Experimental design in intraspecific organelle DNA sequence studies I: haplotype detection methods

Phylogenetic studies of organelle DNA sequences at low taxonomic levels present a researcher with specific experimental design challenges. Such studies require sampling of large numbers of individuals, many of which share identical haplotypes. The process is often limited by time and money required for DNA sequencing. A variety of mutation detection methods has been developed to circumvent this limitation. This paper briefly reviews the available methods and presents some of their advantages and disadvantages. The applicability of these methods to nuclear DNA studies is discussed.