Classification accuracy of algorithms for blood chemistry data for three aquaculture-affected marine fish species

The objective of this study was determination and discrimination of biochemical data among three aquaculture-affected marine fish species (sea bass, Dicentrarchus labrax; sea bream, Sparus aurata L., and mullet, Mugil spp.) based on machine-learning methods. The approach relying on machine-learning methods gives more usable classification solutions and provides better insight into the collected data. So far, these new methods have been applied to the problem of discrimination of blood chemistry data with respect to season and feed of a single species. This is the first time these classification algorithms have been used as a framework for rapid differentiation among three fish species. Among the machine-learning methods used, decision trees provided the clearest model, which correctly classified 210 samples or 85.71%, and incorrectly classified 35 samples or 14.29% and clearly identified three investigated species from their biochemical traits.     

Development of a real‐time PCR assay for rapid detection and quantification of Photobacterium damselae subsp. piscicida in fish tissues

The availability of a rapid and accurate method for the diagnosis of Photobacterium damselae subsp. piscicida (Phdp), able to discriminate its strictly correlated subsp. damselae (Phdd), formally known as Vibrio damsela, is essential for managing fish pasteurellosis outbreaks in farmed fish. A single‐step, high‐sensitivity real‐time PCR assay for simultaneous detection and quantification of P. damselae was designed targeting partial of the sequence of the bamB gene and tested for specificity and sensitivity on laboratory‐generated samples as well as on experimentally infected seabream tissue samples. With a limit of detection (LOD) of one copy in pure bacterial DNA, the sensitivity was higher than all methods previously reported. Validation in target and non‐target bacterial species proved the assay was able to discriminate Phdd‐Phdp subspecies from diverse hosts/geographical origins and between non‐target species. In addition, two SNPs in the target amplicon region determine two distinctive qPCR dissociation curves distinguishing between Phdp‐Phdd. This is the first time that a molecular method for P. damselae diagnosis combines detection, quantification and subspecies identification in one step. The assay holds the potential to improve the knowledge of infection dynamics and the development of better strategies to control an important fish disease.     

Ranking and classification of fishing areas using fuzzy models and techniques

Abstract Fuzzy‐logic‐based methods and fuzzy logic formalism have been demonstrated as appropriate to address the uncertainty and subjectivity in complex environmental problems. This study investigates the use of three fuzzy logic methods in fisheries analysis, aiming towards the grouping and ranking of fishing subareas, according to their fisheries yield. Initially, a simple fuzzy c‐means clustering model was applied to the fishing subareas examined. A rule‐based Mamdani‐type fuzzy inference system was then developed to allow the direct fishing subarea classification. Finally, a species‐economic value weighted global fuzzy membership model was introduced, serving as an indirect classification and ranking scheme. Global memberships were plotted on simple ternary diagrams, producing representations that serve as tools in fisheries management. All methods examined the performance of the Greek fishing subareas, based on the annual landings series of the 10 most abundant fish species in terms of landed biomass, during the period 1985–1999.     

基于RAG2基因序列分析仿石鲈科鱼类及其相关种类系统进化关系

为探讨仿石鲈科鱼类目前存在的分类争议问题,测定了仿石鲈科(Haemulidae),金线鱼科(Nemipteridae),眶棘鲈属(Scolopsis)等相关科属共33种鱼类RAG2基因部分序列,利用最大简约法(MP法)和贝叶斯分析法(BI法),并以黄鹦嘴鱼作为外类群构建分子系统进化树.结果显示,33种鱼类共形成三大类群,其中仿石鲈科8个属聚成一类群,金线鱼属和眶棘鲈属的种类聚成另一类群,眶棘鲈属未能与仿石鲈科形成单系.同时,基于属间遗传距离比较,眶棘鲈属与金线鱼科的遗传距离比其与仿石鲈科各属的遗传距离要小得多,表明眶棘鲈属与金线鱼科有更近的亲缘关系,支持眶棘鲈属隶属于金线鱼科的观点.此外,传统分类资料中归类于仿石鲈科的髭鲷属(Hapalogenys)也没有与仿石鲈科聚成单系,而是独自形成一支,位于进化树基部,显示出髭鲷属与仿石鲈科关系较远,与近年来认为髭鲷属应该从仿石鲈科中划分出去的结果一致.在仿石鲈科内部,少棘胡椒鲷属(Diagramma)中的少棘胡椒鲷与胡椒鲷属(Plectorhinchus)的种类关系很近.在进化树上,少棘胡椒鲷位于胡椒鲷属的内部,花尾胡椒鲷最先分化出来,位于该分支基部,支持少棘胡椒鲷归为胡椒鲷属,名称沿用原来的学名胡椒鲷的观点.     

Genetic identification and phylogenetic inferences in different Mugilidae species using 5S rDNA markers

A DNA methodology was developed to discriminate fry of six Mugilidae species found in the Mediterranean, namely Mugil cephalus, Mugil so‐iuy, Chelon labrosus, Liza aurata, Liza ramada and Liza saliens. Polymerase chain reaction (PCR) amplification of the 5S rDNA gene was used for the identification of the above six species. PCR products of two species showed different patterns on EtBr‐stained agarose gels; M. so‐iuy gave a pattern of three bands, while L. saliens gave a pattern of one band. Mugil cephalus, C. labrosus, L. aurata and L. ramada gave a pattern of two bands. Subsequent sequencing analyses revealed unique haplotypes for each of the remaining four species. This is a genetic technique that could be applied in hatcheries, for identification of fry mullet's species. Furthermore, 5S rDNA sequences of each of five of the studied species (i.e. M. cephalus, C. labrosus, L. aurata, L. ramada and L. saliens), as well as a sequence of Oedalechilus labeo that belongs to the Mugilidae family, were aligned and used for the examination of the phylogenetic relationships among them. Phylogenetic trees produced in our study are in general agreement with those presented in the literature. This is the first study to use a nuclear marker to elucidate the phylogeny of Mugilidae species.