• Animal Systematics, Evolution and Diversity
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• v.29 no.4
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• pp.272-278
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• 2013

Accurate identification of fish and fish products, from eggs to adults, is important in many areas. Grey mullets of the family Mugilidae are distributed worldwide and inhabit marine, estuarine, and freshwater environments in all tropical and temperate regions. Various Mugilid species are commercially important species in fishery and aquaculture of many countries. For the present study we have chosen two Mugilid genes with different phylogenetic signals: relatively variable mitochondrial cytochrome oxidase subunit I (COI) and conservative nuclear rhodopsin (RHO). We examined their diversity within and among 9 Mugilid species belonging to 4 genera, many of which have been examined from multiple specimens, with the goal of determining whether DNA barcoding can achieve unambiguous species recognition of Mugilid species. The data obtained showed that information based on COI sequences was diagnostic not only for species-level identification but also for recognition of intraspecific units, e.g., allopatric populations of circumtropical Mugil cephalus, or even native and acclimatized specimens of Chelon haematocheila. All RHO sequences appeared strictly species specific. Based on the data obtained, we conclude that COI, as well as RHO sequencing can be used to unambiguously identify fish species. Topologies of phylogeny based on RHO and COI sequences coincided with each other, while together they had a good phylogenetic signal.

• Fisheries and Aquatic Sciences
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• v.5 no.3
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• pp.206-211
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• 2002

The aim of this study was to obtain the basic data on the fish school behavior change to approaching vessel and fish species identification by means of their swimming speed. The surveys were carried out for the juvenile southern blue fin tuna and other fish schools off Esperance, western Australia from January to March 1999. We observed changes of fish school behavior in response to the approaching vessel using 360-degree scanning sonar. The results showed that, a horizontal direction index used to quantify a change of fish school behavior did not identify dependence of a radial distance and a swimming speed. A Mann­Whitney test conducted using the horizontal swimming speed of both species identified by sonar specialists, did not reveal a significant difference.

• Journal of fish pathology
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• v.17 no.2
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• pp.145-149
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• 2004

The definitive identification of ciliate species by morphological characteristics relies on time-consuming and laborious staining techniques. Therefore, in this study, we discriminated 3 scuticociliatosis causing species - Pseudocohnilembus persalinus, Uronema marinum and Philasterides dicentrarchi - in cultured olive flounder by multiplex PCR. The multiplex PCR based on the species-specific amplification of small subunit ribosomal RNA (SS rRNA) gene sequence enabled us to distinguish the 3 scuticociliate species in a simple and rapid manner, even in the sample containing the three species simultaneously. These data suggest that the multiplex PCR strategy would make it possible to avoid the cumbersome and time-consuming procedures of morphological analysis for the definitive identification of scuticociliates.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.38 no.4
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• pp.265-275
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• 2005

A prerequisite for deriving the abundance estimates from acoustic surveys for commercially important fish species is the identification of target strength measurements for selected fish species. In relation to these needs, the goal of this study was to construct a data bank for converting the acoustic measurements of target strength to biological estimates of fish length and to simultaneously obtain the target strength-fish length relationship. Laboratory measurements of target strength on 15 commercially important fish species were carried out at five frequencies of 50, 70, 75, 120 and 200 kHz by single and split beam methods under the controlled conditions of the fresh and the sea water tanks with the 389 samples of dead and live fishes. The target strength pattern on individual fish of each species was measured as a function of tilt angle, ranging from $-45^{\circ}$ (head down aspect) to $+45^{\circ}$ (head up aspect) in $0.2^{\circ}$ intervals, and the averaged target strength was estimated by assuming the tilt angle distribution as N $(-5.0^{\circ},\;15.0^{\circ})$. The TS to fish length relationship for each species was independently derived by a least-squares fitting procedure. Also, a linear regression analysis for all species was performed to reduce the data to a set of empirical equations showing the variation of target strength to a fish length, wavelength and fish species. For four of the frequencies (50, 75, 120 and 200 kHz), an empirical model for fish target strength (TS, dB) averaged over the dorsal sapect of 602 fishes of 10 species and which spans the fish length (L, m) to wavelength (\Lambda,\;m)$ ratio between 5 and 73 was derived: $TS=19.44\;Log(L)+0.56\;Log(\Lambda)-30.9,\;(r^2=0.53)$.

• Fisheries and Aquatic Sciences
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• v.27 no.2
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• pp.87-99
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• 2024

Global climate change, followed by an increase in anthropogenic activities in aquatic ecosystems, and species invasions, has resulted in a decline in aquatic organism biodiversity. The Batanghari River, Sumatra's longest river, is polluted by mercury-containing illegal gold mining waste (PETI), industrial pollution, and domestic waste. Several studies have provided evidence suggesting a decline in fish biodiversity within the Batanghari River. However, a comprehensive evaluation of the present status of biodiversity in this river is currently lacking. The species under investigation were identified through various molecular-based identification methods, as well as morphological identification, which involved the use of neighbor-joining (NJ) trees. All collected specimens were initially identified using morphological techniques and subsequently confirmed with molecular barcoding analysis. Morphological and DNA barcoding identification categorized all specimens (1,692) into 36 species, 30 genera and 16 families, representing five orders. A total of 36 DNA barcodes were generated from 30 genera using a 650-bp-long fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene. Based on the Kimura two-parameter model (K2P), The minimum and maximum genetic divergences based on K2P distance were 0.003 and 0.331, respectively, and the average genetic divergence within genera, families, and orders was 0.05, 0.12, 0.16 respectively. In addition, the average interspecific distance was approximately 2.17 times higher than the mean intraspecific distance. Our results showed that the COI barcode enabled accurate fish species identification in the Batanghari River. Furthermore, the present work will establish a comprehensive DNA barcode library for freshwater fishes along Batanghari River and be significantly useful in future efforts to monitor, conserve, and manage fisheries in Indonesia.

• Journal of Internet Computing and Services
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• v.25 no.1
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• pp.17-27
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• 2024

Overfishing, climate change, and competitive fishing have led to a continuous decline in fishery production. To address these issues, the Total Allowable Catch (TAC) system has been established, which sets annual catch quotas for individual fish species and allows fishing only within those limits. As part of the TAC system, land-based investigators measure the length and height of fish species at auction markets to calculate the weight and TAC depletion. However, the accuracy of the acquired data varies depending on the skill level of the land-based investigators, and the labor-intensive nature of the work makes it unsustainable. To address these issues, this paper proposes a fish species recognition and length measurement system that automatically measures the length, height, and weight of eight TAC-managed fish species using the camera of a smart pad that can measure the distance to the water surface. This system can help to automate the current labor-intensive work, minimize data loss, and facilitate the establishment of the TAC system.

• Animal Systematics, Evolution and Diversity
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• v.26 no.2
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• pp.105-114
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• 2010

A study of Han River fish assemblage dynamics for 4 years was conducted. From April 2005 to August, 2008, fishes inhabiting two sites of Han River were sampled for identification. For further analysis, 40 individuals of the dominant species were sampled monthly from March 2006 to November 2008. The fish assemblage at site 1 was dominated by Zacco platypus (32.69%), while the subdominant species were Acheilognathus yamatsutae (14.4%), Acanthorhodeus gracilis (9.43%), Squalidus japonicus coreanus (6.84%), and Tridentiger brevispinis (5.18%). The most abundant species at site 2 was Korean Chub (Zacco koreanus) with relative abundance of 62.45% and followed by Pungtungia herzi (10.29%), Coreoperca herzi (8.67%), and Coreoleuciscus splendidus (6.82%) as the subdominant species. At both sites, the endemics populations show an increasing pattern during the whole survey period, while the natives were declining in the last two years.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.36 no.3
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• pp.317-320
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• 2003

Morphologically similar fish species were subjected to the random amplified polymorphic DNA (RAPD) analysis using universal rice primer (URP). The fish species tested were sea basses (Lateolabrax japonicus and L. maculatus), eels (Anguilla japonica, A. bicolor bicolor, A. rostrata, and A. anguilla), and flounders (Limanda yokohamae and L. herzensteinin). Highly reproducible RAPD patterns were observed with several potential species-specific markers. The results indicate that RAPD technique using URP is useful for distinguishing fish psecies in a rapid manner.

• Fisheries and Aquatic Sciences
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• v.19 no.5
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• pp.26.1-26.8
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• 2016

Background: The nematode species belonging to genus Anisakis occur at their third larval stage in numerous marine teleost fish species worldwide and known to cause accidental human infection through the ingestion of raw or undercooked fish or squids. They may also draw the attention of consumers because of the visual impact of both alive and dead worms. Therefore, the information on their geographical distribution and clear species identification is important for epidemiological survey and further prevention of human infection. Results: For identification of anisakid nematodes species isolated from largehead hairtail (Trichiurus japonicus), polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of internal transcribed spacers of ribosomal DNA were conducted. Mitochondrial cytochrome c oxidase subunit 2 gene was also sequenced, and phylogenetic analysis was conducted. From the largehead hairtail (n = 9), 1259 nematodes were isolated in total. Most of the nematodes were found encapsulated throughout the viscera (56.2 %, 708/1259) or moving freely in the body cavity (41.5 %, 523/1259), and only 0.3 % (4/1259) was found in the muscles. By PCR-RFLP, three different nematode species were identified. Anisakis pegreffii was the most dominantly found (98.7 %, 1243/1259) from the largehead hairtail, occupying 98.7 % (699/708) of the nematodes in the mesenteries and 98.1 % (513/523) in the body cavity. Hybrid genotype (Anisakis simplex ${\times}$ A. pegreffii) occupied 0.5 %, and Hysterothylacium sp. occupied 0.2 % of the nematodes isolated in this study. Conclusions: The largehead hairtail may not significantly contribute accidental human infection of anisakid nematode third stage larvae because most of the nematodes were found from the viscera or body cavity, which are not consumed raw. But, a high prevalence of anisakid nematode larvae in the largehead hairtail is still in concern because they may raise food safety problems to consumers. Immediate evisceration or freezing of fish after catch will be necessary before consumption.

• Fisheries and Aquatic Sciences
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• v.22 no.8
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• pp.18.1-18.5
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• 2019

The development of sex-specific genetic assays in a species provides both a method for identifying the system of sex determination and a valuable tool to address questions of conservation and management importance. In this study, we focused on the identification of single nucleotide polymorphisms (SNPs) that differentiate genetic sex in burbot Lota lota. Burbot are the only true freshwater representative of the cod family and a species of conservation and management importance throughout Eurasia and North America. To identify sex-specific SNPs, we utilized restriction site-associated DNA sequencing (RADseq) to interrogate thousands of SNPs in burbot samples of known phenotypic sex. We discovered 170,569 biallelic SNPs, none of which fit the pattern expected under female heterogamety. However, we identified 22 SNPs that fit the pattern expected under male heterogamety (males heterozygous XY, females fixed XX) and, from these, developed two genetic assays that robustly (~ 97% genotyping success) and accurately (> 99% correct) sexed burbot samples. These sex-specific genetic assays will benefit growing conservation aquaculture programs for this species and allow future assessments of sex-specific migration, growth, and mortality.