The black-fin icefish Chaenocephalus aceratus is among the most abundant fish species on the Antarctic continental shelves of the Scotia Arc, and Bouvet Island. We genotyped 11 microsatellite loci in C. aceratus population samples from South Orkney, southern South Shetlands, and Elephant Island (northern South Shetlands) collected in 2002 and 2006. This investigation further develops a previous study on the species reporting the presence of one panmittic population in southern South Shetlands and Elephant Island, with genetic differentiation between year classes. Our results reveal a more complex pattern of differentiation than shown previously, as genetic differences occur both at the temporal level at Elephant Island and at the geographic scale between southern South Shetland -Elephant Islands and South Orkney population samples. In particular, the magnitude of genetic differentiation at the temporal scale, the relatively high effective population size (N e ) and high gene flow indicate that genetic differentiation is not only driven by geographic distance. At present, our results should be taken into account when defining conservation measures and management boundaries in regions where fishery is still open or where other Antarctic fish species are still exploited.

Chaenocephalus aceratus is one of the most abundant Antarctic icefish species in the Atlantic sector and has been a by-catch species in the fishery for mackerel icefish, Champsocephalus gunnari, between the mid-1970s and mid-1980s at South Georgia, South Orkney, and South Shetland Islands. The species became the target of the fishery in particular seasons, such as at South Georgia in 1977/78. In our paper, we report results on genetic differentiation for 11 microsatellite loci in C. aceratus samples collected at the South Shetlands and Elephant Island. This study represents the first report on microsatellite variability of an icefish species. Our results support the evidence from previous studies on differences in infestation patterns of parasites that a single panmictic population of C. aceratus exists, spanning the two sampling sites separated by about 100 km. Moreover, our study indicates the presence of a significant genetic differentiation between individual year-classes pointing out the existence of dynamic processes acting at the population genetic level, according to recent results for broadly distributed marine species. Both small effective population size and immigration from unsampled differentiated stocks may be at the base of the differentiation found in C. aceratus

We characterized eight polymorphic microsatellites in the Scotia icefish Chaenocephalus aceratus (Perciformes, Notothenioidei, Channichthyidae) that is endemic of Southern Ocean waters surrounding the tip of the Antarctic Peninsula. Microsatellites were isolated from a partial genomic library enriched for an AC motif. The number of alleles ranged from two to 19 with a mean observed hererozygosity of 0.71. Loci were in Hardy–Weinberg equilibrium and no evidence for linkage disequilibrium was found. These molecular markers will be useful to investigate Scotia icefish genetic structure, possibly providing insights on its effective population size and demographic history.