DALP. DALP employs two separate PCRs, each containing one of the primers labeled, for each sample. After separation in denaturing polyacrylamide gel, bands shared by the two reactions are products with different primers at both ends. These bands are compared with those of other samples in order to find the polymorphic bands among the samples. Polymorphic bands can be excised from the gel and sequenced directly using either of the primers.

Selection of appropriate molecular identification methods for (a) species and (b) locality/strain levels. a) For species level, SCAR and ARMS are suitable for detection of a target species or differentiation of species within the same genus. Microarray hybridization is suitable for detection of species within a list of suspected ones. Sequencing of species-specific regions is suitable for identification of samples with its species totally unknown. b) For locality or strain level, species identification should be performed first. Then, depending on whether prior sequence knowledge is available and the integrity of the DNA samples, different methods can be applied. SSR analysis and sequencing of strain-specific sequences are suitable for samples with primer sequences already available and SSR analysis is especially suitable for samples with DNA of low integrity. For samples without prior sequence knowledge, SSR marker development followed by subsequent SSR analysis can be applied for DNA samples of low integrity, while AFLP, RP-PCR, ISSR, DALP and DAMD can be applied for DNA samples of high integrity.

RP-PCR, DALP and DAMD. RP-PCR employs low stringency conditions and unlabeled arbitrary primers, while DALP employs high stringency conditions and both fluorescent-labeled and unlabeled arbitrary primers. DAMD employs high stringency conditions and an unlabeled primer targeting repeat regions.

SSR and ISSR. SSR employs primers targeting a single repeat region, while ISSR employs a single primer containing repeats to amplify regions between two repeats.

Comparison of various regions for use on various taxonomic levels (adapted from [244-246]). The thickness of the lines represents how frequently the regions are used for identification at the levels. The exact taxonomic levels that the regions can be applied to depend on the selected method. Successful application on a species does not guarantee successful application on other species at the same taxonomic level. For nuclear DNA regions, 18S and 5.8S regions are usually used for identification to the order or family levels and 26S is usually used for the order level down to the species level. The two ITS regions and the 5S spacer region are commonly used for identification at the species level, but they can also be applied down to the population/strain/variety level. For chloroplast DNA regions, 16S is suitable for the order level, while rbcL, atpβ and ndhF are suitable for the levels from order to species. The trnL intron, trnL-trnF spacer and matK regions can be applied to the levels from order to population/strain/variety, but the former two are more commonly used for the levels from family to species, while the latter is commonly used for the levels from order to subspecies. The atpβ-rbcL region can be used for the levels from genus to population/strain/variety, but it is more commonly used for the levels from genus to subspecies. For mitochondrial regions, cytochrome b and the control region can be used for identification at the levels from species to population/strain/variety, but the former is more commonly used for the species level and the latter is more commonly used for the subspecies level and lower.