Integrative Biology 200B Spring 2007
"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION"
Most important recommended readings are
in bold face; required readings also have two asterisks
April 3:
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.)
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. Hennig’s
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
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
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.
Wood, S.W. 1994. Monophyly and comparisons between
trees. Cladistics: 10(4):339-346.