3 - First Morphometric Analysis

Basics of performing a Geometric Morphometric Analysis from start to finish.
[Download slides] [Assignment 3 on Faces(PDF) (NB)]

Lecture 3a

Lecture 3B - Face analysis and Morphospace

Results of analysis of face photographs and explanation of morphospace.
[Download slides]

Lecture 4

Lecture 4 - Procrustes and PCA

Explanation of Procrustes superimposition and principal components analysis (morphospace construction).
[Download slides] [Assignment 4 (PDF) (NB)]

Lecture 6

Lecture 6 - Statistical Analysis

Introduction to statistical analyses commonly used in geometric morphometrics.
[Download slides]

Lecture 7

Lecture 7- Bootstrapping and Randomization

Overview of designing bootstrapping and randomization tests, plus two-block partial least squares.
[Download slides] [Assignment 5 (PDF) (NB)]

;
Lecutre 8

Lecture 8 - Analysis of Outlines and Euclidean Distance Matrix Analysis (EDMA)

Introduction to semilandmarks and outlines analysis, plus EDMA for localizing which part of a shape varies.
[Download slides] [Assignment 6 (PDF) (NB)]

Lecture 9

Lecture 9 - Graphics in Mathematica

A little about making graphics in Mathematica.
[Download slides]

;
Lecture 10

Lecture 10 - Phylogeny and Morphometrics

Building trees from morphometrics and comments on the relationship between morphometric variation and phylogenetic history.
[Download slides]
[Assignment 7 simulating evolution (PDF) (NB)]

Lecture 11

Lecture 11 - Phenotypic Evolution: theory and analysis

Models of phenotypic evolution, simulating evolution, adaptive landscapes, and independent contrasts.
[Download slides]
[Assignment 8 phylogeny and morphometrics (PDF) (NB)]
[Assignment 9 phylogenetic correlations (PDF) (NB)]

Lecture 12

Lecture 12 - Collecting Landmarks in Mathematica and Morphing Images

Manipulating images in Mathematica, collecting landmarks, and morphing images.
[Assignment 10 image morphing (PDF)]



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