| Date |
Lecture |
Required Readings
(see also Recommended Readings) |
Lab |
Wednesday,
Jan. 17 |
Introduction - contemporary issues in phylogenetic systematics - what is at stake? (BDM, DDA, CMT) |
Tree Thinking: Chap. 1 |
LAB 01: Discussion: student interests; get acquainted roundtable; tour of systematics collections, labs, and resources in VLSB |
Friday,
Jan. 19 |
Introduction - contemporary issues in comparative methods (DDA) |
Tree Thinking: Chap. 1 |
|
Monday,
Jan. 22 |
Introduction - history & philosophy of phylogenetics; the Hennig Principle: homology; synapomorphy; rooting; integrating fossils (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. 24 |
Morphological data I: ontogeny & structure of plants vs. animals; character analysis; what is a data matrix? (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: How to handle phylogenetic data and trees; Introduction to command line + R; Introduction to Nexus and Newick files; Introduction to FigTree and Mesquite
|
Friday,
Jan. 26 |
Morphological data II: Character coding [primary homology, polarity, additivity, etc.] (guest lecture: Kip Will)
Lecture Notes |
Tree Thinking: pp 77-95, 399-403
Rieppel, O. (2015). Homology: A Philosophical and Biological Perspective. Handbook of Paleoanthropology, 295-315.
|
|
Monday,
Jan. 29
|
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,
Jan. 31
|
Molecular data II: Sequence alignment (BDM)
Lecture Notes |
Tree Thinking: pp 86-89, 195-200 |
PROJECT TOPIC DUE -- turn in 1 paragraph description and discuss in class
Lab 03: introduction to GENBANK and FASTA files; BLAST; sequence analysis and alignment (Clustal, Muscle, AliView)
|
Friday,
Feb. 2
|
Phylogenetic trees I: reconstruction; models, algorithms & assumptions (BDM)
Lecture Notes |
Tree Thinking: pp 35-53. |
|
Monday,
Feb. 5 |
Phylogenetic trees II: Phenetics; distance-based algorithms (BDM)
Lecture Notes |
Tree Thinking: pp 231-238. |
|
Wednesday,
Feb. 7 |
Phylogenetic trees III: Parsimony; Measures of support and robustness (BDM)
Lecture Notes
|
Tree Thinking: pp 95-106, 173-215, 271-284
|
LAB 04: Distance and parsimony inference using PAUP*; UPGMA, neighbor-joining, bootstrap, and jackknife
|
Friday,
Feb. 9 |
Phylogenetic trees IV: Maximum likelihood; molecular evolution and phylogenetics (Tribble)
Lecture Slides |
Required: Tree Thinking: pp 217 - 231, 238 - 247
Recommended:
Felsenstein, Joseph. "Evolutionary trees from DNA sequences: a maximum likelihood approach." Journal of molecular evolution 17.6 (1981): 368-376.
|
|
Monday,
Feb. 12 |
Phylogenetic trees V: Bayesian methods and Markov Chain Monte Carlo (CMT)
Lecture Slides |
Required: Tree Thinking: pp 247 - 258
Recommended: Lecture Notes from 2016
Holder, Mark, and Paul O. Lewis. "Phylogeny estimation: traditional and Bayesian approaches." Nature reviews genetics 4.4 (2003): 275.
|
|
Wednesday,
Feb. 14 |
Phylogenetic trees VI: Dating in the 21st century: clocks, & calibrations; proper use of fossils (BDM)
Lecture Notes
|
Tree Thinking: pp 53-58
Parham, James F., et al. "Best practices for justifying fossil calibrations." Systematic Biology 61.2 (2011): 346-359.
|
LAB 05: Maximum likelihood inference using jModelTest; RAxML; CIPRES supercomputer web interface
|
Friday,
Feb. 16 |
Phylogenetic trees VII: Tree-to-tree comparisons; consensus methods; supertrees (guest lecture: Kip Will)
Lecture Notes
|
NA
|
|
Monday,
Feb. 19 |
Academic and Administrative Holiday - NO CLASS |
Wednesday,
Feb. 21 |
Introduction to statistical thinking in phylogenetics (DDA)
Lecture Notes
|
Tree Thinking: Beginning of Chapter 10 pp. 305 - 312 |
LAB 06: Bayesian inference MrBayes and BEAST; Tracer; molecular clocks and fossil calibrations |
Friday,
Feb. 23 |
Qualitative character evolution within a cladogram I: discrete states; ancestral state reconstructions (DDA)
Lecture Notes
|
Required:
Tree Thinking: pp. 77-99, 312-322
Maddison WP, Maddison DR (2000) MacClade 4 (pdf manual), Sunderland MA: Sinauer, chapters 3, 4, and 22.
Recommended:
Maddison WP, Slatkin M (1991) Null models for the number of evolutionary steps in a character on a phylogenetic tree. Evolution 45: 1184-1197.
|
|
Monday,
Feb. 26 |
Qualitative character evolution within a cladogram II: comparing two or more characters (DDA)
Lecture Notes
|
Required:
Pagel M. (1994) Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proc. R. Soc. Lond. B, 255, 37-45
Schluter D., Price T., Mooers A. & Ludwig D. (1997) Likelihood of ancestor states in adaptive radiation. Evolution, 51, 1699-1711
Recommended:
Pagel M. (1999) The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Syst. Biol., 48, 612-622
|
|
Wednesday,
Feb. 28 |
Quantitative character evolution within a cladogram I: intro; ancestral trait reconstruction; phylogenetic conservatism (DDA)
Lecture Notes
|
Felsenstein J. 1985. Phylogenies and the comparative method. Amer. Nat. 125:1-15
Oakley TH, Cunningham CW. 2000. Independent contrasts succeed where ancestral reconstruction fails in a known bacteriophage phylogeny. Evolution 54:397-405
|
LAB 07: Intro to R for phylogenetics; ancestral state reconstruction and correlated evolution of discrete traits.
Download RMarkdown file here. |
Friday,
Mar. 2 |
Quantitative character evolution within a cladogram II: independent contrasts and trait correlations (DDA)
Lecture Notes
|
Required:
Hansen, T. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution 51:1341- 1351.
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.
Strongly Recommended:
Blomberg, S. P., T. Garland, and A. R. Ives. 2003. Testing for phylogenetic signal in comparative data: Behavioral traits are more labile. Evolution 57:717-745. (Focus on pp. 719-723 on methods for measuring phylogenetic signal.)
Harmon, L. J., J. B. Losos, T. J. Davies, et al.. 2010. EARLY BURSTS OF BODY SIZE AND SHAPE EVOLUTION ARE RARE IN COMPARATIVE DATA Evolution 64:2385-2396.
|
|
Monday,
Mar. 5 |
Phylogenetics and adaptation (DDA)
Lecture Notes
|
Coddington, Jonathan A. "The roles of homology and convergence in studies of adaptation." (1994). |
|
Wednesday,
Mar. 7 |
Phylogenies and Community Ecology I (DDA)
Lecture Notes
|
Required:
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.
Recommended:
Webb, C. O., et al.. 2002. Phylogenies and community ecology. Annu. Rev. Ecol. Syst. 33:475-505.
|
LAB 08: Ancestral state reconstruction and correlated evolution of continuous traits.
Download RMarkdown File Here
|
Friday,
Mar. 9 |
Phylogenies and Community Ecology II (DDA)
|
TBD
|
|
Monday,
Mar. 12 |
Classification I -- introduction to phylogenetic classifications; monophyly, information content (BDM)
Lecture Notes
|
Tree Thinking: pp 107-131
|
|
Wednesday,
Mar. 14 |
Classification II -- phylogenetic taxonomy including incorporation of fossils; Phylocode (BDM)
Lecture Notes
|
Preface to the Phylocode
|
PHYLOGENY FOR YOUR PROJECT DUE in writing + discuss progress on comparative analyses
LAB 09: Community phylogenetics: picante; Online systematic databases: nomenclature, geography, phylogeny, specimens
Download RMarkdown File Here
|
Friday,
Mar. 16 |
Classification III -- species concepts; speciation (BDM)
Lecture Notes
|
B.D. Mishler and J.S. Wilkins. 2018. The hunting of the SNaRC: a snarky solution to the species problem. Philosophy, Theory, and Practice in Biology. 10: 1-18. [accepted, soon to be published] |
QUIZ 1 handed out (due this evening) - see past quizzes |
Monday,
Mar. 19 |
Classification IV -- DNA barcoding and DNA taxonomy (BDM)
Lecture Notes
|
K.W. Will, B.D. Mishler, and Q.D. Wheeler. 2005. The perils of DNA barcoding and the need for integrative taxonomy. Systematic Biology 54: 844-851. |
|
Wednesday,
Mar. 21 |
Classification V -- nomenclature; Zoological & Botanical Codes; practical systematics, monography (guest lecture: Kip Will)
Lecture Notes
|
TBD |
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,
Mar. 23 |
Evolution and development - heterochrony (BDM)
Lecture Notes
|
Fink, W.L. 1982. The Conceptual Relationship Between Ontogeny and Phylogeny. Paleobiology 8: 254-264.
|
|
| Mar. 26 - 30 |
SPRING BREAK |
Monday,
Apr. 2 |
Comparing sister clades within a cladogram: the shape of evolution (DDA)
Lecture Notes
|
Required:
Morlon, H. (2014). Phylogenetic approaches for studying diversification. Ecology Letters, 17(4), 508-525.
Recommended:
Rabosky, D. L., & Glor, R. E. (2010). Equilibrium speciation dynamics in a model adaptive radiation of island lizards. Proceedings of the National Academy of Sciences, 107(51), 22178-22183.
Jetz, W., Thomas, G. H., Joy, J. B., Hartmann, K., & Mooers, A. O. (2012). The global diversity of birds in space and time. Nature, 491(7424), 444-448.
|
|
Wednesday,
Apr. 4 |
Tempo and mode in macroevolution; patterns of diversification and extinction (DDA)
Lecture Notes
|
Goldberg, Emma E., et al. "Species selection maintains self-incompatibility." Science 330.6003 (2010): 493-495.
Lagomarsino, Laura P., et al. "The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae)." New Phytologist 210.4 (2016): 1430-1442.
|
LAB 11: Birth-death models; joint character evolution and diversification analyses using BiSSE
|
Friday,
Apr. 6 |
Adaptive radiations (DDA)
Lecture Notes
|
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. PNAS 106:19699–19706.
|
|
Monday,
Apr. 9 |
Phylogenetic trees VIII: Below the "species level;" phylogeography; dealing with reticulation (BDM)
Lecture Notes
|
Tree Thinking: Chpt 6
|
|
Wednesday,
Apr. 11 |
Molecular evolution (BDM)
Lecture Notes
|
Wolfe KH, Li W (2003) Molecular evolution meets the genomics revolution. Nature Genetics 33(3s), 355-365
|
LAB 12: Coalescence theory: gene tree-species tree reconstruction using RevBayes and the multispecies coalescent
Lecture slides
|
Friday,
Apr. 13 |
Gene family evolution; phylogenomics; 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. 16 |
Biogeography I: basic principles; ecological vs. historical approaches; vicariance vs. dispersal (BDM)
Lecture Notes
|
Tree Thinking: pp 349-355 |
|
Wednesday,
Apr. 18 |
Biogeography II: phylogenetic studies of the niche; range modeling; environmental evolution (DDA)
Lecture Notes
Lecture Slides
|
Crisp, Michael D., et al. "Phylogenetic biome conservatism on a global scale." Nature 458.7239 (2009): 754.
Evans, Margaret EK, et al. "Climate, niche evolution, and diversification of the “bird-cage” evening primroses (Oenothera, sections Anogra and Kleinia)." The American Naturalist 173.2 (2008): 225-240.
|
LAB 13: Probabilistic biogeographic models using RevBayes
Lecture Slides
|
Friday,
Apr. 20 |
Biogeography III: spatial phylogenetics; phylobetadiversity & biome recognition, and other spatial issues (BDM)
Lecture Notes
Lecture Slides
|
A.H. Thornhill, B.D. Mishler, N. Knerr, C.E. Gonzalez-Orozco, C.M. Costion, D.M. Crayn, S.W. Laffan, and J.T. Miller. 2016. Continental-scale spatial phylogenetics of Australian angiosperms provides insights into ecology, evolution and conservation. Journal of Biogeography. 43: 2085–2098. |
|
Monday,
Apr. 23 |
Phylogenetics and conservation biology (DDA)
Lecture Notes
|
Mishler, Brent D., et al. "Phylogenetic measures of biodiversity and neo-and paleo-endemism in Australian Acacia." Nature Communications 5 (2014): 4473.
Pollock, L.J., Thuiller, W. and Jetz, W., 2017. Large conservation gains possible for global biodiversity facets. Nature, 546(7656), p.141.
|
|
Wednesday,
Apr. 25 |
Comparing cladograms; cospeciation methods (DDA)
Lecture Notes
Lecture Slides
|
Percy, Diana M., Roderic DM Page, and Quentin CB Cronk. "Plant–insect interactions: double-dating associated insect and plant lineages reveals asynchronous radiations." Systematic Biology 53.1 (2004): 120-127.
Vienne, DM de, et al. "Cospeciation vs host‐shift speciation: methods for testing, evidence from natural associations and relation to coevolution." New Phytologist 198.2 (2013): 347-385.
|
INITIAL COMPARATIVE ANALYSES DUE in writing + discuss progress on projects in class
LAB 14: BIODIVERSE Demo, phylogenetic alpha- and beta-diversity, mapping
Download BIODIVERSE here
|
Friday,
Apr. 27 |
Coevolution; symbiosis (DDA)
Lecture Notes
Lecture Slides
|
TBD
|
QUIZ 2 handed out (due Sunday night) - see past quizzes |
| April 30- May 11 |
READING & FINALS WEEKS |
Thursday,
May 3 |
Student minisymposium |
| Tuesday, May 8 |
Final projects due by midnight |