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Reading List 7
The required readings are marked with two asterisks**. Highly recommended readings
are marked with one asterisk*; the rest are for background information and to allow
you an entrance into the literature.

March 16, 23: Phylogenetic Trees I and III: reconstruction, algorithms & assumptions; parsimony revisited



Albert VA, Chase MW, and Mishler BD (1993) Character-state weighting for cladistic analysis of protein-coding DNA sequences. Ann. Missouri Bot. Gard. 80:752-766.


Albert VA, and Mishler BD (1992) On the rationale and utility of weighting nucleotide sequence data. Cladistics 8:73-83.


Albert VA, Mishler BD, and Chase MW (1992) Character-state weighting for restriction site data in phylogenetic reconstruction, with an example from chloroplast DNA. In PS Soltis, DE Soltis and JJ Doyle (eds.): Molecular Systematics of Plants. New York:Chapman & Hall, pp. 369-403.


Anderson, J. S. 2001. The phylogenetic trunk: maximal inclusion of missing data in an analysis of the Lepospondyli (Vertebrata, Tetrapoda). Systematic Biology 50: 170-193.


Bininda-Emonds, O. R. P., M. J. Sanderson. 2001. Assessment of the accuracy of matrix representation with parsimony analysis supertree construction. Systematic Biology 50: 565-579.


Bodenbender, B. E. and D. C. Fisher. 2001. Stratocladistic analysis of blastoid phylogeny. Journal of Paleontology 75: 351-369.


Bremer, B., R. K. Jansen, B. Oxelman, M. Backlund, H. Lantz, and K.-J. Kim. 1999. More characters or more taxa for a robust phylogeny – case study from the coffee family (Rubiaceae). Systematic Biology 48: 413-435.


Brochu, C. A. 1999. Taxon sampling and reverse successive weighting. Systematic Biology 48: 808-814.


Camin, J. H. and R. R. Sokal. 1965. A method for deducing branching sequences in phylogeny. Evolution 19:311-326.


Cavalli-Sforza, L. L. and A. W. F. Edwards. 1967. Phylogenetic analysis: Models and estimation procedures. Evolution 32:550-570.


CLYDE, W. C. AND D. C. FISHER. 1997. Comparing the fit of stratigraphic and morphologic data in phylogenetic analysis. Paleobiology 23: 1-19.


Constantinescu, M. and D. Sankoff. 1986. Tree enumeration modulo a consensus. Journal of Classification 3:349-356.


Donoghue, M. J. and W. P. Maddison. 1986. Polarity assessment in phylogenetic systematics: a response to Meacham. Taxon 35:534-545.


Farris, J. S. 1969. A successive approximations approach to character weighting. Systematic Zoology 18:374-385.


Farris, J. S. 1970. Methods for computing Wagner trees. Systematic Zoology 19:83-92.


Farris, J. S. 1972. Estimating phylogenetic trees from distance matrices. American Naturalist 106:645-668.


Farris, J. S. 1977. Phylogenetic analysis under Dollo's Law. Systematic Zoology 26:77-88.


Farris JS (1981) Distance data in phylogenetic analysis. In VA Funk and DR Brooks (eds.): Advances in Cladistics: Proceedings of the First Meeting of the Willi Hennig Society. Bronx, New York:New York Botanical Garden, pp. 3-23.


Farris, J. S. 1982. Outgroups and parsimony. Systematic Zoology 31:328-334.


Farris JS (1983) The logical basis of phylogenetic analysis. In N Platnick and V Funk (eds.): Advances in Cladistics, Volume 2. NY.:Columbia Univ. Press, pp. 7-36.


Farris, J. S. 1988. Hennig86, version 1.5. Distributed by the author, Port Jefferson Station, NY.


Felsenstein, J. 1978. The number of evolutionary trees. Systematic Zoology 27:27-33.


Felsenstein J (1978) Cases in which parsimony and compatibility will be positively misleading. Syst. Zool. 27:401-410.


Felsenstein, J. 1984. The statistical approach to inferring phylogeny and what it tells us about parsimony and compatibility. Pages 169-191 in T. Duncan and T. F. Stuessy (ed.), Cladistics: Perspectives on the Reconstruction of Evolutionary History (Columbia University Press: New York).


FISHER, D. C. 1991. Phylogenetic analysis and its application in evolutionary paleobiology. Pages 103-121 in Analytical Paleobiology (N. L. Gilinsky and P. W. Signor, eds.). Paleontological Society, Knoxville, TN.


FISHER, D. C. 1992. Stratigraphic Parsimony. Pages 124-129 in MacClade: Analysis of Phylogeny and Character Evolution, Version 3 (W. P. Maddison and D. R. Maddison, eds.). Sinauer Associates, Sunderland, MA.


FISHER, D. C. 1994. Stratocladistics: morphological and temporal patterns and their relation to phylogenetic process. Pages 133-171 in Interpreting the Hierarchy of Nature – from systematic patterns to evolutionary theories (L. Grande and O. Rieppel, eds.). Academic Press, San Diego.


Fitch, W. M. 1971. Toward defining the course of evolution: minimal change for a specific tree topology. Systematic Zoology 20:406-416.


Gaffney ES (1979) An introduction to the logic of phylogeny reconstruction. In J Cracraft and N Eldredge (eds.): Phylogenetic Analysis and Paleontology. New York:Columbia University Press, pp. 79-111.


Gascuel, O., D. Bryant, and F. Denis. 2001. Strengths and limitations of the minimum evolution principle. Systematic Biology 50: 621-627.


Hendy, M. D. and D. Penny. 1982. Branch and bound algorithms to determine minimal evolutionary trees. Mathematical Biosciences 59:277-290.


Hendy, M. D., M. A. Steel, D. Penny, and I. M. Henderson. 1988. Families of trees and consensus. Pages 355-362 in H. H. Bock (ed.), Classification and Related Methods of Data Analysis (Elsevier: Amsterdam).


Hennig, W. 1966. Phylogenetic Systematics. (University of Illinois Press: Urbana, Illinois).


Hillis, D. M. 1987. Molecular versus morphological approaches to systematics. Annual Review of Ecology and Systematics 18:23-42.


Hillis DM, Bull JJ, White ME, Badgett MR, and Molineux IJ (1992) Experimental phylogenetics: generation of a known phylogeny. Science 255:589-592.


Houseworth, E. A> and E. P. Martins. 2001. Random sampling of constrained phylogenies: conducting phylogenetic analyses when the phylogeny is partially known. Systematic Biology 50: 628-639.


Huelsenbeck, J. P. 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44: 17-48.


Kim, J. 1996. General inconsistency conditions for maximum parsimony: effects of branch lengths and increasing numbers of taxa. Syst. Biol. 45: 363-374.


Kitching, I. J., P. L. Forey, C. J. Humphries, and D. M. Williams. 1998. Cladistics: The Theory and Practice of Parsimony Analysis. Second Edition. Oxford, Oxford University Press.


Kluge, A. G. and J. S. Farris. 1969. Quantitative phyletics and the evolution of anurans. Systematic Zoology 18:1-32.


Kornet, D. J. and H. Turner. 1999. Coding polymorphism for phylogeny reconstruction. Systematic Biology 48: 365-379.


Lake JA (1987) Determining evolutionary distances from highly diverged nucleic acid sequences: operator metrics. J. Mol. Evol. 26:59-73.


Lundberg, J. G. 1972. Wagner networks and ancestors. Systematic Zoology 21:398-413.


Maddison, D. R. 1991. The discovery and importance of multiple islands of most-parsimonious trees:. Systematic Zoology 40:315-328.


Maddison, W. P. 1989. Reconstructing character evolution on polytomous cladograms. Cladistics 5:365-377.


** Maddison, W. P., and D. R. Maddison. 1992. MacClade: Analysis of Phylogeny and Character Evolution (version 3). Sinauer Associates, Sunderland, MA.


Meacham, C. A. 1984. The role of hypothesized direction of characters in the estimation of evolutionary history. Taxon 33:26-38.


Meacham, C. A. 1986. More about directed characters: a reply to Donoghue and Maddison. Taxon 35:538-540.


Mitchell, A., C. Mitter, and J. C. Regier. 2000. More taxa or more characters revisited: combining data from nuclear protein-encoding genes for phylogenetic analyses of Noctuoidea (Insecta: Lepidoptera). Systematic Biology 49: 202-224.


Nelson G, and Platnick N (1981) Systematics and Biogeography. Cladistics and Vicariance. New York:Columbia Univ. Press.


O’Keefe, F. R. and P. M. Sander. 1999. Paleontological paradigms and inferences of phylogenetic pattern: a case study. Paleobiology 25: 518-533.


Page, R. D. M. 1989. Comments on component-compatibility in historical biogeography. Cladistics 5:167-182.


Penny, D. and M. D. Hendy. 1985. The use of tree comparison metrics. Systematic Zoology 34:75-82.


Penny D, Hendy MD, and Steel MA (1992) Progress with methods for constructing evolutionary trees. Trends Ecol. Evol. 7:73-79.


Pickett KM, Tolman GL, Wheeler WC, et al. Parsimony overcomes statistical inconsistency with the addition of more data from the same gene. CLADISTICS 21 (5): 438-445 OCT 2005


Prendini, L. 2001. Species or supraspecific taxa as terminals in cladistic analysis? Groundplans versus exemplars revisited. Systematic Biology 50: 290-300.


Quicke, D. L. J., J. Taylor, and A. Purvis. 2001. Changing the landscape: a new strategy for estimating large phylogenies. Systematic Biology 50: 60-66.


Sankoff, D., R. J. Cedergren, and W. McKay. 1982. A strategy for sequence phylogeny research. Nucleic Acids Research 10:421-431.


Sankoff, D. D. and R. J. Cedergren. 1983. Simultaneous comparison of three or more sequences related by a tree. Pages 253-263 in D. Sankoff and J. B. Kruskal (ed.), Time Warps, String Edits, and Macromolecules: the Theory and Practice of Sequence Comparison (Addison-Wesley: Reading, Mass.).


Sankoff, D. D. and P. Rousseau. 1975. Locating the vertices of a Steiner tree in an arbitrary metric space. Mathematical Programming 9:240-246.


Simmons, N. B. 2001. Misleading results from the use of ambiguity coding to score polymorphisms in higher-level taxa. Systematic Biology 50: 613-620.


Smith, E. N., and R. L. Gutberlet Jr. 2001. Generalized frequency coding: a method of preparing polymorphic multistate characters for phylogenetic analysis. Systematic Biology 50: 156-169.


Sokal, R. R. and F. J. Rohlf. 1981. Taxonomic congruence in the Leptopodomorpha re-examined. Systematic Zoology 30:309-325.


Sober, Elliott. The contest between parsimony and likelihood. Systematic Biology 53 (4) : 644-653 August 2004


Swofford, D. L. 1991. When are phylogeny estimates from morphological and molecular data incongruent? Pages 295-333 in M. M. a. J. C. Miyamoto (ed.), Phylogenetic Analyis of DNA Sequences (Oxford University Press: New York, N. Y.).


Swofford, D. L. and W. P. Maddison. 1987. Reconstructing ancestral character states under Wagner parsimony. Mathematical Biosciences 87:199-229.


Swofford DL, and Olsen GJ (1990) Phylogeny reconstruction. In DM Hillis and C Moritz (eds.): Molecular Systematics (First Edition). Sunderland, MA:Sinauer Associates, pp. 411-501.


** Swofford, D. L. 1991. PAUP: Phylogenetic Analysis Using Parsimony, 3.1. Illinois Nat. Hist. Surv., Champaign, Illinois.


Templeton, A. R. 1983a. Convergent evolution and non-parametric inferences from restriction fragment and DNA sequence data. Pages 151-179 in B. Weir (ed.), Statistical Analysis of DNA Sequence Data (Marcel Dekker: New York).


Templeton, A. R. 1983b. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and apes. Evolution 37:221-244.


WAGNER, P. J. 1995. Stratigraphic tests of cladistic hypotheses. Paleobiology 21: 153-178.

WAGNER, P. J. 1997. Patterns of morphologic diversification among the rostroconchia. Paleobiology 23: 115-150.


Wiley, E. O. 1981. Phylogenetics. The Theory and Practice of Phylogenetic Systematics. (Wiley and Sons: New York).


Wheeler W.C. and Nixon K. 1994. A novel method for economical, diagnosis of cladograms Sankoff optimization. Cladistics 10(2): 207-213


Wiley, E. O., D. Siegel-Causey, D. R. Brooks, and V. A. Funk. 1991. The Compleat Cladist. A Primer of Phylogenetic Procedures. (University of Kansas Museum of Natural History Special Publ. No. 19: Lawrence, Kansas).

March 21: Phenetics


Barbujani, G., Oden, N.L., & Sokal, R.R. 1989. Detecting regions of abrupt change in maps of biological variables. Systematic Zoology 38(4):37 6-389.


Barrett S.J. & Sneath, P.H.A. 1994. A numerical phenotypic taxonomic study of the genus Neisseria. Microbiology 140:2867-2891.


Blackwelder, R.E. 1967. A critique of numerical taxonomy. Systematic Zoology 16(1):64-72.


* Colless, D.H. 1967. An examination of concepts in phenetic taxonomy. Systematic Zoology 16(1):6-27.


** Farris, J.S. 1967. The meaning of relationship and taxonomic procedure. Systematic Zoology 16(1):44-51.


Felsenstein, J. The troubled growth of statistical phylogenetics. Systematic Biology 50: 465-467.


Huson, Daniel H.; Steel, Mike. Distances that perfectly mislead. Systematic Biology 53 (2) : 327-332 April 2004


* Jacobson, H.R. & Kistner, D.H. 1975. Numeric analyses of the relationships of genera and species of the subtribe Termitusina (Coleoptera: Staphylinidae). Systematic Zoology 24(1):191-198.


* Kim, J., Rohlf, F.J. & Sokal, R.R. 1993. The accuracy of phylogenetic estimation using the neighbor-joining method. Evolution, 47(2): 471-486.


Mayr, E. 1965. Numerical phenetics and taxonomic theory. Systematic Zool.14: 73-97.


Moss, W. 1968. Experiments with various techniques of numerical taxonomy. Systematic Zoology 17(1):31-47.


Nelson, A.D. and W.J. Elisens. 1999. Polyploid evolution and biogeography in Chelone (Scrophulariaceae): Morphological and isozyme evidence. AM J BOT 86: (10) 1487-1501.


Rasnitsyn, A.P. 1996. Conceptual issues in phylogeny, taxonomy, and nomenclature

CONTRIB ZOOL 66: (1) 3-41.


Rohlf, F.J., Chang, W.S., Sokal, R.R. & Kim, J.Y. 1990. Accuracy of estimated phylogenies effects of tree topology and evolutionary model. Evolution 44(6):1671-1684.


Sneath, P. H. A. 1967. Some statistical problems in numerical taxonomy. Statistician17:1-12.


Sneath, P. H. A. 1969. Recent trends in numerical taxonomy. Taxon, 18:14-20.


* Sneath, P. H. A. 1971. Numerical taxonomy: criticisms and critiques. Biol. J. Linn. Soc.3: 147-157.


Sneath, P. H. A. 1961. Recent developments in theoretical and quantitative taxonomy. Systematic Zool. 10: 118-139.


Sneath, P.H.A. 1989. Analysis and interpretation of sequence data for bacterial systematics: The view of a numerical taxonomist. Systematic and Applied Microbiology 12:15-31.


Sneath, P. H. A., and R. R. Sokal 1962. Numerical taxonomy. Nature 193: 855-860.


** Sneath, P.H.A. & Sokal, R.R. 1973. Numerical taxonomy; the principles and practice of numerical classification. W. H. Freeman, San Francisco.


Sokal, R. R. 1965. Statistical methods in systematics. Biol. Rev. 40: 337-391.


Sokal, R. R. 1966. Numerical taxonomy. Sci. Amer. 215(6): 106 116.


Sokal, R. R. 1969. Animal taxonomy: theory and practice. Quart. Rev. Biol. 44: 209-211.


Sokal, R. R., J. H. Camin, F. J. Rohlf, and P. H A. Sneath (1965). Numerical taxonomy: some points of view. Systematic Zool., 14:237-243.


* Sokal, R.R., Kim, J.Y. & Rohlf, F.J. 1992. Character and OTU stability in 5 taxonomic groups. Journal of Classification 9 (1):117-140.


* van der Steen, W.J. & Boontje, W. 1973. Phylogenetic versus phenetic taxonomy: A reappraisal. Systematic Zoology 22(1):55-63.

April 4: Phylogenetic Trees IV: Maximum likelihood


Bergsten J. A review of long-branch attraction . CLADISTICS 21 (2): 163-193 APR 2005


Buckley, T. R., C. Simon, and G. K. Chambers. 2001. Exploring among0site variation models in a maximum likelihood framework using empirical data: effects of model assumptions on estimates of topology, branch lengths, and bootstrap support. Systematic Biology 50: 67-86.


Brinkmann, Henner; Van der Giezen, Mark; Zhou, Yan, et al., An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. Systematic Biology 54 (5) OCT 2005


Caterinno, M. S., R. D. Reed, M. M. Kuo, and F. A. H. Sperling. 2001. A partitioned likelihood analysis of swallowtail butterfly phylogeny (Lepidoptera: Papilionidae). Systematic Biology 50: 106-127.


DeBry, R. W. and N. A. Slade. 1985. Cladistic analysis of restriction endonuclease cleavage maps within a maximum-likelihood framework. Systematic Zoology 34:21-34.


DeQueiroz, K. and S. Poe. 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.


Huelsenbeck, J. P. and B. Rannala. 1997. Maximum likelihood estimation of hpylogeny using stratigraphic data. Paleobiology 23:174-180.


Huelsenbeck, J. P. and B. Rannala. 2000. Using stratigraphic information in phylogenetics. pp. 165-191 in J. J. Wiens (ed.), Phylogenetic Analysis of Morphological Data. Washington DC, Smithsonian Institution Press.


Faith, D. P. and W. H. Trueman. 2001. Towards an inclusive phylogeny for phylgenetic inference. Systematic Biology 50: 331-350.


Farris, J. S. 2000. Corroboration versus "Strongest Evidence. Cladistics 16: 385-393.


** Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.


Haber, Matthew H.

On probability and systematics: Possibility, probability, and phylogenetic inference

Systematic Biology 54 (5) OCT 2005


Kluge, A. G. 2001. Philosophical conjectures and their refutation. Systematic Biology 50: 322-331.


Lewis, P. O. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology 50: 913-925.


Mooers, A. O. and D. Schluter. 1990. Reconstructin ancestor states with maximum likelihood: support for one- and two-rate models. Systematic Biology 48: 612-622.


Pagel, M. 1999. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Systematic Biology 48: 612-622.


Pol, D. and M. E. Siddall. 2001. Biases in Maximum Likelihood and Parsimony: A Simulation Approach to a 10-Taxon Case. Cladistics 17: 266-281.


Rogers, J. S. 2001. Maximum likelihood estimation of phylogenetic trees is consistent when substitution rates vary according to the invariable sites plus gamma distribution. Systematic Biology 50: 713-722.


Salter, L. A. 2001. Complexity of the likelihood surface for a large DNA data set. Systematic Biology 50: 970-978.


Salter, L. A. and D. K Pearl. 2001. Stochastic search strategy for estimation of maximum likelihood phylogenetic trees. Systematic Biology 50: 7-18


Sanderson, M. J. and J. Kim. 2000. Parametric phylogenetics? Systematic Biology 49: 817-829.


Swofford, D. L, P. J. Waddell, J. P. Huelsenbeck, P. G. Foster, P. O. Lewis, and J. S. Rogers. 2001. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Systematic Biology 50: 525-539.


Wagner, P. J. 1998. A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa. Paleobiology 24: 430-449.


WAGNER, P. J. 1999. The utility of fossil data in phylogenetic analyses: a likelihood example using Ordovician-Silurian species of the Lophospiridae (Gastropoda: Murchisoniina). Amer. Malac. Bull. 15: 1-31.


Wagner, P. J. 2000. Phylogenetic analyses and the fossil record: tests and inferences, hypotheses and models. Paleobiology 26 (supplement to 4): 341-371.


Wagner, P. J. 2001. Rate heterogeneity in shell character evolution among lophospirioid gastropods. Paleobiology 27: 290-310.

April 6: Bayesian Methods


Nylander, Johan A. A.; Ronquist, Fredrik; Huelsenbeck, John P., et al. Bayesian phylogenetic analysis of combined data. Systematic Biology 53 (1) : 47-67 February 2004


Pagel, Mark; Meade, Andrew; Barker, Daniel. Bayesian estimation of ancestral character states on phylogenies. Systematic Biology 53 (5) : 673-684 October 2004


Redelings, Benjamin D.; Suchard, Marc A. Joint Bayesian estimation of alignment and phylogeny. Systematic Biology 54 (3) : 401-418 JUN 2005


Yang, Ziheng; Rannala, Bruce. Branch-length prior influences Bayesian posterior probability of phylogeny. Systematic Biology 54 (3) : 455-470 JUN 2005


Zwickl, Derrick J.; Holder, Mark T. Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics. Systematic Biology 53 (6) : 877-888 December 2004