The accuracy of this new molecular tool was tested and validated by comparing multiplex PCR results with species identification based on sequences at mitochondrial and nuclear markers.
But standard DNA tests, based on sequencing segments of the mitochondrial genome, showed no clear divisions in the world's orca population, according to a team of biologists led by Phillip A. Morin of the National Marine Fisheries Service.
A system of specific primers and a Minor Groove Binding (MGB) TaqMan probe based on sequences of the mitochondrial cytochrome b region was designed.
The two species cannot be reliably distinguished using morphological characters, but are readily identified and distinguished by simple, rapid, and inexpensive molecular protocols based on sequence variation of mitochondrial DNA (mtDNA).
Distances are based on sequence differences between mitochondrial D-loop haplotypes, but these species have highly incomplete haplotype lineage sorting.
In general, molecular phylogenetic studies agree with the three major clades proposed by McFadden et al. (2006) based on sequences from two mitochondrial genes (nad2 and mutS).
DNA analyses were based on sequences from partial mitochondrial cytochrome oxidase subunit II gene (COII) and nuclear internal transcribed spacer 2 (ITS2).
This analysis was based on sequences for the mitochondrial region only, since ITS-1 data were only obtained for a limited number of specimens, and were not sufficient for population genetic analysis.
To elucidate evolutionary relationships and to attempt to estimate the number of origins of sociality, we also created a phylogeny based on sequences spanning the mitochondrial genes Cytochrome Oxidase I and II for nine species of Pemphigus.
Phylogeny of the rice tribe has been well resolved by previous studies based on sequences of plastid, mitochondrial and nuclear genes [ 25, 26] and provided an important framework for molecular evolution study for this group (Additional file 1).
