Phylogenetics of notothenioid fishes (Teleostei: Acanthomorpha): Inferences from mitochondrial and nuclear gene sequences

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.

Effect of heat stress on the antioxidant defense system and erythrocyte morphology of Antarctic fishes

This study analyzed the effect of thermal stress on erythrocytes of Notothenia rossii and Notothenia coriiceps, abundant notothenioids in Admiralty Bay, Antarctic Peninsula. In both species, the antioxidant defense system enzymes, superoxide dismutase, catalase, glutathione peroxidase, glutathione-S transferase, glutathione reductase were punctually altered (8°C for 1, 3 and 6 days) in erythrocytes, indicating that these markers are not ideal for termal stress. However, under the influence of thermal stress, morphological changes in Notothenia coriiceps erythrocytes were observed at all exposure times (1, 3 and 6 days at 8°C), and in Notothenia rossii occurred in 6 days. These results suggest that Notothenia corriceps presents a lower tolerance to thermal stress at 8°C for up to 6 days, since the cellular and nuclear alterations recorded are pathological and may be deleterious to the cells. Among the morphological markers analyzed in this work, we believe that the shape change and nuclear bubble formation may be good stress biomarkers in erythrocytes of Notothenia rossii and Notothenia coriiceps.

Understanding the Metabolic Capacity of Antarctic Fishes to Acclimate to Future Ocean Conditions

Antarctic fishes have evolved under stable, extreme cold temperatures for millions of years. Adapted to thrive in the cold environment, their specialized phenotypes will likely render them particularly susceptible to future ocean warming and acidification as a result of climate change. Moving from a period of stability to one of environmental change, species persistence will depend on maintaining energetic equilibrium, or sustaining the increased energy demand without compromising important biological functions such as growth and reproduction. Metabolic capacity to acclimate, marked by a return to metabolic equilibrium through physiological compensation of routine metabolic rate (RMR), will likely determine which species will be better poised to cope with shifts in environmental conditions. Focusing on the suborder Notothenioidei, a dominant group of Antarctic fishes, and in particular four well-studied species, Trematomus bernacchii, Pagothenia borchgrevinki, Notothenia rossii, and N. coriiceps, we discuss metabolic acclimation potential to warming and CO2-acidification using an integrative and comparative framework. There are species-specific differences in the physiological compensation of RMR during warming and the duration of acclimation time required to achieve compensation; for some species, RMR fully recovered within 3.5 weeks of exposure, such as P. borchgrevinki, while for other species, such as N. coriiceps, RMR remained significantly elevated past 9 weeks of exposure. In all instances, added exposure to increased PCO2, further compromised the ability of species to return RMR to pre-exposure levels. The period of metabolic imbalance, marked by elevated RMR, was underlined by energetic disturbance and elevated energetic costs, which shifted energy away from fitness-related functions, such as growth. In T. bernacchii and N. coriiceps, long duration of elevated RMR impacted condition factor and/or growth rate. Low growth rate can affect development and ultimately the timing of reproduction, severely compromising the species' survival potential and the biodiversity of the notothenioid lineage. Therefore, the ability to achieve full compensation of RMR, and in a short-time frame, in order to avoid long term consequences of metabolic imbalance, will likely be an important determinant in a species' capacity to persist in a changing environment. Much work is still required to develop our understanding of the bioenergetics of Antarctic fishes in the face of environmental change, and a targeted approach of nesting a mechanistic focus in an ecological and comparative framework will better aid our predictions on the effect of global climate change on species persistence in the polar regions.

Multiple independent chromosomal fusions accompanied the radiation of the Antarctic teleost genus Trematomus (Notothenioidei:Nototheniidae)

Background

Chromosomal rearrangements are thought to be an important driving force underlying lineage diversification, but their link to speciation continues to be debated. Antarctic teleost fish of the family Nototheniidae (Notothenioidei) diversified in a changing environmental context, which led to ecological, morphological, and genetic differentiation among populations. In addition, extensive chromosomal repatterning accompanied species divergence in several clades. The most striking karyotypic changes involved the recent species radiation (about 10 My) of the genus Trematomus, with chromosomal pair numbers ranging between 29 and 12. These dramatic reductions in chromosome number resulted mostly from large-scale chromosome fusions. Multiple centric and/or tandem fusions have been hypothesized in at least seven of the twelve recognized Trematomus species. To reconstruct their evolutionary history, we employed comparative cytogenomics (BAC-FISH and chromosome painting) to reveal patterns of interspecific chromosomal orthologies across several notothenioid clades.

Results

We defined orthologous chromosomal segments of reference, termed Structural Units (SUs). SUs were identified in a total of 18 notothenioid species. We demonstrated for the first time that SUs were strongly conserved across every specimen examined, with chromosomal syntenies highlighting a paucity of intrachromosomal macro-rearrangements. Multiple independent fusions of these SUs were inferred in the Trematomus species, in contrast to the shared SU fusions in species of the sister lineage Notothenia.

Conclusions

The SU segments were defined units of chromosomal rearrangement in the entire family Nototheiidae, which diverged from the other notothenioid families 20 My ago. Some of the identified chromosomal syntenies within the SUs were even conserved in their closest relatives, the family Eleginopsidae. Comparing the timing of acquisition of the fusions in the closely related genera Notothenia and Trematomus of the nototheniid species family, we conclude that they exhibit distinct chromosomal evolutionary histories, which may be relevant to different speciation scenarios.

The unique structural features of carbonmonoxy hemoglobin from the sub-Antarctic fish Eleginops maclovinus

Tetrameric hemoglobins (Hbs) are prototypical systems for the investigations of fundamental properties of proteins. Although the structure of these proteins has been known for nearly sixty years, there are many aspects related to their function/structure that are still obscure. Here, we report the crystal structure of a carbonmonoxy form of the Hb isolated from the sub-Antarctic notothenioid fish Eleginops maclovinus characterised by either rare or unique features. In particular, the distal site of the α chain results to be very unusual since the distal His is displaced from its canonical position. This displacement is coupled with a shortening of the highly conserved E helix and the formation of novel interactions at tertiary structure level. Interestingly, the quaternary structure is closer to the T-deoxy state of Hbs than to the R-state despite the full coordination of all chains. Notably, these peculiar structural features provide a rationale for some spectroscopic properties exhibited by the protein in solution. Finally, this unexpected structural plasticity of the heme distal side has been associated with specific sequence signatures of various Hbs.

Evolution in chronic cold: varied loss of cellular response to heat in Antarctic notothenioid fish

Background

Confined within the freezing Southern Ocean, the Antarctic notothenioids have evolved to become both cold adapted and cold specialized. A marked signature of cold specialization is an apparent loss of the cellular heat shock response (HSR). As the HSR has been examined in very few notothenioid species to-date, it remains unknown whether HSR loss pervades the Antarctic radiation, or whether the broader cellular responses to heat stress has sustained similar loss. Understanding the evolutionary status of these responses in this stenothermal taxon is crucial for evaluating its adaptive potential to ocean warming under climate change.

Results

In this study, we used an acute heat stress protocol followed by RNA-Seq analyses to study the evolution of cellular-wide transcriptional responses to heat stress across three select notothenioid lineages - the basal temperate and nearest non-Antarctic sister species Eleginops maclovinus serving as ancestral proxy, the cryopelagic Pagothenia borchgrevinki and the icefish Chionodraco rastrospinosus representing cold-adapted red-blooded and hemoglobinless Antarctic notothenioids respectively. E. maclovinus displayed robust cellular stress responses including the ER Unfolded Protein Response and the cytosolic HSR, cementing the HSR as a plesiomorphy that preceded Antarctic notothenioid radiation. While the transcriptional response to heat stress was minimal in P. borchgrevinki, C. rastrospinosus exhibited robust responses in the broader cellular networks especially in inflammatory responses despite lacking the classic HSR and UPR.

Conclusion

The disparate patterns observed in these two archetypal Antarctic species indicate the evolutionary status in cellular ability to mitigate acute heat stress varies even among Antarctic lineages, which may affect their adaptive potential in coping with a warming world.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1254-6) contains supplementary material, which is available to authorized users.

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.

Untargeted metabolic profiling reveals distinct patterns of thermal sensitivity in two related notothenioids

Antarctic marine ectothermal animals may be affected more than temperate species by rising temperatures due to ongoing climate change. Their specialisation on stable cold temperatures makes them vulnerable to even small degrees of warming. Thus, addressing the impacts of warming on Antarctic organisms and identifying their potentially limited capacities to respond is of interest. The objective of the study was to determine changes in metabolite profiles related to temperature acclimation. In a long-term experiment adult fish of two Antarctic sister species Notothenia rossii and Notothenia coriiceps were acclimated to 0°C and 5°C for three months. Impacts and indicators of acclimation at the cellular level were determined from metabolite profiles quantified in gill tissue extracts using nuclear magnetic resonance (NMR) spectroscopy. Furthermore, the metabolite profiles of the two con-generic species were compared. NMR spectroscopy identified 37 metabolites that were present in each sample, but varied in their absolute concentration between species and between treatments. A decrease in amino acid levels indicated an increased amino acid catabolism after incubation to 5°C. In addition, long term warming initiated shifts in organic osmolyte concentrations and modified membrane structure observed by altered levels of phospholipid compounds. Differences in the metabolite profile between the two notothenioid species can be related to their divergent lifestyles, especially their different rates of motor activity. Increased levels of the Krebs cycle intermediate succinate and a higher reduction of amino acid concentrations in warm-acclimated N. rossii showed that N. rossii is more affected by warming than N. coriiceps.

Nutritional Immunity Triggers the Modulation of Iron Metabolism Genes in the Sub-Antarctic Notothenioid Eleginops maclovinus in Response to Piscirickettsia salmonis

Iron deprivation is a nutritional immunity mechanism through which fish can limit the amount of iron available to invading bacteria. The aim of this study was to evaluate the modulation of iron metabolism genes in the liver and brain of sub-Antarctic notothenioid Eleginops maclovinus challenged with Piscirickettsia salmonis. The specimens were inoculated with two P. salmonis strains: LF-89 (ATCC^® VR-1361™) and Austral-005 (antibiotic resistant). Hepatic and brain samples were collected at intervals over a period of 35 days. Gene expression (by RT-qPCR) of proteins involved in iron storage, transport, and binding were statistically modulated in infected fish when compared with control counterparts. Specifically, the expression profiles of the transferrin and hemopexin genes in the liver, as well as the expression profiles of ferritin-M, ferritin-L, and transferrin in the brain, were similar for both experimental groups. Nevertheless, the remaining genes such as ferritin-H, ceruloplasmin, hepcidin, and haptoglobin presented tissue-specific expression profiles that varied in relation to the injected bacterial strain and sampling time-point. These results suggest that nutritional immunity could be an important immune defense mechanism for E. maclovinus against P. salmonis injection. This study provides relevant information for understanding iron metabolism of a sub-Antarctic notothenioid fish.

Cold Fusion: Massive Karyotype Evolution in the Antarctic Bullhead Notothen Notothenia coriiceps

Half of all vertebrate species share a series of chromosome fusions that preceded the teleost genome duplication (TGD), but we do not understand the causative evolutionary mechanisms. The "Robertsonian-translocation hypothesis" suggests a regular fusion of each ancestral acro- or telocentric chromosome to just one other by centromere fusions, thus halving the karyotype. An alternative "genome-stirring hypothesis" posits haphazard and repeated fusions, inversions, and reciprocal and nonreciprocal translocations. To study large-scale karyotype reduction, we investigated the decrease of chromosome numbers in Antarctic notothenioid fish. Most notothenioids have 24 haploid chromosomes, but bullhead notothen (Notothenia coriiceps) has 11. To understand mechanisms, we made a RAD-tag meiotic map with ∼10,000 polymorphic markers. Comparative genomics aligned about a thousand orthologs of platyfish and stickleback genes along bullhead chromosomes. Results revealed that 9 of 11 bullhead chromosomes arose by fusion of just two ancestral chromosomes and two others by fusion of three ancestral chromosomes. All markers from each ancestral chromosome remained contiguous, implying no inversions across fusion borders. Karyotype comparisons support a history of: (1) Robertsonian fusions of 22 ancestral chromosomes in pairs to yield 11 fused plus two small unfused chromosomes, like N. angustata; (2) fusion of one of the remaining two ancestral chromosomes to a preexisting fused pair, giving 12 chromosomes like N. rossii; and (3) fusion of the remaining ancestral chromosome to another fused pair, giving 11 chromosomes in N. coriiceps These results raise the question of what selective forces promoted the systematic fusion of chromosomes in pairs and the suppression of pericentric inversions in this lineage, and provide a model for chromosome fusions in stem teleosts.

Expansion of capacities for iron transport and sequestration reflects plasma volumes and heart mass among white-blooded notothenioid fishes

The family Channichthyidae or “icefishes” (suborder Notothenioidei) represents the only vertebrates lacking hemoglobin (Hb) as adults. Several icefish species also do not express cardiac myoglobin (Mb). We address how levels of proteins involved in iron (Fe) processing (transport, sequestration, and export) vary among white- and red-blooded notothenioids, and whether absence of Hb and/or Mb in channichthyids is accompanied by expansion of contents of Fe-binding proteins to protect against unchaperoned Fe. Levels of transferrin (Tf), ferritin (Ft), ceruloplasmin (Cp), and non-heme Fe were quantified in plasma, serum, and/or nonhematopoietic tissues (cardiac ventricle, skeletal muscle, and liver) from species of white-blooded ( Chaenocephalus aceratus, Champsocephalus gunnari, Chionodraco rastrospinosus, Pseudochaenichthys georgianus) (the first two species not expressing Mb) and red-blooded ( Notothenia coriiceps, Gobionotothen gibberifrons) notothenioids. We also measured levels of ascorbate (Asc), a mediator of Fe uptake. While plasma concentrations of Tf and tissue levels of Asc are similar among species, concentrations of plasma Asc are lower in white-blooded species. Concentrations of Ft and non-heme Fe and activities of Cp are also generally reduced in icefishes compared with red-blooded notothenioids. The presence of cardiac Mb in some icefish species does not appear to influence levels of proteins involved in Fe processing. To address further the question of Fe sequestration within a physiological context, we account for well-characterized differences in blood volume and heart mass among white- and red-blooded notothenioids. We report that total contents of plasma Tf are greater, while ventricle non-heme Fe is at least at parity in white- vs. red-blooded species.

Antarctic notothenioid fish: what are the future consequences of 'losses' and 'gains' acquired during long-term evolution at cold and stable temperatures?

Antarctic notothenioids dominate the fish fauna of the Southern Ocean. Evolution for millions of years at cold and stable temperatures has led to the acquisition of numerous biochemical traits that allow these fishes to thrive in sub-zero waters. The gain of antifreeze glycoproteins has afforded notothenioids the ability to avert freezing and survive at temperatures often hovering near the freezing point of seawater. Additionally, possession of cold-adapted proteins and membranes permits them to sustain appropriate metabolic rates at exceptionally low body temperatures. The notothenioid genome is also distinguished by the disappearance of traits in some species, losses that might prove costly in a warmer environment. Perhaps the best-illustrated example is the lack of expression of hemoglobin in white-blooded icefishes from the family Channichthyidae. Loss of key elements of the cellular stress response, notably the heat shock response, has also been observed. Along with their attainment of cold tolerance, notothenioids have developed an extreme stenothermy and many species perish at temperatures only a few degrees above their habitat temperatures. Thus, in light of today's rapidly changing climate, it is critical to evaluate how these extreme stenotherms will respond to rising ocean temperatures. It is conceivable that the remarkable cold specialization of notothenioids may ultimately leave them vulnerable to future thermal increases and threaten their fitness and survival. Within this context, our review provides a current summary of the biochemical losses and gains that are known for notothenioids and examines these cold-adapted traits with a focus on processes underlying thermal tolerance and acclimation capacity.

Identification of the notothenioid sister lineage illuminates the biogeographic history of an Antarctic adaptive radiation

BACKGROUND

Antarctic notothenioids are an impressive adaptive radiation. While they share recent common ancestry with several species-depauperate lineages that exhibit a relictual distribution in areas peripheral to the Southern Ocean, an understanding of their evolutionary origins and biogeographic history is limited as the sister lineage of notothenioids remains unidentified. The phylogenetic placement of notothenioids among major lineages of perciform fishes, which include sculpins, rockfishes, sticklebacks, eelpouts, scorpionfishes, perches, groupers and soapfishes, remains unresolved. We investigate the phylogenetic position of notothenioids using DNA sequences of 10 protein coding nuclear genes sampled from more than 650 percomorph species. The biogeographic history of notothenioids is reconstructed using a maximum likelihood method that integrates phylogenetic relationships, estimated divergence times, geographic distributions and paleogeographic history.

RESULTS

Percophis brasiliensis is resolved, with strong node support, as the notothenioid sister lineage. The species is endemic to the subtropical and temperate Atlantic coast of southern South America. Biogeographic reconstructions imply the initial diversification of notothenioids involved the western portion of the East Gondwanan Weddellian Province. The geographic disjunctions among the major lineages of notothenioids show biogeographic and temporal correspondence with the fragmentation of East Gondwana.

CONCLUSIONS

The phylogenetic resolution of Percophis requires a change in the classification of percomorph fishes and provides evidence for a western Weddellian origin of notothenioids. The biogeographic reconstruction highlights the importance of the geographic and climatic isolation of Antarctica in driving the radiation of cold-adapted notothenioids.

Diversity and disparity through time in the adaptive radiation of Antarctic notothenioid fishes

According to theory, adaptive radiation is triggered by ecological opportunity that can arise through the colonization of new habitats, the extinction of antagonists or the origin of key innovations. In the course of an adaptive radiation, diversification and morphological evolution are expected to slow down after an initial phase of rapid adaptation to vacant ecological niches, followed by speciation. Such 'early bursts' of diversification are thought to occur because niche space becomes increasingly filled over time. The diversification of Antarctic notothenioid fishes into over 120 species has become one of the prime examples of adaptive radiation in the marine realm and has likely been triggered by an evolutionary key innovation in the form of the emergence of antifreeze glycoproteins. Here, we test, using a novel time-calibrated phylogeny of 49 species and five traits that characterize notothenioid body size and shape as well as buoyancy adaptations and habitat preferences, whether the notothenioid adaptive radiation is compatible with an early burst scenario. Extensive Bayesian model comparison shows that phylogenetic age estimates are highly dependent on model choice and that models with unlinked gene trees are generally better supported and result in younger age estimates. We find strong evidence for elevated diversification rates in Antarctic notothenioids compared to outgroups, yet no sign of rate heterogeneity in the course of the radiation, except that the notothenioid family Artedidraconidae appears to show secondarily elevated diversification rates. We further observe an early burst in trophic morphology, suggesting that the notothenioid radiation proceeds in stages similar to other prominent examples of adaptive radiation.

Complete mitochondrial genome of the Antarctic icefish, Chaenocephalus aceratus (Perciforms, Channichthyidae)

The complete sequence of the mitochondrial genome of the Antarctic icefish Chaenocephalus aceratus was determined to be 17311 bp in length, and to contain 13 protein coding genes (PCGs), 22 tRNA genes and 2 rRNA genes. The total A+T content is 52.8%. The notothenioid-exclusive ND6/tRNAGlu translocation was observed in the mitogenome of C. aceratus. Generally, the order and contents of the other genes are identical with those of other fishes. Antarctic icefishes, the only vertebrates which do not have hemoglobins, have evolved to survive sub-freezing temperature. Therefore, the whole mitogenome sequences of C. aceratus will provide the insights into resolving the evolutionary history of icefish.

Is the species flock concept operational? The Antarctic shelf case

There has been a significant body of literature on species flock definition but not so much about practical means to appraise them. We here apply the five criteria of Eastman and McCune for detecting species flocks in four taxonomic components of the benthic fauna of the Antarctic shelf: teleost fishes, crinoids (feather stars), echinoids (sea urchins) and crustacean arthropods. Practical limitations led us to prioritize the three historical criteria (endemicity, monophyly, species richness) over the two ecological ones (ecological diversity and habitat dominance). We propose a new protocol which includes an iterative fine-tuning of the monophyly and endemicity criteria in order to discover unsuspected flocks. As a result nine « full » species flocks (fulfilling the five criteria) are briefly described. Eight other flocks fit the three historical criteria but need to be further investigated from the ecological point of view (here called "core flocks"). The approach also shows that some candidate taxonomic components are no species flocks at all. The present study contradicts the paradigm that marine species flocks are rare. The hypothesis according to which the Antarctic shelf acts as a species flocks generator is supported, and the approach indicates paths for further ecological studies and may serve as a starting point to investigate the processes leading to flock-like patterning of biodiversity.

ATP regulation of the ligand-binding properties in temperate and cold-adapted haemoglobins. X-ray structure and ligand-binding kinetics in the sub-Antarctic fish Eleginops maclovinus

The major haemoglobin of the sub-Antarctic fish Eleginops maclovinus was structurally and functionally characterised with the aim to compare molecular environmental adaptations in the O(2)-transport system of sub-Antarctic fishes of the suborder Notothenioidei with those of their high-latitude relatives. Ligand-binding kinetics of the major haemoglobin of E. maclovinus indicated strong stabilisation of the liganded quaternary T state, enhanced in the presence of the physiological allosteric effector ATP, compared to that of high-Antarctic Trematomus bernacchii. The activation enthalpy for O(2) dissociation was dramatically lower than that in T. bernacchii haemoglobin, suggesting remarkable differences in temperature sensitivity and structural changes associated with O(2) release and exit from the protein. The haemoglobin functional properties, together with the X-ray structure of the CO form at 1.49 Å resolution, the first of a temperate notothenioid, strongly support the hypothesis that in E. maclovinus, whose life-style varies according to changes in habitat, the mechanisms that regulate O(2) affinity and the ATP-induced Root effect differ from those of high-Antarctic Notothenioids.

Resurrecting prehistoric parvalbumins to explore the evolution of thermal compensation in extant Antarctic fish parvalbumins

Parvalbumins (PVs) from Antarctic notothenioid fishes display a pattern of thermal adaptation that likely reflects evolutionary changes in protein conformational flexibility. We have used ancestral sequence reconstruction and homology modeling to identify two amino acid changes that could potentially account for the present thermal sensitivity pattern of Antarctic fish PVs compared with a PV from a theoretical warm-adapted ancestral fish. To test this hypothesis, ancient PVs were resurrected in the lab using PV from the notothenioid Gobionotothen gibberifrons as a platform for introducing mutations comparable to the reconstructed ancestral PV sequences. The wild-type PV (WT) as well as three mutant expression constructs were engineered: lysine 8 to asparagine (K8N), lysine 26 to asparagine (K26N) and a double mutant (DM). Calcium equilibrium dissociation constants (K(d)) versus temperature curves for all mutants were right-shifted, as predicted, relative to that of WT PV. The K(d) values for the K8N and K26N single mutants were virtually identical at all temperatures and showed an intermediate level of thermal sensitivity. The DM construct displayed a full conversion of thermal sensitivity pattern to that of a PV from a warm/temperate-adapted fish. Additionally, the K(d) versus temperature curve for the WT construct revealed greater thermal sensitivity compared with the mutant constructs. Measurements of the rates of Ca(2+) dissociation (k(off)) showed that all mutants generally had slower k(off) values than WT at all temperatures. Calculated rates of Ca(2+) binding (k(on)) for the K8N and K26N mutants were similar to values for the WT PV at all temperatures. In contrast, the calculated k(on) values for the DM PV were faster, providing mechanistic insights into the nature of potentially adaptive changes in Ca(2+) binding in this PV. The overall results suggest that the current thermal phenotype of Antarctic PVs can be recapitulated by just two amino acid substitutions.

Life history and biogeographic diversification of an endemic western North American freshwater fish clade using a comparative species tree approach

The west coast of North America contains a number of biogeographic freshwater provinces which reflect an ever-changing aquatic landscape. Clues to understanding this complex structure are often encapsulated genetically in the ichthyofauna, though frequently as unresolved evolutionary relationships and putative cryptic species. Advances in molecular phylogenetics through species tree analyses now allow for improved exploration of these relationships. Using a comprehensive approach, we analyzed two mitochondrial and nine nuclear loci for a group of endemic freshwater fish (sculpin-Cottus) known for a wide ranging distribution and complex species structure in this region. Species delimitation techniques identified three novel cryptic lineages, all well supported by phylogenetic analyses. Comparative phylogenetic analyses consistently found five distinct clades reflecting a number of unique biogeographic provinces. Some internal node relationships varied by species tree reconstruction method, and were associated with either Bayesian or maximum likelihood statistical approaches or between mitochondrial, nuclear, and combined datasets. Limited cases of mitochondrial capture were also evident, suggestive of putative ancestral hybridization between species. Biogeographic diversification was associated with four major regions and revealed historical faunal exchanges across regions. Mapping of an important life-history character (amphidromy) revealed two separate instances of trait evolution, a transition that has occurred repeatedly in Cottus. This study demonstrates the power of current phylogenetic methods, the need for a comprehensive phylogenetic approach, and the potential for sculpin to serve as an indicator of biogeographic history for native ichthyofauna in the region.

The reproductive behaviour of Pogonophryne scotti confirms widespread egg-guarding parental care among Antarctic notothenioids

In this paper, the first documentation of egg-guarding behaviour in an artedidraconid species, Pogonophryne scotti, through in situ photographic imagery obtained during video transects is provided. The male specimen was observed closely guarding a well-defined multi-layered egg mass deposited on the sea floor at 240 m on the southern South Orkney Islands shelf in the northern Weddell Sea. Egg-guarding parental care is present in species that are distributed among all of the major lineages of Antarctic notothenioids; however, lack of information on egg-deposition behaviours in Bovichtidae and Pseudaphritis prevents assessment of whether parental care originated prior to the origin of the Antarctic notothenioid radiation.

Application of 16s rDNA and cytochrome b ribosomal markers in studies of lineage and fish populations structure of aquatic species

The most economically important form of aquaculture is fish farming, which is an industry that accounts for an ever increasing share of world fishery production. Molecular markers can be used to enhance the productivity of the aquaculture and fish industries to meet the increasing demand. Molecular markers can be identified via a DNA test regardless of the developmental stage, age or environmental challenges experienced by the organism. The application of 16s and cytochrome b markers has enabled rapid progress in investigations of genetic variability and inbreeding, parentage assignments, species and strain identification and the construction of high resolution genetic linkage maps for aquaculture fisheries. In this review, the advantages of principles and potential power tools of 16s and cytochrome b markers are discussed. Main findings in term of trend, aspects and debates on the reviewed issue made from the model of aquatic species for the benefit of aquaculture genomics and aquaculture genetics research are discussed. The concepts in this review are illustrated with various research examples and results that relate theory to reality and provide a strong review of the current status of these biotechnology topics.

Evolution and function of the globin intergenic regulatory regions of the antarctic dragonfishes (Notothenioidei: Bathydraconidae)

As the Southern Ocean cooled to -1.8 °C over the past 40 My, the teleostean clade Notothenioidei diversified and, under reduced selection pressure for an oxygen-transporting apparatus, became less reliant on hemoglobin and red blood cells. At the extreme of this trend, the crown group of Antarctic icefishes (Channichthyidae) lost both components of oxygen transport. Under the decreased selection scenario, we hypothesized that the Antarctic dragonfishes (Bathydraconidae, the red-blooded sister clade to the icefishes) evolved lower blood hemoglobin concentrations because their globin gene complexes (α- and β-globin gene pairs linked by a regulatory intergene) transcribe globin mRNAs less effectively than those of basal notothenioids (e.g., the Nototheniidae [notothens]). To test our hypothesis, we 1) sequenced the α/β-intergenes of the adult globin complexes of three notothen and eight dragonfish species and 2) measured globin transcript levels in representative species from each group. The typical nototheniid intergene was ∼3-4 kb in length. The bathydraconid intergenes resolved into three subclasses (long [3.8 kb], intermediate [3.0 kb], and short [1.5-2.3 kb]) that corresponded to the three subclades proposed for the taxon. Although they varied in length due to indels, the three notothen and eight dragonfish intergenes contained a conserved ∼90-nt element that we have previously shown to be required for globin gene transcription. Using the quantitative polymerase chain reaction, we found that globin mRNA levels in red cells from one notothen species and from one species of each dragonfish subclade were equivalent statistically. Thus, our results indicate that the bathydraconids have evolved adult globin loci whose regulatory intergenes tend to be shorter than those of the more basal nototheniids yet are equivalent in transcriptional efficacy. Their low blood hemoglobin concentrations are most likely due to reduction in hematocrit.

Characterization and phylogenetic analysis of vitellogenin coding sequences in the Antarctic fish Trematomus bernacchii

Vitellogenin is the yolk protein precursor. Multiple vitellogenins identified in several teleosts have been attributed different roles in the control of egg buoyancy and in early embryonic vs. late larval nutrition. In this study, the cDNA encoding VtgAa was characterized in the Antarctic fish Trematomus bernacchii (suborder Notothenioidei). The sequence contains 4,964 nucleotides and encodes 1,629 amino acids of the precursor molecule. To gain insights into the evolution of vitellogenin in Antarctic fishes, we identified the partial sequence of vtgAb, and vtgAa and vtgAb partial sequences of five other notothenioids. The phylogenetic analysis highlighted a close correlation between the Vtg amino acid sequences of the six Antarctic species and VtgAa and VtgAb of other perciforms. Finally, analysis of the ratio of vtgAa to vtgAb expression, evaluated in T. bernacchii by real-time PCR, showed a considerably greater expression of vtgAa in different periods of austral summer.

On the origin and trigger of the notothenioid adaptive radiation

Adaptive radiation is usually triggered by ecological opportunity, arising through (i) the colonization of a new habitat by its progenitor; (ii) the extinction of competitors; or (iii) the emergence of an evolutionary key innovation in the ancestral lineage. Support for the key innovation hypothesis is scarce, however, even in textbook examples of adaptive radiation. Antifreeze glycoproteins (AFGPs) have been proposed as putative key innovation for the adaptive radiation of notothenioid fishes in the ice-cold waters of Antarctica. A crucial prerequisite for this assumption is the concurrence of the notothenioid radiation with the onset of Antarctic sea ice conditions. Here, we use a fossil-calibrated multi-marker phylogeny of nothothenioid and related acanthomorph fishes to date AFGP emergence and the notothenioid radiation. All time-constraints are cross-validated to assess their reliability resulting in six powerful calibration points. We find that the notothenioid radiation began near the Oligocene-Miocene transition, which coincides with the increasing presence of Antarctic sea ice. Divergence dates of notothenioids are thus consistent with the key innovation hypothesis of AFGP. Early notothenioid divergences are furthermore congruent with vicariant speciation and the breakup of Gondwana.

Identification of a novel helitron transposon in the genome of Antarctic fish

Rolling-circle (RC) eukaryotic transposons, known as helitrons, are found in a wide range of organisms, from protist to mammals. Autonomous helitrons have a distinctive open reading frame (ORF) encoding a polypeptide that contains typical domains for RC replication (RCR): the Rep (RCR initiator) and the DNA helicase domains. These elements are believed to have an important role in the host genome evolution, owing to their frequent capture of host genes, some of which can evolve into novel genes or become essential for helitron transposition. We conducted a molecular analysis of the suborder Notothenioidei, a group of Perciformes that currently dominate the Antarctic waters by virtue of their remarkable cold-adaptation ability. A novel helitron from the genome of the icefish species Chionodraco hamatus, belonging to the Channichthyidae, the most derived Notothenioids family, was isolated, characterized and designated as HeliNoto (8.9 kb). Its ORF was compared to homologous sequences from different species in a comprehensive phylogenetic analysis. For the first time the putative functional domains of a helitron were subjected to a well accurate structural analysis including chromosomal localization. Finally, the distribution of HeliNoto among Notothenioids was investigated.

Genome enablement of the notothenioidei: genome size estimates from 11 species and BAC libraries from 2 representative taxa

The perciform suborder Notothenoidei provides a compelling opportunity to study the adaptive radiation of a marine species flock in the cold Southern Ocean surrounding Antarctica. To enable genome-level studies of these psychrophilic fishes, we estimated the sizes of the genomes of 11 Antarctic species and generated high-quality BAC libraries for 2, the notothen Notothenia coriiceps and the icefish Chaenocephalus aceratus. Our results indicate that evolution of phylogenetically derived notothenioid families, [e.g., the icefishes (Channichthyidae)], was accompanied by genome expansion. Species (n=6) of the basal family Nototheniidae had C values that ranged between 0.98 and 1.20 pg, whereas those of the icefishes, the notothenioid crown group, were 1.66-1.83 pg (n=4 species). The BAC libraries VMRC-19 (N. coriiceps) and VMRC-21 (C. aceratus) comprised 12X and 10X coverage of the respective genomes and had average insert sizes of 138 and 168 kb. Greater than 60% of paired BAC ends sampled from each library ( approximately 0.1% of each genome) contained repetitive sequences, and the repetitive element landscapes of the 2 genomes (13.4% of the N. coriiceps genome and 14.5% for C. aceratus) were similar. The representation and depth of coverage of the libraries were verified by identification of multiple Hox gene contigs: six discrete Hox clusters were found in N. coriiceps and at least five Hox clusters were found in C. aceratus. Given the unusual anatomical and physiological adaptations of the notothenioids, the availability of these BAC libraries sets the stage for expanded analysis of the psychrophilic mode of life.

Antarctic notothenioid fishes: genomic resources and strategies for analyzing an adaptive radiation

The perciform suborder Notothenoidei provides a compelling opportunity to study the adaptive radiation of a marine species-flock in the cold Southern Ocean that surrounds Antarctica. To facilitate genome-level studies of the diversification of these fishes, we present estimates of the genome sizes of 11 Antarctic species and describe the production of high-quality bacterial artificial chromosome (BAC) libraries for two, the red-blooded notothen Notothenia coriiceps and the white-blooded icefish Chaenocephalus aceratus. Our results indicate that evolution of phylogenetically derived notothenioid families (e.g., the crown group Channichthyidae [icefishes]), was accompanied by genome expansion. Six species from the basal family Nototheniidae had C-values between 0.98 and 1.20 pg, a range that is consistent with the genome sizes of proposed outgroups (e.g., percids) of the notothenioid suborder. In contrast, four icefishes had C-values in the range 1.66-1.83 pg. The BAC libraries VMRC-19 (N. coriiceps) and VMRC-21 (C. aceratus) comprise 12× and 10× coverage of the respective genomes and have average insert sizes of 138 and 168 kb. Paired BAC-end reads representing ∼0.1% of each genome showed that the repetitive element landscapes of the two genomes (13.4% of the N. coriiceps genome and 14.5% for C. aceratus) were similar. The availability of these high-quality and well-characterized BAC libraries sets the stage for targeted genomic analyses of the unusual anatomical and physiological adaptations of the notothenioids, some of which mimic human diseases. Here we consider the evolution of secondary pelagicism by various taxa of the group and illustrate the utility of Antarctic icefishes as an evolutionary-mutant model of human osteopenia (low-mineral density of bones).

The Patagonian toothfish: biology, ecology and fishery

Patagonian toothfish (Dissostichus eleginoides) is a large notothenioid fish that supports valuable fisheries throughout the Southern Ocean. D. eleginoides are found on the southern shelves and slopes of South America and around the sub-Antarctic islands of the Southern Ocean. Patagonian toothfish are a long-lived species (>50 years), which initially grow rapidly on the shallow shelf areas, before undertaking an ontogenetic migration into deeper water. Although they are active predators and scavengers, there is no evidence of large-scale geographic migrations, and studies using genetics, biochemistry, parasite fauna and tagging indicate a high degree of isolation between populations in the Indian Ocean, South Georgia and the Patagonian Shelf. Patagonian toothfish spawn in deep water (ca. 1000 m) during the austral winter, producing pelagic eggs and larvae. Larvae switch to a demersal habitat at around 100 mm (1-year-old) and inhabit relatively shallow water (<300 m) until 6-7 years of age, when they begin a gradual migration into deeper water. As juveniles in shallow water, toothfish are primarily piscivorous, consuming the most abundant suitably sized local prey. With increasing size and habitat depth, the diet diversifies and includes more scavenging. Toothfish have weakly mineralised skeletons and a high fat content in muscle, which helps neutral buoyancy, but limits swimming capacity. Toothfish generally swim with labriform motion, but are capable of more rapid sub-carangiform swimming when startled. Toothfish were first caught as a by-catch (as juveniles) in shallow trawl fisheries, but following the development of deep water longlining, fisheries rapidly developed throughout the Southern Ocean. The initial rapid expansion of the fishery, which led to a peak of over 40,000 tonnes in reported landings in 1995, was accompanied by problems of bird by-catch and overexploitation as a consequence of illegal, unreported and unregulated fishing (IUU). These problems have now largely been addressed, but continued vigilance is required to ensure that the species is sustainably exploited and the ecosystem effects of the fisheries are minimised.

Comparison of fatty acid composition in nine organs of the sympatric Antarctic teleost fish species Notothenia coriiceps and Notothenia rossii (Perciformes: Nototheniidae)

Fatty acid (FA) composition of nine organs from two closely related Antarctic fish species, Notothenia coriiceps and Notothenia rossii, was determined through gas chromatography with flame ionization detection. A data set for each species was obtained using major FA profiles from specimens caught in the sea waters of Admiralty Bay during the summer season. The FA profiles for both species are overall similar, but organ peculiarities have been found, which could reflect metabolic specificities and feeding habits between species. With the exception of liver, the most abundant FA in organs was the n-3 polyunsaturated FA. The total n-6 polyunsaturated FAs were minor components in all evaluated organs. Palmitic acid was identified as the major saturated FA, whereas oleic acid was the most represented of the monounsaturated FA in almost all assessed organs of both species. The n-3/n-6 ratios of all organs were higher than 3.5. Differences in individual FA and FA metabolic profiles of some organs observed between N. coriiceps and N. rossii suggest specific requirements in the mobilization, transport, incorporation, and/or catabolism of lipids that were reinforced by differences on some FA ratios expressing the activity coefficient of enzymes implicated on the FA pathway flux.

Evolution of the Antarctic teleost immunoglobulin heavy chain gene

Notothenioid teleosts underwent major modifications of their genome to adapt to the cooling of the Antarctic environment. In order to identify specific features of the Antarctic teleost immunoglobulin, transcripts encoding the constant region of the IgM heavy chain from 13 Antarctic and non-Antarctic notothenioid species were sequenced. The primary mRNA splicing for the membrane form was found to be atypical in the majority of Antarctic species, because it led to exclusion of two entire constant exons, and to inclusion of 39-nucleotide exons encoding an unusually long Extracellular Membrane-Proximal Domain (EMPD). Genomic DNA analysis revealed that each 39-nucleotide exon fell within a long sequence that was the reverse complement of an upstream region. Deduced amino acid sequence analysis lead to the identification of cysteine encoding codons in the 39-nucleotide exons, but not in the respective sequence counterpart, suggesting that these residues might play an important role in the folding of the EMPD.