Utility of 18S rDNA and ITS sequences as population markers for Lepeophtheirus salmonis (Copepoda : Caligidae) parasitising Atlantic salmon (Salmo salar) in Scotland

Genetic differentiation within the salmon louse Lepeophtheirus salmonis (Kr oyer, 1837), was investigated by the sequencing of specific nucleotide regi ons. Partial sequences of the 18S ribosomal RNA gene and the ribosomal inte rnal transcribed spacer (ITS-I) region from single sea lice were amplified by the polymerase chain reaction (PCR). Lice were collected from wild and f armed Atlantic salmon (Salmo salar L., 1758) from nine selected localities around the Scottish coastline. A 0.9kb fragment of the 18S ribosomal RNA ge ne was amplified and compared for several samples of lice which showed no o bservable differences between the lice from different collection sites conf irming the absence of cryptic species. The 454 nucleotide ITS-I sequence sh owed differences between derived sequences from 13 sea lice samples from 4 collection sires which included 2 farm sites and 2 sites where lice were ta ken from wild fish. Across all samples, there was a 92.14% similarity in th e ITS-I sequence. The percentage similarity in the ITS-1 sequence in sample s of lice from two fish farms were 99.71% (site A) and 95.72% (site D) but only 86.90% (site B) and 86.03% (site C) similarity was shown in lice sampl es taken from sites where wild salmonids were caught. The greater similarit y between the ITS-1 sequence within farm sites may be attributed to a restr icted gene flow within lice populations in Atlantic salmon cage sites.