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Background  Dispersal ability, population genetic structure and species divergence in marine nematodes are still poorly understood, especially in remote areas such as the Southern Ocean. We investigated genetic differentiation of species and populations of the free-living endobenthic nematode genera  Sabatieria  and  Desmodora  using nuclear 18S rDNA, internal transcribed spacer (ITS) rDNA, and mitochondrial cytochrome oxidase I (COI) gene sequences. Specimens were collected at continental shelf depths (200–500 m) near the Antarctic Peninsula, Scotia Arc and eastern side of the Weddell Sea. The two nematode genera co-occurred at all sampled locations, but with different vertical distribution in the sediment. A combination of phylogenetic (GMYC, Bayesian Inference, Maximum Likelihood) and population genetic (AMOVA) analyses were used for species delimitation and assessment of gene flow between sampling locations.    Results  Sequence analyses resulted in the delimitation of four divergent species lineages in  Sabatieria , two of which could not be discriminated morphologically and most likely constitute cryptic species. Two species were recognised in  Desmodora , one of which showed large intraspecific morphological variation. Both genera comprised species that were restricted to one side of the Weddell Sea and species that were widely spread across it. Population genetic structuring was highly significant and more pronounced in the deeper sediment-dwelling  Sabatieria  species, which are generally less prone to resuspension and passive dispersal in the water column than surface  Desmodora  species.    Conclusions  Our results indicate that gene flow is restricted at large geographic distance in the Southern Ocean, which casts doubt on the efficiency of the Weddell gyre and Antarctic Circumpolar Current in facilitating circum-Antarctic nematode species distributions. We also show that genetic structuring and cryptic speciation can be very different in nematode species isolated from the same geographic area, but with different habitat preferences (surface versus deeper sediment layers).    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-017-0968-1) contains supplementary material, which is available to authorized users.

Distinct genetic differentiation and species diversification within two marine nematodes with different habitat preference in Antarctic sediments