Integrative Biology 200A
Syllabus and Handouts

Syllabus pdf; see also 2010 handouts, 2008 handouts

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

Last update 20 January 2012
by Michael J. Landis