Seth D Dobson Dartmouth College Department of Anthropology Why take into account phylogeny Because any given correlation may be the result of stochastic evolution Brownian motion t ime ID: 1034365
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1. Comparative Analyses in COMPARE: A Model-Selection ApproachSeth D. DobsonDartmouth CollegeDepartment of Anthropology
2. Why take into account phylogeny?Because any given correlation may be the result of stochastic evolution.
3. Brownian motiontime*Revell et al.(2008)
4. Brownian motionMartins and Garland (1991)Computer simulations of two traits evolving under Brownian motion along a specified phylogenyDistribution of correlation coefficients centered on zero (N = 1000)Some runs produced strong correlations (r ≥ 0.70)Correlation is not adaptationmoderate to strong~25% chance
5. Ornstein-UhlenbeckTimePhenotype*Butler and King (2004)Weak constraintStrong constraintOptimum
6. Alpha parameterOrnstein-Uhlenbeck branch-length transformation*Figures from Blomberg et al. (2003)Log-likelihood: An amount proportional to the probability of observing the data given some model (Pagel, 1999)Starter tree“Star phylogeny”Small alphaMedium alphaLarge alpha
7. Inside the black boxAlpha is used to transform an OU process into Brownian motion which renders the GLS error term independentMartins EP. 1994. Estimating the rate of phenotypic evolution from comparative data. American Naturalist 144: 193-209.
8. Inferring adaptationStep 1: Significance of slope(s)Calculate p-values or confidence intervalsSubtract a degree of freedom for ML alphaStep 2: OU model goodness-of-fitCalculate likelihood-ratio test (chi-square)LR = -2*(lnL1-lnL2)
9. What about phylogenetic signal?Small alphaLarge alpha*Blomberg et al. (2003)
10. Other stuff COMPARE doesResults for multiple trees (e.g., 10kTrees)Independent contrasts (Felsenstein, 1985)Rates of evolution (Martins, 1994)Phylogenetic mixed model (Housworth et al., 2004)Hansen adaptation model (Hansen, 1997)Spatial autocorrelation (Martins, 1996)Ancestor reconstruction (Martins, 1999)Random trees (Housworth and Martins, 2001)
11. Take home messageAlways consider models of trait evolution when planning, conducting, and interpreting comparative analyseswww.indiana.edu/~martinsl/compare/
12. ReferencesBlomberg SP, Garland T, and Ives AR. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57(4):717-745.Butler MA, and King AA. 2004. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. American Naturalist 164(6):683-695.Felsenstein J. 1985. Phylogenies and the comparative method. American Naturalist 125(1):1-15.Freckleton RP, Harvey PH, and Pagel M. 2002. Phylogenetic analysis and comparative data: A test and review of evidence. American Naturalist 160(6):712-726.Hansen TF. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution 51(5):1341-1351.Housworth EA, and Martins EP. 2001. Random sampling of constrained phylogenies: Conducting phylogenetic analyses when the phylogeny is partially known. Systematic Biology 50(5):628-639.Housworth EA, Martins EP, and Lynch M. 2004. The phylogenetic mixed model. American Naturalist 163(1):84-96.Martins EP. 1994. Estimating the rate of phenotypic evolution from comparative data. American Naturalist 144(2): 193-209.Martins EP. 1995. Phylogenies and comparative data, a microevolutionary perspective. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences 349(1327):85-91.Martins EP. 1996. Phylogenies, spatial autoregression, and the comparative method: A computer simulation test. Evolution 50(5):1750-1765.Martins EP. 1999. Estimation of ancestral states of continuous characters: A computer simulation study. Systematic Biology 48(3):642-650.Martins EP, and Garland T. 1991. Phylogenetic analyses of the correlated evolution of continuous characters: a simulation study. Evolution 45(3):534-557.Martins EP, and Hansen TF. 1997. Phylogenies and the comparative method: A general approach to incorporating phylogenetic information into the analysis of interspecific data. American Naturalist 149(4):646-667.Pagel M. 1999. Inferring the historical patterns of biological evolution. Nature 401(6756):877-884.Revell LJ, Harmon LJ, and Collar DC. 2008. Phylogenetic Signal, Evolutionary Process, and Rate. Systematic Biology 57(4): 591-601.