Genetic variation between outer-coastal and fjord populations of Pacific herring (Clupea pallasii) in the eastern Gulf of Alaska

Pacific herring (Clupea pallasii) from the Gulf of Alaska were screened for temporal and spatial genetic variation with 15 microsatellite loci. Thirteen collections were examined in this study: 11 from Southeast Alaska and 2 from Prince William Sound, Alaska. Although FST values were low, a neighbor-joining tree based on genetic distance, homogeneity, and FST values revealed that collectively, the Berners Bay and Lynn Canal (interior) collections were genetically distinct from Sitka Sound and Prince of Wales Island (outer-coastal) collections. Temporal genetic variation within regions (among three years of Berners Bay spawners and between the two Sitka Sound spawners) was zero, whereas 0.05% was attributable to genetic variation between Berners Bay and Sitka Sound. This divergence may be attributable to environmental differences between interior archipelago waters and outer-coast habitats, such as differences in temperature and salinity. Early spring collections of nonspawning Lynn Canal herring were nearly genetically identical to collections of spawning herring in Berners Bay two months later—an indication that Berners Bay spawners over-winter in Lynn Canal. Southeast Alaskan herring (collectively) were significantly different from those in Prince William Sound. This study illustrates that adequate sample size is needed to detect variation in pelagic fish species with a large effective population size, and microsatellite markers may be useful in detecting low-level genetic divergence in Pacific herring in the Gulf of Alaska.

Genetic enhancement and conservation of aquatic biodiversity in Africa

There is a pressing need to enhance fish production in Africa through improved farm management and the use of improved fish breeds and/or alien species in aquaculture while at the same time conserve the aquatic genetic diversity. This paper presents the outcome of the Expert Consultation on Biosafety and Environmental Impact of Genetic Enhancement and Introduction of Improved Tilapia Strains/Alien Species in Africa held in Nairobi, Kenya on 20-23 February 2002. The main topics discussed were status of aquaculture in Africa and the role of genetic enhancement; potential benefits and risks involved in introduction of genetically improved strains and/or alien species with specific reference to tilapias; existing policies and legislation for the conservation of biodiversity, their strengths and weaknesses; capacity for undertaking genetic enhancement research and implementation of policies for the conservation of aquatic biodiversity.

The genetic structure and phylogenetics of pikeperch (Sander lucioperca) Anzali and Amirkolaye wetlands and perch (Perca fluviatilis) populations in Aras Dam and south-west of the Caspian Sea

The genetic structure of pikeperch (Sander lucioperca) and perch (Perca fluviatilis) populations was studied using microsatellite technique. A total of 207 specimens of adult pikeperch were collected from Aras dam (57 specimens), Anzali wetland (50 specimens), Talesh (50 specimens) and Chaboksar (50 specimens) coasts. Also a total of 158 specimens of adult perch were collected from Anzali (Abkenar (50 specimens)and Hendekhale(48 specimens)) and Amirkolaye(60 specimens) wetlands. About 2 g of each specimen's dorsal fin was removed, stored in 96% ethyl alcohol and transferred to the genetic laboratory of the International Sturgeon Research Institute. Genomic DNA was extracted using ammonium-acetate method. The quality and quantity of DNA was assessed using 1% agarose gel electrophoresis. Polymerase Chain Reaction (PCR) was conducted on the target DNA using 15 pairs of microsatellite primers. PCR products were electrophoresed on poly acryl amide gels (6%) that were stained that were stained using silver nitrate. DNA bands were analyzed with BioCapt software. Allele count and frequency, genetic diversity, expected and observed heterozygosity , allele number and the effective allele number, genetic similarity and genetic distance, Fst, Rst, Hardy Weinberg Equilibrium based on X2 and Analysis of Molecular Variance (AMOVA) at 10% confidence level was calculated using the Gene Alex software. Dendogram for genetic distances and identities were calculated using TFPGA program for any level of hierarchy. The results for P. fluviatilis showed that from 15 pair of primers that were examined 6 polymorphic and 7 monomorphic loci were produced, while 2 loci didn't produce any DNA bands. Mean allele number was 4.1±1.1 and mean observed and expected heterozygosity was 0.56±0.12 and 0.58±0.14 respectively. It was also seen that specimens from all regions were not in Hardy Weinberg Equilibrium in some of loci (P<0.001). Highest Fst (0.095) with Nm=2.37 was observed between Hendekhale and Amirkolaye and the lowest Fst (0.004) with Nm=59.31 was observed between Abkenar and Hendekhale. According to AMOVA Significant difference (P<0.05) was observed between recorded Rst in the studied regions in Anzali and Amirkolaye lagoons. In another words there are two distinct populations of this species in Anzali and Amirkolaye lagoons. The highest genetic distance (0.181) and lowest genetic resemblance (0.834) were observed between specimens from Hendekhale and Amirkolaye and the lowest genetic distance (0.099) and highest genetic 176 resemblance (0.981) were observed between specimens from Abkenar and Hendekhale. Based on the genetic dendogram tree derived by applying UPGMA algorithm, specimens from Anzali and Amirkolaye wetlands have the same ancestor. On the other hand there is no noticeable genetic distance between the specimens of these two regions. Also the results for S. lucioperca showed that from 15 pair of primers that were examined 6 polymorphic and 7 monomorphic loci were produced, while 2 loci didn't produce any DNA bands. Mean allele number was 3.0±0.6 and mean observed and expected heterozygosity was 0.52±0.21 and 0.50±0.14 respectively. It was also seen that specimens from all regions were not in Hardy Weinberg Equilibrium in some of loci (P<0.001). Highest Fst (0.093) with Nm=2.43 was observed between Aras dam and Anzali wetland and the lowest Fst (0.022) with Nm=11.27 was observed between Talesh and Chaboksar coasts. Significant differences (P<0.05) were observed between recorded Rst in the studied regions exept for Talesh and Chaboksar Coasts. In another words there are three distinct populations of this species in Caspian sea, Anzali wetland and Aras dam. Highest genetic distance (0.110) and lowest genetic resemblance (0.896) were observed between specimens from Aras dam and Anzali wetland and the lowest genetic distance (0.034) and highest genetic resemblance (0.966) were observed between specimens from Talesh and Chaboksar coasts. Based on the genetic dendogram tree derived by applying UPGMA algorithm, specimens from Talesh and Chaboksar coasts have the lowest genetic distance. On the other hand the main population of this species belongs to Anzali wetland. Phylogenetic relationship of these two species was inferred using mitochondrial cytochrome b gene sequencing. For this purpose 2 specimens of P. fluviatilis from Anzali wetland, 2 specimens of S. lucioperca from Aras dam and 2 specimens of S. lucioperca from Anzali wetland were sequenced and submitted in Gene Bank. These sequences were aligned with Clustal W. The phylogenic relationships were assessed with Mega 4. The results of evolutionary history studies of these species using Neighbor-Joining and Maximum Parsimony methods showed that the evolutionary origin of pikeperch in Aras Dam and Anzali wetland is common. On the other hand these two species had common ancestor in about 4 million years ago. Also different sequences of any region specimens are supposed as different haplotypes. 177 As a conclusion the results of this study showed that microsatellite and mtDNA sequencing methods respectively are effective in genetic structure and phylogenic studies of P. fluviatilis and S. lucioperca.

Ecology of aquaculture species and enhancement of stocks: proceedings of the thirtieth U.S. - Japan meeting on aquaculture, Sarasota, FL, Dec. 3-4, 2001

CONTENTS: I. U.S.-Japan Cooperation Open Ocean Aquaculture – A Venue for Cooperative Research Between the United States and Japan.............................................................................. 1 C. Helsley II. Growth, Nutrition and Genetic Diversity Daily Ration of Hatchery-Reared Japanese Flounder Paralichthys olivaceus as an Indicator of Release Place, Time and Fry Quality. In situ Direct Estimation and Possibility of New Methods by Stable Isotope............................ 7 O. Tominaga, T. Seikai, T. Tsusaki, Y. Hondo, N. Murakami, K. Nogami, Y. Tanaka and M. Tanaka Nucleic Acids and Protein Content as a Measure to Evaluate the Nutritional Condition of Japanese Flounder Paralichthys olivaceus Larvae and Juveniles........................................................................................................ 25 W. Gwak Genetic Diversity Within and Between Hatchery Strains of Flounder Paralichthys olivaceus Assessed by Means of Microsatellite and Mitochondrial DNA Sequencing Analysis...................................................................... 43 M. Sekino, M. Hara and N. Taniguchi Tracking Released Japanese Flounder Paralichthys olivaceus by Mitochondrial DNA Sequencing................................................................................ 51 T. Fujii Preliminary Aspects of Genetic Management for Pacific Threadfin Polydactylus sexfilis Stock Enhancement Research in Hawaii........................................ 55 M. Tringali, D. Ziemann and K. Stuck Enhancement of Pacific Threadfin Polydactylus sexfilis in Hawaii: Interactions Between Aquaculture and Fisheries............................................................. 75 D. Ziemann Aquaculture and Genetic Structure in the Japanese Eel Anguilla japonica..................... 87 M. Katoh and M. Kobayashi Comparative Diets and Growth of Two Scombrid Species, Chub Mackerel Scomber japonicus and Japanese Spanish Mackerel Scomberomorus niphonius, in the Central Seto Inland Sea, Japan.................................. 93 J. Shoji, M. Tanaka and Tsutomu Maehara iii Evaluating Stock Enhancement Strategies: A Multi-disciplinary Approach................... 105 T. M. Bert, R.H. McMichael, Jr., R.P. Cody, A. B. Forstchen, W. G. Halstead, K. M. Leber, J. O’Hop, C. L. Neidig, J. M. Ransier, M. D. Tringali, B. L. Winner and F. S. Kennedy III. Physiological and Ecological Applications Predation on Juvenile Chum Salmon Oncorhynchus keta by Fishes and Birds in Rivers and Coastal Oceanic Waters of Japan................................... 127 K. Nagasawa and H. Kawamura Interaction Between Cleaner and Host: The Black Porgy Cleaning Behavior of Juvenile Sharpnose Tigerfish Rhyncopelates Oxyrhynchus in the Seto Inland Sea, Western Japan............................................................................. 139 T. Shigeta, H. Usuki and K. Gushima IV. Case Studies Alaska Salmon Enhancement: A Successful Program for Hatchery and Wild Stocks............................................................................................... 149 W. Heard NMFS Involvement with Stock Enhancement as a Management Tool........................... 171 T. McIlwain Stock Enhancement Research with Anadromous and Marine Fishes in South Carolina...................................................................................... 175 T. I. J. Smith, W. E. Jenkins, M. R. Denson and M. R. Collins Comparison of Some Developmental, Nutritional, Behavioral and Health Factors Relevant to Stocking of Striped Mullet, (Mugilidae), Sheepshead (Sparidae), Common Snook (Centropomidae) and Nassau Groupers (Serranidae)........................... 191 J. W. Tucker Jr. and S. B. Kennedy Participants in the Thirtieth U.S.-Japan Meeting on Aquaculture................. Inside Back Cover iv (PDF has 204 pages.)

Evaluation of the carcass and commercial characteristics of carps

The role of carcass evaluation techniques in aquaculture research programs, especially in genetics, breeding, production management, feeding and nutrition, cannot be overemphasized. Knowledge of production efficiencies and growth potentials in relation to desired carcass attributes has provided an impetus to improvements in genetic selection techniques and management of aquatic food animals. Accurate, standard and uniform methods of carcass evaluation are critically important. A standard format developed for collection of data on carps is presented in this paper.

History of the Fisheries of Raritan Bay, New York and New Jersey

Raritan Bay is the body of water bounded by New York and New Jersey and lying immediately south of New York City (Fig. 1). It has close proximity to the most concentrated urban and industrial area in the United States. Its history has been one of extensive multiple use by the surrounding human population. Dating from the precolonial and colonial periods, people have employed many types of gear to catch and gather its once abundant fishes and shellfishes. Its beaches were once popular for sun bathing and swimming, but after the 1940's they were essentially abandoned because the water became too polluted. Another large use has been for pleasure boating and the transit and dockage of merchant, passenger, and military vessels. Channels and basins were dug in the bay, bulkheads and jetties were constructed along its shores, and it was a donor source of sand and gravel for construction projects. It has also been a receptor for large quantities of domestic and industrial wastes and, mainly for this reason, it is one ofthe most deteriorated estuaries in the United States.

Genetic diversity study of Caspian brown trout (Salmo trutta caspius Kessler, 1877) population in five rivers in the southern part of Caspian Sea, Iran

For study the genetic diversity of Caspian brown trout population in five rivers in the southern part of Caspian Sea in Iran 182 number generators in the fall and winter of 1390 were collected in Chalus, Sardab Rud, Cheshmeh Kileh, Kargan Rud and Astara rivers. Then about 3-5 g of soft and fresh tissue from the bottom fin fish removed and were fixed in ethanol 96°. Genomic DNA was extracted by using ammonium acetate, then quantity and quality of the extracted DNA were determined by using spectrophotometry and horizontal electrophoresis in 1% agarose gel. The polymerase chain reaction was performed by using 16 SSR primers and sequencing primers (D-Loop) and the quality of PCR products amplified by SSR method were performed by using horizontal electrophoresis in 2% agarose gel. Alleles and their sizes were determined by using vertical electrophoresis in 6% polyacrylamide gel and silver nitrate staining method. Gel images were recorded by gel documentarian, the bands were scored by using Photo- Capt software and statistical analysis was performed by using Gene Alex and Pop Gene software. Also the PCR sequencing products after quality assessment by usinghorizontal electrophoresis in 1.5% agarose gel were purified and sent to South Korea Bioneer Corporation for sequencing. Sequencing was performed by chain termination method and the statistical analysis was performed by using Bio- Edit, Mega, Arlequin and DNA SP software. The SSR method, 5 pairs of primers produced polymorphic bands and the average real and effective number of alleles were calculated 5.60±1.83 and 3.87±1.46 in the Cheshmeh Kileh river and 7.60±1.75 and 5.48±1.32 in the Karganrud river and the mean observed and expected heterozygosity were calculated 0.44 ±0.15 and 0.52 ±0.16 in the Cheshmeh Kileh river and 0.50 ±0.11 and 0.70±0.13 in the Karganrud river. Analysis of Molecular Variance results showed that significant differences in genetic diversity between and within populations and between and within individuals in the studied rivers (P<0.01). The sequencing method identified 35 different haplotype, the highest number of polymorphic position (251) and haplotype (14) were observed in the Chalus river. The highest mean observed number of alleles (2.24±0.48) was calculated in the Sardabrud river, the highest mean observed heterozygosity (1.00±0.03) was calculated in the Chalus river and the highest mean nucleotide diversity (0.13±0.07) was observed in the Sardabrud river and mean haplotype diversity was obtained (1) in three studied rivers. The overall results show that there are no same population of this fish in the studied rivers and Karganrud and Chalus rivers in the SSR and sequencing methods had the highest levels of genetic diversity.

The genetic diversity of Acipenser stellatus populations in the Caspian Sea was studied using microsatellite technique

A total of 361 caudal fin samples were collected from adult A. stellatus specimens caught in the north Caspian Sea, including specimens from Kazakhstan (Ural River), Russia (Volga River), Azerbaijan (Kura River), specimens caught in the south Caspian Sea including specimens from Fishery Zone 1 (from Astara to Anzali), Fishery Zone 2 (from Anzali to Ramsar), Fishery Zone 3 (from Nowshahr to Babolsar), Fishery Zone 4 (from Miyankaleh to Gomishan) as well as from specimens caught in Turkmenistan (all specimens were collected during the sturgeon stock assessment survey). About 2 g of fin tissue was removed from each caudal fin sample, stored in 96% ethyl alcohol and transferred to the genetic laboratory of the International Sturgeon Research Institute. Genomic DNA was extracted using phenol-chloroform method. The quality and quantity of DNA was assessed using 1% Agarose gel electrophoresis and Polymerase Chain Reaction (PCR) was conducted on the target DNA using 15 paired microsatellite primer. PCR products were electrophoresed on polyacrylamide gels (6%) that were stained using silver nitrate. Electrophoretic patterns and DNA bands were analyzed with BioCapt software. Allele count and frequency, genetic diversity, expected heterozygosity and observed heterozygosity allele number, and the effective allele number, genetic similarity and genetic distance, FST and RST were calculated. The Hardy Wienberg Equilibrium based on X2 and Analysis of Molecular Variance (AMOVA) at 10% confidence level was calculated using the Gene Alex software. Dendrogram for genetic distances and identities were calculated using TFPGA program for any level of the hierarchy. It is evident from the results obtained that the 15 paired primers studied, polymorphism was observed in 10 pairs in 12 loci, while one locus did not produce DNA bands. Mean allele number was 13.6. Mean observed and expected heterozygosity was 0.86 and 0.642, respectively. It was also seen that specimens from all regions were not in Hardy Wienberg Equilibrium in most of the loci (P≤0.001). Highest Fst (0.063) was observed when comparing specimens from Fishery Zone 2 and Fishery Zone 4 (Nm=3.7) and lowest FST (0.028) was observed when comparing specimens from the Volga River and those from the Ural River (8.7). Significant differences (P<0.01) were observed between RST recorded in the specimens studied. Highest genetic distance (0.604) and lowest genetic resemblance (0.547) were observed between specimens from Fishery zones 2 and 4. Lowest genetic distance (0.311) and highest genetic resemblance (0.733) was observed between specimens from Turkmenistan and specimens from Fishery zone 1. Based on the genetic dendrogeram tree derived by applying UPGMA algorithm, A. stellatus specimens from Fishery zone 2 or in other words specimens from the Sepidrud River belong to one cluster which divides into two clusters, one of which includes specimens from Fishery zones 1, 3 and 4 and specimens from Turkmenistan while the other cluster includes specimens from Ural, Volga and Kura Rivers. It is thus evident that the main population of this species belongs to the Sepidrud River. Results obtained from the present study show that at least eight different populations of A. stellatus are found in the north and south Caspian Sea, four of which are known populations including the Ural River population, the Volga River population, the Kura River population and the Sepidrud River populations. The four other populations identified belonging to Fishery zones 1, 3, and 4 and to Turkmenistan are most probably late or early spawners of the spring run and autumn run of each of the major rivers mentioned. Specific markers were also identified for each of the populations identified. The Ural River population can be identified using primers Spl-68, 54b and Spl-104, 163 170, 173, the Volga River population can be identified using primers LS-54b and Spl-104, 170, 173 113a and similarly the population from the Kura River can be identified using primers LS-34, 54b and Spl-163, 173 and that from the Sepidrud River can be identified using primers LS-19, 34, 54b and Spl-105, 113b. This study gives evidence of the presence of different populations of this species and calls for serious measures to be taken to protect the genetic stocks of these populations. Considering that the population of A. stellatus in Fishery zone 2 is an independent population of the Sepidrud River in the Gilan Province, the catch of these fishes in the region needs to be controlled and regulated in order to restore the declining stocks of this species.

Genetic viability of Nabugabo lakes (LVR satellite lakes) fish species

Natural populations of fish species in Lake Victoria Region (LVR) have under gone dramatic changes including severe reduction in sizes, division of original stocks into disjunct subunits, and segregation into several isolated population units either within a single water body or even worse into separate waters. In addition, these changes have been either preceded or precipitated by introductions of non-indigenous species that out competed the native forms and in case of closely related species genetically swamped them through hybridisation. The latter is especially the case in Nabugabo lakes. Such events lead to fragmentation of populations, which results in reduction in genetic diversity due to genetic drift, inbreeding and reduced or lack of gene flow among independent units. Such phenomena make the continued existence of fisheries stocks in the wild precarious, more so in the face of the competition from exotic species. Species introductions coupled with growing exploitation pressure of the fisheries of these lakes have put the native stocks at risk. Nabugabo lakes harbor cichlid species that are unique to these lakes more so species of the cichlid complex. In this paper the ecological status and genetic viability of key Nabugabo lakes fish species is examined and management options are discussed.

Report of the Indian Mackerel Working Group Meeting, Colombo, Sri Lanka, 28-29 May, 2012

Stock structure approaches and consequences of management in the eight member countries. Indian mackerel (Rastrelliger kanagurta) genetic stock studies and workplan