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.
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Module 1 - Introduction
Module 1 - Introduction
Course overview and software installation.Â
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Week 1 - Introduction.pdfModule 2 - MySQL and Mathematica
Module 2 - MySQL and Mathematica
Introduction to software, SQL queries, Mathematica interface, programming, and data queries. See handouts in right column of this page.
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Week 2 - Software and data.pdfModule 3 - Time series and random walks
Module 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.
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Week 3 - Trait evolution, random walks.pdfModule 4 - Rates and modes of evolution
Module 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
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Week 4 - Rates and modes of evolution.pdfModule 5 - Rates of evolution within lineages
Module 5 - Rates 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.
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Week 5 - LineageEvolution and real data.pdfModule 6 - Quantitative traits and phylogeny
Module 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.
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Week 6 - Quantitative Traits and Phylogeny.pdfModule 7 - Phylogeny, parsimony, and tree support
Module 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.
Week 7 - phylogenetic reconstruction.pdfModule 8 - Tree support and disparity
Module 8 - Tree support and disparity
Review assignment; tree support, and bootstrapping; ML phylogenetics; disparity; taxon distances
Week 8 - Disparity.pdfModule 9 - Empirical diversity patterns
Module 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.
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Week 9 - Diversity curves.pdfModule 10 - Simulated diversity patterns
Module 10 - Simulated diversity patterns
Discusison of Raup (1985); Diversity curves; extinction and speciation rates; cohort analysis; paraclade dynamics.
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Week 10 - Mathematica and Diversity curves.pdfModule 11 - Introduction to Finite Element Analysis (FEA)
Module 11 - Introduction to Finite Element Analysis (FEA)
Lecture on FEA, introduction to FARO Arm laser scanner.
Week 12 - Finite Element Analysis.pdfModule 12 - Climate
Module 12 - Climate
Introduction to climate and global climate models.
Week 13 - Climate.pdfPage updated
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