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Experimental design in intraspecific organelle DNA sequence studies III: statistical measures of sampling success

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Abstract:

Statistical methods are proposed for analyzing the experimental design, preliminary results, and final results of phylogenetic studies of organelle DNA sequence at low taxonomic levels. Such studies require sampling numerous individuals, many of which share identical haplotypes. The proportions of the haplotypes sampled can help answer the following questions: (1) Is one haplotype so dominant that the particular DNA region is without meaningful variation within the scope of the study? (2) Were all prevalent haplotypes found? (3) What are the proportions of each haplotype within the studied group? (4) What percentage of the studied group can be confidently asserted to belong to the haplotypes that were found? Examples are given in which the statistics techniques are applied to data drawn from the botanical literature. Tables are included as a quick reference for the researcher who wishes to circumvent calculation. A Microsoft® Excel 2000 spreadsheet (titled "HaploPro.xls") for performing some of the more complicated calculations is offered online. Finally, the limitations of these methods and their applicability to nuclear DNA and other characters studies are discussed.

Keywords: BULKING; HAPLOTYPE FREQUENCY CONFIDENCE INTERVALS; INCLUSION-EXCLUSION PRINCIPLE; INTRASPECIFIC SEQUENCE STUDIES; PHYLOGEOGRAPHY; PROPORTION ESTIMATES

Document Type: Research Article

Affiliations: 1: Box 37, Hinsdale, Montana 59241, U.S.A. 2: Box 37, Hinsdale, Montana 59241, U.S.A.; Institute of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno 611 37, Czech Republic 3: Institute of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno 611 37, Czech Republic

Publication date: August 1, 2007

iapt/tax/2007/00000056/00000003/art00021
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