Cyprinidae Fish Research Articles

Preserving the tree of life of the fish family Cyprinidae in Africa in the face of the ongoing extinction crisis 1.

Our understanding of how the phylogenetic tree of fishes might be affected by the ongoing extinction risk is poor. This is due to the unavailability of comprehensive DNA data, especially for many African lineages. In addition, the ongoing taxonomic confusion within some lineages, e.g., Cyprinidae, makes it difficult to contribute to the debate on how the fish tree of life might be shaped by extinction. Here, we combine COI sequences and taxonomic information to assemble a fully sampled phylogeny of the African Cyprinidae and investigate whether we might lose more phylogenetic diversity (PD) than expected if currently threatened species go extinct. We found evidence for phylogenetic signal in extinction risk, suggesting that some lineages might be at higher risk than others. Based on simulated extinctions, we found that the loss of all threatened species, which approximates 37% of total PD, would lead to a greater loss of PD than expected, although highly evolutionarily distinct species are not particularly at risk. Pending the reconstruction of an improved multi-gene phylogeny, our results suggest that prioritizing high-EDGE species (evolutionary distinct and globally endangered species) in conservation programmes, particularly in some geographic regions, would contribute significantly to safeguarding the tree of life of the African Cyprinidae.

Identification and phylogenetic analysis of the mitogenome from Acrossocheilus wenchowensis

In the present study, the complete mitogenome sequence of Acrossocheilus wenchowensis was obtained using PCR amplification. The complete mitochondrial genome of A. wenchowensis was 16,591 bp in length, it contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one non-coding region. The gene arrangement and organization in the mitogenome of A. wenchowensis were consistent with other Cyprinidae fishes. The phylogenetic analysis was carried out, and the results showed that the mitogenome sequence could be useful data in the field of population genetics and conservation biology for A. wenchowensis and other Cyprinidae fishes.

KEANEKARAGAMAN DAN KEKERABATAN IKAN FAMILI CYPRINIDAE PADA EKOSISTEM BENDUNGAN COLO SUKOHARJO JAWA TENGAH

The Cyprinidae fish family is a family of freshwater fish with the largest number of species and its presence is widespread almost all of the world. The main habitat of this family is the river's ecosystem, river damming changing the environmental conditions between the ecosystems before and after the dam's watergate. Such as Colo Dam that dammed Bengawan Solo River that allegedly affects the diversity of species of Cyprinidae fish. So this study was conducted in order to determine the diversity and kinship of the Cyprinidae fish family in the ecosystem before and after the Colo Dam watergate. Sampling was conducted September-October 2017 at Sukoharjo Colo Dam by Purposive sampling method. Identify fish species used Kottelat identification books. The diversity of fish species was calculated by Shannon Wiener's diversity index. The correlation between abiotic factor and fish diversity was analyzed by a regression test. The kinship of the fish was analyzed by the Ntsys cluster method (2.02i). The results showed that the Cyprinidae fish species that live in the Colo Dam ecosystem contain 10 species, the diversity of Cyprinidae fish in the fast-water ecosystem of station I is higher (0,96) then the slow-water ecosystem of station II, III, and IV (0,47; 0,73, and 0,58). Abiotic factors of current velocity affect the level of fish diversity reaches 91%. The Cyprinidae fish kinship rate has a coefficient of resemblance between 60% - 85%, fish with the same genus and many similarities in morphological characters and their behavior is categorized as having a close kinship.

Non-invasive sampling: reliable methods for DNA extraction and PCR amplification from a single scale of small Cyprinidae fish

The present study was aimed to DNA extraction and PCR amplification of mitochondrial DNA of a varied size range using the non-invasive samples of fish. As many obstacles arise when obtaining an ade...

Studying embryotoxicity of petroleum products for carp fish family

To study the embryotoxicity of the oil fraction Karakuduk locality (Kazakhstan, oil deposit) for zebrafish Danio rerio (family Cyprinidae), in the conditions of the experiment. The method of breeding fishes of Danio rerio, receiving, and incubating zebrafish in vitro. Experiments have been carried out on the development of Danio rerio embryos in the oil-bearing fraction (Karakuduk locality) in various in vitro concentrations. The paper presents the results of experiments on exposure zebrafish embryos (Danio rerio) oil fractions in different concentrations and shows data on mortality of embryos and embryonic development violations. The originality of studying embryotoxicity of petroleum products for Cyprinidae fish family is that the object of our experiment is the most vulnerable age group in the population-fish larvae. Due to investigations, number of eggs could exactly determine the vitality of the fish population in general and can counter the number of the population through a certain period. Following the epidemic of mass mortality of caviar and larvae from oil pollution, the toxicant acts in the role of the immunosuppressive agent. Thus, it leads to the reduction of resistance to various infections with the reduction of the variability of even slight temperature and salinity fluctuations.

Effects of Environment and Physiological State of an Organism on the Activity and Content of Lysozyme in Fishes of the Family Cyprinidae: A Review

The effect of environmental factors such as water temperature, experimental conditions (fish in control), toxicants (heavy metals, herbicides, insecticides, etc.), and features of physiological state (starvation, early ontogenesis, reproduction, and relationship) on the activity and content of lysozyme in serum/plasma and some immune organs in fishes of the family Cyprinidae have been reviewed. Similar and multidirectional reactions of the enzyme under the influence of the same factors, as well as a wide range of variation, various units, and dimensions of the studied parameter of nonspecific resistance, have been shown. This review presents research materials that have been published in the past 15 years.

The role of the Liwonde National Park in conserving fish species diversity in the upper Shire River, Malawi

Tremendous decline of fish catches in Lake Malawi, mainly due to uncontrolled fishing, is a clear evidence of challenges of managing a common/open resource. East of the Shire River lies the protected area known as Liwonde National Park about 538 km2. Species diversity around the National Park including the southeast arm of Lake Malawi, Lake Malombe, and the upper Shire River were studied to determine if the moratorium in the park has any impact to the fishery in these areas. Fish samples were collected using a variety of fishing gears including mosquito nets, gill nets, scoop nets, cast nets, and hand lines from southeast arm of Lake Malawi, Upper Shire River, Lake Malombe, and the area near the Liwonde Barrage. Over 40 species belonging to 27 genera and 6 families were sampled compared to 50 species recorded in earlier studies suggesting that, despite the general decline in the fish species diversity, this area still maintains its resilience. The family Cichlidae was the most diverse with 19 genera followed by the Cyprinidae with 4 genera. These results showed that Cichlidae and Cyprinidae fish species that have nearly disappeared in Lake Malawi are still found in considerable abundance in the Shire River especially in areas around the National Park. Most of the determined fish species originated from surrounding areas to the park suggesting that it is a breeding area for fishes that are caught upstream and downstream. Findings underpin the importance of managing and protecting the National Park or even establishing other moratoriums for the same.

Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae).

Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for phylogenetic comparative analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.

Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)

Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for comparative phylogenetic analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.

Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae)

Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for phylogenetic comparative analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.

Prevalence and Intensity of Clonorchis sinensis Metacercariae in Freshwater Fish from Wicheon Stream in Gunwi-gun, Gyeongsangbuk-do, Korea.

The infection status of Clonorchis sinensis metacercariae (CsMc) was examined in freshwater fish from a highly prevalent site, Wicheon (a branch of Nakdong-gang), which is located in Gunwi-gun, Gyeongsangbuk-do, the Republic of Korea. Total 1,162 fish in 32 species were examined by the artificial digestion method through 6 years. CsMc were detected in 720 (67.5%) out of 1,067 fish (26 spp.) and their density was 610 per fish infected. In the susceptible gobioninid fish group, i.e., Pungtungia herzi, Squalidus gracilis majimae, Squalidus japonicus coreanus, Sarcocheilichthys variegatus wakiyae and Pseudorasbora parva, all of 323 fish were infected with an average of 1,310 CsMc. Total 23 (95.8%) gobioninid fish, i.e., Pseudogobio esocinus, Abbottina springeri, Hemibarbus longirostris, Microphysogobio koreensis, and Microphysogobio jeoni, were infected with 127 CsMc in average. In the acheilognathinid fish (bitterlings) group, the prevalence was 77.0%, and the density was 50 CsMc per fish infected. In the rasborinid fish (chubs) group, i.e., Zacco platypus, Zacco temminckii, Zacco koreanus, and Opsariichthys uncirostris amurensis, 147 (36.5%) out of 403 fish examined were infected with 15 CsMc in average. The susceptibility indices of CsMc were 412 in the overall positive fish group, 1,310 in the gobioninid group-1, 122 in the gobioninid group-2, 38.5 in the acheilognathinid group, and 5.5 in the rasborinid fish group. Conclusively, it was confirmed that CsMc are highly prevalent in fish from Wicheon, and their infection tendency varied according to the subfamily groups in Cyprinidae fish hosts.

Polymeric immunoglobulin receptor in dojo loach (Misgurnus anguillicaudatus): Molecular characterization and expression analysis in response to bacterial and parasitic challenge

The polymeric immunoglobulin receptor (pIgR) is an essential component of the mucosal immune system in jawed vertebrates including teleost fish, which mediate transepithelial transport of secretory immunoglobulins (sIgs) to protect organisms against environmental pathogens. In this study, we firstly cloned and identified the pIgR from dojo loach (Misgurnus anguillicaudatus). The full-length cDNA of Ma-pIgR was of 1145 bp, containing an open reading frame (ORF) of 1101 bp encoded a predicted protein of 336 amino acids. The structure of Ma-pIgR is comprised of a signal peptide, a transmembrane region, an intracellular region and an extracellular region with two Ig-like domains (ILDs), which are similar to their counterparts described in other teleosts. Multiple sequence alignment and phylogenetic analysis showed the dojo loach is closely related to the fish family Cyprinidae. The transcriptional level of Ma-pIgR was detected by quantitative real-time PCR (qRT-PCR) in different tissues and high expression was found in liver, skin, kidney, eye, fin and gills. Two infection models of the loach with bacteria (Aeromonas hydrophila) and parasite (Ichthyophthirius multifiliis) were constructed for the first time. Histological studies showed the goblet cells in skin significantly increased and the ratio of gill length to width also significantly changed after challenged with A.hydrophila. Both challenge experiments resulted in the significant up-regulated expression of Ma-pIgR not only in kidney and spleen, but also in skin and gills. Our results suggest that pIgR may play an important role in skin and gill mucosal immunity to protect the loach against bacteria and parasite.

Occurrence and distribution of yellow grub trematodes (Clinostomum complanatum) infection in Taiwan.

Digenetic trematodes of the genus Clinostomum are widely distributed in many species of freshwater fish and are known to cause the zoonotic disease Halzoun. Humans may become accidental hosts if they ingest raw freshwater fish containing metacercaria of Clinostomum complanatum, which causes pharyngitis or laryngitis. The yellow grub parasitizing cultivated ayu (Plecoglossus altivelis) and loach (Misgurnus anguillicaudatus) was one of the most serious problems in fish farms from 1977 to 1979 in Taiwan. The present study revealed, for the first time, frequent occurrence of C. complanatum metacercaria in various fish species in a natural environment, the Dahan River, in Taiwan. We examined 1503 fish specimens belonging to four families and 162 snails representing six species. C. complanatum metacercaria was mainly from the fish family Cyprinidae, and only cercaria from the snail Radix swinhoei was recovered. The prevalence and mean intensity of metacercaria were 9.8% and 9.35 parasites/infected fish, respectively. The prevalence of cercaria was low, 0.62%, in snails. Acrossocheilus paradoxus, Zacco barbata, Zacco pachycephalus, Zacco platypus, Onychostoma barbatula, and Hemibarbus labeo are new host records. Metacercariae were primarily found in the operculum, mandible, muscle, and oral cavity of fish. Morphological description and molecular analysis with 18S rDNA sequencing allowed for rapidly identifying C. complanatum. Encysted and excysted metacercariae cultivated at 22°C in physiological saline died within 60h. The mean intensity of infection increased with an increasing length of Z. pachycephalus. We found no association between monthly parasite prevalence and mean intensity at each sampling location. No C. complanatum metacercaria survived after 8h of salting. The Dahan River has suitable conditions and hosts (snails, fish, and fish-eating birds) for maintaining the life cycle of C. complanatum.

BIOCHEMICAL CHANGES OF MERCURY CHLORIDE ON BLOOD METABOLITE LEVELS OF A FRESHWATER FISH, LABEO ROHITA

Rohu (Labeo rohita) is a fish of the carp family Cyprinidae, found commonly in rivers and fresh water lakes in and around South Asia and South - East Asia. The freshwater fish Labeo rohita were exposed to Mercury chloride (0.25 ppm) for 10, 20 and 30 days and its effect on blood – bio chemical properties in the form of hyperglycemia, hypoproteinemia and hypercholesteromia. The results of the present study that the blood – biochemical changes may lead to the fish morbidity and mortality.

The genetic map of goldfish (Carassius auratus) provided insights to the divergent genome evolutions in the Cyprinidae family.

A high-density linkage map of goldfish (Carassius auratus) was constructed using RNA-sequencing. This map consists of 50 linkage groups with 8,521 SNP markers and an average resolution of 0.62 cM. Approximately 84% of markers are in protein-coding genes orthologous to zebrafish proteins. We performed comparative genome analysis between zebrafish and medaka, common carp, grass carp, and goldfish to study the genome evolution events in the Cyprinidae family. The comparison revealed large synteny blocks among Cyprinidae fish and we hypothesized that the Cyprinidae ancestor undergone many inter-chromosome rearrangements after speciation from teleost ancestor. The study also showed that goldfish genome had one more round of whole genome duplication (WGD) than zebrafish. Our results illustrated that most goldfish markers were orthologous to genes in common carp, which had four rounds of WGD. Growth-related regions and genes were identified by QTL analysis and association study. Function annotations of the associated genes suggested that they might regulate development and growth in goldfish. This first genetic map enables us to study the goldfish genome evolution and provides an important resource for selective breeding of goldfish.

PERBANDINGAN MORPHOMETRIK - MERISTIK JANTAN DAN BETINA IKAN KERLING (Tor tambroides) DARI DAS DI ACEH BARAT

Kerling fish (Tor spp) is a species of freshwater fish, belonging to the family Cyprinidae. In Aceh Province there are three species of fish of very commercial i.e. Tor tambroides,Tor soro and Tor tambra. In this author's research focuses on Tor tambriodes. Survey results obtained by researchers in field description of the species is quite difficult to distinguish the character of males and females (unlike other Cyprinidae fish). Because that's what needs to be done comparative studies of characters within the same species morphometric and meristic approach. These are qualitative research (survey), is a method for the measurement of morphometric and character counting/meristic refers to the twinkle and Menezes (1974), and Jayaram (1981, 2002). The number of specimens to be analyzed i.e. 20 species (10 females: 10 males). The research results obtained that based on the characteristics of the morphometric there is no noticeable difference between females and males. However the qualitative character of morphometric visible presence of noticeable difference between females and males in character: body color, the profile of the muzzle, the thickness of the lips. While the study does not look meristic the existence of the real difference between females and males. Thus to view differences characterized the fish are females and the male Tor tambroides saw enough character body color (bright golden yellow: female, dark: male), the profile of the muzzle (convex: female, flat: male) and the profile lip up/down (thin, thick: females: males).

DNA barcoding and evaluation of genetic diversity in Cyprinidae fish in the midstream of the Yangtze River.

The Yangtze River is the longest river in China and is divided into upstream and mid‐downstream regions by the Three Gorges (the natural barriers of the Yangtze River), resulting in a complex distribution of fish. Dramatic changes to habitat environments may ultimately threaten fish survival; thus, it is necessary to evaluate the genetic diversity and propose protective measures. Species identification is the most significant task in many fields of biological research and in conservation efforts. DNA barcoding, which constitutes the analysis of a short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) sequence, has been widely used for species identification. In this study, we collected 561 COI barcode sequences from 35 fish from the midstream of the Yangtze River. The intraspecific distances of all species were below 2% (with the exception of Acheilognathus macropterus and Hemibarbus maculatus). Nevertheless, all species could be unambiguously identified from the trees, barcoding gaps and taxonomic resolution ratio values. Furthermore, the COI barcode diversity was found to be low (≤0.5%), with the exception of H. maculatus (0.87%), A. macropterus (2.02%) and Saurogobio dabryi (0.82%). No or few shared haplotypes were detected between the upstream and downstream populations for ten species with overall nucleotide diversities greater than 0.00%, which indicated the likelihood of significant population genetic structuring. Our analyses indicated that DNA barcoding is an effective tool for the identification of cyprinidae fish in the midstream of the Yangtze River. It is vital that some protective measures be taken immediately because of the low COI barcode diversity.

Ion Torrent next-generation sequencing reveals the complete mitochondrial genome of koi carp (Cyprinus carpio, Cyprinidae)

The complete mitochondrial genome of the koi carp (Cyprinus carpio, Cyprinidae) was sequenced in the present study by using Ion Torrent Personal Genome Machine (PGM) platform for the first time. The mitochondrial genome sequence is 16 581 bp in size and consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one control region. The gene order and organization were similar to most of the other teleost. The nucleotide compositions of the light strand are 24.82% of A, 31.92% of T, 27.53% of G and 15.73% of C. With the exception of eight tRNA genes and the NADH dehydrogenase subunit 6 (ND6), all other mitochondrial genes are encoded on the heavy strand. The phylogenetic tree constructed using a maximum-likelihood model showed sister relationship of koi carp to other Cyprinidae fishes.

An N-targeting real-time PCR strategy for the accurate detection of spring viremia of carp virus

Spring viremia of carp virus (SVCV) is a highly pathogenic agent of several economically important Cyprinidae fish species. Currently, there are no effective vaccines or drugs for this virus, and prevention of the disease mostly relies on prompt diagnosis. Previously, nested RT-PCR and RT-qPCR detection methods based on the glycoprotein gene G have been developed. However, the high genetic diversity of the G gene seriously limits the reliability of those methods. Compared with the G gene, phylogenetic analyses indicate that the nucleoprotein gene N is more conserved. Furthermore, studies in other members of the Rhabdoviridae family reveals that their gene transcription level follows the order N>P>M>G>L, indicating that an N gene based RT-PCR should have higher sensitivity. Therefore, two pairs of primers and two corresponding probes targeting the conserved regions of the N gene were designed. RT-qPCR assays demonstrated all primers and probes could detect phylogenetically distant isolates specifically and efficiently. Moreover, in artificially infected fish, the detected copy numbers of the N gene were much higher than those of the G gene in all tissues, and both the N and G gene copy numbers were highest in the kidney and spleen. Testing in 1100 farm-raised fish also showed that the N-targeting strategy was more reliable than the G-targeting methods. The method developed in this study provides a reliable tool for the rapid diagnosis of SVCV.

Efficiency of a modified Ice Harbor-type fishway for Korean freshwater fishes passing a weir in South Korea

The effectiveness of a modified Ice Harbor-type fishway on the Geum River in South Korea was investigated for native freshwater fishes, using trap and passive integrated transponder (PIT) telemetry. The traps were installed at the exit part of the fishway, and fish use was monitored monthly from June to October 2012. Fishes were caught by a cast net and a fyke net at the lower part of the Gongju weir for PIT tagging. The tagged fishes were released downstream of the fishway. Three antenna lines (entrance, middle, and exit) were installed along the 70-m stretch of the fishway to investigate fish passage. A total of 1114 individuals, classified into 21 species and 4 families, were collected by the traps, with fishes of family Cyprinidae being dominant. The total length (TL) of fishes collected by the traps ranged from 40 mm (Rhinogobius brunneus) to 504 mm (Erythroculter erythropterus), with a mean of 161.3 ± 82.3 mm. The overall attraction and passing rate of the fishway were 15.3 and 43.2 %, respectively. TL had no effect on the attraction and passing rate of tagged fishes. Even though some Cyprinidae species required >6 h to move through the fishway, most fishes passed through within 6 h. Most fish detections occurred when the water level in the fishway exceeded the management level. To our knowledge, this study is the first to investigate the use of a fishway by Korean freshwater fishes, demonstrating the high use of a modified Ice Harbor-type fishway. To confirm whether this type of fishway is ideal for Korean freshwater fishes, other fishways must be evaluated. Such research would contribute towards the development of optimal fishways for this location and towards the establishment of operational strategies that facilitate the passage of more fishes.