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Reading List 5
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.

Feb 21 & 23: Molecular data


Albert, V. A. and B. D. Mishler. 1992. On the rationale and utility of weighting nucleotide sequence data. Cladistics 8:73-83.


Albert, V. A., B. D. Mishler and M. W. Chase. 1992. Character-state weighting for restriction site data in phylogenetic reconstruction, with an example from chloroplast DNA. Pages 369-403 in Molecular Systematics of Plants (Soltis, P. S., D. E. Soltis and J. J. Doyle, ed.). Chapman & Hall, New York.


Avise, J. C., J. Arnold, R. M. Ball, E. Bermingham, T. Lamb, J. E. Neigel, C. A. Reeb and N. C. Saunders. 1987. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Ann. Rev. Ecol. Syst. 18:489-522.


Avise, J. C. 1989. Gene trees and organismal histories: a phylogenetic approach to population biology. Evol. 43:1192-1208.


Baker, R. H., G. S. Wilkinson, R. DeSalle. 2001. Phylogenetic utility of different types of molecular data used to infer evolutionary relationships among stalk-eyed flies (Diopsidae). Systematic Biology 50: 87-105.


Bledsoe, A. H. and R. J. Raikow. 1990. A quantitative assessment of congruence between molecular and nonmolecular estimates of phylogeny. J. Mol. Evol. 30:247-259.


Bremer, K. 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evol. 42:795-803.


Broughton, R. E., S. E. Stanley, and R. T. Durrett. 2000. Quantification of homoplasy for nucleotide transitions and transversions and a reexamination of assumptions in weighted phylogenetic analyses. Systematic Biology 49: 617-627.


Bruns, T. D., T. J. White and J. W. Taylor. 1991. Fungal molecular systematics. Annu. Rev. Ecol. Syst. 22:525-564.

Cladistics. 2001. Supplement to Volume 17 (1).


Collins, Timothy M.; Fedrigo, Olivier; Naylor, Gavin J. P..Choosing the best genes for the job: The case for stationary genes in genome-scale phylogenetics. Systematic Biology 54 (3) : 493-500 JUN 2005


* Cracraft, J. 1987. DNA hybridization and avian phylogenetics. Evol. Biol. 21:47-96.


Creer S, Malhotra A, Thorpe RS, et al. Targeting optimal introns for phylogenetic analyses in non-model taxa: experimental results in Asian pitvipers . CLADISTICS 21 (4): 390-395 AUG 2005


DeBry, R. W. 1999. Maximum likelihood analysis of gene-based and structure-based process partitions, using mammalian mitochondrial genomes. Systematic Biology 48: 286-299.


DeSalle, R. and D. A. Grimaldi. 1991. Morphological and molecular systematics of the Drosophilidae. Ann. Rev. Ecol. Syst. 22:447-475.


** Donoghue, M. J. and M. J. Sanderson. 1992. The suitability of molecular and morphological evidence in reconstructing plant phylogeny. Pages 340-368 in Molecular Systematics of Plants (Soltis, P. S., D. E. Soltis and J. J. Doyle, ed.). Chapman & Hall, New York.


Doyle, J. J. 1992. Gene trees and species trees: molecular systematics as one-character taxonomy. Syst. Bot. 17:144-163.


Fleissner, Roland; Metzler, Dirk; Von Haeseler, Arndt. Simultaneous statistical multiple alignment and phylogeny reconstruction. Systematic Biology 54 (4) : 548-561 AUG 2005


Giribet G. Generating implied alignments under direct optimization using POY . CLADISTICS 21 (4): 396-402 AUG 2005


Givnish, T. J. and K. J. Sytsma (1997). Homoplasy in molecular vs. morphological data: the likelihood of correct phylogenetic inference. Molecular Evolution and Adaptive Radiation. (T. J. Givnish and K. J. Sytsma, eds). Cambridge, Cambridge University Press: 55-101.


Hillis, D. M. 1987. Molecular versus morphological approaches to systematics. Ann. Rev. Ecol. Syst. 18:23-42.


Hillis, D. M., J. J. Bull, M. E. White, M. R. Badgett and I. J. Molineux. 1992. Experimental phylogenetics: generation of a known phylogeny. Science 255:589-592.


Hillis, D.M. 1995. Approaches for assessing phylogenetic accuracy. Systematic Biology 44(1):3-16.


Hillis, D. M., C. Moritz and B. K. Mable (eds.). 1996. Molecular Systematics, second edition. Sinauer, Sunderland, MA. 655 pp.


Hillis, D. M. and J. J. Wiens. 2000. Molecules versus morphology in systematics: conflicts, artifacts, and misconceptions. pp. 1-19 in J. J. Wiens (ed.), Phylogenetic Analysis of Morphological Data. Washington DC, Smithsonian Institution Press.


Huelsenbeck, J. P. and R. Nielsen. 1999. Effect of non-independent substitution on phylogenetic accuracy. Systematic Biology 49: 317-328.


Laamanen TR, Meier R, Miller MA, et al. Phylogenetic analysis of Themira (Sepsidae : Diptera): sensitivity analysis, alignment, and indel treatment in a multigene study. CLADISTICS 21 (3): 258-271 JUN 2005


Lutzoni, F., P. Wagner, V. Reeb and S. Zoller. 2000. Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Systematic Biology 49: 628-651.


Macey, J. R., J. A. Schulte II, and A. Larson. 2000. Evolution and phylogenetic information content of mitochondrial genomic structural features illustrated with acrodont lizards. Systematic Biology 49: 257-277.


Mindell, D. P. and R. L. Honeycutt. 1990. Ribosomal RNA in vertebrates: evolution and phylogenetic applications. Ann. Rev. Ecol. Syst. 21:541-566.


** Mishler, B. D. (1994). The cladistic analysis of molecular and morphological data. American Journal of Physical Anthropology 94: 143-156.


Mishler, B. D., K. Bremer, C. J. Humphries and S. P. Churchill. 1988. The use of nucleic acid sequence data in phylogenetic reconstruction. Taxon 37:391-395.


* Miyamoto, M. M. and J. Cracraft (eds.). 1991. Phylogenetic analysis of DNA sequences. Oxford University Press, New York. 358 pp.


Nei, M. and F. Tajima. 1987. Problems arising in phylogenetic inference from restriction-site data. Mol. Biol. Evol. 4: 320-323.


Palmer, J. D., R. K. Jansen, H. J. Michaels, M. W. Chase and J. R. Manhart. 1988. Chloroplast DNA variation and plant phylogeny. Ann. Mo. Bot. Gard. 75:1180-1206.


Palmer, J. D. and L. A. Herbon. 1988. Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. J. Mol. Evol. 28: 87-97.


Patterson, C. (ed.). 1987. Molecules and Morphology in Evolution: Conflict or Compromise. Cambridge Univ. Press, Cambridge.


Patterson, C., D. M. Williams and C. J. Humphries. 1993. Congruence between molecular and morphological phylogenies. Ann. Rev. Ecol. Syst. 24:153-188.


Penny, D., M. Hasegawa, P. J. Waddell, and M. D. Hendy. 1999. Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition. Systematic Biology 48: 76-93.


Pisani, Davide. Identifying and removing fast-evolving sites using compatibility analysis: An example from the arthropoda. Systematic Biology 53 (6) : 978-989 December 2004


Posada, D. and K. A. Crandall. Selecting the ebst fit model of nucleotide substitution. Systematic Biology 50: 580-601.


Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.


Sanderson, M. J. and M. J. Donoghue. 1989. Patterns of variation in levels of homoplasy. Evol. 43:1781-1795.


Sarich, V. M., C. W. Schmid and J. Marks. 1989. DNA hybridization as a guide to phylogenies: a critical analysis. Cladistics 5:3-32.


Sennblad, B. and B. Bremer. 2000. Is there justification for differential a priori weighting in coding sequences? A case study from rbcL abd Apocynaceae s.l. Systematic Biology 49: 101-113.


* Sibley, C. G. and J. E. Ahlquist. 1986. Reconstructing bird phylogeny by comparing DNA's. Sci. Am. 254: 82-92.


Simmons, M. P. 2000. A Fundamental Problem with Amino-Acid-Sequence Characters for Phylogenetic Analyses. Cladistics 16: 274-282.


Simmons, M. P. and H. Ochoterena. 2000. Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49: 369-381.


Simmons, M. P., H. Ochoterena, and T. G. Carr. 2001. Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses. Systematic Biology 50: 454-462.


Slowinski, J. B. and B. S. Arbogast. 1999. Is the rate of molecular evolution inversely related to body size? Systematic Biology 48: 396-399.


Smith, A. B. 1989. RNA sequence data in phylogenetic reconstruction: testing the limits of its resolution.


Smith, R. L. and K. J. Sytsma. 1990. Evolution of Populus nigra (sect. Aigeiros): introgressive hybridization and the chloroplast contribution of Populus alba (sect. Populus ). Am. J. Bot. 77:1176-1187.


Springer, M. S., H. M. Amrine, A. Burk, and M. J. Stanhope. 1999. Additional support for Afrotheria and Paenungulata, the performance of mitochondrial versus nuclear genes, and the impact of data partitions with heterogeneous base composition. Systematic Biology 48: 65-75.


Steel, M., D. Huson, and P. J. Lockhart. 2000. Invariable sites models and their use in phylogeny reconstruction. Systematic Biology 49: 225-232.


Sytsma, K. J., J. F. Smith and L. D. Gottlieb. 1990. Phylogenetics in Clarkia (Onagraceae): restriction site mapping of chloroplast DNA. Syst. Bot. 15: 280-295.


Sytsma, K. J. 1990. DNA and morphology: inference of plant phylogeny. Trends Ecol. Evol. 5:104-110.


Terry MD, Whiting MF. Comparison of two alignment techniques within a single complex data set: POY versus Clustal. CLADISTICS 21 (3): 272-281 JUN 2005


Van Dijk, M. A. M., E. Paradis, F. Catzeflis, and W. W. De Jong. 1999. The virtues of gaps: Xenarthran (edentate) monophyly supported by a unique deletion in aA-Crystallin. Systematic Biology 48: 94-106.


Waddell, P. J., Y. Cao, J. Hauf, M. Hasegawa. 1999. Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid-invariant sites-LogDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant. Systematic Biology 48: 31-53.


Wheeler, W. C. 1995. Sequence alginment, parameter sensistivity and the phylogenetic analysis of molecular data. Syst. Biol. 44(3): 321-331.


Wheeler, W. C. 2001. Homology and the Optimization of DNA Sequence Data. Cladistics 17: S3-S11.


Wilgenbusch, J. and K. deQueiroz. 2000. Phylogenetic relationships among the phyrnosomatid sand lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes. Systematic Biology 49: 592-612.


Xia, X. 2000. Phylogenetic relationship among horseshoe crab species: effect of substitution models on phylogenetic analyses. Systematic Biology 49: 87-100.


Yang, Z. 1996. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evol. 11: 367-372.


Zimmer, E. A., R. K. Hamby, M. L. Arnold, D. A. LeBlanc and E. C. Theriot. 1989. Ribosomal RNA phylogenies and flowering plant evolution. Pages 205-214 in The Hierarchy of Life (Fernholm, B., K. Bremer and H. Jornvall, ed.). Elsevier, Amsterdam.


Zurawski, G. and M. T. Clegg. 1987. Evolution of higher-plant chloroplast DNA-encoded genes: Implications for structure-function and phylogenetic studies. Ann. Rev. Plant Physiol. 38:391-418.