Sculpin Fishes Research Articles

Freshwater Habitats Promote Rapid Rates of Phenotypic Evolution in Sculpin Fishes (Perciformes: Cottoidea).

AbstractInvasions of freshwater habitats by marine fishes provide exceptional cases of habitat-driven biological diversification. Freshwater habitats make up less than 1% of aquatic habitats but contain ∼50% of fish species. However, while the dominant group of freshwater fishes (Otophysi) is older than that of most marine fishes (Percomorphaceae), it is less morphologically diverse. Classically, scientists have invoked differences in the tempo and/or mode of evolution to explain such cases of unequal morphological diversification. We tested for evidence of these phenomena in the superfamily Cottoidea (sculpins), which contains substantial radiations of marine and freshwater fishes. We find that the morphology of freshwater sculpins evolves faster but under higher constraint than that of marine sculpins, causing widespread convergence in freshwater sculpins and more morphological disparity in marine sculpins. The endemic freshwater sculpins of Lake Baikal, Siberia, are exceptions that demonstrate elevated novelty akin to that of marine sculpins. Several tantalizing factors may explain these findings, such as differences in habitat stability and/or habitat connectivity between marine and freshwater systems.

Molecular dynamics-guided insight into the adsorption–inhibition mechanism for controlling ice growth/melt of antifreeze protein type IV mutant from longhorn sculpin fish

Molecular dynamics-guided insight into the adsorption–inhibition mechanism for controlling ice growth/melt of antifreeze protein type IV mutant from longhorn sculpin fish

The Summer Distribution of Sculpin Fish (Cottidae) on the Continental Margin of the Sea of Japan from Cape Povorotny to Cape Mapatsa

The Summer Distribution of Sculpin Fish (Cottidae) on the Continental Margin of the Sea of Japan from Cape Povorotny to Cape Mapatsa

The Summer Distribution of Sculpin Fish (Cottidae) on the Continental Margin of the Sea of Japan from Cape Povorotny to Cape Mapatsa

We identified Gymnocanthus detrisus as the absolute dominant species in the taxocene of sculpins (family Cottidae), caught below 20 m water depth in the aquatic area between Cape Povorotny and Cape Mapatsa. Myoxocephalus polyacanthocephalus, Gymnocanthus herzensteini, Enophrys diceraus and Triglops pingelii are dominant as well. Subdominant species are Triglops septicus, Icelus cataphractus, Hemilepidotus gilberti, Myoxocephalus brandtii, Myoxocephalus jaok, Taurocottus bergii and Gymnocanthus pistilliger. Other types of fishes identified in this area are insignificant in abundance. Sculpins aggregate at greater depth in the southern aquatic areas, from Cape Povorotny to Olga Bay, and from Olga Bay to Cape Belkin, than in the northern areas, between Cape Belkin and Cape Zolotoy, particularly between Cape Zolotoi and Cape Mapatsa. We attribute this phenomenon to the differences in water regimes. The highest densities of sculpins are generally typical for the southern area. Conversely the lowest densities are typical in the northern area. However, some species prefer northern areas. The minimum depths habitat for different species varying from less than 20 m to 82 m; the maximum depths range from 80 to 530 m. Due to the high species diversity, aggregations of sculpins are observed in a wide bathymetric range from 20 to 300 m, with peak values at depths of 150–200 m. Sculpins live in summer at water temperatures above 0.4°C. The shallow water species of sculpins tolerate much greater temperature ranges then deep water species. Hence, the stenotherm increases in deep water species.

Nanopore Sequencing and Hi-C Based De Novo Assembly of Trachidermus fasciatus Genome.

Trachidermus fasciatus is a roughskin sculpin fish widespread across the coastal areas of East Asia. Due to environmental destruction and overfishing, the population of this species is under threat. In order to protect this endangered species, it is important to have the genome sequenced. Reference genomes are essential for studying population genetics, domestic farming, and genetic resource protection. However, currently, no reference genome is available for Trachidermus fasciatus, and this has greatly hindered the research on this species. In this study, we integrated nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C methods to thoroughly assemble the Trachidermus fasciatus genome. Our results provided a chromosome-level high-quality genome assembly with a predicted genome size of 542.6 Mbp (2n = 40) and a scaffold N50 of 24.9 Mbp. The BUSCO value for genome assembly completeness was higher than 96%, and the single-base accuracy was 99.997%. Based on EVM-StringTie genome annotation, a total of 19,147 protein-coding genes were identified, including 35,093 mRNA transcripts. In addition, a novel gene-finding strategy named RNR was introduced, and in total, 51 (82) novel genes (transcripts) were identified. Lastly, we present here the first reference genome for Trachidermus fasciatus; this sequence is expected to greatly facilitate future research on this species.

Genetic Evidence for a Mixed Composition of the Genus Myoxocephalus (Cottoidei: Cottidae) Necessitates Generic Realignment.

Sculpin fishes belonging to the family Cottidae represent a large and complex group, inhabiting a wide range of freshwater, brackish-water, and marine environments. Numerous studies based on analysis of their morphology and genetic makeup frequently provided controversial results. In the present work, we sequenced complete mitochondrial (mt) genomes and fragments of nuclear ribosomal DNA (rDNA) of the fourhorn sculpin Myoxocephalus quadricornis and some related cottids to increase the power of phylogenetic and taxonomic analyses of this complex fish group. A comparison of the My. quadricornis mt genomes obtained by us with other complete mt genomes available in GenBank has revealed a surprisingly low divergence (3.06 ± 0.12%) with Megalocottus platycephalus and, at the same time, a significantly higher divergence (7.89 ± 0.16%) with the species of the genus Myoxocephalus. Correspondingly, phylogenetic analyses have shown that My. quadricornis is clustered with Me. platycephalus but not with the Myoxocephalus species. Completely consistent patterns of divergence and tree topologies have been obtained based on nuclear rDNA. Thus, the multi-gene data in the present work indicates obvious contradictions in the relationships between the Myoxocephalus and Megalocottus species studied. An extensive phylogenetic analysis has provided evidence for a closer affinity of My. quadricornis with the species of the genus Megalocottus than with the species of the genus Myoxocephalus. A recombination analysis, along with the additional GenBank data, excludes introgression and/or incorrect taxonomic identification as the possible causative factors responsible for the observed closer affinity between the two species from different genera. The above facts necessitate realignment of the genera Myoxocephalus and Megalocottus. The genetic data supports the two recognized genera, Myoxocephalus and Megalocottus, but suggests changing their compositions through transferring My. quadricornis to the genus Megalocottus. The results of the present study resolve the relationships within a complex group of sculpin fishes and show a promising approach to phylogenetic systematics (as a key organizing principle in biodiversity research) for a better understanding of the taxonomy and evolution of fishes and for supplying relevant information to address various fish biodiversity conservation and management issues.

Complete mitochondrial genome of the plain sculpin Myoxocephalus jaok (Cottoidei: Cottidae)

The complete mitochondrial (mt) genome was sequenced in two specimens of the plain sculpin Myoxocephalus jaok by high-throughput sequencing technology (Ion S5 platform). The sequences were 16,653 bp in size, and the gene content, gene arrangement, and size were very similar to other sculpin mt genomes published previously. Comparison of the two M. jaok mt genomes now obtained with other complete mt genomes available in GenBank reveals an affinity to the sculpin fishes from the genus Myoxocephalus. The low level of sequence divergence (1.6%) detected between the genome of M. jaok and the GenBank complete mitochondrial genomes of Myoxocephalus polyacanthocephalus (MK621914, MK621915) may likely be due to recent divergence of the species and/or historical hybridization.

Complete mitochondrial genome of the Belligerent sculpin Megalocottus platycephalus (Cottoidei: Cottidae)

The complete mitochondrial (mt) genome was sequenced in two specimens of the Belligerent sculpin Megalocottus platycephalus by high-throughput sequencing technology (Ion S5 platform). The sequences are 16,673 bp in size, and the gene arrangement, composition, and size are very similar to the other sculpin mt genomes published previously. Comparison of the two M. platycephalus mt genomes now obtained with other complete mt genomes available in GenBank reveals an affinity to the sculpin fishes from the genus Myoxocephalus. The intergeneric difference between the Megalocottus and Myoxocephalus is 0.0757 ± 0.0019, which is significantly less than the corresponding value, 0.1240 ± 0.0120, obtained previously for the sculpin fishes based on the COI barcoding marker.

Contrasting life histories contribute to divergent patterns of genetic diversity and population connectivity in freshwater sculpin fishes

BackgroundLife history characteristics are considered important factors influencing the evolutionary processes of natural populations, including the patterns of population genetic structure of a species. The sister species Cottus hangiongensis and C. koreanus are small bottom-dwelling freshwater sculpin fishes from South Korea that display marked life history divergence but are morphologically nearly indistinguishable. Cottus hangiongensis evolved an ‘amphidromous’ life history with a post-hatching pelagic larval phase. They spawn many small eggs in the low reaches of rivers, and hatched larvae migrate to the sea before returning to grow to maturity in the river mouth. In contrast, C. koreanus evolved a ‘fluvial’ landlocked type with benthic larvae. They release a smaller number of larger eggs, and the larvae undergo direct development, remaining benthic in the upstream rivers throughout their entire lives. We tested whether there were differences in patterns and levels of within-population genetic diversities and spatial population structure between the two closely related Korean sculpins using mitochondrial DNA control region sequences and seven nuclear microsatellite loci.ResultsThe combined analyses of both marker sets revealed that C. hangiongensis harboured considerably higher levels of within-population genetic diversities (e.g. haplotype/allelic richness, heterozygosities) than C. koreanus. In contrast, the fluvial sculpin exhibited noticeably more spatial population structure than did the amphidromous sculpin, as suggested by pairwise FST statistics. The finding that C. hangiongensis individuals comprised a single random mating population across the east-flowing river basins in the Korean Peninsula, whereas C. koreanus individuals comprised genetically discrete individual populations, was further supported by an individual-based Bayesian population assignment and also factorial correspondence analyses.ConclusionsThe higher genetic diversity, but lower population structure, of the amphidromous sculpin relative to the fluvial sculpin may have resulted from its greater larval dispersal and also possibly, higher fecundity accompanied by an amphidromous life history. Hence, we conclude that contrasting early life histories – including the presence or absence of the pelagic larval phase – may have led to divergent patterns of within-population genetic diversities and spatial population structure between the sister Cottus species following speciation from a common ancestor of marine sculpin.

Interspecific variation in brain mitochondrial complex I and II capacity and ROS emission in marine sculpins.

Environmental hypoxia presents a metabolic challenge for animals because it inhibits mitochondrial respiration and can lead to the generation of reactive oxygen species (ROS). We investigated the interplay between O2 use for aerobic respiration and ROS generation among sculpin fishes (Cottidae, Actinopterygii) that are known to vary in whole-animal hypoxia tolerance. We hypothesized that mitochondria from hypoxia-tolerant sculpins would show more efficient O2 use with a higher phosphorylation efficiency and lower ROS emission. We showed that brain mitochondria from more hypoxia-tolerant sculpins had lower complex I and higher complex II flux capacities compared with less hypoxia-tolerant sculpins, but these differences were not related to variation in phosphorylation efficiency (ADP/O) or mitochondrial coupling (respiratory control ratio). The hypoxia-tolerant sculpins had higher mitochondrial H2O2 emission per O2 consumed (H2O2/O2) under oligomycin-induced state 4 conditions compared with less hypoxia-tolerant sculpins. An in vitro redox challenge experiment revealed species differences in how well mitochondria defend their glutathione redox status when challenged with high levels of reduced glutathione, but the redox challenge elicited the same H2O2/O2 in all species. Furthermore, in vitro anoxia recovery lowered absolute H2O2 emission (H2O2 per mg mitochondrial protein) in all species and negatively impacted state 3 respiration rates in some species, but the responses were not related to hypoxia tolerance. Overall, we clearly demonstrate a relationship between hypoxia tolerance and complex I and II flux capacities in sculpins, but the differences in complex flux capacity do not appear to be directly related to variation in ROS metabolism.

Site fidelity and homing behaviour of intertidal sculpins revisited.

To assess the repeatability of an ecological study, this study both partially replicates and extends a previous study on the site fidelity and homing ability of two abundant and ecologically important species of rocky intertidal sculpin fishes, Oligocottus maculosus and Oligocottus snyderi. A traditional mark and recapture approach was utilized and found that both of these species display high site fidelity to a home range of tidepools and homing ability to these pools, confirming the findings of previous work. Unlike the previous study, however, there was no effect of body size on homing ability and a modelling approach that incorporates encounter probability provided evidence for a sex effect on homing ability. In addition, this study extends the maximum homing ability of O. snyderi to 179 m and O. maculosus to 218 m, which were the maximum displacement distances for each species in this study, suggesting they may be capable of even greater homing distances. This work, however, finds that homing success was negatively related to displacement distance. These findings suggest adult sculpin populations are likely to be highly sub-structured geographically, possibly contributing to the exceptionally high species richness of the group.

Ultrastructure of saccular epithelium sensory cells of four sculpin fish species (Cottoidei) of Lake Baikal in relation to their way of life

Various structural elements of the apical region of hair cells and their location in the saccular macula of four sculpin fish species (Cottoidei) of Lake Baikal—two oilfish species (big golomyanka Comephorus baicalensis and small golomyanka C. dybowski), Severobaikalsk yellowfin Cottocomephorus alexandrae, and stone sculpin Paracottus knerii—were studied by scanning electron microscopy. In stone sculpin Paracottus knerii, which inhabits the coastal areas and leads a benthic lifestyle, the diversity of hair cells (in terms of the height of kinocilium and stereocilia) is big than that in the secondary pelagic species big and small golomyankas and in Severobaikalsk yellowfin, which inhabits the near-slope areas. Stereocilia of hair cells of stone sculpin and Severobaikalsk yellowfin are shorter than in the other species studied. The presence of such cells in the macula can ensure the sensitivity to more high-frequency acoustic signals and facilitate their perception by fish against the background of low-frequency noises characteristic of the coastal zone of the lake.

Mass leech infestation of sculpin fish in Lake Baikal, with clarification of disease-prone species and parasite taxonomy

Sculpin fish bdellosis in Lake Baikal is caused by leech ectoparasites, which are identified as belonging to the genus Baicalobdella. In addition to Cottocomephorus grewinkii, eight sculpin hosts for Baicalobdella are newly recorded: Paracottus knerii (Cottocomephorinae), and Abyssocottus korotneffi, Asprocottus platycephalus, Batrachocottus baicalensis, Batrachocottus multiradiatus, Cyphocottus megalops, Limnocottus griseus and Procottus major (Abyssocottinae). These host fishes are mass infected by Baicalobdella leeches (up to 75%) in different sites of Lake Baikal. Comparative morphological analysis of Baicalobdella infecting sculpin fishes vs. Baicalobdella torquata proper revealed nine distinctive features that allow confirming a separate systematic position and revalidating original name Baicalobdella cottidarum Dogiel, 1957.

Critical oxygen tensions as predictors of hypoxia tolerance and tissue metabolic responses during hypoxia exposure in fishes

An organism's critical oxygen tension (Pcrit) reflects its ability to extract environmental O2. Consequently, Pcrit has been used as an indicator of hypoxia tolerance in aquatic animals. The relationship between Pcrit and hypoxia tolerance and hypoxic metabolic responses, however, remains incompletely understood. Among several species of sculpin fishes (superfamily Cottoidea), we previously demonstrated a correlation between Pcrit and hypoxia tolerance, as measured as the time required for 50% of a group of fish to lose equilibrium (LOE50) at a water PO2 of 6.4Torr. In the present study, we further investigated the relationship between Pcrit, hypoxia tolerance, and hypoxic metabolic responses by examining the effects of hypoxia exposure at a fixed percentage of Pcrit (30%; termed relative hypoxia exposure) on LOE50 and metabolic responses in brain, liver, and white muscle in three sculpin species that differ in Pcrit and hypoxia tolerance at 6.4Torr. We also assessed the tissue metabolic responses underlying hypoxic loss of equilibrium (LOE). The species, from most to least hypoxia-tolerant at 6.4Torr and from lowest to highest Pcrit values, were the tidepool sculpin (Oligocottus maculosus), staghorn sculpin (Leptocottus armatus), and silverspotted sculpin (Blepsias cirrhosus). If Pcrit predicts hypoxia tolerance, then we expected similar LOE50 values and similar tissue metabolic responses across all species during relative hypoxia exposure. LOE50 values were similar in staghorn sculpins and tidepool sculpins, but not in silverspotted sculpins, which had a comparatively lower relative hypoxia LOE50 value. Thus, Pcrit, and consequently the ability to extract environmental O2, cannot predict hypoxia tolerance in all species, at least at a water PO2 of 30% of Pcrit. During relative hypoxia exposure, tissue lactate accumulation and ATP levels were similar between species, suggesting that the ability to extract environmental O2 is an important determinant of cellular energy status and reliance on anaerobic glycolysis in hypoxic sculpins. However, whereas tissue glycogen content and utilization were similar between tidepool sculpins and staghorn sculpins, there were lower normoxic levels and greater hypoxic depletion in silverspotted sculpins, potentially explaining their poorer relative hypoxia tolerance. In all species, LOE was associated with depletion of brain [ATP]. Overall, caution is warranted when Pcrit is used as an indicator of hypoxia tolerance, especially when considering temporal aspects of hypoxia tolerance and related metabolic characteristics (e.g. glycogen availability). Ideally, comparative studies of hypoxia tolerance should feature multiple measures (e.g. Pcrit and LOE50) in order to assess the overall responses of fishes to hypoxia.

Diet of a Population of Western Terrestrial Garter Snake, Thamnophis elegans, Along the Grande Ronde River, Southeastern Washington

Abstract We investigated the diet of the western terrestrial garter snake (Thamnophis elegans) along the Grande Ronde River in southeastern Washington. Snakes were collected with mass, snout-vent length and sex recorded. Of the 38 snakes collected 27 contained 31 prey items. The most abundant prey item was sculpin fish (Cottus spp.) (81.5%). There was no statistically significant relationship between size or sex of snake and prey presence, absence or size. Our data demonstrate that there is no change in prey base in relation to snake size or age. This is also the first population of Thamnophis elegans shown to specialize on Cottid fish in October, pre-overwintering hibernation.

The Second Northernmost Cave-Adapted Fish in the World? Groundwork on the Tytoona Cave Sculpin Population

A new cave population of sculpin fish from Central Pennsylvania is described that, if confirmed to be cave adapted, would become the second northernmost cave-adapted fish in the world. The Tytoona Cave fish lack the suite of modifications typical of troglomorphic populations. Their eyes, pectoral fins, and mouths appear to be as large as those of their surface counterparts, they have the same number of cephalic lateralis pores, and their pigmentation levels do not appear to be much lower. Nonetheless, they are considered to be cave adapted due to the presence of ovigerous females, a lack of evidence for starvation, and primarily because the cephalic lateralis pores (part of the lateral line system) are significantly larger than those of similar-sized surface fish. It may be that the Tytoona Cave population only has some emergent cave adaptations because in high latitudes the extent of polar ice sheet migration during the Pleistocene era restricted colonization by fish at least until 12 ka ago, when the ice age ended.

Adaptive morphological shifts to novel habitats in marine sculpin fishes

Sculpin fishes of the North American Pacific Coast provide an ideal opportunity to examine whether adaptive morphological character shifts have facilitated occupation of novel habitat types because of their well-described phylogeny and ecology. In this group, the basal-rooted species primarily occupy the subtidal habitat, whereas the species in the most distal clades are found in the intertidal. We tested multiple evolutionary models to determine whether changes in body size and changes in number of scales are adaptive for habitat use in sculpins. Based on a statistically robust, highly resolved molecular phylogeny of 26 species of sculpins, in combination with morphometric and habitat affinity data, our analyses show that an adaptive model based on habitat use best explains changes in body size and number of scales. The habitat model was statistically supported over models of neutral evolution, stabilizing selection across all habitats, and three clade-based models. We suggest that loss of scales and reduction of body size in the intertidal may facilitate cutaneous breathing in air when tidepools become hypoxic during low tides. This study demonstrates how the combined use of phylogenetic, ecological and statistical approaches helps to identify traits that are likely adaptive to novel habitats.

BIOCOMPUTATIONAL ANALYSIS AND CHARACTERIZATION OF SOME ANTIFREEZE PROTEINS

Novel bioinformatic procedures and computational methods have been used to analyze, characterize and provide more detailed description of some selected fish antifreeze proteins (AFPs) retrieved from Swiss–Prot database. Analysis shows that AFPs are rich in non-polar residues and that the AFPs Q01758 and P05140 contain SS bonds. The aliphatic index computed by ExPasy's ProtParam infers that AFPs may be stable for a wide range of temperatures and the AFP P80961 is classified as an unstable protein. The very low GRAVY index of AFP P80961 infers its higher hydrosolubility. Secondary structure analysis shows that the flounder and sculpin fish AFPs are found to be of predominant ∝–helical structures and the rest of them are with mixed secondary structures. The average molecular weight of AFPs computed is 9584 Da. SOSUI server predicts one transmembrane region in P04002 (winter flounder fish) and two regions in P09031 (yellowtail flounder fish). The predicted transmembrane regions were visualized and analyzed using helical wheel plots generated by EMBOSS pepwheel tool. The residues A, L, G and N are identified as the antigenic sites by EMBOSS antigenic program. The presence of 11 Cys residues in AFPs Q01758 (rainbow smelt fish) and P05140 (sea raven fish) indicates the presence of disulfide bridges (SS bonds) in these AFPs, and it is also recognized by CYS_REC tool and well documented from the three dimensional structure using Rasmol tool.

Intensive genetic assessment of the mating system and reproductive success in a semi-closed population of the mottled sculpin, Cottus bairdi.

Most genetic surveys of parentage in nature sample only a small fraction of the breeding population. Here we apply microsatellite markers to deduce the genetic mating system and assess the reproductive success of females and males in an extensively collected, semi-closed stream population of the mottled sculpin fish, Cottus bairdi. In this species, males guard nest rocks where females deposit the eggs for fertilization. The potential exists for both males and females to mate with multiple partners and for males to provide parental care to genetically unrelated offspring. Four hundred and fifty-five adults and subadults, as well as 1,259 offspring from 23 nests, were genotyped at five polymorphic microsatellite loci. Multilocus maternal genotypes, deduced via genetic analyses of embryos, were reconstructed for more than 90% of the analysed nests, thus allowing both male and female reproductive success to be estimated accurately. There was no genetic evidence for cuckoldry, but one nest probably represents a takeover event. Successful males spawned with a mean of 2.8 partners, whereas each female apparently deposited her entire clutch of eggs in a single nest (mean fecundity = 66 eggs/female). On average, genetically deduced sires and dams were captured 1.6 and 9.3 metres from their respective nests, indicating little movement by breeders during the spawning season. Based on a 'genetic mark-recapture' estimate, the total number of potentially breeding adults (c. 570) was an order-of-magnitude larger than genetically based estimates of the effective number of breeders (c. 54). In addition, significantly fewer eggs per female were deposited in single than in multidam nests. Not only were perceived high-quality males spawning with multiple partners, but they were receiving more eggs from each female.