A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. 4. Nested analyses with cladogram uncertainty and recombination

Journal Article · Tue Jun 01 04:00:00 EDT 1993 · Genetics; (United States)

OSTI ID:6180468

Templeton, A R ^[1]; Sing, C F ^[2]

---

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

The authors previously developed an analytical strategy based on cladistic theory to identify subsets of haplotypes that are associated with significant phenotypic deviations. Their initial approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site data to estimate the evolutionary steps that interrelate the observed haplotypes to one another. The cladogram is then used to define a nested statistical design for identifying mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that a mutation responsible for a particular phenotypic effect is embedded within the evolutionary history that is represented by the cladogram. The power of this approach depends on the accuracy of the cladogram in portraying the evolutionary history of the DNA region. This accuracy can be diminished both by recombination and by uncertainty in the estimated cladogram topology. In a previous paper, the authors presented an algorithm for estimating the set of likely cladograms and recombination events. In this paper they present an algorithm for defining a nested statistical design under cladogram uncertainty and recombination. Given the nested design, phenotypic associations can be examined using either a nested analysis of variance (for haploids or homozygous strains) or permutation testing (for outcrossed, diploid gene regions). In this paper they extend this analytical strategy to include categorical phenotypes in addition to quantitative phenotypes. Some worked examples are presented using Drosophila data sets. These examples illustrate that having some recombination may actually enhance the biological inferences that may be derived from a cladistic analysis. In particular, recombination can be used to assign a physical localization to a given subregion for mutations responsible for significant phenotypic effects. 14 refs., 10 figs., 7 figs.

• OSTI ID: 6180468
• Journal Information: Genetics; (United States), Journal Name: Genetics; (United States) Vol. 134:2; ISSN GENTAE; ISSN 0016-6731
• Country of Publication: United States
• Language: English

Related Subjects

550400* -- Genetics
59 BASIC BIOLOGICAL SCIENCES
ALGORITHMS
BIOLOGICAL EVOLUTION
BIOLOGICAL VARIABILITY
DNA
GENE MUTATIONS
GENE RECOMBINATION
GENETIC VARIABILITY
MATHEMATICAL LOGIC
MATHEMATICAL MODELS
MUTATIONS
NUCLEIC ACIDS
ORGANIC COMPOUNDS
PHENOTYPE
STATISTICAL MODELS