A Cladistic Analysis of Phenotypic Associations With Haplotypes Inferred From Restriction Endonuclease Mapping and DNA Sequence Data. III. Cladogram Estimation

INVESTIGATIONS

A Cladistic Analysis of Phenotypic Associations With Haplotypes Inferred From Restriction Endonuclease Mapping and DNA Sequence Data. III. Cladogram Estimation

A. R. Templeton, K. A. Crandall and C. F. Sing
Department of Biology, Washington University, St. Louis, Missouri 63130

We previously developed a cladistic approach to identify subsets of haplotypes defined by restriction endonuclease mapping or DNA sequencing that are associated with significant phenotypic deviations. Our approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site or sequence data that represents the evolutionary steps that interrelate the observed haplotypes. The cladogram is used to define a nested statistical design to identify mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that any undetected mutation causing a phenotypic effect is embedded within the same evolutionary history that is represented by the cladogram. The power of this approach depends upon the confidence one has in the particular cladogram used to draw inferences. In this paper, we present a strategy for estimating the set of cladograms that are consistent with a particular sample of either restriction site or nucleotide sequence data and that includes the possibility of recombination. We first evaluate the limits of parsimony in constructing cladograms. Once these limits have been determined, we construct the set of parsimonious and nonparsimonious cladograms that is consistent with these limits. Our estimation procedure also identifies haplotypes that are candidates for being products of recombination. If recombination is extensive, our algorithm subdivides the DNA region into two or more subsections, each having little or no internal recombination. We apply this estimation procedure to three data sets to illustrate varying degrees of cladogram ambiguity and recombination.

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				K.-F. Chung, C.-I Peng, S. R. Downie, K. Spalik, and B. A. Schaal Molecular systematics of the trans-Pacific alpine genus Oreomyrrhis (Apiaceae): phylogenetic affinities and biogeographic implications Am. J. Botany, December 1, 2005; 92(12): 2054 - 2071. [Abstract] [Full Text] [PDF]

				M. J. Stanhope, S. L. Walsh, J. A. Becker, M. J. Italia, K. A. Ingraham, M. N. Gwynn, T. Mathie, J. A. Poupard, L. A. Miller, J. R. Brown, et al. Molecular Evolution Perspectives on Intraspecific Lateral DNA Transfer of Topoisomerase and Gyrase Loci in Streptococcus pneumoniae, with Implications for Fluoroquinolone Resistance Development and Spread Antimicrob. Agents Chemother., October 1, 2005; 49(10): 4315 - 4326. [Abstract] [Full Text] [PDF]

				A. Wattanathum, S. Manocha, H. Groshaus, J. A. Russell, and K. R. Walley Interleukin-10 Haplotype Associated With Increased Mortality in Critically Ill Patients With Sepsis From Pneumonia But Not in Patients With Extrapulmonary Sepsis Chest, September 1, 2005; 128(3): 1690 - 1698. [Abstract] [Full Text] [PDF]

				M. Perez-Losada, R. P. Viscidi, J. C. Demma, J. Zenilman, and K. A. Crandall Population Genetics of Neisseria gonorrhoeae in a High-Prevalence Community Using a Hypervariable Outer Membrane porB and 13 Slowly Evolving Housekeeping Genes Mol. Biol. Evol., September 1, 2005; 22(9): 1887 - 1902. [Abstract] [Full Text] [PDF]

				J. Mu, D. A. Joy, J. Duan, Y. Huang, J. Carlton, J. Walker, J. Barnwell, P. Beerli, M. A. Charleston, O. G. Pybus, et al. Host Switch Leads to Emergence of Plasmodium vivax Malaria in Humans Mol. Biol. Evol., August 1, 2005; 22(8): 1686 - 1693. [Abstract] [Full Text] [PDF]

				V. Ketmaier and C. Bernardini Structure of the Mitochondrial Control Region of the Eurasian Otter (Lutra lutra; Carnivora, Mustelidae): Patterns of Genetic Heterogeneity and Implications for Conservation of the Species in Italy J. Hered., July 1, 2005; 96(4): 318 - 328. [Abstract] [Full Text] [PDF]