A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation

Journal Article · · Genetics; (United States)

OSTI ID:7285333

Templeton, A R; Crandall, K A ^[1]; Sing, C F ^[2]

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1. Washington Univ., St. Louis, MO (United States)
2. Univ. of Michigan, Ann Arbor, MI (United States)

The authors 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. The 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, the authors 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. They first evaluate the limits of parsimony in constructing cladograms. Once these limits have been determined, they construct the set of parsimonious and nonparsimonious cladograms that is consistent with these limits. The estimation procedure also identifies haplotypes that are candidates for being products of recombination. If recombination is extensive, the algorithm subdivides the DNA region into two or more subsections, each having little or no internal recombination. The authors apply this estimation procedure to three data sets to illustrate varying degrees of cladogram ambiguity and recombination. 26 refs., 9 figs., 1 tab.

• OSTI ID: 7285333
• Journal Information: Genetics; (United States), Journal Name: Genetics; (United States) Vol. 132; ISSN GENTAE; ISSN 0016-6731
• Country of Publication: United States
• Language: English

Related Subjects

550400* -- Genetics
59 BASIC BIOLOGICAL SCIENCES
99 GENERAL AND MISCELLANEOUS
990200 -- Mathematics & Computers
BIOLOGICAL MARKERS
BIOLOGICAL VARIABILITY
CHROMOSOMES
DNA SEQUENCING
GENETIC MAPPING
GENETIC VARIABILITY
MAPPING
MATHEMATICAL MODELS
RFLPS
STATISTICAL MODELS
STRUCTURAL CHEMICAL ANALYSIS