Larval stages of the Antarctic dragonfish Akarotaxis nudiceps (Waite, 1916), with comments on the larvae of the morphologically similar species Prionodraco evansii Regan 1914 (Notothenioidei: Bathydraconidae)

The notothenioid family Bathydraconidae is a poorly understood family of fishes endemic to the Southern Ocean. There is especially little information on Akarotaxis nudiceps, one of the deepest-dwelling and least fecund bathydraconid species. Using genetic and morphological data, we document and describe the larval stages of this unique species, offer a novel characteristic to distinguish it from the morphologically similar bathydraconid Prionodraco evansii and use the sampling locations to infer a possible spawning area of A. nudiceps along the western Antarctic Peninsula. These results provide important baseline information for locating, identifying and studying the biology of A. nudiceps, an important component of the Southern Ocean ecosystem.

The evolutionary puzzle solution for the origins of the partial loss of the Cτ2 exon in notothenioid fishes

Cryonotothenioidea is the main group of fishes that thrive in the extremely cold Antarctic environment, thanks to the acquisition of peculiar morphological, physiological and molecular adaptations. We have previously disclosed that IgM, the main immunoglobulin isotype in teleosts, display typical cold-adapted features. Recently, we have analyzed the gene encoding the heavy chain constant region (CH) of the IgT isotype from the Antarctic teleost Trematomus bernacchii (family Nototheniidae), characterized by the near-complete deletion of the CH2 domain. Here, we aimed to track the loss of the CH2 domain along notothenioid phylogeny and to identify its ancestral origins. To this end, we obtained the IgT gene sequences from several species belonging to the Antarctic families Nototheniidae, Bathydraconidae and Artedidraconidae. All species display a CH2 remnant of variable size, encoded by a short Cτ2 exon, which retains functional splicing sites and therefore is included in the mature transcript. We also considered representative species from the three non-Antarctic families: Eleginopsioidea (Eleginops maclovinus), Pseudaphritioidea (Pseudaphritis urvillii) and Bovichtidae (Bovichtus diacanthus and Cottoperca gobio). Even though only E. maclovinus, the sister taxa of Cryonotothenioidea, shared the partial loss of Cτ2, the other non-Antarctic notothenioid species displayed early molecular signatures of this event. These results shed light on the evolutionary path that underlies the origins of this remarkable gene structural modification.

Phylogenomic species delimitation dramatically reduces species diversity in an Antarctic adaptive radiation

Application of genetic data to species delimitation often builds confidence in delimitations previously hypothesized using morphological, ecological, and geographic data and frequently yields recognition of previously-undescribed cryptic diversity. However, a recent critique of genomic data-based species delimitation approaches is that they have the potential to conflate population structure with species diversity, resulting in taxonomic oversplitting. The need for an integrative approach to species delimitation, in which molecular, morphological, ecological, and geographic lines of evidence are evaluated together, is becoming increasingly apparent. Here, we integrate phylogenetic, population genetic, and coalescent analyses of genome-wide sequence data with investigation of variation in multiple morphological traits to delimit species within the Antarctic barbeled plunderfishes (Artedidraconidae: Pogonophryne). Pogonophryne currently comprises 29 valid species, most of which are distinguished solely by variation in ornamentation of the mental barbel that projects from the lower jaw, a structure previously shown to vary widely within a single species. However, our genomic and phenotypic analyses result in a dramatic reduction in the number of distinct species recognized within the clade, providing evidence to support the recognition of no more than six species. We propose to synonymize 24 of the currently recognized species with five species of Pogonophryne. We find genomic and phenotypic evidence for a new species of Pogonophryne from specimens collected in the Ross Sea. Our findings represent a rare example in which application of molecular data provides evidence of taxonomic oversplitting on the basis of morphology, clearly demonstrating the utility of an integrative species delimitation framework.

Accumulation of PBDEs and MeO-PBDEs in notothenioid fish from the South Shetland Islands, Antarctica: An interspecies comparative study

Concentrations of polybrominated diphenyl ethers (PBDEs) and methoxylated polybrominated diphenyl ethers (MeO-PBDEs); are reported in specimens of fish notothenioids Chaenocephalus aceratus (SSI), Trematomus bernacchii (ERN), and Nototheniops nudifrons (NOD) from the South Shetland Islands, Antarctica. Significant differences in the accumulation of 2'-MeO-BDE-68 and 6-MeO-BDE-47 were detected among the analysed species. MeO-BDEs were significantly higher in SSI (11.7, 8.6, and 14.1 ng g^-1 lw) than in NOD (1.63, 1.63, and 3.0 ng g^-1 lw) in muscle, liver, and gill, respectively. Feeding ecology traits explain the accumulation patterns of MeO-PBDEs. SSI has a higher feeding activity with a broader diet, followed by ERN, whereas NOD is a benthic/sedentary fish with a narrower diet. The accumulation of PBDEs was neither species-, nor tissue-specific. The current study expands the knowledge concerning the accumulation of PBDEs and MeO-PBDEs in Antarctic marine fish and supports the importance of species-specificity in the accumulation of MeO-PBDEs.

Not Frozen in the Ice: Large and Dynamic Rearrangements in the Mitochondrial Genomes of the Antarctic Fish

The vertebrate mitochondrial genomes generally present a typical gene order. Exceptions are uncommon and important to study the genetic mechanisms of gene order rearrangements and their consequences on phylogenetic output and mitochondrial function. Antarctic notothenioid fish carry some peculiar rearrangements of the mitochondrial gene order. In this first systematic study of 28 species, we analyzed known and undescribed mitochondrial genome rearrangements for a total of eight different gene orders within the notothenioid fish. Our reconstructions suggest that transpositions, duplications, and inversion of multiple genes are the most likely mechanisms of rearrangement in notothenioid mitochondrial genomes. In Trematominae, we documented an extremely rare inversion of a large genomic segment of 5,300 bp that partially affected the gene compositional bias but not the phylogenetic output. The genomic region delimited by nad5 and trnF, close to the area of the Control Region, was identified as the hot spot of variation in Antarctic fish mitochondrial genomes. Analyzing the sequence of several intergenic spacers and mapping the arrangements on a newly generated phylogeny showed that the entire history of the Antarctic notothenioids is characterized by multiple, relatively rapid, events of disruption of the gene order. We hypothesized that a pre-existing genomic flexibility of the ancestor of the Antarctic notothenioids may have generated a precondition for gene order rearrangement, and the pressure of purifying selection could have worked for a rapid restoration of the mitochondrial functionality and compactness after each event of rearrangement.

The genome sequence of the channel bull blenny, Cottoperca gobio (Günther, 1861)

We present a genome assembly for Cottoperca gobio (channel bull blenny, (Günther, 1861)); Chordata; Actinopterygii (ray-finned fishes), a temperate water outgroup for Antarctic Notothenioids. The size of the genome assembly is 609 megabases, with the majority of the assembly scaffolded into 24 chromosomal pseudomolecules. Gene annotation on Ensembl of this assembly has identified 21,662 coding genes.

The complete mitochondrial genome of the Antarctic marbled rockcod, Notothenia rossii (Perciformes, Nototheniidae)

The complete mitochondrial genome of Notothenia rossii was obtained using PacBio Sequel long-read sequencing platform. The mitogenome of N. rossii was circular form and 18,274 bp long, which consists of 13 protein-coding genes, 24 tRNAs, 2 rRNAs, and non-coding control region. Particularly, we found duplicated tRNA^Thr and tRNA^Pro in addition to the typical 22 tRNAs. The phylogenetic tree revealed that N. rossii was most closely related to N. coriiceps among species in the Nototheniidae clade within the suborder Notothenioidei.

Cytogenetic characterization of the Antarctic silverfish Pleuragramma antarctica (Boulenger 1902) through analysis of mitotic chromosomes from early larvae

This paper describes the cytogenetic features of the Antarctic silverfish Pleuragramma antarctica (Boulenger 1902), a keystone species of the Antarctic coastal marine ecosystem. Conventional cytogenetic analyses and physical mapping of repetitive DNA sequences were performed on metaphase plates obtained through direct chromosome preparation from P. antarctica early larvae. The Antarctic silverfish have a diploid number (2n) = 48, and a karyotype made up of a majority of two-armed chromosomes (karyotype formula36m/sm + 10st + 2a, fundamental number = 94). Major ribosomal gene repeats were detected on three chromosome pairs (20, 21, and 23), in correspondence of dim DAPI stained regions. Long Interspersed Nuclear Elements (LINEs) were abundant and wide spread over all chromosomes. Overall, the cytogenetic data presented herein are consistent with a long independent cytogenetic and evolutionary history for the species. The large number of two-armed chromosomes, indicative of highly-rearranged karyotype, coupled with a diploid number of 48, a presumed primitive character for this fish group, and the spread of the major ribosomal genes on three chromosome pairs, make the Antarctic silverfish distinct from all other notothenioid species.

Concentrations of Thirteen Trace Metals in Scales of Three Nototheniid Fishes from Antarctica (James Ross Island, Antarctic Peninsula)

In this study, we assessed concentrations of 13 trace metals in the scales of Notothenia coriiceps, Trematomus bernacchii and Gobionotothen gibberifrons caught off the coast of James Ross Island (Antarctic Peninsula). Overall, our results for scales broadly match those of previous studies using different fish and different organs, with most metals found at trace levels and manganese, aluminium, iron and zinc occurring at high levels in all species. This suggests that scales can serve as a useful, non-invasive bioindicator of long-term contamination in Antarctic fishes. High accumulation of manganese, aluminium, iron and zinc is largely due to high levels in sediments associated with nearby active volcanic sites. Manganese, vanadium and aluminium showed significant positive bioaccumulation in T. bernacchii (along with non-significant positive accumulation of iron, zinc, cobalt and chromium), most likely due to greater dietary specialisation on sediment feeding benthic prey and higher trophic species. Levels of significance in bioaccumulation regressions were strongly affected by large-scale variation in the data, driven largely by individual differences in diet and/or changes in habitat use and sex differences associated with life stage and reproductive status. Increased levels of both airborne deposition and precipitation and meltwater runoff associated with climate change may be further adding to the already high levels of manganese, aluminium, iron and zinc in Antarctic Peninsula sediments. Further long-term studies are encouraged to elucidate mechanisms of uptake (especially for aluminium and iron) and possible intra- and interspecific impacts of climate change on the delicate Antarctic food web.

Mechanosensory system of the lateral line in the subantarctic Patagonian blenny Eleginops maclovinus

This study describes the cephalic and trunk lateral line systems in Patagonian blenny Eleginops maclovinus juveniles, providing morphological details for pores, canals and neuromasts. Eleginops maclovinus juveniles possess a complete laterodorsal lateral line that extends from the upper apex of the gill opening along the trunk as far as the caudal fin. The lateral line was ramified through pores and canals. The following pores were recorded: four supraorbital pores, with two along the eye border and two on the snout; seven infraorbital pores, with three on the lacrimal bone and four being infraorbital; five postorbital pores, with three along the preopercular border (upper preoperculum branch) and two on the bone curvature (inferior preoperculum branch); and four mandibular pores aligned along the jaw. Furthermore, five narrow-simple and interconnected canals were found (i.e. preopercular, mandibular, supraorbital and infraorbital canals). Histologically, the dorsal lateral line presented thin neuromasts (350 μm) with short hair cells. By contrast, the cranial region presented long, thick neuromasts. Infraorbital and mandibular neuromasts had a major axis length of 260 μm and respective average diameters of 200 and 185 μm. Sensory system variations would be due to a greater concentration of neuromasts in the cranial region, allowing for a greater perception of changes in water pressure. Scarce morphological information is available for the lateral sensory system in Eleginopsidae, particularly compared to Channichthyidae, Bovichthydae, Artedidraconidae and Bathydraconidae. Therefore, the presented results form a fundamental foundation of knowledge for the lateral-line system in juvenile E. maclovinus and provide a basis for future related research in this taxon as well as within the Notothenioidei suborder.

First data on uranium uptake in three nototheniid fishes from Antarctica (James Ross Island)

Recent studies have confirmed historic atmospheric deposition of uranium in Antarctica, with a steep and significant increase in levels deposited since the 1980s in Antarctic Peninsula ice core samples. To date, however, there has been little or no attention paid to uranium in the Antarctic food web. Here, we present results for uranium content in scales of three common nototheniid species (Trematomus bernacchii, Gobionotothen gibberifrons, Notothenia coriiceps) from coastal waters off James Ross Island (Antarctic Peninsula). While mean total uranium levels (mean ± SD) were low and similar between species (N. coriiceps 0.08 μg g^-1 ± 0.01, T. bernacchii 0.17 μg g^-1 ± 0.10; G. gibberifrons 0.11 μg g^-1 ± 0.04), linear regressions against standard length indicated bioaccumulation in T. bernacchii (ANOVA, F = 7.8349, P = 0.0076). We suggest this may be the result of dietary specialisation on prey with calcareous shells that accumulate uranium. To the best of our knowledge, this paper provides the first quantitative baseline data on uranium levels in coastal Antarctic nototheniids. While the low levels recorded are unlikely to represent a threat within the food chain, we suggest that further long-term trophic studies (including stable isotope analysis) are needed, recognising that the feeding ecology of individual species (and even individuals) can have a strong effect on overall trends.

Phylogenetic analysis of Antarctic notothenioids illuminates the utility of RADseq for resolving Cenozoic adaptive radiations

Notothenioids are a clade of ∼120 species of marine fishes distributed in extreme southern hemisphere temperate near-shore habitats and in the Southern Ocean surrounding Antarctica. Over the past 25 years, molecular and morphological approaches have redefined hypotheses of relationships among notothenioid lineages as well as their relationships among major lineages of percomorph teleosts. These phylogenies provide a basis for investigation of mechanisms of evolutionary diversification within the clade and have enhanced our understanding of the notothenioid adaptive radiation. Despite extensive efforts, there remain several questions concerning the phylogeny of notothenioids. In this study, we deploy DNA sequences of ∼100,000 loci obtained using RADseq to investigate the phylogenetic relationships of notothenioids and to assess the utility of RADseq loci for lineages that exhibit divergence times ranging from the Paleogene to the Quaternary. The notothenioid phylogenies inferred from the RADseq loci provide unparalleled resolution and node support for several long-standing problems including, (1) relationships among species of Trematomus, (2) resolution of Indonotothenia cyanobrancha as the sister lineage of Trematomus, (3) the deep paraphyly of Nototheniidae, (4) the paraphyly of Lepidonotothen s.l., (5) paraphyly of Artedidraco, and 6) the monophyly of the Bathydraconidae. Assessment of site rates demonstrates that RADseq loci are similar to mtDNA protein coding genes and exhibit peak phylogenetic informativeness at the time interval during which the major Antarctic notothenioid lineages originated and diversified. In addition to providing a well-resolved phylogenetic hypothesis for notothenioids, our analyses quantify the predicted utility of RADseq loci for Cenozoic phylogenetic inferences.

Implications of biological factors on accumulation of persistent organic pollutants in Antarctic notothenioid fish

In the present study, the possible associations between selected persistent organic pollutants (POPs) and biological factors were assessed in different tissues of two Antarctic notothenioid fish: Notothenia rossii (NOR) and Trematomus newnesi (TRN) collected at Potter Cove, King George Island/Isla 25 de Mayo, South Shetland Islands. Specifically, association patterns between biological factors (body size, lipid content, body condition) and POP concentrations (polychlorinated biphenyls (PCBs), dichlorodiphenyltrichloroethane (DDT) and metabolites, polybrominated diphenyl ethers (PBDEs), and hexachlorocyclohexane (HCH), hexachlorobenzene (HCB), chlordanes (CHLs) and methoxylated polybrominated diphenyl ethers (MeO-PBDEs)), were explored by using two approaches: multivariate analyses (principal component analysis: PCA) and intraspecific correlations. Integrating results suggest that biological factors such as size, KI and tissue type seemed to be associated to selective accumulation of POPs for immature specimens of N. rossii, and KI and tissue type for mature specimens of T. newnesi. Each particular factor should be considered when choosing N. rossii or T. newnesi as sentinels for POPs pollution in Antarctic marine environments. Further, both nototheniids showed a selective accumulation pattern in their gonads of penta-chlorinated biphenyls (penta-CBs; 55.5 and 29ngg^-1 lw for N. rossii and T. newnesi, respectively) and organochlorine pesticides such as DDTs (199 and 13.3ngg^-1 lw, for N. rossii and T. newnesi respectively), and of polybrominated diphenyl ethers (PBDEs) in gills (97.2 and 22.1 for ngg^-1 lw, for N. rossii and T. newnesi, respectively), highlighting the importance of these tissues in monitoring studies of pollution in fish. The current study expands the knowledge concerning the biological factors to be investigated when specific pollutants are monitored and supports the importance of tissue type for the selective accumulation of POPs in Antarctic fish. Additionally, a contribution to the scarce data on concentration of MeO-PBDEs in Antarctic marine organisms, particularly in the highly diverse perciform suborder Notothenioidei is provided.

Genomic conservation of erythropoietic microRNAs (erythromiRs) in white-blooded Antarctic icefish

White-blooded Antarctic crocodile icefish are the only vertebrates known to lack functional hemoglobin genes and red blood cells throughout their lives. We do not yet know, however, whether extinction of hemoglobin genes preceded loss of red blood cells or vice versa, nor whether erythropoiesis regulators disappeared along with hemoglobin genes in this erythrocyte-null clade. Several microRNAs, which we here call erythromiRs, are expressed primarily in developing red blood cells in zebrafish, mouse, and humans. Abrogating some erythromiRs, like mir144 and mir451a, leads to profound anemia, demonstrating a functional role in erythropoiesis. Here, we tested two not mutually exclusive hypotheses: 1) that the loss of one or more erythromiR genes extinguished the erythropoietic program of icefish and/or led to the loss of globin gene expression through pseudogenization; and 2) that some erythromiR genes were secondarily lost after the loss of functional hemoglobin and red blood cells in icefish. We explored small RNA transcriptomes generated from the hematopoietic kidney marrow of four Antarctic notothenioids: two red-blooded species (bullhead notothen Notothenia coriiceps and emerald notothen Trematomus bernacchii) and two white-blooded icefish (blackfin icefish Chaenocephalus aceratus and hooknose icefish Chionodraco hamatus). The N. coriiceps genome assembly anchored analyses. Results showed that, like the two red-blooded species, the blackfin icefish genome possessed and the marrow expressed all known erythromiRs. This result indicates that loss of hemoglobin and red blood cells in icefish was not caused by loss of known erythromiR genes. Furthermore, expression of only one erythromiR, mir96, appears to have been lost after the loss of red blood cells and hemoglobin-expression was not detected in the erythropoietic organ of hooknose icefish but was present in blackfin icefish. All other erythromiRs investigated, including mir144 and mir451a, were expressed by all four species and thus are present in the genomes of at least the two white-blooded icefish. Our results rule out the hypothesis that genomic loss of any known erythromiRs extinguished erythropoiesis in icefish, and suggest that after the loss of red blood cells, few erythromiRs experienced secondary loss. Results suggest that functions independent of erythropoiesis maintained erythromiRs, thereby highlighting the evolutionary resilience of miRNA genes in vertebrate genomes.

Total Mercury in Six Antarctic Notothenioid Fishes

We analyzed white muscle samples from six species of Antarctic fish (suborder Notothenioidei) collected in 2011 from McMurdo Sound, Ross Sea, Antarctica, to assess levels of total mercury (THg). Gymnodraco acuticeps and Trematomus bernacchii exhibited the highest concentrations of THg followed by Trematomus pennellii, Trematomus nicolai, Trematomus newnesi and Pagothenia borchgrevinki, (71.3, 53.9±32.1, 45.8±27.3, 37.2±18.6, 35.7±23.6, and 21.9±2.8 ng/g wet weight, respectively). The results from this study suggest that THg has the potential to bioaccumulate from various marine Antarctic ecosystems into biota.