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

• DOI: 10.1093/genetics/132.2.619
• Publication Date: 2021-01-13T19:04:38Z
• Authors: A R Templeton; K A Crandall; C F Sing
• Keywords: Cladogram; Restriction site

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