Genetics, Vol 132, 619-633, Copyright © 1992


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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P. L. Morrell, K. E. Lundy, and M. T. Clegg
Distinct geographic patterns of genetic diversity are maintained in wild barley (Hordeum vulgare ssp. spontaneum) despite migration
PNAS, September 16, 2003; 100(19): 10812 - 10817.
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J HeredHome page
B. A. Schaal, J. F. Gaskin, and A. L. Caicedo
The Wilhelmine E. Key 2002 Invitational Lecture. Phylogeography, Haplotype Trees, and Invasive Plant Species
J. Hered., May 1, 2003; 94(3): 197 - 204.
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Mol Biol EvolHome page
A. Gandolfi, I. R. Sanders, V. Rossi, and P. Menozzi
Evidence of Recombination in Putative Ancient Asexuals
Mol. Biol. Evol., May 1, 2003; 20(5): 754 - 761.
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GeneticsHome page
R. E. Broughton and R. G. Harrison
Nuclear Gene Genealogies Reveal Historical, Demographic and Selective Factors Associated With Speciation in Field Crickets
Genetics, April 1, 2003; 163(4): 1389 - 1401.
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GeneticsHome page
J.-Z. Lin, P. L. Morrell, and M. T. Clegg
The Influence of Linkage and Inbreeding on Patterns of Nucleotide Sequence Diversity at Duplicate Alcohol Dehydrogenase Loci in Wild Barley (Hordeum vulgare ssp. spontaneum)
Genetics, December 1, 2002; 162(4): 2007 - 2015.
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GeneticsHome page
T. C. Nesbitt and S. D. Tanksley
Comparative Sequencing in the Genus Lycopersicon: Implications for the Evolution of Fruit Size in the Domestication of Cultivated Tomatoes
Genetics, September 1, 2002; 162(1): 365 - 379.
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GeneticsHome page
G. Gentile, A. della Torre, B. Maegga, J. R. Powell, and A. Caccone
Genetic Differentiation in the African Malaria Vector, Anopheles gambiae s.s., and the Problem of Taxonomic Status
Genetics, August 1, 2002; 161(4): 1561 - 1578.
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Mol Biol EvolHome page
A. Antunes, A. R. Templeton, R. Guyomard, and P. Alexandrino
The Role of Nuclear Genes in Intraspecific Evolutionary Inference: Genealogy of the transferrin Gene in the Brown Trout
Mol. Biol. Evol., August 1, 2002; 19(8): 1272 - 1287.
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Am. J. Bot.Home page
E. Emshwiller and J. J. Doyle
Origins of domestication and polyploidy in oca (Oxalis Tuberosa: Oxalidaceae). 2. Chloroplast-expressed glutamine synthetase data
Am. J. Botany, July 1, 2002; 89(7): 1042 - 1056.
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Proc. Natl. Acad. Sci. USAHome page
K. Saltonstall
Cryptic invasion by a non-native genotype of the common reed, Phragmites australis, into North America
PNAS, February 19, 2002; 99(4): 2445 - 2449.
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Biol. Bull.Home page
J. P. Wares
Biogeography of Asterias: North Atlantic Climate Change and Speciation
Biol. Bull., August 1, 2001; 201(1): 95 - 103.
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GeneticsHome page
T. Y. James, J.-M. Moncalvo, S. Li, and R. Vilgalys
Polymorphism at the Ribosomal DNA Spacers and Its Relation to Breeding Structure of the Widespread Mushroom Schizophyllum commune
Genetics, January 1, 2001; 157(1): 149 - 161.
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GeneticsHome page
A. R. Templeton, K. M. Weiss, D. A. Nickerson, E. Boerwinkle, and C. F. Sing
Cladistic Structure Within the Human Lipoprotein Lipase Gene and Its Implications for Phenotypic Association Studies
Genetics, November 1, 2000; 156(3): 1259 - 1275.
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Proc. Natl. Acad. Sci. USAHome page
B. A. Schaal and K. M. Olsen
Gene genealogies and population variation in plants
PNAS, June 20, 2000; 97(13): 7024 - 7029.
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GeneticsHome page
M. T. Hamblin and M. Veuille
Population Structure Among African and Derived Populations of Drosophila simulans: Evidence for Ancient Subdivision and Recent Admixture
Genetics, September 1, 1999; 153(1): 305 - 317.
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GeneticsHome page
N. Davies, F. X. Villablanca, and G. K. Roderick
Bioinvasions of the Medfly Ceratitis capitata: Source Estimation Using DNA Sequences at Multiple Intron Loci
Genetics, September 1, 1999; 153(1): 351 - 360.
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GeneticsHome page
C. L. Nesbo, M. O. Arab, and K. S. Jakobsen
Heteroplasmy, Length and Sequence Variation in the mtDNA Control Regions of Three Percid Fish Species (Perca fluviatilis, Acerina cernua, Stizostedion lucioperca)
Genetics, April 1, 1998; 148(4): 1907 - 1919.
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ScienceHome page
C. Vila, P. Savolainen, J. E. Maldonado, I. R. Amorim, J. E. Rice, R. L. Honeycutt, K. A. Crandall, J. Lundeberg, and R. K. Wayne
Multiple and Ancient Origins of the Domestic Dog
Science, June 13, 1997; 276(5319): 1687 - 1689.
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Proc. Natl. Acad. Sci. USAHome page
J. A. Leonard, R. K. Wayne, and A. Cooper
From the Cover: Population genetics of Ice Age brown bears
PNAS, February 15, 2000; 97(4): 1651 - 1654.
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