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
March
15: RETICULATION AND PHYLOGENETICS
Arnold, M. L., C. M.
Buckner and J. J. Robinson. 1991.
Pollen-mediated introgression and hybrid speciation in
Arnold, M. L., J. J.
Robinson, C. M. Buckner and B. D. Bennet.
1992. Pollen dispersal and interspecific gene flow in
**Avise, J. C.
1989. Gene trees and organismal histories: a phylogenetic approach to population
biology. Evol. 43: 1192-1208.
Avise, J. C. and R. M. Ball. 1990.
Principles of geneological concordance in
species concepts and biological taxonomy.
Baum, D. 1992.
Phylogenetic species concepts. Trends Ecol. Evol. 7: 1-2.
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.)
Crandall, K. A. 1994. Intraspecific cladogram
estimation: accuracy at higher levels of divergence. Syst. Biol. 43:
222-235.
Doyle, J. J. 1992. Gene trees and species
trees: Molecular systematics
as one-character taxomony. Syst.
Bot. 17: 144-163.
Funk, V. A. 1985. Phylogenetic
patterns and hybridization. Ann.
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.
Heiser, C. B.
1973. Introgression
re-examined. Bot. Rev. 39: 347-366.
Hudson,
R. R. 1991. Gene genealogies and the coalescent
process.
Hudson, R. R., M. Slatkin and W. P. Maddison.
1992. Estimation of levels of
gene flow from DNA sequence data.
Genetics 132: 583-589.
Kidwell, M. G. 1993. Lateral transfer in
natural populations of eukaryotes. Annu. Rev. Genet. 27: 235-256.
Maddison, W. P.
1997. Gene trees in species
trees. Syst.
Biol. 46: 523-536.
McDade, L.
1990. Hybrids and phylogenetic systematics. I. Patterns of character expression in hybrids
and their implications for cladistic analysis. Evol. 44: 1685-1700.
McDade, L. A.
1992. Hybrids and phylogenetic systematics II. The impact of hybrids on cladistic
analysis. Evol. 46: 1329-1346.
McDade, L. A.
1995. Hybridization and phylogenetics. in
Experimental and molecular approaches to plant biosystematics (Hoch, P. C. and A. G. Stephenson, ed.).
McDade, L A. 1997. Hybrids
and phylogenetic systematics III. Comparison with distance methods. Systematic Botany, v.22,
n.4, (1997): 669-683.
Mountain, J. L., J. M. Hebert, S.
Bhattacharyya, P. A. Underhill, C. Ottolenghi, M. Gadgil and L. L. Cavalli-Sforza. 1995.
Demographic history of
Nason, J. D., N. C. Ellstrand and M. I. Arnold.
1992. Patterns of hybridization
and introgression in populations of oaks, manzanitas,
and irises. Am. J. Bot.
79: 101-111.
Nieto, F.G., A.J. Fuertes, and J.A. Rossello. 2001. Can extensive reticulation and
concerted evolution result in a cladistically
structured mmolecular data set? Cladistics. 17(4):301-312.
Rieseberg, L. H.
1991. Homoploid
reticulate evolution in Helianthus (Asteraceae):
evidence from ribosomal genes. Amer. J. Bot 78: 1218-1237.
Rieseberg, L. H., R. Carter and
S. Zona. 1990. Molecular
tests of the hypothesized hybrid origin of two diploid Helianthus species (Asteraceae). Evol. 44: 1498-1511.
Schlefer, E. K., M. A. Romano,
S. I. Guttman and S. B. Ruth.
1986. Effects of twenty years of
hybridization in a disturbed habitat on Hyla cinerea and Hyla gratiosa. J.
of Herpetology 20: 210-221.
Skala, Z.
and Zrzavy J. 1994.
Phylogenetic reticulations and cladistics
- discussion of methodological concepts.
Cladistics 10(3): 305-313.
Slatkin, M. and W. Maddison. 1989.
A cladistic measure of gene flow inferred from
the phylogenies of alleles. Genetics
123: 603-613.
Slatkin, M. and W. Maddison. 1990.
Detecting isolation by distance using phylogenies of genes. Genetics 126: 249-260.
Vrana, P. and W. Wheeler.
1992. Individual organisms as
terminal entities: laying the species problem to rest. Cladistics 8:
67-72.
Wagner, W. H. 1983. Reticulistics: the recognition of hybrids and their role in
cladistics and classification. Pages 63-79 in
Advances in Cladistics, Volume 2 (Platnick,
N. I. and V. A. Funk, ed.).
Woodruff, D. S. and S.
J. Gould. 1987.
Fifty years of interspecific hybridization:
genetics and morphometrics of a controlled experiment
on the land snail Cerion in the