Phylogenetic comparative methods, CEB Spring 2010 [Revised April 22, 2010]

Transcription

1 Phylogenetic comparative methods, CEB Spring 2010 [Revised April 22, 2010] Instructors: Andrew Hipp, Herbarium Curator, Morton Arboretum Rick Ree, Associate Curator, Botany Dept., Field Museum. Time: Spring quarter 2010, Wednesdays, 9:30 to 11:30 a.m. Location: Zoology classroom, the Field Museum Prerequisites: Systematics, or general familiarity with methods for estimating phylogenies Software / computer requirements: Computer tutorials will be held in class, primarily utilizing the opensource R and Python languages. Students will need to have a laptop computer with them or share a laptop with a classmate. Overview: This is a graduate seminar course about the uses of phylogenetic trees in evolution and ecology, emphasizing historical inference of phenotypic traits, geographic ranges, and community ecology. (This is not a course on how to infer phylogenies, or their uses in studies of molecular evolution and population genetics.) Within this scope we will focus on topics of popular interest and relevance to student research, working our way from model assumptions and statistical underpinnings to practical implementation of methods. The 2-hour weekly meeting will include lectures on main topics, discussion of primary literature, and tutorials on and opportunities to work hands-on with software (bring your own laptop). Additionally, each week one student will present a case study from the literature or from their own research. Focus in these presentations will be on the comparative questions and approaches taken by the authors. Grades will be based on the clarity of the presentations as well as on class participation. Each week, all students will be expected to to the instructor two questions they have based on the readings. Questions should be mailed by Monday evening, and they will be considered a part of class participation. Students who are presenting in a given week will not be required to submit questions, but they will be required to send a copy of the paper(s) they ll be presenting to all class participants by Monday evening. Week 1 (March 31): Independent contrasts and phylogenetic regression I Tutorial: Regression in R [Hipp] Prior to class, install R ( and the packages ape, geiger, nlme * Felsenstein J Phylogenies and the comparative method. Am Nat 125: * Freckleton RP The seven deadly sins of comparative analysis. J Evol Biol 22(7): * Garland T, Ives AR Using the past to predict the present: Confidence intervals for regression equations in phylogenetic comparative methods. Am Nat 155: Felsenstein J Comparative Methods with Sampling Error and Within-Species Variation: Contrasts Revisited and Revised. The American Naturalist 171(6): Garland T, Midford PE, Ives AR An Introduction to phylogenetically based statistical methods, with a new method for confidence intervals on ancestral values. Am Zool 39: Garland T, Harvey PH, Ives AR Procedures for the analysis of comparative data using phylogenetically independent contrasts. Syst Biol 41: Housworth EA, Martins EP, Lynch M The phylogenetic mixed model. Am Nat 163(1): Ives AR, Midford PE, Garland T Within-Species variation and measurement error in phylogenetic comparative methods. Syst Biol 56(2):

2 Lynch M Methods for the analysis of comparative data in evolutionary biology. Evolution 45(5): Paradis E, Claude J Analysis of comparative data using generalized estimating equations. J Theor Biol 218(2): Revell LJ Size-correction and principal components for interspecific comparative studies. Evolution 63(12): Revell LJ, Harrison AS PCCA: a program for phylogenetic canonical correlation analysis. Bioinformatics 24(7): Week 2 (April 7): Regression II: Model fit and phylogenetic rates Tutorial: Regression in R part II, model-fitting in R [Hipp] * Blomberg, S., Garland, T. & Ives, A., Testing for phylogenetic signal in comparative data: Behavioral traits are more labile. Evolution, 57(4), p * O Meara, B. et al., Testing for different rates of continuous trait evolution using likelihood. Evolution, 60(5), p * Pagel, M., Inferring evolutionary processes from phylogenies. Zoologica Scripta, 26(4), p * Pagel M Inferring the historical patterns of biological evolution. Nature (Lond) 401(6756): Burnham KP, Anderson DR Model selection and multimodel inference: a practical information-theoretic approach. 2nd ed. New York: Springer. [selections] Hunt, G., The relative importance of directional change, random walks, and stasis in the evolution of fossil lineages. Proceedings of the National Academy of Sciences of the United States of America, 104(47), p Week 3 (April 14): Adaptation (continuous characters) * Butler M, King AA Phylogenetic comparative analysis: a modeling approach for adaptive evolution. Am Nat 164: * Hansen TF, Pienaar J, Orzack SH A Comparative Method for Studying Adaptation to a Randomly Evolving Environment. Evolution 62(8): * Hansen TF Stabilizing selection and the comparative analysis of adaptation. Evolution 51(5): * Martins EP, Hansen TF Phylogenies and the comparative method: A general approach to incorporating phylogenetic information into analysis of interspecific data. Am Nat 149: Baum DA, Larson A Adaptation revisited: a phylogenetic methodology for studying character macroevolution. Syst Zool 40: Hansen TF, Martins EP Translating between microevolutionary process and macroevolutionary patterns: the correlation structure of interspecific data. Evolution 50: Hansen TF, Orzack SH Assessing current adaptation and phylogenetic inertia as explanations of trait evolution: The need for controlled comparisons. Evolution 59(10): King AA, Butler MA ouch: Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses (R package). Maddison, W.P., Squared-change parsimony reconstructions of ancestral states for continuous-valued characters on a phylogenetic tree. Systematic Zoology, 40(3), p Martins EP Estimation of ancestral states of continuous characters: A computer simulation study. Syst Biol 48:

3 Schluter, D. et al., Likelihood of Ancestor States in Adaptive Radiation. Evolution, 51(6), p Week 4 (April 21): Reconstructing the evolutionary history of discrete traits * Huelsenbeck, J.P., Nielsen, R. & Bollback, J.P., Stochastic Mapping of Morphological Characters. Systematic Biology, 52(2), p * Maddison, D. R. M. & Maddison, W. P. Reconstructing character evolution using parsimony. Chapter in MacClade Manual (v. 3 or 4). Sunderland, MA: Sinauer Associates. * Pagel, M., The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Systematic Biology, 48(3), p Cunningham, C.W., Some Limitations of Ancestral Character-State Reconstruction When Testing Evolutionary Hypotheses. Systematic Biology, 48(3), p Igic, B., Bohs, L. & Kohn, J., Ancient polymorphism reveals unidirectional breeding system shifts. Proceedings of the National Academy of Sciences 103(5), p Lewis, P.O., A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data. Systematic Biology, 50(6), p Mayrose I, Barker MS, Otto SP Probabilistic Models of Chromosome Number Evolution and the Inference of Polyploidy. Syst Biol: syp083. Mooers, A.O. & Schluter, D., Reconstructing Ancestor States with Maximum Likelihood: Support for One- and Two-Rate Models. Systematic Biology, 48(3), p.623. Nielsen, R., Mapping mutations on phylogenies. Systematic Biology, 51(5), p Ree, R.H. & Donoghue, M.J., Inferring Rates of Change in Flower Symmetry in Asterid Angiosperms. Systematic Biology, 48(3), p.633. Schultz, T.R. & Churchill, G.A., The Role of Subjectivity in Reconstructing Ancestral Character States: A Bayesian Approach to Unknown Rates, States, and Transformation Asymmetries. Systematic Biology, 48(3), p.651. Week 5 (April 28): Correlated trait evolution * Maddison, W.P., A method for testing the correlated evolution of 2 binary characters - are gains or losses concentrated on certain branches of a phylogenetic tree? Evolution, 44(3),p * Pagel, M., Detecting Correlated Evolution on Phylogenies: A General Method for the Comparative Analysis of Discrete Characters. Proceedings of the Royal Society B: Biological Sciences, 255(1342), p * Pagel, M. and Meade, A Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo. American Naturalist, 167, * Revell LJ, Collar DC Phylogenetic analysis of the evolutionary correlation using likelihood. Evolution 63(4): Ackerly DD Taxon sampling, correlated evolution, and independent contrasts. Evolution 54(5): Diaz-Uriarte R, Garland T, Jr Testing hypotheses of correlated evolution using phylogenetically independent contrasts: sensitivity to deviations from brownian motion. Syst Biol 45(1): Moles, A. et al., A brief history of seed size. Science, 307(5709), p Organ CL, Janes DE, Meade A, Pagel M Genotypic sex determination enabled adaptive radiations of extinct marine reptiles. Nature (Lond) 461(7262): Week 6 (May 5): Diversification rates and patterns

4 * Chan, K.M.A. & Moore, B.R., Whole-tree methods for detecting differential diversification rates. Systematic Biology, 51(6), p * Nee S Birth-Death Models in Macroevolution. Annual Review of Ecology, Evolution, and Systematics 37(1): * Rabosky DL Extinction Rates Should Not Be Estimated from Molecular Phylogenies. Evolution, doi /j x. * Ricklefs, R.E., Estimating diversification rates from phylogenetic information. Trends in Ecology and Evolution, 22(11), p * Sanderson, M.J. & Donoghue, M.J., Reconstructing shifts in diversification rates on phylogenetic trees. Trends in Ecology and Evolution, 11(1), p Alfaro ME, Santini F, Brock C, Alamillo H, Dornburg A, Rabosky DL, et al Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proceedings of the National Academy of Sciences 106(32): Nee S, Holmes EC, May RM, Harvey PH Extinction rates can be estimated from molecular phylogenies. Philos Trans R Soc Lond B Biol Sci 344(1307): Rabosky DL Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions. Ecol Lett 12(8): Rabosky DL Heritability of Extinction Rates Links Diversification Patterns in Molecular Phylogenies and Fossils. Syst Biol 58(6): Ricklefs, R.E., Schwarzbach, A.E. & Renner, S.S., Rate of lineage origin explains the diversity anomaly in the world's mangrove vegetation. American Naturalist, 168(6), p Sanderson, M.J. & Donoghue, M.J., Shifts in diversification rate with the origin of angiosperms. Science, 264(5165), p Week 7 (May 12): Key innovations * Moore BR, Donoghue MJ A Bayesian approach for evaluating the impact of historical events on rates of diversification. Proceedings of the National Academy of Sciences 106(11): * Paradis, E., Statistical analysis of diversification with species traits. Evolution, 59(1), p * Ree RH Detecting the historical signature of key innovations using stochastic models of character evolution and cladogenesis. Evolution 59(2): * Slowinksi, J.B. & Guyer, C., Testing whether certain traits have caused amplified diversification - an improved method based on a model of random speciation and extinction. American Naturalist, 142(6), p Guyer, C. & Slowinksi, J.B., Adaptive radiation and the topology of large phylogenies. Evolution, 47(1), p Paradis E Asymmetries in phylogenetic diversification and character change can be untangled. Evolution 62(1): Rabosky DL, McCune AR Reinventing species selection with molecular phylogenies. Trends Ecol Evol 25(2): Sargent, R., Floral symmetry affects speciation rates in angiosperms. Proceedings of the Royal Society B: Biological Sciences, 271(1539), p Week 8 (May 19): Integrative approaches to diversification and trait evolution * FitzJohn RG, Maddison WP, Otto SP Estimating Trait-Dependent Speciation and Extinction Rates from Incompletely Resolved Phylogenies. Syst Biol 58(6): * Goldberg EE, Igic B On Phylogenetic Tests of Irreversible Evolution. Evolution 62(11):

5 * Maddison, W.P., Confounding asymmetries in evolutionary diversification and character change. Evolution, 60(8), p * Maddison, W., Midford, P. & Otto, S., Estimating a binary character's effect on speciation and extinction. Systematic Biology, 56(5), p Whittall, J. & Hodges, S., Pollinator shifts drive increasingly long nectar spurs in columbine flowers. Nature, 447(7145), p Week 9 (May 26): Historical biogeography Tutorial: Using Lagrange [Ree] * Ree, R. & Smith, S., Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology, 57(1), p * Ree, R.H. et al., A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Evolution, 59(11), p * Ronquist, F., Dispersal-vicariance analysis: A new approach to the quantification of historical biogeography. Systematic Biology, 46(1), p Hausdorf, B., Weighted Ancestral Area Analysis and a Solution of the Redundant Distribution Problem. Systematic Biology, 47(3), p Week 10 (June 2): Phylogenetics and community ecology * Cavender-Bares J, Ackerly D, Baum D, Bazzaz F Phylogenetic overdispersion in Floridian oak communities. Am Nat 163(6): * Cavender-Bares J, Kozak KH, Fine PVA, Kembel SW The merging of community ecology and phylogenetic biology. Ecol Lett 12(7): * Graham CH, Fine PVA Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time. Ecol Lett 11(12): * Webb CO, Ackerly DD, McPeek MA, Donoghue MJ Phylogenies and community ecology. Annu Rev Ecol Syst 33: Cavender-Bares J, Keen A, Miles B Phylogenetic structure of Floridian plant communities depends on taxonomic and spatial scale. Ecology 87(7 Suppl): S Faith DP Threatened species and the potential loss of phylogenetic diversity: conservation scenarios based on estimated extinction probabilities and phylogenetic risk analysis. Conserv Biol 22(6): Helmus MR, Bland TJ, Williams CK, Ives AR Phylogenetic measures of biodiversity. The American Naturalist 169(3): E68-E83. Kembel SW Disentangling niche and neutral influences on community assembly: assessing the performance of community phylogenetic structure tests. Ecol Lett 12(9): Losos JB Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecol Lett 11(10): Vamosi SM, Heard SB, Vamosi JC, Webb CO Emerging patterns in the comparative analysis of phylogenetic community structure. Mol Ecol 18(4):