Examination of unidentifiable spined loach individuals found in the overlap zone of two tetraploid species within a single river in Japan

An endangered tetraploid spined loach species, Cobitis takenoi (Cypriniformes: Cobitidae; hereafter called Tango loach) is known to inhabit only a single river in Kyoto Prefecture, Japan. Since Tango loach was discovered recently, in 2010, and only described in 2016, its morphology, ecology, and genetics are not well studied. Another tetraploid spined loach species Cobitis sp. BIWAE type A (hereafter, called Ohshima loach) inhabits the same river. The two loaches are reported as morphologically distinguishable from each other. Although the habitats of the two species in the river are segregated (Ohshima loach and Tango loach inhabit the upper and lower reaches, respectively), they overlap to a small degree in the boundary area. Recently, some individuals with morphological characteristics that are intermediate between the two species were found in the overlap zone. It was suspected that hybrids between the two species were produced since breeding seasons of the two species overlapped. To investigate whether the two species produce hybrids, we performed mitochondrial and nuclear DNA analyses on the unidentifiable individuals. Eight individuals unidentifiable to the species level collected in the river between 2017 and 2018 were examined and compared with the Tango and Ohshima loach species. Using mitochondrial DNA (mtDNA) cytochrome b analysis, we found that six individuals had mtDNA types identical to Tango loach and two individuals had mtDNA types identical to Ohshima loach. Furthermore, sequencing analysis of nuclear recombination activating gene 1 (RAG-1) revealed that each species had species-specific alleles. The phylogenetic analysis indicated that alleles in Tango loach were divided into two clusters and those from Ohshima loach formed a single cluster. There were no discrepancies in the combination between mtDNA and nuclear DNA species types within each specimen. DNA fingerprinting analysis (AFLP) showed that the species-unidentifiable individuals exhibited distinctly segregated genetic groups corresponding with Tango and Ohshima loaches. In summary, no hybrids were detected from among any unidentifiable individual examined in this study. New conventional genetic method for discriminating the two sympatric loach species developed here can be effective tool for the conservation of the Tango loach since there was no strict diagnostic morphological character between them.     

Evidence of a secondary interspecific mitochondrial DNA introgression in the pond loach Misgurnus dabryanus (Teleostei: Cobitidae) population introduced in Japan

The pond loach Misgurnus dabryanus is a freshwater fish with a distribution range spanning the eastern part of the Asian continent, the Korean Peninsula, and Taiwan. The pond loach was transplanted to the Japanese archipelago through the co-inclusion with dojo loach (Misgurnus anguillicaudatus species complex) populations, which were imported live from China for food materials, and it is currently distributed widely across Japan. A previous mitochondrial DNA (mtDNA) analysis revealed that a pond loach population in Ehime Prefecture (Shikoku Island, Japan) included two highly diverged mtDNA groups (Groups I and II). To examine the origin of these two distinct forms of mtDNA within the Japanese pond loach population, we performed phylogenetic analyses using sequences based on the mtDNA of cytochrome oxidase b (cyt b) and the nuclear DNA recombination activating gene 1 (RAG-1). We also conducted a random amplified polymorphic DNA (RAPD) analysis to examine the establishment of reproductive isolation between sympatric pond loaches with two different mtDNA groups. Our mtDNA phylogenetic results indicated that the two diverged pond loach mtDNA sequences showed polyphyletic relationships among Misgurnus species and its related genus Cobitis. In contrast, there were no clear divergence in nuclear DNA among the pond loaches irrespective of their mtDNA groups, and they all formed monomorphic clades in the phylogenetic relationships among the species. The discrepancy between the mtDNA and nuclear DNA genes support that the existence of two diverged forms of DNA within the pond loach population could be attributed to past mtDNA introgressions from other species rather than convergent evolution. Previous mtDNA phylogenetic studies among Cobitidae revealed that the dojo loach also consisted of two genetically diverged polyphyletic clades: an original Misgurnus mtDNA and an introgressed mtDNA from Cobitis species. In our mtDNA result, the Group II haplotype of the pond loach was included in the mtDNA from the introgressed dojo loach. This suggested that the Group II haplotype was derived from introgressed dojo loach mtDNA. The close relationships between the introgressed dojo loach and the pond loach mtDNA indicated that this secondary introgression had recently occurred via hybridization in a recent artificial aquaculture or transportation process. Common RAG-1 alleles and RAPD bands were shared between the sympatric pond loaches with original and introgressed mtDNAs. This indicates that the introgressed mtDNA haplotype is included as one of the polymorphic genotypes within the pond loach populations, and does not represent existence of different cryptic species.     

Production of a mutant of large-scale loach Paramisgurnus dabryanus with skin pigmentation loss by genome editing with CRISPR/Cas9 system

CRISPR/Cas9 system has been developed as a highly efficient genome editing technology to specifically induce mutations in a few aquaculture species. In this study, we described induction of targeted gene (namely tyrosinase, tyr) mutations in large-scale loach Paramisgurnus dabryanus, an important aquaculture fish species and a potential model organism for studies of intestinal air-breathing function, using the CRISPR/Cas9 system. Tyr gene in large-scale loach was firstly cloned and then its expressions were investigated. Two guide RNAs (gRNAs) were designed and separately transformed with Cas9 in the loach. 89.4% and 96.1% of injected loach juveniles respectively displayed a graded loss of pigmentation for the two gRNAs, in other words, for target 1 and target 2. We classified the injected loach juveniles into five groups according to their skin color phenotypes, including four albino groups and one wild-type-like group. And one of them was clear albino group, which was of high ornamental and commercial value. More than 50 clones for each albino transformant with a visible phenotype in each target were randomly selected and sequenced. Results obtained here showed that along with the increase of pigmentation, wild-type alleles appeared in the injected loach juveniles more often and insertion/deletion alleles less frequently. This study demonstrated that CRISPR/Cas9 system could be practically performed to modify large-scale loach tyr to produce an albino mutant of high ornamental and commercial value, and for the first time showed successful use of the CRISPR/Cas9 system for genome editing in a Cobitidae species.

     

Detection of hybridization between two loach species (<Emphasis Type="Italic">Paramisgurnus dabryanus</Emphasis> and <Emphasis Type="Italic">Misgurnus anguillicaudatus</Emphasis>) in wild populations

Artificial interspecific hybrids between large scale loach P. dabryanus and tetraploid pond loach M. anguillicaudatus (Cobitidae, Cypriniformes) are viable. To detect the occurrence of possible natural hybridization, genetic analyses by using microsatellite markers were performed for natural populations of large scale loach and pond loach, the reciprocal laboratory hybrids, and “supposed hybrids” with ambiguous morphology. The fertility of the artificial hybrids was also tested. At one diagnostic microsatellite (Mac50), one out of 20 “supposed hybrids” was identified to be F₁ hybrid between the two loach species because it had the same genotype as that of the laboratory hybrids. The triploid hybrids between the two species were confirmed to be female-sterile. The results show that rare hybridization has occurred between diploid large scale loach and tetraploid pond loach in nature although it may have little effect in genetic introgression. This study is helpful for fish conservation and encourages further investigation on natural hybridization and introgression of loaches.     

Morphological features of mucous secretory organ and mucous secretion of loach Misgurnus anguillicaudatus skin for friction drag reduction

We examined the functional morphology of loach Misgurnus anguillicaudatus skin by using synchrotron X-ray micro-computed tomography (SR-μCT) and high-contrast staining using osmium tetroxide or phosphotungstic acid (PTA), which enhances the image contrast of soft tissues. The captured high-spatial resolution images revealed that the surface ornamentations were stuck in the basement membrane of the loach scales. The ornamentations consisting of grooves (radii) and ridges (circuli) that can move freely and bend flexibly. The cross-sectional lateral microstructures of flat, concave and convex loach skins were observed from a live image of loach skin obtained through dark-field optical coherence tomography (OCT) imaging. The thickness of loach skin was changed with varying empty space between the mucous-cell layer and the scales by bending motion of loach. In addition, through direct measurement of drag reduction of loach skin, the mucous layer was found to have a strong influence on the reduction of skin friction. The present results enhance the understanding of the functional morphologies of mucous layer of loach to secrete mucus for skin friction reduction.     

Distribution of the oriental weatherloach, Misgurnus anguillicaudatus, in paddy fields and its implications for conservation in Sado Island, Japan

The distribution of the oriental weatherloach, Misgurnus anguillicaudatus, together with related environmental factors were surveyed at 185 paddy field locations on Sado Island in Japan. This was associated with the reintroduction of the Japanese crested ibis, Nipponia nippon, which prefers to feed on the loach. Loach were found to be present at 90 locations (49%). Analysis with GIS, GLM and AIC revealed that positive factors for the loach distribution included the presence of an earth ditch, the connections at outlets and the proportion of paddy field area within an 800 m radius. Conversely, pumping-up water irrigation and flow irrigation affected loach distribution negatively. In an interview survey that was conducted concurrently, older farmers in the area recalled that the loach had once been distributed over almost the entire island (89/96, 93%) about half a century ago. The farmers also suggested that the impact of agricultural chemicals was one of the main reasons for loach reduction or local extinction. A map of the current potential loach distribution was made using the best fit model from GIS variables. The loach was expected to be distributed in the Kuninaka region with high probability (60–100%) and in patches in the Osado and Kosado regions with low–medium probability (10–50%). As a feasible scenario for the conservation of the loach, another predictive map of the loach distributions was made using a model fit based on the GIS variables and outlet connection, in which the all of the outlets were presumed to be connected to the ditches without gaps. In this case, the loach were expected to be distributed almost throughout the paddy fields with medium–high probability (40–100%). In another scenario that presumed the complete land consolidation of all the paddy fields, the probability of loach occurrence was low (0–30%) throughout the island with the exception of the island’s center in the Kuninaka region.     

Spatial and ontogenetic variability in the microhabitat use of stream-dwelling spined loach (Cobitis taenia) and stone loach (Barbatula barbatula)

Ontogenetic and spatial variability in microhabitat use of spined loach Cobitis taenia (Linnaeus), considered as one species for the purposes of this study, and stone loach Barbatula barbatula (Linnaeus) were examined in the River Great Ouse basin, England, using multivariate and habitat suitability methods, including a technique for handling spatial variation in collections of preference curves. Distinct ordinations of spined age classes and stone loach developmental stages, respectively, in canonical correspondence analysis of species × variables × samples relationships suggest that the two species occupy completely different microhabitats; however, young‐of‐the‐year spined loach occurred more often than expected with all developmental stages of stone loach except young larvae. Water velocity and filamentous algae were the most influential microhabitat variables, the latter decreasing in importance with increasing age of both fish species. Preferred water velocities generally decreased with age in spined loach and increased in stone loach, with substratum size generally increasing with fish age in both species. Spatial variation in microhabitat preferences was great in both species but less so in the spined loach, suggesting that limited plasticity in habitat use could account, at least in part, for the latter species’ limited distribution and abundance in the catchment. Preference curves for a species, if generated and verified for all life intervals and all seasons, could be used as a management tool for a given stream or sector of river basin. But preference curves should be generated for each location to ensure that river management decisions with regard habitat and species conservation consider local‐level species requirements. Thus, a multi‐(eco)species and multi‐scale approach is required in habitat suitability assessments.     

Comparative and evolutionary analysis in natural diploid and tetraploid weather loach Misgurnus anguillicaudatus based on cytochrome b sequence data in central China

To obtain the phylogenetic relationship between diploid and tetraploid Misgurnus anguillicaudatus, the mitochondrial cyt b gene in the diploid and tetraploid weather loach were isolated and sequenced. The DNA sequences were analyzed using MEGA 3.0 software to determine the phylogenetic relationship. Forty-five variable sites among cyt b gene sequences and 18 amino acid substitutions occurred within the diploid and tetraploid loaches as deduced from the nucleotide sequences analysis of the cyt b gene. The nucleotide pairwise distance between diploid and tetraploid loach ranged from 0.001 to 0.025. Phylogenetic analysis revealed evolutionary relationships between diploid and tetraploid loach. Our results indicated a significant difference between diploid and tetraploid loach about the cyt b gene. AMOVA analysis indicated that there were no significant genetic variations within diploid loaches (Fst = 0.2529, P > 0.05) and within tetraploid loaches (Fst = 0.0564, P > 0.05), neither. However, significant genetic differences were found between diploid and tetraploid loaches (Fst = 0.7634, P < 0.05). Thus, it is concluded that no reproductive isolation was found within the same cytotypes of different localities, but there was reproductive isolation between these two cytotypes. The diploid loach existed before the tetraploid loach in nature. The present study is the first to describe the phylogenetic relationships of natural polyploidy weather loach using mtDNA cyt b gene.     

Test of Competitive Interactions for Space Between Two Benthic Fish Species, Burbot Lota lota, and Stone Loach Barbatula barbatula

The substrate preferences, growth rates and foraging efficiency of two small benthic fish species, juvenile burbot, Lota lota, and stone loach, Barbatula barbatula, were compared in combined outdoor mesocosm and indoor laboratory experiments. Both species preferred the same stony substrate when alone, but significant differences in habitat selection were found between the two species under food deprivation and competition conditions. In burbot, preference for the stony habitat was reinforced under food-deprivation conditions and became even stronger when a potential competitor, the stone loach, was present. In contrast, stone loach switched to the gravel substrate when either starving or in the presence of a heterospecific competitor. Growth rates and foraging efficiency of burbot were significantly highest in the stony substrate and decreased with finer substrates. In stone loach, neither growth rates nor foraging efficiency were significantly different among the different substrates. The results provide an example of habitat partitioning by means of different competition styles, with a stenoecious, dominant style of the burbot and an euryoecious, evasive style of stone loach allowing coexistence of two sympatric fish species by graded interactions at an individual level in the littoral zone of a large lake.     

Habitat factors affecting the distribution and abundance of the spinous loach <Emphasis Type="Italic">Cobitis shikokuensis</Emphasis> in southwestern Japan

We examined habitat factors related to the distribution and abundance of the spinous loach Cobitis shikokuensis, an endangered benthic fish, in the Shigenobu River system, southwestern Japan. In the study river, the spinous loach was distributed widely along the main stem, from headwater to near the mouth, whereas it was rarely found in tributary streams. Classification tree analysis showed that the presence/absence of spinous loach was explained by a combination of percent pebble and length of river fragment between artificial barriers. Spinous loach incidence was high in sites with abundant pebble (>27.7%), but low in sites with short river fragment (≤0.97 km) even if pebbles were abundant. A regression tree model for loach density retained only percent pebble as a single best predictor, with sites with higher percent pebble (>40.4%) having higher density. These results suggest that substrate condition is an important factor determining the distribution and abundance of spinous loach and also that habitat fragmentation by artificial barriers has great potential to threaten the spinous loach population in this river. Considering the highly fragmented situation of the study river and prevention of upstream migration by barriers, we conclude that maintenance of suitable habitats in upper reaches has high priority for conservation of the spinous loach.     

Spermatozoa of the Loach Misgurnus fossilis in the Identification of New Centrosome Proteins

We studied the possibility of using the spermatozoa of the loach Misgurnus fossilis L. in the identification of centrosome proteins. It has been shown that the centrosome of the loach spermatozoa consists of a pair of centrioles of the standard structure and contains the marker protein -tubulin, cytoplasmic microtubules branch out from it, and it does not contain any additional structures characteristic of the centrosomes of spermatozoa of many other fishes. A preparation enriched with intact centrosomes was obtained from the loach spermatozoa. These centrosomes contained -tubulin, although they had lost their ability to induce the polymerization of microtubules. The preparation of loach centrosomes was successfully used to obtain a set of monoclonal antibodies against the mammalian centrosome. A new protein kinase LOSTEK was identified with the help of one of these monoclonal antibodies, SN2-3D2, which was localized in the centrosome and then on microtubules in both loach spermatozoa and cultured mammalian cells. Hence, the loach spermatozoa are a promising means to identify new proteins in the mammalian centrosome.     

Edward Smith Deevey 1914–1988

Stone loach and bullhead were given a choice of Chironomus and Asellus prey in experiments using solitary fish and fish in company. Solitary fish ate more than fish in company. The effect of light and substratum type on feeding was investigated. Both species ate more prey items on gravel than silt when a significant difference was observed. Bullhead ate more than loach in the light on both substrata. The only experiment in which loach ate more than bullhead was on a silt substratum in the dark. It is concluded that these two species utilise different components of the available food resources in chalk streams by adopting different habitats.     

Molecular and morphological analyses revealed a cryptic species of dojo loach Misgurnus anguillicaudatus (Cypriniformes: Cobitidae) in Japan

Although it has been reported that populations of the Japanese dojo loach Misgurnus anguillicaudatus (Cypriniformes: Cobitidae) belong to two distinct mitochondrial (mt)DNA (Type I and Type II), the taxonomic status of the species remains unresolved. To address this question, nuclear DNA and morphological analyses were performed on M. anguillicaudatus population in the Nakaikemi Wetland, where Type I and Type II lineages are sympatric. Results suggest the existence of a cryptic species (Type I) within the Japanese dojo loach.     

Molecular phylogeny of the Cobitoidea (Teleostei: Cypriniformes) revisited: position of enigmatic loach Ellopostoma resolved with six nuclear genes

Molecular variation in six nuclear genes provides substantive phylogenetic evidence for the recognition of a new cypriniform family, the Ellopostomatidae, to include the enigmatic Southern Asia loach genus Ellopostoma. The current six loach families form a monophyletic group, with the Nemacheilidae as the sister group to Ellopostomatidae; Vaillantellidae forms the sister group to all families exclusive of Botiidae. While the superfamily Cobitoidea includes eight families, the monophyly of this large clade within the Cypriniformes remains a vexing problem despite extensive molecular analyses and is in need of further investigation.     

Temporal Organization in Locomotor Activity of the Hypogean Loach, Nemacheilus Evezardi, and its Epigean Ancestor

Locomotor activity rhythm in the hypogean population of Nemacheilus evezardi was recorded first under light-to-dark (LD) 12 : 12 h cycle and then DD. The results were compared with that of its epigean counterpart held under comparable regimes. In LD 12 : 12, while hypogean loach exhibited a distinct bimodality in its locomotor activity rhythm, it was altogether absent in the case of epigean population. In hypogean loach, dark-to-light transition peak in LD was observed to free-run under DD. The same was not discernible in case of epigean loach. The locomotor activity rhythm in epigean fish was noticed to free-run in DD either from the dawn peak or dusk peak in LD. It is hypothesized that the hypogean fish still possesses a functional oscillator underlying its overt circadian rhythm in locomotor activity. The ecophysiological significance of these findings is yet to be fully understood.     

Ontogenetic changes in RNA,DNA and protein contents of Chinese loach,Paramisgurnus dabryanus (Dabry de Thiersant, 1872), larvae and juveniles

The changes in nucleic acid‐based indices and protein variables of Chinese loach, Paramisgurnus dabryanus, larvae and juveniles from hatching to 60 days after hatching (DAH) were conducted to assess its growth potential. The nucleic acid contents were analysed using a UV‐based method (n = 3, rearing temperature 24.4 ± 0.4°C, dissolve oxygen 7.1 ± 0.5 mg L^?1, pH 7.9 ± 0.4). Ribonucleic acid (RNA) concentration significantly decreased from 2 to 5 DAH, then increased rapidly until 10 DAH, declining slightly thereafter. Deoxyribonucleic acid (DNA) concentration increased 2–5 DAH, decreased until 9 DAH, slightly increased again around 26 DAH, and then declined to a relatively stable level. Both RNA‐DNA and protein‐DNA ratios showed a statistically obvious relationship with growth rates. A significantly positive relationship was found between RNA‐DNA ratio and growth rates during the early life stage of Chinese loach. According to the results, growth of Chinese loach is characterized by rapid hyperplasia from hatching through completion of the yolk‐sac stage followed by continued rapid hyperplasia combined with increasing hypertrophy after feeding commences. The stage preceding 17 DAH of Chinese loach P. dabryanus is presumed to be critical for its survival and growth at 24°C.     

Alterations of selected metabolic enzymes in fish following long-term exposure to contaminated streams

In order to assess the suitability ofalterations in activities of selected metabolicenzymes as biomarkers of chemicalcontamination, juvenile brown trout (Salmotrutta f. fario) and adult loach (Barbatula barbatula) were exposed to nativesurface waters from Krähenbach andKörsch, two differently polluted smallstreams in Southern Germany. As biomarkers ofexposure, a set of metabolic enzymes comprisinghexokinase, phosphofructokinase,glucose-6-P-dehydrogenase, malic enzyme,cytochrome c oxidase, succinate dehydrogenase,citrate synthase, alanine aminotransferase,esterase, superoxide dismutase, catalase, acidphosphatase as well as acetylcholinesterase(brain) were measured by means of establishedenzyme assays. In parallel studies, loach andbrown trout sampled from corresponding fieldsites were investigated to elucidate therepresentativeness of a stream bypass system.Although the episodic exposure scenarios ineither natural stream resulted in considerablevariability of enzyme activities, biochemicalchanges in both species allowed a cleardiscrimination between the two differentlypolluted streams. Similarities in changes ofenzyme activities between fish exposed in thebypass system and the field reached levels of63% and 73.1% in brown trout and loach,respectively. In conjunction with biomarkersfrom other studies, alterations in metabolicenzyme activities were able to serve as a toolfor the sensitive identification ofenvironmental pollutants, which in turn form fromthe basis for an improved understanding ofunderlying toxic processes and an interpretationof toxicant-related effects.     

A sperm cryopreservation protocol for the loach Misgurnus anguillicaudatus and its applicability for other related species

The aim of the present study was to establish a protocol of sperm cryopreservation in Misgurnus anguillicaudatus and verify the applicability of the obtained protocol in other loach species. We evaluated the following parameters: inseminating dose, thawing temperatures (20, 25 and 30 °C for 10 s), extenders (loach or cyprinid extenders), internal cryoprotectants (dimethyl sulfoxide (DMSO), dimethylacetamide (DMA), glycerol (Gly), ethylene glycol (EG), and methanol (MeOH) at 0, 5, 10 and 15%), external cryoprotectants (bovine serum albumin 1 and 2%; sucrose 0.5 and 1%; glucose 0.5 and 1%; glycine 0.5 and 1%), activating solutions (distilled water, dechlorinated tap water, 25 mM NaCl and 50 mM NaCl), and hatchability of the eggs when fertilized with fresh or cryopreserved sperm. After the evaluation of these parameters, we optimized the cryopreservation using the following procedure: thawing temperature at 25 °C for 10 s; loach or cyprinid extenders; methanol at 10 or 15% as internal cryoprotectants; glycine 0.5% or bovine serum albumin 1% as external cryoprotectants and 50 mM NaCl for sperm activation. Using this procedure, the fertilizability of the post-thawed sperm was 47% in comparison to the fresh sperm, at the minimum inseminating dose (687.65 spermatozoa egg⁻¹ mL⁻¹). Based on this protocol, sperm from other loach species Lefua nikkonis, Misgurnus mizolepis and Barbatula toni were cryopreserved successfully.     

Fish abundance and habitat relationships in forest and grassland streams, northern Hokkaido, Japan

The relationships between habitat variables and population densities of masu salmon (Oncorhynchus masou), rosyface dace (Leuciscus ezoe), Siberian stone loach (Noemacheilus barbatulus) and wrinklehead sculpin (Cottus nozawae) were examined by data collected at 55 reaches in forest and grassland streams in northern Hokkaido, Japan. Regression analysis suggested that salmon and dace densities were affected by water temperature (negative for salmon, positive for dace) and structural habitat factors (woody debris for salmon, pools for dace). Salmon density was higher in forest reaches than in grassland reaches, whereas dace density was higher in grassland reaches, suggesting that the removal of riparian forest had raised water temperature and allowed upstream invasions by dace. In contrast to salmon and dace, neither the density of loach nor sculpin differed between the forest and grassland reaches. For their densities, a negative effect of each on the other was most important, suggesting a strong effect of interspecific competition between loach and sculpin on their distributions. However, regression models also suggested that substrate heterogeneity mediated the outcome of their interspecific competition. On the basis of the results, a scenario is predicted for a fish-assemblage change with a typical land-development process in Hokkaido, and the importance of leaving or restoring riparian buffer for conservation and restoration of stream habitat is emphasized.     

Length‐weight relationships of diploid and tetraploid loach Misgurnus anguillicaudatus (Cantor, 1842) from the Yangtze River basin,China

Length‐weight relationships (LWRs) of diploid and tetraploid loach Misgurnus anguillicaudatus from the Yangtze River basin, China were estimated and compared.