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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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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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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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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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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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.

Module 8 - Tree support and disparity

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

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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Module 10 - Simulated diversity patterns

Discusison of Raup (1985); Diversity curves; extinction and speciation rates; cohort analysis; paraclade dynamics.

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Module 11 - Introduction to Finite Element Analysis (FEA)

Lecture on FEA, introduction to FARO Arm laser scanner.

Module 12 - Climate

Introduction to climate and global climate models.