Molecular taxonomy (molecular systematics / molecular phylogenetics)

Molecular taxonomy (molecular systematics / molecular phylogenetics) is the branch of phylogeny that analyses hereditary molecular differences - mainly in DNA sequences - to gain information and establish genetic relationships between members of different taxonomic categories, with results expressed as a phylogenetic tree. The advent of DNA cloning and sequencing methods has driven the field forward hugely.

A range of molecular markers is used: allozyme electrophoresis (detects variation at the enzyme level); mitochondrial DNA markers (non-nuclear, non-recombining, so homologous markers); microsatellites (short, highly variable tandem-repeat DNA sequences); RFLP - Restriction Fragment Length Polymorphism (identifies taxa from unique patterns of restriction sites, i.e. differences in the LENGTHS of DNA fragments after cutting with restriction enzymes); RAPD - Random Amplified Polymorphic DNA (uses a randomly synthesised primer to amplify unknown regions of DNA; useful within and between closely related species, though results are hard to replicate); AFLP - Amplified Fragment Length Polymorphism (similar to RFLP but the fragments each terminate in a characteristic sequence; used in population genetics and higher-level cladistic analysis); SNPs - Single Nucleotide Polymorphisms (the most abundant genome polymorphism, arising from single-nucleotide substitutions/insertions/deletions, detected via PCR, microchip arrays or fluorescence); and DNA microarrays/chips (immobilised DNA fragments on a slide/chip that match a known probe against an unknown sample, useful for species-specific identification). …