Integrative Biology 200
Syllabus and Handouts



Download syllabus as pdf.
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.
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

Background image adapted from a phylogeny of all organisms with complete genome sequences.

Last update Spring 2016 by Will Freyman