Cemal Turan

Microsatellite DNA analysis of population structure in Atlantic herring (Clupea harengus), with direct comparison to allozyme and mtDNA RFLP analyses

Previous attempts to test for small-scale stock structuring within Atlantic herring (Clupea harengus L.) with molecular markers have been hampered by uninformative levels of genetic variation. Here we report the first application of microsatellite DNA markers to investigate population subdivision in Atlantic herring from Norwegian waters and the Barents Sea, and also examine microsatellite differentiation between C. harengus and Pacific herring (C. pallasi). Results from four microsatellite loci indicate high, and informative, variation compared to molecular markers used previously: number of alleles per locus=18–41; mean expected heterozygosity within samples=0.90–0.93. Significant genetic differences were detected between almost all samples representing postulated Icelandic summer-spawner, Norwegian spring-spawner and Norwegian fjord stocks, using Fisher’s exact test, FST and RST values. Levels of allele frequency differentiation between Atlantic and Pacific herring overlapped the range seen among Atlantic herring samples, indicating that microsatellites are poor indicators of the degree of species differentiation. Comparison with allozyme and mitochondrial DNA restriction fragment length polymorphism (RFLP) datasets from the same samples suggests that microsatellites may detect structuring at a finer scale, but are less informative at larger scales of divergence.

Identifying fishes through DNA barcodes and microarrays.

Background International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. Methodology/Principal Findings This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of “DNA barcoding” and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the “position of label” effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology. Conclusions/Significance Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products.

DNA Microarrays for Identifying Fishes

In many cases marine organisms and especially their diverse developmental stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. In this study, a DNA microarray has been developed to be able to investigate its potential as a tool for the identification of fish species from European seas based on mitochondrial 16S rDNA sequences. Eleven commercially important fish species were selected for a first prototype. Oligonucleotide probes were designed based on the 16S rDNA sequences obtained from 230 individuals of 27 fish species. In addition, more than 1200 sequences of 380 species served as sequence background against which the specificity of the probes was tested in silico. Single target hybridisations with Cy5-labelled, PCR-amplified 16S rDNA fragments from each of the 11 species on microarrays containing the complete set of probes confirmed their suitability. True-positive, fluorescence signals obtained were at least one order of magnitude stronger than false-positive cross-hybridisations. Single nontarget hybridisations resulted in cross-hybridisation signals at approximately 27% of the cases tested, but all of them were at least one order of magnitude lower than true-positive signals. This study demonstrates that the 16S rDNA gene is suitable for designing oligonucleotide probes, which can be used to differentiate 11 fish species. These data are a solid basis for the second step to create a “Fish Chip” for approximately 50 fish species relevant in marine environmental and fisheries research, as well as control of fisheries products.

Towards the Ictalurid Catfish Transcriptome: Generation and Analysis of 31,215 Catfish ESTs.

BackgroundEST sequencing is one of the most efficient means for gene discovery and molecular marker development, and can be additionally utilized in both comparative genome analysis and evaluation of gene duplications. While much progress has been made in catfish genomics, large-scale EST resources have been lacking. The objectives of this project were to construct primary cDNA libraries, to conduct initial EST sequencing to generate catfish EST resources, and to obtain baseline information about highly expressed genes in various catfish organs to provide a guide for the production of normalized and subtracted cDNA libraries for large-scale transcriptome analysis in catfish.ResultsA total of 17 cDNA libraries were constructed including 12 from channel catfish (Ictalurus punctatus) and 5 from blue catfish (I. furcatus). A total of 31,215 ESTs, with average length of 778 bp, were generated including 20,451 from the channel catfish and 10,764 from blue catfish. Cluster analysis indicated that 73% of channel catfish and 67% of blue catfish ESTs were unique within the project. Over 53% and 50% of the channel catfish and blue catfish ESTs, respectively, had significant similarities to known genes. All ESTs have been deposited in GenBank. Evaluation of the catfish EST resources demonstrated their potential for molecular marker development, comparative genome analysis, and evaluation of ancient and recent gene duplications. Subtraction of abundantly expressed genes in a variety of catfish tissues, identified here, will allow the production of low-redundancy libraries for in-depth sequencing.ConclusionThe sequencing of 31,215 ESTs from channel catfish and blue catfish has significantly increased the EST resources in catfish. The EST resources should provide the potential for microarray development, polymorphic marker identification, mapping, and comparative genome analysis.

Phylogenetic relationships of nine mullet species (Mugilidae) in the Mediterranean Sea

Phylogenetic relationships among four genera and nine species (Mugil cephalus, Mugil soiuy, Liza ramada, Liza aurata, Liza abu, Liza saliens, Liza carinata, Chelon labrosus, Oedalechilus labeo) of the Mediterranean mullets (Mugilidae) were investigated by means of allozyme electrophoresis using a seven-enzyme system (CK*, GAPDH*, G3PDH*, IDHP*, ME*, MDH*, PGM*) comprising eleven putative loci. The highest genetic divergence was 1.299, detected between M. cephalus and L. aurata and the lowest (0.280) was found between L. carinata and L. saliens. The amount of genetic divergence between the genera Chelon and Oedalechilus did not appear to be high (0.285). In a UPGMA tree, all nine species were grouped in two main branchings. In the first branch, C. labrosus and O. labeo clustered as closest taxa and were sister group to L. ramada. The other four Liza species produced two sub-branching in this group; L. carinata branched together with L. saliens, and L. aurata branched together with L. abu. In the second branch the two species of the genus Mugil, M. cephalus and M. soiuy, clustered together and were clearly isolated from the other three genera.

Threatened fishes of the world: Capoeta antalyensis (Battalgil, 1943) (Cyprinidae)

Common name: Antalya barb (English), Antalya Saribaligi (Turkish). Conservation status: Vulnerable VU D2 (Crivelli 2006). Identification: D III/8–9, A III/5, P I/15–17, V I/7–8 and Ll. 50–56. Reachs 195 mm TL. Body elongated and fusiform. The mouth is ventral and like a half-moon, two pairs of barbels. Body covered by moderate scales. Last unbranched ray of the dorsal fin thickened, slightly emarginated and denticulated up to 2/3 of its length. Grey to blackish coloration on dorsal and sides, and silver-grey ventrally (Karaman 1969; Erk’akan and Kuru 1983). Distribution: The Antalya barb has a very restricted distribution. There are three populations, Aksu, Koprucay and Boga Streams (Kucuk and Ikiz 2004). Abundance: It is abundant in the Aksu, but is rare in the Koprucay and Boga (Kucuk and Guclu 2006). Habitat and ecology: This species prefers upper reaches, with high flow, clear and cold water, and inhabits shallow streams with sandy and pebbly bottom, being concurrently with Salmo trutta macrostigma (Kucuk and Ikiz 2004). Reproduction: Very few data are available. Breeding takes place from May to June (Kucuk and Ikiz 2004). Threats: C. antalyensis is threatened due to its limited distribution. Furthermore, river damming for hydroelectricity resulted in destruction of shallow water habitats and in the decline of their populations. Conservation action and recommendations: Besides the inclusion in the IUCN International Red List, no specific legal protection or conservation actions have yet been taken. In order to implement future management and protection programs, further research addressing the biology, ecology, genetic diversity and population status of the species is required. However, future conservation efforts should include the protection of the species natural habitats. Remarks: C. antalyensis is highly endemic with restricted distribution.

The effect of relocation on the morphology of Green Turtle, Chelonia mydas (Linnaeus, 1758), hatchlings on Samandağ beach, Turkey

Abstract We studied the impact of nest relocation in Green Turtles, Chelonia mydas (Linnaeus, 1758), on hatchling morphology at Samandağ, Turkey, and examined 350 hatchlings taken equally from both natural nests and relocated nests. The nuchal, vertebral and costal series were the most variable and the supracaudal scutes were almost stable for the hatchlings in both groups. There were significant differences in all sets of nuchal, costal and marginal except vertebral scutes between hatchlings from natural and relocated nests. Hatchlings from relocated nests also had a smaller straight carapace width and lower weight than hatchlings from natural nests. Furthermore, hatchlings from relocated nests had smaller left and right fore limb lengths than hatchlings from natural nests. There were significant differences between both nests in incubation duration and moisture content. Relocation thus has a negative effect on hatchling morphology and consequently on the fitness of hatchlings. The smaller size of hatchlings (with scute variations) results in reduced fitness. In spite of the relocation of nests being an important protection technique, it has a negative effect on the morphology and probably on the viability of hatchlings.

Classification of fish species with two dorsal fins using centroid-contour distance

Color, texture and shape are generally used features in order to recognise an object from an image. In this study centroid-contour distance method is used in order to classify fish species with two dorsal fins. Therefore, fish images with two dorsal fins were used from fish images database taken under specific conditions. Various image processing methods were applied on images in order to extract centroid-contour distances. These distances were used as features and Nearest Neighbour algorithm was used for classification. 15 species from 427 fish images were classified with 95% general accuracy achievement.

A second observation ofDendrodoris fumata(Rüppell & Leuckart, 1830) from the Mediterranean Sea (Nudibranchia: Dendrodorididae)

The nudibranch Dendrodoris fumata (Rüppell & Leuckart, 1830) was originally described from the Red Sea, and has been observed throughout the tropical Indo-Pacific region, from East Africa up to the Galapagos Islands and the Pacific coasts of Mexico and Costa Rica (ZENETOS et al. 2011, VALDES et al. 1996). BARASH & DANIN (1986) found it in the vicinity of Dor, Israel, in 1980. However, they misidentified it as Dendrodoris nigra (ZENETOS et al. 2011). BRODIE et al. (1997) have provided a comprehensive analysis of the differences between D. nigra and D. fumata. In a recent review of marine alien species in the Mediterranean, ZENETOS et al. (2005) classify the occurrence D. fumata as casual, as only one record is known. We found a single living specimen of D. fumata in Yumurtal k, Adana (36°46’N, 35°47’E) in shallow (15 cm) and calm water on 15 March 2010, more than 30 years after the first observation of it in the Mediterranean Sea. The temperature, salinity and oxygen saturation of the region were 17°C, 38.5 psu and 7.8 mg/L, respectively. The length of the specimen was measured as 25 mm. The specimen has been deposited in the museum of the Çukurova University, Faculty of Fisheries, Turkey (CSFM-GAS/09–08). When the specimen was examined, the following characteristics were observed which fit the description as given on the CIESM web page (ZENETOS et al. 2011): Body dorsoventrally flattened, soft and slimy. It had a characteristic mantle: it was broad, smooth-thin and wavy (Figs 1-2). However, the wavy edges were not remarkable. Head very small and containing a small pore-like mouth. The rhinophores seemed bulbous, lamellated and contained thick stalks (Fig. 2). Branchial plumes were located at the end of the dorsum and it was interrupted by the anal papilla. The gills of D. fumata were finely subdivided as shown in Fig. 1. The colour of the specimen was brownish in contrast to the specimen that was first recorded from the Mediterranean Sea. The colour of the specimen from Israel was reported as being grey (ZENETOS et al. 2011). The possible vector for this introduction can be

Image analysis methods on fish recognition

The aim of study is creating a new database which contains fish species and classifying this fish species. A new fish database was created by using the fish photos in seas of Turkey. The new feature set are obtained by marking the biometric points on fish to identify family and species of fishes. The features were obtained by using the three different biometric measurement techniques (Euclidean network technique, quadratic network technique, triangulation technique). A classifications system was created by using Naive Bayesian classifier. The obtained accuracy is 93.10% for 7 families on family classification and 75.71% for 15 species on species classification.