Integrative Biology 200A
Syllabus and Handouts

Syllabus html pdf; see also 2008 handouts

Date Lecture Assigned Readings
(see also Recommended Readings by topic)
Lab
Tuesday, Jan. 19 Introduction (see syllabus)   Discussion
Thursday, Jan. 21 History and Philosophy 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. 26 Hennig Principle 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. 28 Morphological Data I - character coding Maddison, W. P., and D. R. Maddison. (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." Intro to PHYLIP AzollaITS.txt Caminalcules.nex MollyNickEric.nex
Tuesday, Feb. 2 Morphological Data II - fossils (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) Project Topic Due; discuss project
Thursday, Feb. 4 Morphological Data III - ontogeny & animal structure Winsor, Mary Pickard (1995). "The english debate on taxonomy and phylogeny." History and Philosopy of the Life Sciences, 17(2), 227-252. Introduction to Mesquite Amblygnathus.nex
Tuesday, Feb. 9 Morphological Data IV - ontogeny & plant structure Fink, William L. (1982). The Conceptual Relationship Between Ontogeny and Phylogeny. Paleobiology, 8(3), 254-264. (JSTOR) Discussion with Quentin Wheeler
Thursday, Feb. 11 Molecular Data I - intro (repeat) 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 Introduction to TNT dq_v2b.tnt
Tuesday, Feb. 16 Molecular Data II - Sequence alignment Morrison, David A. (2009). Why Would Phylogeneticists Ignore Computerized Sequence Alignment?, Systematic Biology, 58(1), 150-158. doi: 10.1093/sysbio/syp009.

Brower, Andrew V. Z., Schawaroch, Valerie (1996). "Three steps of homology assessment." Cladistics, 12(3), 265–272. doi: 10.1111/j.1096-0031.1996.tb00014.x

Phillips, Aloysius; Janies, Daniel; Wheeler, Ward (2000). "Multiple Sequence Alignment in Phylogenetic Analysis." Molecular Phylogenetics and Evolution, 16(3), 317-330. doi: 10.1006/mpev.2000.0785
Genebank, JALVIEW, alignments, ClustalW
Thursday, Feb. 18 Phylogenetic trees I - assumptions, reconstructions Sober, E. (1988). Reconstructing the Past: Parsimony, Evolution, and Inference. Chapter 1. MIT Press. Preview available at Google Books. Intro to PAUP
primate-mtDNA.nex
Tuesday, Feb. 23 Phylogenetic trees II - phenetics, distance-based 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. 25 Phylogenetic trees III - parsimony Siddall, M. and A. Kluge (1997). Probabilism and phylogenetic inference. Cladistics 13, 313-336. (DOI) Introduction to POY
cephalopod_COI.txt
mol1.txt
POY_tutorial_commands.txt
POY4beta_commands.pdf
docs.zip
Tuesday, March 2 Phylogenetic trees IV - maximum likelihood; molecular evolution 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 4 Phylogenetic trees V - measures of support, bootstrap etc. 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 9 Phylogenetic trees VI - Bayesian methods (NJM) Sober, E. (2008). Evidence and Evolution: the logic behind the science, Cambridge University Press. Chapter 1 excerpt.

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 11 Phylogenetic trees VII - tree-to-tree comparisons; consensus methods
(separate figures)
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
graphic of 3 trees of rays
MrBayesCephalopodConsensus.nex
MrBayesCephalopodTprobs.nex
RayMatrix.nex
Tuesday, March 16 Classification I - Biological Systematics | Classification and Phylocode Philip D. Cantino, Harold N. Bryant, Kevin De Queiroz, Michael J. Donoghue, Torsten Eriksson, David M. Hillis and Michael S. Y. Lee (1999). Species Names in Phylogenetic Nomenclature. Systematic Biology, 48(4), 790-807. (JSTOR)

Kevin de Queiroz (2006). The PhyloCode and the Distinction between Taxonomy and Nomenclature. Systematic Biology, 55(1), 160-162. doi:10.1080/10635150500431221
Discuss project progress
Thursday, March 18 Classification II - integrating fossils   QUIZ 1 (covers through March 11)
March 22 - 26: Spring Break
Tuesday, March 30 Classification III - phylogenetic taxonomy; phylocode (short, 1.5 pages) Laurin, M.; de Queiroz, K.; Cantino, P. D. (2006). Sense and stability of taxon names. Zoologica Scripta, 35(1), 113–114. (DOI | Scholar)

Laurin, M.; Cantino, P.D. (2007). Second Meeting of the International Society for Phylogenetic Nomenclature: a Report. Zoologica Scripta, 36(1), 109–117. (Scholar | DOI)
Discussion of phylogenetic taxonomy (using the papers below, and to the left, for today as a framework)

De Queiroz, K., Gauthier, J. (1992). Phylogenetic Taxonomy. Annual Review of Ecology and Systematics, 23, 449-480. (Journal | DOI | JSTOR)

Keller, Roberto A.; Boyd, Richard N.; Wheeler, Quentin D. (2003). The illogical basis of phylogenetic nomenclature. The Botanical Review 69: 93-110. (DOI | Scholar)
Thursday, April 1 Classification IV - 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)
Discussion of species concepts (see papers to left)
Tuesday, April 6 Classification V - nomenclature, Zoological & Botanical Codes   basic intro to scripting in R and mesquite (zipfile with lab and data)
(NOTE: Updated ClustalW script for Macs)
Thursday, April 8 Classification VI - DNA barcoding, DNA taxonomy (KWW) Hebert, P. D. and Gregory, T. R. (2005). “The promise of DNA barcoding for taxonomy.” Systematic Biology 54(5): 852-859. (Pubmed | DOI | Scholar)

Smith, V. S. (2005). “DNA barcoding: perspectives from a "Partnerships for Enhancing Expertise in Taxonomy" (PEET) debate.” Systematic Biology 54(5): 841-844. (Pubmed | DOI | Scholar)

Will, K. W., Mishler, B. D. and Wheeler, Q. D. (2005). “The perils of DNA barcoding and the need for integrative taxonomy.” Systematic Biology 54(5): 844-851. (Pubmed | DOI | Scholar)

Stoeckle, M. Y. and Hebert, P. D. N. (2008). “Bar Code of Life: DNA Tags Help Classify Animals.” Scientific American 299(4): 82-88. (HTML | Scholar)

Meier, R. and Zhang, G. (2009). DNA barcoding and DNA taxonomy in Diptera: An assessment based on 4261 COI sequences for 1001 species. Diptera Diversity: Status, Challenges, and Tools. Pape, T., Bickel, D. and Meier, R. New York, Brill Academic Publishers, 349-380. (Scholar)
Discussion of molecular application papers (students each bring a paper)
Tuesday, April 13 Phylogenetic trees VIII: below the "species level" phylogeography, reticulation 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)
Project Progress Reports
Thursday, April 15 Morphometrics Zelditch, Miriam Leah, Fink, William L., Swiderski, Donald L. and Lundrigan, Barbara L. (1998). “On Applications of Geometric Morphometrics to Studies of Ontogeny and Phylogeny: A Reply to Rohlf.” Systematic Biology. 47(1): 159-167. (Pubmed | DOI)

Ivanović, Ana, Sotiropoulos, Konstantinos, Džukić, Georg and Kalezić, Miloš (2009). “Skull size and shape variation versus molecular phylogeny: a case study of alpine newts ( Mesotriton alpestris , Salamandridae) from the Balkan Peninsula.” Zoomorphology. 128(2): 157-167. (DOI)

de Bivort, Benjamin. L., Clouse, Ronald M. and Giribet, Gonzalo (2010). “A morphometrics-based phylogeny of the temperate Gondwanan mite harvestmen (Opiliones, Cyphophthalmi, Pettalidae).” Journal of Zoological Systematics and Evolutionary Research. (DOI)

Felsenstein, J. (2002). Quantitative characters, phylogenies, and morphometrics. Morphology, shape and phylogeny. MacLeod, N. and Forey, P. L., Eds. London ; New York, Taylor & Francis: 27-44. (Google books)
Morphometrics
Tuesday, April 20 Dating in the 21st century: divergence times, clocks, calibrations   LR tests of molecular clock, R8S, BEAST

CEPHALAPOD.nex

cephalopod_COI_Clustalw.nex

cephalopod_COI.fasta

CephSeq.nuc

CephTree.trees

Thursday, April 22 Historical Biogeography - Kip

Historical Biogeography: event-based methods - Nick
Brooks, D. R., van Veller, M. G. P. and McLennan, D. A. (2002). “How to do BPA, really.” Journal of Biogeography. 28(3): 345-358. (DOI)

Clark, J. R., Ree, R. H., Alfaro, M. E., King, M. G., Wagner, W. L. and Roalson, E. H. (2008). “A comparative study in ancestral range reconstruction methods: retracing the uncertain histories of insular lineages.” Systematic Biology. 57(5): 693-707. (DOI)

Donoghue, M. J. and Moore, B. R., 2003. Toward an Integrative Historical Biogeography. Integrative and Comparative Biology. 43 (2), 261-270. (DOI)

Historical Biogeography with DIVA and Lagrange (zipfile)
Tuesday, April 27 Introduction to Macroevolution Alfaro, M. E., Santini, F., Brock, C., Alamillo, H., Dornburg, A., Rabosky, D. L., Carnevale, G. and Harmon, L. J. (2009). “Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates.” Proceedings of the National Academy of Sciences. 106(32): 13410. (DOI)

Simons, A. M. (2002). “The continuity of microevolution and macroevolution.” Journal of Evolutionary Biology. 15(5): 688-701. (DOI)
Discussion: future of phylogenetic systematics
Thursday, April 29 Introduction to Comparative Methods   QUIZ 2 (covers March 16th-April 29th)
   
May 3-14 Reading & Finals Weeks - Student Symposium will be at:VLSB 2063, 1-4 pm, Thursday May 6.
Wednesday, May 12 Final projects due at 5:00 pm, Wednesday May 12.
Background image adapted from a phylogeny of all organisms with complete genome sequences.

Last update 20 January 2012
by Michael J. Landis