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


Quantitative Paleontology is the practical application of quantitative analysis to paleontology, including the analysis of diversity through time, analysis of diversity in space, analysis of morphological disparity, and reconstruction of phylogenetic relationships.  Skills include Monte Carlo statistical tests, analysis of large data sets, use of relational SQL databases, and the application of finite element analysis to paleontological problems.

[Course Syllabus]


Lecture 1

Week 1 - Introduction

Course overview and software installation.
[Download slides] [Download handout]

Week 2 - MySQL and Mathematica

Introduction to software, SQL queries, Mathematica interface, programming, and data queries.

See handouts in upper right column of this page.
[Download slides] [Download assignment] [Download data]

Week 3 - Time series and random walks

Discussion of papers, discussion of properties of time series and random walks, discussion of methods for assessing trends and correlations within and between time series.

[Download lecture as Mathematica notebook]
[Download lecture as PDF]
[Download assignment notebook]

Week 4 - Rates and modes of evolution

Discussion of papers, review of properties of time series and random walks, discussion of directional and stabilizing modes of evolution, discussion of step rates and net rates, discussion of expected scaling of net rates to directional, random, and stabilizing modes of evolution

[Download lecture and assigment as Mathematica notebook]
[Download lecture and assigment as PDF]

Week 5 - Review of evolution within lineages

Review discussion of the LineageEvolution function; modes of evolution, rates of evolution, thinking of step rate as a statistical distribution, LRI method for estimating step rate and mode, time series properties, serial correlation, McKinney's equation for time series process, correlation between time series. Introduction to evolution of quantitative trait on a phylogenetic tree.

[Download assigment as Mathematica notebook]
[Download assigment as PDF]

Week 6 - Quantitative traits and phylogeny

Review of properties of random walks; discussion of assignment; star phylogenies and their properties; Simulating star phylogenies; expected covariances from phylogeny; C matrix; birth-death models; reconstructing ancestral nodes.

[Download assigment as Mathematica notebook]
[Download assigment as PDF]

Week 7 - Phylogeny, parsimony, and tree support

Review assignment; trees; continuous versus discrete characters; parsimony; character polarity; tree support, consistency index, retention index, bootstrapping; ML and Bayesian approaches; stratigraphy and phylogeny.

[Download assigment as PDF]

Week 8 - Tree support and disparity

Review assignment; tree support, and bootstrapping; ML phylogenetics; disparity; taxon distances.

[Download assignment as Word file]
[Download assigment as PDF]

Lecture 1

Week 9 - Empirical diversity patterns

Review assignment; what is diversity or taxonomic richness; how is it estimated; first and last occurrences; rates or probabilities of origination and extinction.

[Download assigment as PDF]

Week 10 - Empirical and simulated diversity analysis

Discusison of Raup (1985); Diversity curves; extinction and speciation rates; cohort analysis; paraclade dynamics.
[Download assigment as Word File]

Week 11 - Introduction to Finite Element Analysis

Lecture on FEA, introduction to FARO Arm laser scanner.
[Download slides as PDF]

Week 12 - Finite Element Analysis with FEBio

Lecture on FEA, introduction to FARO Arm laser scanner.
[Download handout as PDF]

 

Mathematica Quantitative Paleontology Package

Download Quantitative Paleontology for Mathematica and other Mathematica packages here.

Handouts

Getting Started with MySQL
SQL primer
Getting Started with Mathematica
Mathematica Quick Guide
Diversity curve calculations (Foote and Miller)
Project Report Instructions

Data files

Carnivore limb measurements [CSV]
Creodont parsimony data [PHY]
Marmot continuous trait data [PHY]


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 Paleontological Data

CladeStore
TreeBase
MorphoBank
NCBI Taxonomy
Molecular Data from Extinct Species