"PRINCIPLES OF PHYLOGENETICS:
ECOLOGY AND EVOLUTION"

Jan. 19th - 28th.  GENERAL PHYLOGENETICS:

Those references preceded by ** are required. Those preceded by * are highly suggested.  The others are suggested, but we all can only read so much. Go for it...

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.

Bremer, K. 1994. Branch support and tree stability. Cladistics 10(3):295-304

Donoghue, M.J. and J.W. Kadereit. 1992. Walter Zimmermann and the growth of phylogenetic theory. Systematic Biology 41(1): 74-84.

de Queiroz, K. and J. Gauthier. 1992. Phylogenetic taxonomy.  Ann. Rev. Ecol. Syst. 23: 449-480.

Farris J.S.  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.

Forey, P. L., C. J. Humphries, I. L. Kitching, R. W. Scotland, D. J. Siebert, and D. M. Williams.  1992.  Cladistics.  The Systematics Association Publication No.10.  Oxford University Press, New York

Hennig, W. 1965. Phylogenetic systematics. Ann. Rev. of Entomology 10: 97-116.

Hennig, W.  1966.  Phylogenetic systematics. University of Illinois Press, Urbana.

Hull, D. L.  1988.  Science as a process: an evolutionary account  of the social and conceptual development of science.  University  of Chicago Press, Chicago. [an already classic work on the recent, violent history of systematics; used as data for Hull's general theories about scientific change].

Kluge, A.G. 1994. Moving targets and shell games. Cladistics 10(4): 403-413.

Lundberg, J. G. and L. A. McDade.  1990.  Systematics. Pages 65-108 in Methods for Fish Biology, American Fisheries Society.

Lindberg, D.R. Systematic paleontology, pp. 31-37.

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

Mishler, B. D. and E. De Luna. 1991. The use of ontogenetic data in phylogenetic analyses of mosses. Advances in Bryology 4:121-167. [especially pages 129-143]

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

Patterson, C. 1982. Morphological characters and homology. pp. 21-74 in Josey, K.A. and Friday, A.E. (eds.) Problems of Phylogenetic Reconstruction. Academic Press.

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

Sober, E.  1988.  Reconstructing the past.  MIT Press.

Stevens, P. F.  1994.  The development of biological systematics. Columbia University Press, New York.

Wiley, E. O.  1975.  Karl R. Popper, systematics, and classification: a reply to Walter Bock and other evolutionary taxonomists.  Syst. Zool. 24: 233-243.
 

Feb. 2nd.  GENERAL COMPARATIVE METHODS REFERENCES
(just to get started)

*Brooks, D.R., & D. McLennan. 1991. Phylogeny, Ecology, and Behavior. University of Chicago Press.

Burt, A.  1989.  Comparative methods using phylogenetically independent contrasts.  Oxford Surveys in Evolutionary Biology  6:33-53.

Cheverud, J., and M.  Dow.  1985.  An autocorrelation analysis of the effect of lineal fission on  genetic variation among social groups.  Amer.  J.  Phys.  Anthropol.  67:113-121.

Cheverud, J. M., M. M. Dow, and W. Leutenegger.  1985.  The quantitative assessment of phylogenetic constraints in comparative analyses:  Sexual dimorphism in body weight among primates.  Evolution, 39, 1335-1351.

Cliff, A. D., and Ord, J. K.  1973.  Spatial Autocorrelation.  London:  Pion.

Coddington, J. 1988. Cladistic tests of adaptational hypotheses. Cladistics 4:3-22.

de Queiroz, K. 1996. Including the characters of interest during tree reconstruction and the problems of circularity and bias in studies of character evolution. Am. Nat. 148: 700-708.

**Donoghue, M.J. 1989. Phylogenies and analysis of evolutionary sequences, with examples from seed plants. Evolution 43:1137-1156. (maddisonís test)

Felsenstein, J.  1985.  Phylogenies and the comparative method.  Am.  Nat.   125:1-15.

Funk, V.A. and D.R. Brooks. 1990. Phylogenetic systematics as the basis of comparative biology. Smithsonian Institution Press.

*Harvey, P.H. and M.D. Pagel. 1991. The comparative method in evolutionary biology. Oxford University Press.

Martins, E. P.  1996.  Phylogenies, spatial autoregression, and the  comparative method: A computer simulation test.  Evolution, v.50, n.5, 1750-1765.

Martins, E. P., and Hansen, T. F.  1997.  Phylogenies and the comparative method:  A  general approach to incorporating phylogenetic information into the analysis of interspecific data.  Am.  Nat.

Miles, D. B. and A. E. Dunham. 1993. Historical perspectives in ecology and evolutionary biology: the use of phylogenetic comparative analyses. Ann. Rev. Ecol. Syst. 24: 587-619.

**Sillin-Tullberg, B. 1988. Evolution of gregariousness in aposematic butterfly larvae: a phylogenetic analysis. Evolution 42: 293-305.

Vogl, C., and G. P. Wagner.  1990.  Interspecific variability in randomly evolving clades:  models for testing hypotheses on the relative evolutionary flexibility of quantitative traits.  Sys.  Zool.  39:109-123.149:646-667.

Feb. 4th.  CONSENSUS TECHNIQUES AND TREE CONGRUENCE

Avise, J. C., J. F. Shapiro, S. W. Danila, C. F. Aquadro, and R. A. Lansman. 1983. Mitochondrial DNA differentiation during the speciation process in Peromyscus. Mol. iol. Evol. 1:38-56.

Baum, D. A., and K. L. Shaw. 1995. Genealogical perspectives on the species problem. Pages 289-303 in Experimental and molecular approaches to plant biosystematics. Monographs in systematics, Volume 53 (P. C. Hoch and A. G., Stevenson, eds.) Missouri Botanical Garden, St, Louis.

Adams, E. N., III. 1972. Consensus techniques and the comparison of taxonomic trees. Systematic Zoology 21:390-397.

Barrett M, Donoghue MJ, and Sober E (1991) Against consensus. Syst. Zool. 40:486-493.

Bremer, K. 1990. Combinable component consensus. Cladistics 6:369-372.

Brooks, D. R. 1981. Hennigís parasitoligical method: A proposed solution. Syst. Zool. 30: 229-249.

Brooks, D. R. 1990. Parsimony analyisis in historical biogeography and coevolution: Methodological and theoretical update. Syst. Zool. 39: 14-30.

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

Doyle, J. L. Doyle, and A. H. D. Brown. 1990. A chloroplast DNA phylogeny of the wild perennial relatives of soybean (Glycine subgenus Glycine): Congruence with morphological and crossing groups. Evolution 44: 371-389.

Dvorak, J. and R. Appels. 1982. Chromosome and nucleotide sequence differentiation in genomes of polyploid Triticum species. Theoretical and Applied Genetics 63: 349-360.

Farris, J. S., M. Kallersjo, A. G. Kluge, and C. Bult. 1994. Testing significance of incongruence. Cladistics 10: 315-319.

Felsenstein, J. 1978. Cases in which parsimony or compatability methods will be positively misleading. Systematic Zoology 27: 401-410.

Felsenstein, J. 1988. Phylogenies from molecular sequences: inferences and reliability. Annual Review of Genetics 22: 521-565.

Farris J.S., Kallersjo, M., Kluge, A.G. and Bult, C. 1994. Testing significance of incongruence.Cladistics 10(3): 315-319

Funk, V. A. 1985. Phylogenetic patterns and hybridization. Annals of the Missouri Botanical Garden 72: 681-715.

Goodman, M., J. Czelusniak, G. W. Moore, A. E. Romero-Herrera, and G. Matsuda. 1979. Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool. 28: 132-163.

Hudson, R. R. 1990. Gene genealogies and the coalescent process. Oxf. Surv. Evol. Biol. 7: 1-44.

Hudson, R. R. 1992. Gene trees, species trees, and the segregation of ancestral alleles. Genetics 131: 509-512.

Kidwell, M. G. 1993. Lateral transfer in natural populations of eukaryotes. Annu. Rev. Genet. 27: 235-256.

Kirkpatrick, M. and Slatkin, M. 1993. Searching for evolutionary patterns in the shape of a phylogenetic tree. Evolution 47: 1171-1181.

Mason-Gamer, R. J. and E. A. Kellogg. 1996. Testing for phylogenetic conflict among molecular data sets in the Triticeae. Systematic Biology 45: In press.

McDade, L. 1990. Hybrids and phylogenetic systematics. I. Patterns of character expression in hybrids and their implications for cladistic analysis. Evolution 44: 1685-1700.

McDade, L. 1992. Hybrids and phylogenetic systematics. II. The impact of hybrids on cladistic analysis.  Evolution 46: 1329-1346.

Mickevich, M. F. and J. S. Farris. 1981. The implications of congruence in Menidia. Systematic Zoology 30: 351-370.

Miyamoto MM (1985) Consensus cladograms and general classifications. Cladistics 1:186-189.

Miyamoto, M.M. and M.W. Fitch. 1995. Testing species phylogenies and phylogenetic methods with congruence. Syst. Biol. 41(1): 64-76.

Neigel, J. E., and J. C. Avise. 1986. Phylogenetic relationships of mitochondrial DNA under various demographic models of speciation. Pages 515-534 in Evolutionary processes and theory (E. Nevo and S. Karlin, eds.). Academic Press, New York.

Page, R. D. M. 1993. Genes, organisms, and areas: The problem of multiple lineages. Syst. Biol. 42: 77-84.

Page, R.D.M. 1994a. Maps between trees and cladistic analysis of historical associations among genes, organisms and areas. Syst. Biol. 42: 58-77.

Page, R. D. M. 1994b. Parallel phylogenies: Reconstructing the history of host-parasite assemblages. Cladistics 10: 155-173.

Pamilo, P., and M Nei. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5: 568-583.

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

Rohlf, F. J. 1982. Consensus indices for comparing classifications. Mathematical Biosciences 59:131-144.

Seberg, O. 1989. Genome analysis, phylogeny, and classification. Plant Systematics and Evolution 166: 105-122.

Swenson, U. and K. Bremer. 1997. Pacific Biogeography of the Asteraceae genus Abrotanella (Senecioneae, Belnnospermatinae). Systematic Botany 22: 493-508.

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

Swofford, D. L. 1991. When are phylogeny estimates from molecular and morphological data incongruent? Pp. 295-333 in M. M. Miyamoto &J. Cracraft (ed.), Phylogenetic analysis of DNA sequences. Oxford University Press, New York.

Wood, S.W. 1994. Monophyly and comparisons between trees. Cladistics: 10(4):339-346.