| Date | Lecture | Assigned Readings
(see also Recommended Readings by topic) |
Lab |
| Tuesday, Jan. 18 | Introduction to aims of course (syllabus) / Phylogenetic reconstruction in a nutshell: homology & characters (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 | Local PDF)
(recommended) Pleijel, F. (1995). "On character coding for phylogeny reconstruction." Cladistics 11(3): 309-315. (Scholar | DOI | Link) |
Get acquainted roundtable (all) |
| Thursday, Jan. 20 | Phylogenetic reconstruction in a nutshell: trees (BDM) | Sober, E. (1988). Reconstructing the Past: Parsimony, Evolution, and Inference. Chapter 1. MIT Press. Preview available at Google Books.
|
Tour of systematics collections & resources in VLSB |
| Tuesday, Jan. 25 | What can we do with trees once we have them? 1. Classification classical and modern (DRL) | Laurin, Michel (2008). "The splendid isolation of biological nomenclature." Zoologica Scripta 37(2), 223-233. (Scholar | DOI | Link)
O'Malley, Maureen A.; Martin, William; Dupré, John (2010). "The tree of life: introduction to an evolutionary debate." Biology and Philosophy 25(4), 441-453. (Scholar | DOI | Link -- this was part of a Special Issue on the Tree of Life, 25(4), September 2010) Readings/authors mentioned in class, during discussion of species, essentialism, and the long delay between the Origin and the cladistics revolution: |
Introduction to Statistical Thinking (all)
Background reading on Frequentism and Bayesianism: Efron, B. (1986). "Why isn't everyone a Bayesian?" American Statistician 40(1), 1-5. (Scholar | Link)Doug Theobald on testing Universal Common Ancestry (Theobald will be visiting IB to speak for the Thursday seminar in April): Theobald, Douglas L. (2010). "A formal test of the theory of universal common ancestry." Nature 465(7295), 219-222. (Scholar | DOI | Link) |
| Thursday, Jan. 27 | Qualitative character evolution within a cladogram (discrete states; ancestral state reconstructions; single characters - BDM) | Maddison, W. P.; Slatkin, M. (1991). "Null models for the number of evolutionary steps in a character on a phylogenetic tree." Evolution 45(5), 1184-1197. (Scholar | Link)
Maddison, D. R.; Maddison, W. P. (2000). MacClade 4. Sunderland, Mass., Sinauer Associates, 1-492. (Scholar | Link to MacClade website; PDFs of the manual are linked from Google Scholar) |
Lab #1: Introduction to Mesquite; Discrete character reconstruction
Amblygnathus.nex If you don't have your own data (DNA or character data), or don't want to make it up, trying using theses Pictures of fake "Lundbergidae"; code your own characters -- but here are hints PhyloWiki page for notes and questions (feel free to register if you want to post questions/notes there) |
| Tuesday, Feb. 1 | Qualitative character evolution (comparing two or more characters - BDM) | 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(3), 539-557. (Scholar | DOI | Link)
Pagel, M. (1999). "The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies." Systematic Biology 48(3), 612-622. (Scholar | DOI | Link) |
LAB #2: Phylogenetic Conservatism and Correlation of Discrete Characters (Mesquite - Matzke) Amblygnathus.nex Concentrated_Changes.nex Dess200B.nx Notes on PhyloWiki |
| Thursday, Feb. 3 | Quantitative character evolution within a cladogram (intro; ancestral trait reconstruction; phylogenetic conservatism - BDM) |
Maddison, Wayne P. (1991). "Squared-Change Parsimony Reconstructions of Ancestral States for Continuous-Valued Characters on a Phylogenetic Tree." Systematic Zoology 40(3), 304-314. (Scholar | DOI | Link)
Blomberg, S. P.; Theodore Garland, J. R.; Ives, A. R. (2003). "Testing for phylogenetic signal in comparative data: behavioral traits are more labile." Evolution 57(4), 717-745. (Scholar | DOI | Link) |
PhyloWiki link: LAB #3: Introduction to R (Matzke)
If you want the same thing as just a text file, download it here (I have now added the answers/descriptions, and some bug fixes, 2/8/11): _Nicks_intro_to_R_v4.R Scripts that are being sourced in the lab: _genericR_v1.R _R_tree_functions_v1.R A file we are using (downloaded from TreeBase, here): Caetano-anolles_2002_JME_ToL.newick Note: Introductory books on R and statistics, phylogenetics (Berkeley has online access to all of them): Paradis, E. (2006). Analysis of Phylogenetics and Evolution with R. Springer Verlag. (Scholar | Link) |
| Tuesday, Feb. 8 | Evolution and development - heterochrony (DRL) | Maxwell, E. E.; Harrison, L. B. (2009). "Methods for the analysis of developmental sequence data." Evolution & Development 11(1), 109-119. (Scholar | DOI)
Hunt, G.; Yasuhara, M. (2010). "A fossil record of developmental events: variation and evolution in epidermal cell divisions in ostracodes." Evolution & Development 12(6), 635-646. (Scholar | DOI) |
LAB #4: Intro to R continued: Phylogenies; Continuous characters
_ib200b_lab4_R_continuous_characters_v1.R chronogram_bkup.R anoles_continuous.nex anoles_continuous_data_table.txt |
| Thursday, Feb. 10 | Independent contrasts and trait correlations (Ginger Jui) | From Ginger: "PICs are introduced in the first reading, Ackerly 2009. Just read the
first 5 pages of this summary article. It actually doesn't have any of the
math in it; we'll cover this in class. I'll then introduce model-testing approaches for the comparative analysis of trait evolution. We'll talk about the Orhnstein-Uhlenbeck model (Butler 2004) and the use of maximum likelihood approaches for model inference (Harmon 2010)." PIC_exercise_v1.R Ackerly, David D. (2009). "Phylogenetic Methods in Ecology." Encyclopedia of Life Sciences. (Scholar | DOI | Link) |
LAB #5: Correlations between variables/characters: correlation, Principle Components, and Phylogenetically Independent Contrasts (R)
_ib200b_lab5_R_PICs_v1.R (text file of the above) Data: anoles_continuous.nexScripts: The lab sources these scripts remotely, but you may want to have them for future reference. You can source scripts locally by using the command source like this: source("insert_file_path_and_name")
Eventually, once you get good at R, many of your own analyses will be done in scripts you source from your main analysis script. _genericR_v1.R |
| Tuesday, Feb. 15 | Morphometrics (DRL) | Catalano, S. A.; Goloboff, P. A.; Giannini, N. P. (2010). "Phylogenetic morphometrics (I): the use of landmark data in a phylogenetic framework." Cladistics 26(5), 539-549. (Scholar | DOI | Link)
Sidlauskas, B. (2008). "Continuous and arrested morphological diversification in sister clades of characiform fishes: a phylomorphospace approach." Evolution 62(12), 3135-3156. (Scholar | DOI | Link) |
LAB #6: morphometrics applications
(PhyloWiki notes, if any) LAB #6: morphometrics applications We will use the software installed on the lab computers. However, if you ever need it, it is online here (typically you will need Windows, or a Windows emulator on a Mac (perhaps "Wine" is an option): http://life.bio.sunysb.edu/morph/soft-dataacq.html http://www3.canisius.edu/%7Esheets/morphsoft.html We are using the "standard" tool for morphometrics, but much morphometrics analysis can now be done in R. See: Claude, J. (2008). Morphometrics with R, Springer Verlag, 298. (Scholar | Link) ...or talk to Liz & Jessie, who took a short course on this. |
| Thursday, Feb. 17 | Fossil data in phylogenetics (DRL) | Magallon, S. (2010). "Using fossils to break long branches in molecular dating: a comparison of relaxed clocks applied to the origin of angiosperms." Systematic Biology. (Scholar)
Zhao, J.; Zhao, Y.; Shih, C.; Ren, D.; Wang, Y. (2010). "Transitional fossil earwigs- a missing link in Dermaptera evolution." BMC Evolutionary Biology 10(1), 344. (Scholar) |
LAB: PROJECT TOPIC DUE: discuss your potential project in class |
| Tuesday, Feb. 22 | Tempo in macroevolution (DRL) |
Wright, Sewall (1945). "Review: Tempo and Mode in Evolution: A Critical Review." Ecology 26(4), 415-419. (Scholar | DOI | Link)
Baker, Allan J.; Huynen, Leon J.; Haddrath, Oliver; Millar, Craig D.; Lambert, David M. (2005). "Reconstructing the tempo and mode of evolution in an extinct clade of birds with ancient DNA: The giant moas of New Zealand." Proceedings of the National Academy of Sciences of the United States of America 102(23), 8257-8262. (Scholar | DOI | Link) McPeek, Mark A.; Shen, Li; Torrey, John Z.; Farid, Hany (2008). "The Tempo and Mode of Three-Dimensional Morphological Evolution in Male Reproductive Structures." The American Naturalist 171(5), E158-E178. (Scholar | DOI | Link) Also: Purvis, Andy (2008). "Phylogenetic Approaches to the Study of Extinction." Annual Review of Ecology, Evolution, and Systematics 39(1), 301-319. (Scholar | DOI | Link) Krug, Andrew Z.; Jablonski, David; Valentine, James W.; Roy, Kaustuv (2009). "Generation of Earth's First-Order Biodiversity Pattern." Astrobiology 9(1), 113-124. (Scholar | DOI | Link) Rabosky, Daniel (2009). "Ecological Limits on Clade Diversification in Higher Taxa." The American Naturalist 173(5), 662-674. (Scholar | DOI | Link) |
Note: much of this is unpublished data which I will take down after the lab. Do not re-use e.g. for publications or othe courses without talking to me. Thanks! LAB #7: testing molecular clock, r8s, BEAST (Matzke) (txt file: _dating_code_v1.R) PDF of lab r8s and R: cons_Ecab_chrM_12May2010.fasta_nn.aln_prc.nexus_reroot.nexus cons_Ecab_chrM_12May2010.fasta_nn.aln_prc.nexus.phy cons_Ecab_chrM_12May2010.fasta_nn.aln_prc.nexus compare_Rchrono_r8s.pdf BEAST Tutorial: do the primates tutorial (online here) Local backup: dating_primates.pdf primates.nex Simulated fossils in BEAST (EXPERIMENTAL!): simt_connected100_86_newick.txt simmorph_4states100.nex Download one or more of these XML control files for BEAST: http://ib.berkeley.edu/courses/ib200b/labs/beast_inputs/ For the 200A lab on molecular clock: Cephalopod.nex |
| Thursday, Feb. 24 | Dating in the 21st Century: putting dates on nodes, characters, and events (DRL) | Marshall, Charles R. (2008). "A Simple Method for Bracketing Absolute Divergence Times on Molecular Phylogenies Using Multiple Fossil Calibration Points." The American Naturalist 171(6), 726-742. (Scholar | DOI | Link)
Sorhannus, U. (1993). "Relative-rate tests versus paleontological divergence data for diatoms and vertebrates." Acta Palaeontologica Polonica 38(3-4), 199-214. (Scholar | Link) |
LAB: discussion: the use of fossil data in phylogenetic reconstruction (all) |
| Tuesday, March 1 | Molecular evolution (BDM) | Wolfe, Kenneth H.; Li, Wen-Hsiung (2003). "Molecular evolution meets the genomics revolution." Nature Genetics 33(3s), 355-365. (Scholar | DOI | Link)
|
LAB #8: analysis of molecular evolution; substitution models, Modeltest, etc (Matzke)
PTK_Nem_phyl.txt PTK_Nem_small.nex Parts.txt Also, we don't have time for it here, but if you start doing likelihood phylogenies with DNA data, you need to assess the different DNA substitution models and pick best one with a Likelihood Ratio Test or with AIC. This is typically done with ModelTest and PAUP; see the IB200a lab: ib200a_lab09_ML_PAUP_modeltest.pdf cephalopod_COI_Clustalw.nex modelblockPAUPb10.nex |
| Thursday, March 3 | Gene family evolution; comparative genomics (Matzke) | Phylogenomics and genome phylogenetics:
Eisen, Jonathan A.; Fraser, Claire M. (2003). "Phylogenomics: Intersection of Evolution and Genomics." Science 300(5626), 1706-1707. (Scholar | DOI | Link)Phylostratigraphy and the developmental hourglass observed in relative diversification of transcriptome timepoints: Prud'Homme, B.; Gompel, N. (2010). "Evolutionary biology: Genomic hourglass." Nature 468(7325), 768-769. (Scholar | DOI | Link) |
LAB #9: tools for comparative genomics; BLAST, etc. (Matzke) Mystery.fasta Nematode_lin-39.fasta |
| Tuesday, March 8 | Evolution and Development (DRL) | Jacobs, David K.; Hughes, Nigel C.; Fitz-Gibbon, Sorel T.; Winchell, Christopher J. (2005). "Terminal addition, the Cambrian radiation and the Phanerozoic evolution of bilaterian form." Evolution & Development 7(6), 498-514. (Scholar | DOI | Link)
Grande, Cristina; Patel, Nipam H. (2009). "Nodal signalling is involved in left-right asymmetry in snails." Nature 457(7232), 1007-1011. (Scholar | DOI | Link) |
LAB #10: tools for evo-devo (Matzke) (PhyloWiki version) ib200b_lab10_evodevo_v2.R The other files you need are here (temporarily available, as this is unpublished): http://ib.berkeley.edu/courses/ib200b/labs/lab10/ These are useful papers giving background on models of evolution for continuous traits: Pagel, Mark (1999). "Inferring the historical patterns of biological evolution." Nature 401(6756), 877-884. (Scholar | DOI | Link) |
| Thursday, March 10 | Comparing sister clades within a cladogram: the shape of evolution (DRL) |
Greenhill, S. J.; Atkinson, Q. D.; Meade, A.; Gray, R. D. (2010). "The shape and tempo of language evolution." Proceedings of the Royal Society B: Biological Sciences 277(1693), 2443-2450. (Scholar | DOI | Link)
Nat's notes have a great list of references on this topic, here are a few highlights: Maddison, W. P.; Slatkin, M. (1991). "Null models for the number of evolutionary steps in a character on a phylogenetic tree." Evolution 45(5), 1184-1197. (Scholar | Link) Paradis, Emmanuel (2008). "Asymmetries in phylogenetic diversification and character change can be untangled." Evolution 62(1), 241-247. (Scholar | DOI | Link) Moore, Brian R.; Donoghue, Michael J. (2007). "Correlates of Diversification in the Plant Clade Dipsacales: Geographic Movement and Evolutionary Innovations." The American Naturalist 170(S2), S28-S55. (Scholar | DOI | Link) |
This lab has a PDF/Mesquite section, and an R code section: LAB #11: generating random trees; testing cladogram imbalance (Matzke) ib200b_lab11_tree_shape_clade_imbalance_v1.R (PhyloWiki version) Colless_example.nex Comparing_Clades.xls Compare_Clades.exe (optional bit of the lab, for those who can run Windows executables) |
| Tuesday, March 15 | Phylogenetics and adaptation (BDM) | Gould, S. J.; Lewontin, R. C. (1979). "The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme." Proceedings of the Royal Society of London. Series B, Biological Sciences 205(1161), 581-598. (Scholar | Link) | LAB: discussion of adaptation (all) |
| Thursday, March 17 | Adaptive radiations (BDM) | Ackerly, David (2009). "Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal." Proceedings of the National Academy of Sciences 106(Supplement 2), 19699-19706. (Scholar | DOI | Link) | LAB #12: lineages through time; diversification analyses (Matzke) Several useful references: Rabosky, Daniel L. (2006). "Likelihood methods for detecting temporal shifts in diversification rates." Evolution 60(6), 1152-1164. (Scholar | DOI | Link) |
| March 21 - 25: | Spring Break | ||
| Tuesday, March 29 | Speciation and related issues: species revisited (BDM) | Mishler, Brent D. (2009). "Species are not Uniquely Real Biological Entities." Contemporary Debates in Philosophy of Biology. F. Ayala and R. Arp, Wiley-Blackwell, 110-122. (Scholar | DOI | Link | Local PDF) | LAB: QUIZ 1 (see past quizzes) |
| Thursday, March 31 | Reticulation and phylogenetics; "phylogeography" and population biology (BDM) | Posada, David; Crandall, Keith A. (2001). "Intraspecific gene genealogies: trees grafting into networks." Trends in Ecology & Evolution 16(1), 37-45. (Scholar | DOI | Link) | LAB: discussion of species (all) (your project data set should be complete) |
| Tuesday, April 5 | Phylogenetics and conservation biology (BDM) | Faith, Daniel P. (1992). "Conservation evaluation and phylogenetic diversity." Biological Conservation 61(1), 1-10. (Scholar | DOI | Link)
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LAB #13: coalescence theory in Mesquite (Matzke) Coalescence_Example_1.nex Coalescence_Example_1.nex Coalescence_Example_1.nex Temp.nex |
| Thursday, April 7 | Modes in macroevolution - patterns of diversification and extinction (DRL) | Valentine, James W.; Jablonski, David (2010). "Origins of marine patterns of biodiversity: some correlates and applications." Palaeontology 53(6), 1203-1210. (Scholar | DOI | Link)
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LAB: discussion on levels of selection (all) |
| Tuesday, April 12 | Comparing cladograms; supertrees; coevolution; symbiosis (BDM) | Page, Roderic D. M.; Charleston, Michael A. (1998). "Trees within trees: phylogeny and historical associations." Trends in Ecology & Evolution 13(9), 356-359. (Scholar | DOI | Link) | LAB #14: consensus methods; Brooks parsimony (Matzke) Get the files here (you might have to try an alternative from the ones mentioned in the lab text, but probably the one in the text will work). Cited articles: Rosen, Donn Eric (1979). "Fishes from the uplands and intermontane basins of Guatemala: revisionary studies and comparative geography." Bulletin of the American Museum of Natural History 162, 269-375. (Scholar | Link) |
| Thursday, April 14 | Biogeography I -- basic principles; ecological vs. historical approaches; vicariance biogeography (DRL) | Crisp, Michael D.; Trewick, Steven A.; Cook, Lyn G. (2011). "Hypothesis testing in biogeography." Trends in Ecology & Evolution 26(2), 66-72. (Scholar | DOI | Link)
Buerki, Sven; Forest, Félix; Alvarez, Nadir; Nylander, Johan A. A.; Arrigo, Nils; Sanmartín, Isabel (2011). "An evaluation of new parsimony-based versus parametric inference methods in biogeography: a case study using the globally distributed plant family Sapindaceae." Journal of Biogeography 38(3), 531-550. (Scholar | DOI | Link) |
LAB #15: Biogeographic software; DIVA, Lagrange
All files (except some of the executables, see lab) are available here: http://ib.berkeley.edu/courses/ib200b/labs/lab15/ (download the lab15.zip zipfile) Reading: Donoghue, Michael J.; Moore, Brian R. (2003). "Toward an Integrative Historical Biogeography." Integrative and Comparative Biology 43(2), 261-270. (Scholar | DOI | Link) |
| Tuesday, April 19 | Biogeography II -- New tools, databases, and research possibilities (Matzke) | TBA | LAB: discuss progress on projects in class (hand in outline of project April 18th, details TBA) |
| Thursday, April 21 | Interactions among clades in macroevolution (DRL) |
Heard, Stephen B.; Cox, Graham H. (2007). "The Shapes of Phylogenetic Trees of Clades, Faunas, and Local Assemblages: Exploring Spatial Pattern in Differential Diversification." The American Naturalist 169(5), E107-E118. (Scholar | DOI | Link)
Briggs, John C. (1998). "Biotic Replacements: Extinction or Clade Interaction?" BioScience 48(5), 389-395. (Scholar | Link) |
LAB: discussion of application papers (students to bring papers from their groups) |
| Tuesday, April 26 | Phylogenies and Community Ecology; Assembly of Regional Biota (Ginger Jui) | Cavender-Bares, J.; Ackerly, D. D.; Baum, D. A.; Bazzaz, F. A. (2004). "Phylogenetic Overdispersion in Floridian Oak Communities." The American Naturalist 163(6), 823-843. (Scholar | DOI | Link)
Swenson, Nathan G.; Enquist, Brian J.; Pither, Jason; Thompson, Jill; Zimmerman, Jess K. (2006). "The problem and promise of scale dependency in community phylogenetics." Ecology 87(10), 2418-2424. (Scholar | DOI | Link) Background: Webb, Campbell O.; Ackerly, David D.; McPeek, Mark A.; Donoghue, Michael J. (2002). "Phylogenies and Community Ecology." Annual Review of Ecology and Systematics 33, 475-505. (Scholar | DOI | Link) |
LAB #16: phylocom, picante (Matzke)
oaksample.txt oakphylo.txt |
| Thursday, April 28 | Glimpses of the future - comparative and functional genomics; integrating genetics, physiology, ecology and evolution (all) | LAB: QUIZ 2 | |
| May 2-13 | Reading & Finals Weeks - Student Symposium will be at: VLSB 2063, TBA. | ||
| Wednesday, May TBA | Final projects due at TBA. | ||