Date | Lecture | Assigned Readings
(see also Recommended Readings by topic) |
Lab |
Tuesday, Jan. 17 |
Introduction (see syllabus) | Discussion | |
Thursday, Jan. 19 |
History and Philosophy (BDM) | Mishler, Brent D. (2009). Three centuries of paradigm changes in biological classification: Is the end in sight? Taxon, 58(1), 61-67. | Museum Tour |
Tuesday, Jan. 24 |
Hennig Principle (BDM) | Mishler, Brent D. (2005). The logic of the data matrix in phylogenetic analysis. In V.A. Albert (ed.), Parsimony, Phylogeny, and Genomics, Oxford University Press, 57-70. doi:10.1093/acprof:oso/9780199297306.003.0004 | Parsimony by hand (Wagner tree exercise, courtesy of John Lundberg); starting character matrix; empty difference matrix; see also another version of this exercise (the homework for which includes Mishleridae). |
Thursday, Jan. 26 |
Lab Day (MJL) | No assigned reading. | Intro to PHYLIP AzollaITS.txt Caminalcules.nex MollyNickEric.nex Introduction to Mesquite Amblygnathus.nex |
Tuesday, Jan. 31 |
Morphological Data I - Ontogeny and structure of Animals(DRL) Morphological Data II - Fossils(DRL) |
(recommended) Kenneth D. Angielczyk and David L. Fox (2006). Exploring new uses for measures of fit of phylogenetic hypotheses to the fossil record. Paleobiology 32(1):147-165. doi: 10.1666/05016.1 (bioone) Edgecombe G. D. (2010). Palaeomorphology: fossils and the inference of cladistic relationships. Acta Zoologica 91(1):72-80. Escapa, I. H. and Pol, D. (2011). Dealing with incompleteness: New advances for the use of fossils in phylogenetic analysis. Palaios. 26(3):121-124. |
Project topic due |
Thursday, Feb. 2 |
Morphological Data II - Character coding (KWW) | Maddison, W. P. (1993). Missing Data Versus Missing Characters in Phylogenetic Analysis, Systematic Biology, 42(4):576-581 Maddison, W. P. and Maddison D. R. (2002) MacClade: Analysis of Phylogeny and Character Evolution (version 4), Sinauer Associates, Sunderland, MA. Chapter 3, "Overview of Phylogenetic Inference." Chapter 4, "Reconstructing Character Evolution Using Parsimony." |
Introduction to Mesquite (cont'd) |
Tuesday, Feb. 7 |
Morphological Data IV - Ontogeny and structure of plants (BDM) | Fink, William L. (1982). The Conceptual Relationship Between Ontogeny and Phylogeny. Paleobiology, 8(3), 254-264. (JSTOR) | Introduction to TNT dq_v2b.tnt |
Thursday, Feb. 9 |
Molecular Data I - intro (BDM) | Mishler, Brent D. (2005). The logic of the data matrix in phylogenetic analysis. In V.A. Albert (ed.), Parsimony, Phylogeny, and Genomics, Oxford University Press, 57-70. doi: 10.1093/acprof:oso/9780199297306.003.0004 | Intro to PAUP primate-mtDNA.nex |
Tuesday, Feb. 14 |
Molecular Data II - Sequence alignment (KWW) | Anisimova, M., Cannarozzi, G. and Liberles, D. (2010). Finding the balance between the mathematical and biological optima in multiple sequence alignment. Trends in Evolutionary Biology, North America, 2(11). Brower, A. V. Z. and Schawaroch, V. (1996). Three steps of homology assessment. Cladistics, 12(3):265–272. |
GenBank, JALVIEW, alignments, ClustalW |
Thursday, Feb. 16 |
Phylogenetic trees I - assumptions, reconstructions (BDM) | Sober, E. (1988). Reconstructing the Past: Parsimony, Evolution, and Inference. Chapter 1. MIT Press. | Discussion of molecular applications papers; Students to bring papers from their groups |
Tuesday, Feb. 21 |
Phylogenetic trees II - Phenetics and Distance Metrics | Saitou, Naruya; Nei, Masatoshi (1987). The Neighbor-joining Method: A New Method for
Reconstructing Phylogenetic Trees. Molecular Biology and Evolution, 4(4), 406-425. (Scholar; P.S., "Cited by 21061"!!)
Backeljau, Thierry; De Bruyn, Luc; De Wolf, Hans; Jordaens, Kurt; Van Dongen, Stefan; Winnepenninckx, Birgitta (1995). Multiple UPGMA and Neighbor-joining Trees and the Performance of Some Computer Packages. Molecular Biology and Evolution, 13(2), 309-313. (Scholar) |
UPGMA and Neighbor-joining using PAUP cephalopod_COI.txt cephalopod_COI.nex |
Thursday, Feb. 23 |
Phylogenetic trees III - parsimony (BDM) | Siddall, M. and A. Kluge (1997). Probabilism and phylogenetic inference. Cladistics 13, 313-336. (DOI) | Introduction to POY; CIPRES data analysis cephalopod_COI.txt mol1.txt POY_tutorial_commands.txt POY4beta_commands.pdf docs.zip |
Tuesday, Feb. 28 |
Phylogenetic trees IV - maximum likelihood; molecular evolution (KWW) | 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, 305-321. (DOI | JSTOR) | ML using PAUP and Modeltest cephalopod_COI_Clustalw.nex modelblockPAUPb10.nex |
Thursday, March 1 |
Phylogenetic trees V - measures of support, bootstrap etc. (KWW) | Grant, T., Kluge, A.G. (2003). Data exploration in phylogenetic inference: scientific, heuristic, or neither. Cladistics 19, 379-418. (DOI)
Giribet, G.; DeSalle, R.; Wheeler, W. (2002). 'Pluralism' and the aims of phylogenetic research. In: R. DeSalle, G. Giribet and W. Wheeler, editors, Molecular Systematics and Evolution: Theory and Practice, Birkhauser, Basel, 92, 141-146. (Scholar | online PDF) |
Bootstrap, Jackknife, and Bremer support anolis.nex primates.nex primate-mtDNA.nex |
Tuesday, March 6 |
Phylogenetic trees VI - Bayesian phylogenetics (MJL) | Huelsenbeck, John P.; Larget, Bret; Miller, Richard E.; Ronquist, Fredrik (2002). Potential Applications and Pitfalls of Bayesian Inference of Phylogeny. Systematic Biology, 51(5), 673-688. doi:10.1080/10635150290102366 (Scholar) | MrBayes primates.nex |
Thursday, March 8 |
Dating in the 21st century: divergence times, clocks, calibrations (DRL) | Ho Y. W. S., Lanfear R., Bromham L., Phillips M. J., Soubrier J., Rodrigo A. G., Cooper A. (2011) Time-dependent rates of molecular evolution. Molecular Ecology. 20:3087-3101 Link Lanfear R., Welch J. J., Bromham L. (2010) Watching the clock: Studying variation in rates of molecular evolution between species. Trends Eco. Evo.. 25:495-503. Link |
LR tests of molecular clock, R8S, BEAST CEPHALAPOD.nex cephalopod_COI_Clustalw.nex cephalopod_COI.fasta CephSeq.nuc CephTree.trees CEPHr8s.NEX CEPHr8s_NPRS.NEX |
Tuesday, March 13 |
Phylogenetic trees VIII - tree-to-tree comparisons; consensus methods (KWW) |
Bryant, David (2003). A Classification of Consensus Methods for Phylogenetics. DIMACS Series in Discrete Mathematics and Theoretical Computer Science. DIMACS Working Group Meetings on Bioconsensus, October 25-26, 2000, and October 2-5, 2001. 61, 163-184. (Scholar) | Tree comparisons MrBayesCephalopodConsensus.nex MrBayesCephalopodTprobs.nex RayMatrix.nex |
Thursday, March 15 |
Classification I - Phylogenetic Classification (DRL) |
Tassy P. (2010). Trees before and after Darwin. J Zoo Syst Evo Res. 49(2):89-101. Wilkinson B. H. (2011). On taxonomic membership. Paleobiology. 37(3):519-536. Wägele H. et al. (2011). The taxonomist - an endangered race. A practical proposal for its survival. Frontiers in Zoology. 8:25. |
Discuss progress on projects in class; present initial analysis of project dataset |
Thursday, March 20 |
Classification II - integrating fossils (DRL) | Parham et al. (2012). Best Practices for Justifying Fossil Calibrations Syst Biol. 61(2):346-359. | QUIZ 1 (covers through March 11) |
Tuesday, March 22 |
Classification III - Phylogenetic taxonomy; Phylocode |
Sereno, P. C. (2004). The logical basis of phylogenetic taxonomy. Syst Biol, 54(4):595-619. Rieppel, O. (2006). The PhyloCode: a critical discussion of its theoretical foundation. Cladistics, 22(2):186-197. |
Discussion of phylogenetic taxonomy (using the papers to the left as a framework) |
March 26 - March 30 |
Spring Break | ||
Tuesday, April 3 |
Classification IV - DNA barcoding, DNA taxonomy (KWW) | Taylor H. R. and Harris W. E. (2012). An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. Molecular Ecology. DOI: 10.1111/j.1755-0998.2012.03119.x. | Basic intro to scripting in R and mesquite (zipfile with lab and data) (NOTE: Updated ClustalW script for Macs) |
Thursday, April 5 |
Classification V - nomenclature, Zoological & Botanical Codes (KWW) | No assigned reading. | Online systematic databases: nomenclature, species, geography, phylogeny |
Thursday, April 10 |
Classification VI - Species concepts (BDM) | Claridge, M. F. (2010). Species Are Real Biological Entities, in: Ayala, F. and Arp, R. (Eds.), Contemporary Debates in Philosophy of Biology, Wiley-Blackwell, Singapore, pp. 87-109. (Scholar) Mishler, B. D. (2010). Species Are Not Uniquely Real Biological Entities, in: Ayala, F. and Arp, R. (Eds.), Contemporary Debates in Philosophy of Biology, Wiley-Blackwell, Singapore, pp. 110-122. (Scholar) | R packages for evolutionary biology |
Thursday, April 12 |
Phylogenetic trees IX - below the species level (BRM) | Knowles LL, Maddison WP (2002) Statistical phylogeography. Molecular Ecology, 11, 2623-2635. (DOI | PubMed | Scholar) Strangely, this paper is missing from the online archives. Millstein, Roberta L. (2009), “Populations as Individuals.” Biological Theory: Integrating Development, Evolution and Cognition, 4(3), 267-273. (DOI | Scholar) |
Discuss progress on projects in class |
Thursday, April 17 |
Morphometrics (DRL) |
Windhager S. et al. (2012). Cars have their own faces: cross-cultural ratings of car shapes in biological (stereotypical) terms. Evolution & Human Behavior. 33(2):109-120. Klingenberg C. P. et al. (2011). Developmental plasticity, morphological variation and evolvability: a multilevel analysis of morphometric integration in the shape of compound leaves. J Evol Biol. 25(1):115-129. |
Morphometrics |
Thursday, April 19 |
Historical Biogeography (KWW) Supplementary figures |
Crisp, M. D., Trewick, S. A., and Cook, L. G. (2011). Hypothesis testing in biogeography. Trends Evol. Ecol. 26(2):66-72. Ronquist, F. and Sanmartin, I. (2011). Phylogenetic Methods in Biogeography. Annu. Rev. Ecol. Evol. 42:441-464. |
Historical Biogeography with DIVA and Lagrange (zipfile) |
Tuesday, April 24 |
Introduction to Macroevolution (DRL) | Hallinan, N. M. and Lindberg, D. R. (2011). Comparative Analysis of Chromosome Counts Infers Three Paleopolyploidies in the Mollusca. Genome Biol. Evol. 3:1150-1163. Donoghue, M. J. (2005). Key innovations, convergence, and success: macroevolutionary lessons from plant phylogeny. Paleobiology. 31(2):77-93. |
Concluding discussion: Phylogenetics, systematics, future directions |
Thursday, April 26 |
Introduction to Comparative Methods (BRM) | Webb, C.O.. D.D. Ackerly, M.A McPeek, and M.J. Donoghue 2002. Phylogenies and community ecology. Annual Review of Ecology and Systematics. 33: 475-505. | QUIZ 2 (covers March 16th-April 29th) |
April 30 - May 11 |
Reading & Finals Weeks | ||
Monday, April 30 |
Draft projects due at 5:00 pm, Monday April 30. | ||
Wednesday, May 2 (??) |
Student Mini-Symposium, TBA | ||
Friday, May 4 |
Peer review due at 5:00 pm, Friday May 4. | ||
Wednesday, May 9 |
Final projects due at 5:00 pm, Wednesday May 9. |