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24 results for “notothenioid”
Data from: Physical, chemical, and functional properties of neuronal membranes vary between species of Antarctic notothenioids differing in thermal tolerance
Disruption of neuronal function is likely to influence limits to thermal tolerance. We hypothesized that with acute warming the structure and function of neuronal membranes in the Antarctic notothenioid fish Chaenocephalus aceratus are more vulnerable to perturbation than membranes in the more thermotolerant notothenioid Notothenia coriiceps. Fluidity was quantified in synaptic membranes, mitochondrial membranes, and myelin from brains of both species of Antarctic fishes. Polar lipid compositions and cholesterol contents were analyzed in myelin; cholesterol was measured in synaptic membranes. Thermal profiles were determined for activities of two membrane-associated proteins, acetylcholinesterase (AChE) and Na+/K+-ATPase (NKA), from brains of animals maintained at ambient temperature or exposed to their critical thermal maxima (CTMAX). Synaptic membranes of C. aceratus were consistently more fluid than those of N. coriiceps (P < 0.0001). Although the fluidities of both myelin and mitochondrial membranes were similar among species, sensitivity of myelin fluidity to in vitro warming was greater in N. coriiceps than in C. aceratus (P < 0.001), which can be explained by lower cholesterol contents in myelin of N. coriiceps (P < 0.05). Activities of both enzymes, AChE and NKA, declined upon CTMAX exposure in C. aceratus, but not in N. coriiceps. We suggest that hyper-fluidization of synaptic membranes with warming in C. aceratus may explain the greater stenothermy in this species, and that thermal limits in notothenioids are more likely to be influenced by perturbations in synaptic membranes than in other membranes of the nervous system.
Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes
<p>Mitochondrial genomes are known for their compact size and conserved gene order, however, recent studies employing long-read sequencing technologies have revealed the presence of atypical mitogenomes in some species. In this study, we assembled and annotated the mitogenomes of five Antarctic notothenioids, including four icefishes (Champsocephalus gunnari, C. esox, Chaenocephalus aceratus, and Pseudochaenichthys georgianus) and the cold-specialized Trematomus borchgrevinki. Antarctic notothenioids are known to harbor some rearrangements in their mt genomes, however the extensive duplications in icefishes observed in our study have never been reported before. In the icefishes, we observed duplications of the protein coding gene ND6, two transfer RNAs, and the control region with different copy number variants present within the same individuals and with some ND6 duplications appearing to follow the canonical Duplication-Degeneration-Complementation (DDC) model in C. esox and C. gunnari. In addition, using long-read sequencing and k-mer analysis, we were able to detect extensive heteroplasmy in C. aceratus and C. esox. We also observed a large inversion in the mitogenome of T. borchgrevinki, along with the presence of tandem repeats in its control region. This study is the first in using long-read sequencing to assemble and identify structural variants and heteroplasmy in notothenioid mitogenomes and signifies the importance of long-reads in resolving complex mitochondrial architectures. Identification of such wide-ranging structural variants in the mitogenomes of these fishes could provide insight into the genetic basis of the atypical icefish mitochondrial physiology and more generally may provide insights about their potential role in cold adaptation.</p>
Genomics of cold adaptations in the Antarctic notothenioid fish radiation
<p>Numerous novel adaptations characterise the radiation of notothenioids, the dominant fish group in the freezing seas of the Southern Ocean. To improve understanding of the evolution of this iconic fish group, we generated and analysed new genome assemblies for 24 species covering all major subgroups of the radiation, including five long-read assemblies. We present a new estimate for the onset of the radiation at 10.7 million years ago, based on a time-calibrated phylogeny derived from genome-wide sequence data. We identify a two-fold variation in genome size, driven by expansion of multiple transposable element families, and use the long-read data to reconstruct two evolutionarily important, highly repetitive gene family loci. First, we present the most complete reconstruction to date of the antifreeze glycoprotein gene family, whose emergence enabled survival in sub-zero temperatures, showing the expansion of the antifreeze gene locus from the ancestral to the derived state. Second, we trace the loss of haemoglobin genes in icefishes, the only vertebrates lacking functional haemoglobins, through complete reconstruction of the two haemoglobin gene clusters across notothenioid families. Both the haemoglobin and antifreeze genomic loci are characterised by multiple transposon expansions that may have driven the evolutionary history of these genes.</p>
Genomics of cold adaptations in the Antarctic notothenioid fish radiation
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Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes
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Data from: Physical, chemical, and functional properties of neuronal membranes vary between species of Antarctic notothenioids differing in thermal tolerance
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Data from: Gene flow by larval dispersal in the Antarctic notothenioid fish Gobionotothen gibberifrons
The diversification of the teleost suborder Notothenioidei (Perciformes) in Antarctic waters provides one of the most striking examples of a marine adaptive radiation. Along with a number of adaptations to the cold environment, such as the evolution of antifreeze glycoproteins, notothenioids diversified into eight families and at least 130 species. Here, we investigate the genetic population structure of the humped rockcod (Gobionotothen gibberifrons), a benthic notothenioid fish. Six populations were sampled at different locations around the Scotia Sea, comprising a large part of the species' distribution range (N=165). Our analyses based on mitochondrial DNA sequence data (352 bp) and eight microsatellite markers reveal a lack of genetic structuring over large geographic distances (ΦST≤0.058, F ST≤0.005, p-values nonsignificant). In order to test whether this was due to passive larval dispersal, we used GPS-tracked drifter trajectories, which approximate movement of passive surface particles with ocean currents. The drifter data indicate that the Antarctic Circumpolar Current (ACC) connects the sampling locations in one direction only (West-East), and that passive transport is possible within the four-months larval period of G. gibberifrons. Indeed, when applying the isolation-with-migration model in IMA, strong unidirectional West-East migration rates are detected in the humped rockcod. This leads us to conclude that, in G. gibberifrons, genetic differentiation is prevented by gene flow via larval dispersal with the ACC.
Data from: 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.
Data from: 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.
Data from: Phylogenomics of an extra-Antarctic notothenioid radiation reveals a previously unrecognized lineage and diffuse species boundaries
Background: The impressive adaptive radiation of notothenioid fishes in Antarctic waters is generally thought to have been facilitated by an evolutionary key innovation, antifreeze glycoproteins, permitting the rapid evolution of more than 120 species subsequent to the Antarctic glaciation. By way of contrast, the second-most species-rich notothenioid genus, Patagonotothen, which is nested within the Antarctic clade of Notothenioidei, is almost exclusively found in the non-Antarctic waters of Patagonia. While the drivers of the diversification of Patagonotothen are currently unknown, they are unlikely to be related to antifreeze glycoproteins, given that water temperatures in Patagonia are well above freezing point. Here we performed a phylogenetic analysis based on genome-wide single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (RADseq) in a total of twelve Patagonotothen species. Results: We present a well-supported, time-calibrated phylogenetic hypothesis including closely and distantly related outgroups, confirming the monophyly of the genus Patagonotothen with an origin approximately 3 million year ago and the paraphyly of both the sister genus Lepidonotothen and the family Notothenidae. Our phylogenomic and population genetic analyses highlight a previously unrecognized linage and provide evidence for shared genetic variation between some closely related species. We also provide a mitochondrial phylogeny showing mitonuclear discordance. Conclusions: Based on a combination of phylogenomic and population genomic approaches, we provide evidence for the existence of a new, potentially cryptic, Patagonotothen species, and demonstrate that genetic boundaries between some closely related species are diffuse, likely due to recent introgression and/or incomplete linage sorting. The detected mitonuclear discordance highlights the limitations of relying on a single locus for species barcoding. In addition, our time calibrated phylogenetic hypothesis shows that the early burst of diversification roughly coincides with the onset of the intensification of Quaternary glacial cycles and that the rate of species accumulation may have been stepwise rather than constant. Our phylogenetic framework not only advances our understanding of the origin of a high-latitude marine radiation, but also provides the basis for the study of the ecology and life history of the genus Patagonotothen, as well as for their conservation and commercial management.
Data from: Mitochondrial membranes in cardiac muscle from Antarctic notothenioid fishes vary in phospholipid composition and membrane fluidity
Antarctic notothenioid fishes are highly stenothermal, yet their tolerance for warming is species-dependent. Because a body of literature points to the loss of cardiac function as underlying thermal limits in ectothermic animals, we investigated potential relationships among properties of ventricular mitochondrial membranes in notothenioids with known differences in both cardiac mitochondrial metabolism and organismal thermal tolerance. Fluidity of mitochondrial membranes was quantified by fluorescence depolarization for the white-blooded Chaenocephalus aceratus and the red-blooded Notothenia coriiceps. In these same membranes, lipid compositions and products of lipid peroxidation, the latter of which can disrupt membrane order, were analyzed in both species and in a second icefish, Pseudochaenichthys georgianus. Mitochondrial membranes from C. aceratus were significantly more fluid than those of the more thermotolerant species N. coriiceps (P < .0001). Consistent with this, ratios of total phosphatidylethanolamine (PE) to total phosphatidylcholine (PC) were lower in membranes from both species of icefishes, compared to those of N. coriiceps (P < .05). However, membranes of N. coriiceps displayed a greater unsaturation index (P < .0001). No differences among species were found in membrane products of lipid peroxidation. With rising temperatures, greater contents of PC in mitochondrial membranes from ventricles of icefishes are likely to promote membrane hyperfluidization at a lower temperature than for cardiac mitochondrial membranes from the red-blooded notothenioid. We propose that physical and chemical properties of the mitochondrial membranes may contribute to some of the observed differences in thermal sensitivity of physiological function among these species.
Figure 5 in The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids
Figure 5. Phylogenetic relationships of control regions inferred by the maximum likelihood (ML) method. Statistical support is shown on the branches: bootstrap values (above) and posterior probability (below). BI, Bayesian inference; CR, control region.
Figure 1 in The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids
Figure 1. Evolution of mitochondrial genomes in Antarctic notothenioids modified from Zhuang & Cheng (2010). Abbreviations: 12S, 12S ribosomal RNA; CR, control region; Cyt b, cytochrome b; E, tRNAGlu; F, tRNAPhe; ND, nicotinamide adenine dinucleotide (reduced form) dehydrogenase; P, tRNAPro; T, tRNAThr.
Figure 4. A in The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids
Figure 4. A, linear representation of three types of gene content from the partial cytochrome b (Cyt b) to 12S rRNA in the mitochondrial (mt) genome of the mackerel icefish. Black and dark grey arrows respectively represent the first and the second duplicates. The first duplicate of the type-1 genome contains full-length nicotinamide adenine dinucleotide (reduced form) dehydrogenase subunit 6 (ND6) and tRNAGlu. Type-2 contains a half-sized ND6 only. Type-3 does not contain ND6 or tRNAGlu. B, PCR amplifications for detecting ND6 and tRNAGlu in the three types of mt genome of the mackerel icefish. PCR fragments between Cyt b and control region (CR) 2 (Cyt b-CR2) and between CR2 and CR3 (CR2-CR3) contain the first and second copies of ND6, respectively. The PCR fragment between ND5 and Cyt b (ND5-Cyt b) did not contain ND6 or tRNAGlu. M, size marker. Lanes 1, 2, 7, and 10 are type-1 individuals. Lanes 3, 4, 8 and 11 are type-2 individuals. Lanes 5, 6, 9, and 12 are type-3 individuals. Abbreviations: E, tRNAGlu; F, tRNAPhe; P, tRNAPro; T, tRNAThr.
Figure 3 in The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids
Figure 3. Map of the mackerel icefish mitochondrial (mt) genome as a circular diagram. The map represents the mt genome of a type-1 individual in which ND6 and tRNAGlu were transposed to a position between tRNAThr and tRNAPro flanked by intergenic spacers (UN3 and UN4), and the ND6- to -CR segment was duplicated once. Fourteen protein-coding genes, two rRNA genes, and noncoding regions are labelled with abbreviations. Twenty-four tRNA genes are shown by a one-letter amino acid code. Different codons used by each of tRNALeu and tRNASer are shown in parentheses. Genes transcribed from the heavy strand and light strand are respectively presented outside and inside the circle. Heavy- and light-strand replication origins are represented by OH and OL, respectively. Abbreviations: 12S, 12S ribosomal RNA; 16S, 16S ribosomal RNA; A, tRNAAla; ATP, ATP synthase; C, tRNACys; CO, cytochrome oxidase; Cyt b, cytochrome b; D, tRNAAsp; E, tRNAGlu; F, tRNAPhe; G, tRNAGly; H, tRNAHis; I, tRNAIle; K, tRNALys; L, tRNALeu; M, tRNAMet; N, tRNAAsn; ND, nicotiamide adenine dinucleotide (reduced form) dehydrogenase; P, tRNAPro; Q, tRNAGln; R, tRNAArg; S, tRNASer; T, tRNAThr; V, tRNAVal; W, tRNATrp; Y, tRNATyr.
Data from: Genetic relationships between Atlantic and Pacific populations of the notothenioid fish Eleginops maclovinus: the footprints of Quaternary glaciations in Patagonia
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Data from: Gene flow by larval dispersal in the Antarctic notothenioid fish Gobionotothen gibberifrons
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Data from: Diversity and disparity through time in the adaptive radiation of Antarctic notothenioid fishes
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Data from: Phylogenomics of an extra-Antarctic notothenioid radiation reveals a previously unrecognized lineage and diffuse species boundaries
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Data from: Mitochondrial membranes in cardiac muscle from Antarctic notothenioid fishes vary in phospholipid composition and membrane fluidity
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