Date | Lecture | Required Readings (see also Recommended Readings) |
Lab |
Wednesday, Jan. 20 |
Introduction - contemporary issues in phylogenetic systematics - what is at stake? (KWW) | Tree Thinking: Chap. 1 | LAB 01: discussion: student interests; get acquainted roundtable; Tour of systematics collections, labs, and resources in VLSB |
Friday, Jan. 22 |
Introduction - contemporary issues in comparative methods (DDA) | Coddington, J. A. 1994. The roles of homology and convergence in studies of adaptation. Academic Press, London. Ackerly, D.D. 2009. Phylogenetics and comparative methods. Pages 117-125 in Levin et al., eds. The Princeton guide to ecology. Princeton University Press, 2009. |
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Monday, Jan. 25 |
History & philosophy of phylogenetics; the Hennig Principle: homology; synapomorphy (BDM)
Lecture Notes |
Required reading: Tree Thinking: Chap. 2 Supplemental: B.D. Mishler. 2009. Three centuries of paradigm changes in biological classification: is the end in sight? Taxon 58: 61-67. B.D. Mishler. 2014. History and theory in the development of phylogenetics in botany. In A. Hamilton (ed.), The Evolution of Phylogenetic Systematics, pp. 189-210. UC Press. |
|
Wednesday, Jan. 27 |
Morphological data I: Character analysis; What is a data matrix?
Homoplasy; Ontogeny & structure of plants & animals; The role of morphology (BDM)
Lecture Notes |
B.D. Mishler. 2005. The logic of the data matrix in phylogenetic analysis. In V.A. Albert (ed.), Parsimony, Phylogeny, and Genomics, pp. 57-70. Oxford University Press. | LAB 02: Discussion about homology; Introduction to Nexus and Newick files; Introduction to FigTree and Mesquite Please do Part 1 before coming to lab (installing software). |
Friday, Jan. 29 |
Morphological data II: Character coding [primary homology, polarity, additivity, etc.]; (KWW)
Lecture Notes |
Tree Thinking: pp 77-95, 399-403
Rieppel, O. (2015). Homology: A Philosophical and Biological Perspective. Handbook of Paleoanthropology, 295-315. |
|
Monday, Feb. 1 |
Molecular data I: General introduction; types of molecular data (DNA hybridization; allozymes; restriction sites, DNA sequences, ESTs; comparative genomics) (BDM)
Lecture Notes |
Maddison, W. P. and D.R. Maddison. 2011. Mesquite: a modular system for evolutionary analysis. Version 2.75 Chapter on Molecular Data | |
Wednesday, Feb. 3 |
Molecular data II: Sequence alignment (KWW)
Lecture Notes |
Tree Thinking: pp 86-89, 195-200 | PROJECT TOPIC DUE -- discuss in class LAB 03: Introduction to GenBank, BLAST, and FASTA files; sequence analysis and alignment (Clustal, Muscle, AliView) |
Friday, Feb. 5 |
Phylogenetic trees I: reconstruction; models, algorithms & assumptions (BDM)
Lecture Notes |
Tree Thinking: pp 35-53 | |
Monday, Feb. 8 |
Phylogenetic trees II: Phenetics; distance-based algorithms (KWW)
Lecture Notes |
Tree Thinking: pp 231-238 | |
Wednesday, Feb. 10 |
Phylogenetic trees III: Parsimony; Measures of support and robustness (KWW)
Lecture Notes |
Tree Thinking: pp 95-106, 173-215, 271-284
Anisimova, M., Cannarozzi, G., & Liberles, D. A. (2010). Finding the balance between the mathematical and biological optima in multiple sequence alignment. Trends in Evolutionary Biology, 2(1), 7. Grant, T., & Kluge, A. G. (2003). Data exploration in phylogenetic inference: scientific, heuristic, or neither. Cladistics, 19(5), 379-418. |
LAB 04: Distance and parsimony inference using PAUP*; UPGMA, neighbor-joining, bootstrap, and jackknife |
Friday, Feb. 12 |
Phylogenetic trees IV: Maximum likelihood; molecular evolution and phylogenetics (KWW)
Lecture Notes |
Tree Thinking: pp 217-231, 238-247
De Queiroz, K., & Poe, S. (2001). Philosophy and phylogenetic inference: a comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroboration. Systematic Biology, 50(3), 305-321. |
|
Monday, Feb. 15 |
Academic and Administrative Holiday - NO CLASS | ||
Wednesday, Feb.17 |
Phylogenetic trees V: Bayesian methods and Markov chain Monte Carlo (WF)
Lecture Notes |
Tree Thinking: pp 247-258 Huelsenbeck, J. P., Larget, B., Miller, R. E., & Ronquist, F. 2002. Potential applications and pitfalls of Bayesian inference of phylogeny. Systematic Biology, 51(5), 673–88. http://doi.org/10.1080/10635150290102366 Holder, M., & Lewis, P. O. 2003. Phylogeny estimation: traditional and Bayesian approaches. Nature Reviews. Genetics, 4(4), 275–84. http://doi.org/10.1038/nrg1044 |
LAB 05: Maximum likelihood inference; models of DNA sequence evolution; jModelTest and PAUP*; RAxML and CIPRES supercomputer web interface |
Friday, Feb. 19 |
Phylogenetic trees VI: Dating in the 21st century: clocks, & calibrations; proper use of fossils (KWW)
Lecture Notes |
Tree Thinking: pp 53-58
Parham et al. (2011). Best practices for justifying fossil calibrations. Systematic Biology, syr107. |
|
Monday, Feb. 22 |
Phylogenetic trees VII: Tree-to-tree comparisons; consensus methods; supertrees (KWW)
Lecture Notes |
Tree Thinking: pp 58-60
Bryant, D. (2003). A classification of consensus methods for phylogenetics. DIMACS series in discrete mathematics and theoretical computer science, 61, 163-184. |
|
Wednesday, Feb. 24 |
Introduction to statistical thinking in phylogenetics (DDA)
Lecture Notes |
none | LAB 06: Bayesian inference using MrBayes and BEAST; Tracer; molecular clocks and fossil calibrations |
Friday, Feb. 26 |
Qualitative character evolution within a cladogram I: discrete states; ancestral state reconstructions (DDA)
Lecture Notes Example R Script |
Tree Thinking: pp 77-99, 305-322 Maddison WP, Maddison DR (2000) MacClade 4 (pdf manual), Sunderland MA: Sinauer, chapters 3, 4 and 22. [pdf] |
|
Monday, Feb. 29 |
Qualitative character evolution within a cladogram II: comparing two or more characters (DDA)
Lecture Notes |
Tree Thinking: pp 323-327 Maddison, W.P. 1990. A method for testing the correlated evolution of two binary characters: are gains or losses concentrated on certain branches of a phylogenetic tree? Evolution 44, 539-557. Donoghue, M. J. 1989. Phylogenies and the analysis of evolutionary sequences, with examples from the seed plants. Evolution 43:1137-1156. (just read to top of p. 1148) Pagel, M., 1994. Detecting Correlated Evolution on Phylogenies : A General Method for the Comparative Analysis of Discrete Characters. Proceedings R. Soc. Lond B 255:37–45. |
|
Wednesday, Mar. 2 |
Quantitative character evolution within a cladogram I: intro; ancestral trait reconstruction; phylogenetic conservatism (DDA)
Lecture Notes |
Tree Thinking: pp 327-336 Felsenstein, J. 1985. Phylogenies and the comparative method. Amer Nat 125:1–15. Ackerly, D. D. 2009. Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal. Proceedings of the National Academy of Sciences USA 106:19699–19706. Blomberg, S. P., and T. Garland, Jr. 2002. Tempo and mode in evolution: phylogenetic inertia, adaptation and comparative methods. J. Evol. Biol. 15:899-910. |
LAB 07: Intro to R and Basic Phylogenetic Functions in R |
Friday, Mar. 4 |
Quantitative character evolution within a cladogram II: independent contrasts and trait correlations (DDA)
Lecture Notes Lecture Slides |
Tree Thinking: pp 336-340 Oakley TH, Cunningham CW. 2000. Independent contrasts succeed where ancestral reconstruction fails in a known bacteriophage phylogeny. Evolution 54:397-405 Garland Jr, T., P. H. Harvey, and A. R. Ives. 1992. Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology 41:18–32. |
|
Monday, Mar. 7 |
Phylogenetics and adaptation (DDA)
Lecture Notes |
Tree Thinking: pp 77-99, 305-316 (reread) Donoghue, M. J. 1989. Phylogenies and the analysis of evolutionary sequences, with examples from the seed plants. Evolution 43:1137-1156. (pp. 1148 - end) Gould SJ, Vrba ES. 1982. Exaptation-a missing term in the science of form. Paleobiology. Jan 1:4-15. |
|
Wednesday, Mar. 9 |
Classification I -- introduction to phylogenetic classifications; monophyly, information content (KWW)
Lecture Notes |
Tree Thinking: pp 107-131 | LAB 08: Intro to R continued: ancestral state reconstruction, simulating under Brownian motion and Ornstein-Uhlenbeck, and phylogenetically independent contrasts |
Friday, Mar. 11 |
Classification II -- phylogenetic taxonomy including incorporation of fossils; Phylocode (BDM)
Lecture Notes |
Preface to the Phylocode | |
Monday, Mar. 14 |
Classification III -- species concepts; speciation (BDM)
Lecture Notes |
Mishler, Brent D. 2010. Species are not Uniquely Real Biological Entities. Contemporary Debates in Philosophy of Biology. F. Ayala and R. Arp, Wiley-Blackwell, 110-122 | |
Wednesday, Mar. 16 |
Classification IV -- DNA barcoding and DNA taxonomy (KWW)
Lecture Notes |
Collins, R. A., & Cruickshank, R. H. (2013). The seven deadly sins of DNA barcoding. Molecular ecology resources, 13(6), 969-975. | Discuss progress on projects LAB 09: Phylogenetic, Specimen, and Taxonomic Databases and R Packages QUIZ 1 handed out (due Friday evening) - see past quizzes |
Friday, Mar. 18 |
Classification V -- nomenclature; Zoological & Botanical Codes; practical systematics, monography (KWW)
Lecture Notes QUIZ 1 due tonight! |
International Code of Zoological Nomenclature [read preface and skim preamble]
International Code of Nomenclature for algae, fungi, and plants [read preface and skim preamble] |
|
Mar. 21 - 25 | SPRING BREAK | ||
Monday, Mar. 28 |
Evolution and development - heterochrony (BDM)
Lecture Notes |
Fink, W.L. 1982. The Conceptual Relationship Between Ontogeny and Phylogeny. Paleobiology 8: 254-264. | |
Wednesday, Mar. 30 |
Molecular evolution (BDM)
Lecture Notes |
Wolfe KH, Li W (2003) Molecular evolution meets the genomics revolution. Nature Genetics 33(3s), 355-365 | LAB 10: Introduction to RevBayes: phylogenetic analysis using graphical models and Markov chain Monte Carlo
Install RevBayes before coming to lab. It is a command line program, please make sure you can run it before lab. |
Friday, Apr. 1 |
Gene family evolution; comparative genomics; evo-devo (BDM)
Lecture Notes |
Boussau B, Daubin V (2010) Genomes as documents of evolutionary history. Trends in Ecology & Evolution 25(4), 224-232. | |
Monday, Apr. 4 |
Phylogenetic trees VIII: Below the "species level;" phylogeography; dealing with reticulation (BDM)
Lecture Notes |
Tree Thinking: Chap. 6 | |
Wednesday, Apr. 6 |
Tempo and mode in macroevolution; patterns of diversification and extinction (BDM)
Lecture Notes |
Jablonski D (2008) Species Selection: Theory and Data. Annual Review of Ecology Evolution and Systematics, 39:501-524. | Lecture on coalescent theory (WAF) Lecture Slides LAB 11: Coalescence theory: gene tree-species tree reconstruction using RevBayes and the multispecies coalescent |
Friday, Apr. 8 |
Phylogenetics and conservation biology (BDM)
Lecture Notes Lecture Slides |
Faith DP (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation, 61(1): 1-10. | |
Monday, Apr. 11 |
Comparing sister clades within a cladogram: the shape of evolution (DDA)
Lecture Notes Lecture Slides |
Tree Thinking: pp 370-375 Morlon, H. (2014). Phylogenetic approaches for studying diversification. Ecology Letters, 17(4), 508-525. |
|
Wednesday, Apr. 13 |
Adaptive radiations (DDA)
Lecture Notes Lecture Slides |
Tree Thinking: pp 375-381 Hodges, S. 1995. Spurring plant diversification: Are floral nectar spurs a key innovation? Proc. Roy. Soc. London Ser. B 262:343-348. Harmon, L. J., J. A. Schulte, II, A. Larson, and J. B. Losos. 2003. Tempo and mode of evolutionary radiation in Iguanian lizards. Science 301:961-964. Ackerly, D. D. 2009. Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal. Proceedings of the National Academy of Sciences USA 106:19699–19706. (reread) |
Discuss progress on projects in class; present initial analysis of project dataset
LAB 12: Probabilistic Models of Geographic Range Evolution LAB 12: Lecture Slides |
Friday, Apr. 15 |
Phylogenies and Community Ecology I (DDA)
Lecture Notes Lecture Slides |
Tree Thinking: pp 359-362 Cavender-Bares, J., D. D. Ackerly, D. Baum, and F. A. Bazzaz. 2004. Phylogenetic overdispersion in Floridian oak communities. Amer. Nat. 163:823-843. Cavender-Bares, J., K. H. Kozak, P. V. A. Fine, and S. W. Kembel. 2009. The merging of community ecology and phylogenetic biology. Ecology letters 12:693-715. |
|
Monday, Apr. 18 |
Phylogenies and Community Ecology II (DDA)
Same notes as 4/15 |
Godoy O, Kraft NJ, Levine JM. 2014. Phylogenetic relatedness and the determinants of competitive outcomes. Ecology letters. Jul 1;17(7):836-44. Kraft, N.J.B., W.K. Cornwell, C.O. Webb, and D.D. Ackerly. 2007. Trait evolution, community assembly and the phylogenetic structure of ecological communities. American Naturalist 170: 271-283. |
|
Wednesday, Apr. 20 |
Biogeography I: basic principles; ecological vs. historical approaches (KWW)
Lecture Notes |
Biogeography: Chapter 1 |
LAB 13:
Estimating Diversification Rates:
Heterogenous and Character Dependent Processes
LAB 13: Lecture Slides |
Friday, Apr. 22 |
Biogeography II: vicariance biogeography; detecting dispersal (KWW)
Lecture Notes |
Tree Thinking: pp 349-355 Biogeography: pp 260-278 |
|
Monday, Apr. 25 |
Biogeography III: phylogenetics and range modeling; biome recognition and other spatial issues (BDM)
Lecture Notes Lecture Slides |
Graham CH & Fine PVA (2008) Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time. Ecology Letters, 11: 1265-1277. | |
Wednesday, Apr. 27 |
Comparing cladograms; cospeciation methods (DDA)
Lecture Notes Lecture Slides |
Tree Thinking: pp 355-358 Page, R. D. M. 1996. Temporal congruence revisited: Comparison of mitochondrial DNA sequence divergence in cospeciating pocket gophers and their chewing lice. Systematic Biology 45:151-167. Percy, D. M., R. D. M. Page, and Q. C. B. Cronk. 2004. Plant-insect interactions: Double-dating associated insect and plant lineages reveals asynchronous radiations. Systematic Biology 53:120- 127. |
Discuss progress on projects in class
LAB 14: Community and spatial phylogenetics: Introduction to Biodiverse and the picante R package QUIZ 2 handed out (due Friday evening) - see past quizzes |
Friday, Apr. 29 |
Coevolution; symbiosis (DDA) |
Rezende EL, Lavabre JE, Guimarães PR, Jordano P, Bascompte J. 2007. Non-random coextinctions in phylogenetically structured mutualistic networks. Nature. Aug 23;448(7156):925-8. | |
May 2-13 | READING & FINALS WEEKS | ||
Monday, May 9 |
Student minisymposium: 1 - 4:30 PM in 3083 VLSB | ||
Friday, May 13 | Final projects due by midnight |