Gyrodactylus molecular markers successfully employed to date fall into the following categories:

Genomic markers

• Ribosomal loci including Internal Transcribed Spacers (ITS-1, ITS-2) and the 5.8S rDNA gene. These loci have the advantage of being under the influence of concerted evolution, and thus being sensitive markers of panmictic populations, but not under selective pressure so they show rapid evolution when panmixis is disrupted. The best marker for distinguishing closely related taxa, widely used (perhaps incorrectly) for phylogenies. Over 100 sequences now in Genbank. Being flanked by conservative regions, easy to amplify.
• V4 region of the 18S rDNA. Originally sequenced by Cunningham et al. (1995), the first locus to be sequenced. Chosen because variable, but flanked by highly conserved sites making primer design easy. Used particularly for salmonid-infecting gyrodactylids, but fallen into disuse now.
• Intergenic Spacer region (IGS) of the ribosomal cassette. Properties not fully understood, but probably under control of concerted evolution. Only sequenced in G. salaris and G. thymalli, in which numerous repeats are present. Specialist locus, but highly valuable in plotting evolutionary pathways of gyrodactylids.
• Tubulin locus. Only single copy nuclear gene so far isolated or sequenced from Gyrodactylus

Mitochondrial markers

• Mitochondrial Cytochrome Oxidase I. Extensively sequenced for G. salaris and G. thymalli, providing important evidence of evolutionary pathways in these species. Important maternal marker for other species, but bear in mind different method of inheritance (maternal) may be particularly important in a parthenogen such as Gyrodactylus
• Work is underway (Huyse, Littlewood) to sequence entire mitochondrial genome.

• RAPDs - highly unreliable, outmoded now, used once on G. salaris.
• AFLP - like RAPDs, a 'whole genome scanning' approach. Have been used by Cable group fairly extensively. Reliable, repeatable, but interpretation difficult.