Antarctic notothenioids radiated over millions of years in subzero waters, evolving peculiar features, such as antifreeze glycoproteins and absence of heat shock response. Icefish, family Channichthyidae, also lack oxygen-binding proteins and display extreme modifications, including high mitochondrial densities in aerobic tissues. A genomic expansion accompanying the evolution of these fish was reported, but paucity of genomic information limits the understanding of notothenioid cold adaptation. We reconstructed and annotated the first skeletal muscle transcriptome of the icefish Chionodraco hamatus providing a new resource for icefish genomics (http://compgen.bio.unipd.it/chamatusbase/, last accessed December 12, 2012). We exploited deep sequencing of this energy-dependent tissue to test the hypothesis of selective duplication of genes involved in mitochondrial function. We developed a bioinformatic approach to univocally assign C. hamatus transcripts to orthology groups extracted from phylogenetic trees of five model species. Chionodraco hamatus duplicates were recorded for each orthology group allowing the identification of duplicated genes specific to the icefish lineage. Significantly more duplicates were found in the icefish when transcriptome data were compared with whole-genome data of model species. Indeed, duplicated genes were significantly enriched in proteins with mitochondrial localization, involved in mitochondrial function and biogenesis. In cold conditions and without oxygen-carrying proteins, energy production is challenging. The combination of high mitochondrial densities and the maintenance of duplicated genes involved in mitochondrial biogenesis and aerobic respiration might confer a selective advantage by improving oxygen diffusion and energy supply to aerobic tissues. Our results provide new insights into the genomic basis of icefish cold adaptation.

Aim Pleuragramma antarctica is an Antarctic notothenioid fish with a pelagic life-cycle. It plays a major trophic role in coastal Antarctic waters as a predator of krill and as prey for penguins and seals. A previous study, using mtDNA to investigate Pleuragramma population structure at multiple Antarctic sites was unable to discriminate between hypotheses of panmixia, with occasional fluctuations of allelic frequencies, and population structure. The aim of the present study was to investigate the population structure of P. antarctica along the Antarctic Peninsula (AP) shelf by microsatellite genotyping.Location Four areas along the AP shelf: Charcot Island, Marguerite Bay, Joinville Island and the Larsen Ice Shelf.Methods A total of 562 individuals from nine population samples were genotyped at 16 expressed sequence tag (EST)-linked microsatellites. Genetic variability, Hardy-Weinberg probabilities and F-statistics were calculated, and a hierarchical analysis of molecular variance was carried out. A Bayesian method was applied to estimate the migration rates between geographical localities.Results We found one genetically homogeneous population with no interannual variability in the south-western AP and one off the northern tip of the AP. Significant differences were recorded between the two geographical regions, which also differed from the eastern AP. The extent of differentiation changed between years and significant genetic differentiation was found between clusters of individuals of different length modes collected at Joinville Island in 2010. Bayesian analysis suggested weak gene flow along the western AP, with a prevailing direction from north to south, following the anticlockwise-flowing Coastal Current.Main conclusions Population genetic structure can be detected in AP shelf samples of P. antarctica. Thus, even in this area characterized by strong oceanographic currents, genetic mixing is not complete. Temporal fluctuations of allelic frequencies and genetic differentiation between individuals of different length collected at the same location suggest the importance of genetic drift in this highly abundant species.

Determining the timing, extent and underlying causes of interspecific gene exchange during or following speciation is central to understanding species' evolution. Antarctic notothenioid fish, thanks to the acquisition of antifreeze glycoproteins during Oligocene transition to polar conditions, experienced a spectacular radiation to >100 species during Late Miocene cooling events. The impact of recent glacial cycles on this group is poorly known, but alternating warming and cooling periods may have affected species' distributions, promoted ecological divergence into recurrently opening niches and/or possibly brought allopatric species into contact. Using microsatellite markers and statistical methods including Approximate Bayesian Computation, we investigated genetic differentiation, hybridization and the possible influence of the last glaciation/deglaciation events in three icefish species of the genus Chionodraco. Our results provide strong evidence of contemporary and past introgression by showing that: (i) a substantial fraction of contemporary individuals in each species has mixed ancestry, (ii) evolutionary scenarios excluding hybridization or including it only in ancient times have small or zero posterior probabilities, (iii) the data support a scenario of interspecific gene flow associated with the two most recent interglacial periods. Glacial cycles might therefore have had a profound impact on the genetic composition of Antarctic fauna, as newly available shelf areas during the warmer intervals might have favoured secondary contacts and hybridization between diversified groups. If our findings are confirmed in other notothenioids, they offer new perspectives for understanding evolutionary dynamics of Antarctic fish and suggest a need for new predictions on the effects of global warming in this group.

Using monoclonal antibodies (MoAbs) termed GL183 and EB6, directed to a novel family of natural killer (NK) specific triggering molecules, four functional subsets of NK cells have been recently defined (GL183+EB6-; GL183+EB6+; GL183-EB6+; GL183-EB6-). In healthy individuals, all these subsets are represented in variable portion. The expression of EB6 and GL183 surface antigens has been analyzed in a series of 14 patients with lymphoproliferative disease of granular lymphocytes (LDGL) characterized by a chronic CD3-CD16+ lymphocytosis. Our data showed that in 11 of 14 cases, the proliferation was specifically sustained by one of the four possible subsets of granular lymphocytes (GLs) (seven cases: EB6-GL183-; three cases: EB6+GL183-; one case: EB6-GL183+). In the remaining three cases, a pattern was demonstrated that is consistent with that of healthy individuals (ie, the presence of all four subsets). When expressed on GL surfaces, in the majority of cases tested both EB6 and GL183 MoAbs behave as functional surface molecules as assessed in the redirected killing of P815 target cells. We also provided evidence that EB6+GL183+ proliferating cells show a definite (type 1) in vitro NK specificity as do their normal counterparts. The unique expansion of a defined subset of NK cells in most patients with LDGL suggests that the pathologic noxa leading to GL proliferation selectively acts on a specific subset of NK lymphocytes.

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This article documents the addition of 139 microsatellite marker loci and 90 pairs of singlenucleotide polymorphism sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Aglaoctenus lagotis, Costus pulverulentus, Costus scaber, Culex pipiens, Dascyllus marginatus, Lupinus nanus Benth, Phloeomyzus passerini, Podarcis muralis, Rhododendron rubropilosum Hayata var. taiwanalpinum and Zoarces viviparus. These loci were cross-tested on the following species: Culex quinquefasciatus, Rhododendron pseudochrysanthum Hay. ssp. morii (Hay.) Yamazaki and R. pseudochrysanthum Hayata. This article also documents the addition of 48 sequencing primer pairs and 90 allele-specific primers for Engraulis encrasicolus. et al.

The identification of loci under selection (outliers) is a major challenge in evolutionary biology, being critical to comprehend evolutionary processes leading to population differentiation and speciation, and for conservation purposes, also in light of recent climate change. However, detection of selected loci can be difficult when populations are weakly differentiated. This is the case of marine fish populations, often characterized by high levels of gene flow and connectivity, and particularly of fish living in the Antarctic marine environment, characterized by a complex and strong circulating system promoting individual dispersal all around the continent. With the final aim of identifying outlier loci putatively under selection in the Chionodraco genus, we used 21 microsatellites, including both genomic (Type II) and EST-linked loci (Type I), to investigate the genetic differentiation among the three recently derived Chionodraco species that are endemic to the freezing Antarctic waters. Neutrality tests were applied in interspecific comparisons in order to identify candidate loci showing high levels of genetic differentiation, which might reveal imprints of past selection.Three outlier loci were identified, detecting a higher differentiation between species than did neutral loci. Outliers showed sequence similarity to a calmodulin gene, to an antifreeze glycoprotein/trypsinogen-like protease gene and to nonannotated fish mRNAs. Selective pressures acting on outlier loci identified in this study might reflect past evolutionary processes, which led to species divergence and local adaptation in the Chionodraco genus. Used loci will provide a valuable tool for future population genetic studies in Antarctic notothenioids.

This article documents the addition of 234 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acipenser sinensis, Aleochara bilineata, Aleochara bipustulata, Barbus meridionalis, Colossoma macropomum, Delia radicum, Drosophila nigrosparsa, Fontainea picrosperma, Helianthemum cinereum, Liomys pictus, Megabalanus azoricus, Pelteobagrus vachelli, Pleuragramma antarcticum, Podarcis hispanica type 1A, Sardinella brasiliensis and Sclerotinia homoeocarpa. These loci were cross-tested on the following species: Acipenser dabryanus, Barbus balcanicus, Barbus barbus, Barbus cyclolepis, Drosophila hydei, Drosophila melanogaster, Drosophila obscura, Drosophila subobscura, Fontainea australis, Fontainea fugax, Fontainea oraria, Fontainea rostrata, Fontainea venosa, Podarcis bocagei, Podarcis carbonelli, Podarcis liolepis, Podarcis muralis and Podarcis vaucheri.