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Experimental design in intraspecific organelle DNA sequence studies III: statistical measures of sampling success
Author(s) -
Holt Jason A.,
Stoneberg Holt Sierra D.,
Bureš Petr
Publication year - 2007
Publication title -
taxon
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.819
H-Index - 81
eISSN - 1996-8175
pISSN - 0040-0262
DOI - 10.2307/25065866
Subject(s) - haplotype , sampling (signal processing) , phylogenetic tree , evolutionary biology , sequence (biology) , intraspecific competition , biology , statistics , computer science , genetics , mathematics , paleontology , genotype , filter (signal processing) , gene , computer vision
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.