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 GIS to paleontological problems.

[Course Syllabus]


Lecture 1

Week 1 - Introduction

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

Session 2 - SQL

Week 2 - SQL and data summaries

Review of downloading data, introduction to client-server concept, introduction to mySQL, instructions for importing data into mySQL, introduction to the Structured Query Language (SQL).

[Download slides] [Assignment Sheet] [SQL primer]

Lecture 3

Week 3 - Mathematica and Diversity Curves

Introduction to the estimation of taxonomic diversity curves and to programming in Mathematica..

[Download slides] [Assignment Sheet] [Calculating Diversity Curves from Foote and Miller]

Week 4 - Diversity curves and Quantitative Paleontology Package

More about taxonomic diversity curves and an introduction to working with the Quantitative Paleontology add-in package for Mathematica.

[Get Quantitaive Paleontology Package] [Assignment Sheet]

Lecture 5

Week 5 - Monte Carlo modeling of taxonomic diversity

Discussion of Raup's (1985) paper on mathematical modeling of diversity and cohort analysis, emphasizing understanding of the equations, parameters, and consequences. Discussion of the uses of modeling, assignment to use modeling to better understand the uncertainty (and certainty) of estimated parameters such as rates of extinction and origination.

[Assignment Sheet]

Week 7 - Habitat distribution modeling

Discussion of Townsend and Soberón papers: niche modeling, species distribution modeling, suitable habitat modeling, climate envelopes, BIOCLIM, GARP.

[Assignment Sheet]

Week 10 - Habit distribution modeling and paleontology

Discussion of Svenning et al, 2011, and Macguire and Stigall, 2008. Introduction to Cenozoic and Quaternary climates and climate modeling, construction of habitat distribution models with Mathematica and mySQL.

[Assignment Sheet] [Supplement on Occurrence Points]

Week 11 - Phylogeny 1

Discussion of Baldauf (2003), Maddison, Donoghue and Maddison (1984), and Holder and Lewis (2003). Parsimony, discrete characters, likelihood for continous traits, Newick Format trees.

[Assignment Sheet]
[creodont discrete character data in PHYLIP format]
[creodont data in nexus format]
[marmot continuous character data in PHYLIP format]

Week 12 - Phylogeny 2

Discussion of Gingerich (1979), Fisher (2008), Wagner (2000), relevance and issues with including stratigraphic data in phylogenetic analysis, concept of stratigraphic debt, concept of stratigraphic likelihood.

[Assignment Sheet]

Gerber et al, 2007

Week 15 - Traits and Disparity

Discussion of Foote (1994), Gerber et al. (2007), and Mitteroecker & Hutteger (2009). Morphospaces, PCA and PCO, distances, disparity, measures of disparity.

[Assignment Sheet]

Polly et al, 2010

Week 16 - Functional traits and community ecometrics

Discussion of Polly et al, (2010) and Jablonski (2005). Functional traits, communities, taxon-free measures, synthesis of diversity, geography, phylogeny, and traits.

 

 

Mathematica Quantitative Paleontology Package

Download Quantitative Paleontology for Mathematica and other Mathematica packages here.

Handouts

Downloading data
SQL primer

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