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Background  The salmon louse  Lepeophtheirus salmonis  is a parasitic copepod that infects salmonids in the Pacific and Atlantic oceans. Although considered as a single species, morphological and biological differences have been reported between lice from the two oceans. Likewise, studies based on nucleotide sequencing have demonstrated that sequence differences between Atlantic and Pacific  L. salmonis  are highly significant, albeit smaller than the divergence observed between congeneric copepod species.    Results  We demonstrated reproductive compatibility between  L. salmonis  from the two oceans and successfully established F2 hybrid strains using separate maternal lines from both the Pacific and Atlantic. The infection success for the F2 hybrid strains were similar to results typically observed for non hybrid lice strains in the rearing facility used.  Lepeophtheirus salmonis  COI and 16S sequences divergence between individuals from the Pacific and the Atlantic oceans was high compared to what may be expected within a copepod species and phylogenetic analysis showed that they consistently formed monophyletic clades representing their origin from the Pacific or Atlantic oceans.    Conclusions   Lepeophtheirus salmonis  from the Pacific and Atlantic oceans are reproductively compatible at least until adults at the F2 hybrid stage, and should not be regarded as separate species based on reproductive segregation or sequence divergence levels. Reported biological and genetic differences in  L. salmonis  seen in conjunction with the reported genetic diversity commonly observed between and within species demonstrate that Atlantic and Pacific  L. salmonis  should be regarded as two subspecies:  Lepeophtheirus salmonis salmonis  and  L. salmonis oncorhynchi  subsp. nov.

bmc genomic data

Pacific and Atlantic Lepeophtheirus salmonis (Krøyer, 1838) are allopatric subspecies: Lepeophtheirus salmonis salmonis and L. salmonis oncorhynchi subspecies novo