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.

Population genetic structure of Neogobius caspius (Eichwald ,1831) in the South Caspian Sea using PCR-RFLP Marker

Neogobius caspius is a small benthic fish that is native to the Caspian Sea. The importance of this fish is because of it is role as a main food resource of the sturgeon fish. The genetic diversity of N. caspius population in the Caspian Sea was studied using PCR- RFLP technique. A total of 135 samples of N. caspius were collected from coastal line in the north Caspian sea, including specimens from coasts of Anzali , Torkman Port and Chalus. Genomic DNA was extracted by phenol-chloroform method and then was amplified using a pair primer of cytochrom b gene, 2 tRNA gene and the control region sequences by a thermal cycler. D2 (5'-CCGGAGTATGTAGGGCATTCTCAC-3'), CY1 (5'-YYTAACCRRGACYAATGACTTGA-3') 12 restriction enzyme were used to digest the target gene region including: Alul HincII —Tas1 —Rsa1 -MboI -DraI -BSeNI(BSRI) Alw261(BsmAI). Bsul 51 Hin11 Bsh12851- BsuRI(HaeIII) digested PCR products were observed by silver staining method followed by Polyacrylamide gel electrophoresis (PAGE). The results were shown the same pattern among the species. There was no polymorphism and no differentiation in population in the Neogobius caspius fish and all individuals have shown homogenous genotype.

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.)

Lessons from established breeding programs: terrestrial and aquatic animals

Some relevant components of selection program theory and implementation are reviewed. This includes pedigree recording, genetic evaluation, balancing genetic gains and genetic diversity and tactical integration of key issues. Lessons learned are briefly described – illustrating how existing method and tools can be useful when launching a program in a novel species, and yet highlighting the importance of proper understanding and custom application according to the biology and environments of that species.

Panama City Fisheries Resources Office: FY 2009 Annual Report

HIGHLIGHTS FOR FY 2009 1. Completed the second of a two-year Gulf sturgeon population study on the Choctawhatchee River, Florida. The juvenile, sub adult and adult Gulf sturgeon population was estimated at 3,400 fish. 2. Three young of year Gulf sturgeon were collected by Corps of Engineers biologists in the upper Brothers Rivers. 3. Two YCC enrollees spent eight weeks assisting PCFO biologists and Tyndall AFB with various projects. 4. The Gulf Sturgeon 5-Year Summary and Evaluation was completed. 5. Karen Herrington co-authored a peer-reviewed journal article for a striped bass symposium at the annual American Fisheries Society meeting, which will be published in the symposium proceedings. The article reviews the past 25 years of striped bass restoration in the ACF and is titled “Restoration of Gulf Striped Bass: Lessons and Management Implications”. 6. We documented recent purple bankclimber recruitment in the Ochlockonee River for the first time in several years. 7. We provided over 200 genetic samples to Warm Springs Fish Technology Center to compare mussel populations and genetic diversity, rank populations by status, and facilitate recovery actions. 8. We established permanent mussel monitoring locations in Sawhatchee Creek and the Flint River to examine trends in population size, survival, and recruitment. 9. We provided a prioritized list to the Federal Emergency Management Agency of 197 stream crossings that occur near freshwater mussel populations in order to facilitate habitat restoration following major flooding in Alabama, Florida, and Georgia in the spring of 2009.

The impact of molecular biology on assessment of water quality: advantages and limitations of current techniques

The advent of molecular biology has had a dramatic impact on all aspects of biology, not least applied microbial ecology. Microbiological testing of water has traditionally depended largely on culture techniques. Growing understanding that only a small proportion of microbial species are culturable, and that many microorganisms may attain a viable but non-culturable state, has promoted the development of novel approaches to monitoring pathogens in the environment. This has been paralleled by an increased awareness of the surprising genetic diversity of natural microbial populations. By targeting gene sequences that are specific for particular microorganisms, for example genes that encode diagnostic enzymes, or species-specific domains of conserved genes such as 16S ribosomal RNA coding sequences (rrn genes), the problems of culture can be avoided. Technical developments, notably in the area of in vitro amplification of DNA using the polymerase chain reaction (PCR), now permit routine detection and identification of specific microorganisms, even when present in very low numbers. Although the techniques of molecular biology have provided some very powerful tools for environmental microbiology, it should not be forgotten that these have their own drawbacks and biases in sampling. For example, molecular techniques are dependent on efficient lysis and recovery of nucleic acids from both vegetative forms and spores of microbial species that may differ radically when growing in the laboratory compared with the natural environment. Furthermore, PCR amplification can introduce its own bias depending on the nature of the oligonucleotide primers utilised. However, despite these potential caveats, it seems likely that a molecular biological approach, particularly with its potential for automation, will provide the mainstay of diagnostic technology for the foreseeable future.

Population structure of pink salmon (Oncorhynchus gorbuscha) in British Columbia and Washington, determined with microsatellites

Population structure of pink salmon (Oncorhynchus gorbuscha) from British Columbia and Washington was examined with a survey of microsatellite variation to describe the distribution of genetic variation. Variation at 16 microsatellite loci was surveyed for approximately 46,500 pink salmon sampled from 146 locations in the odd-year broodline and from 116 locations in the even-year broodline. An index of genetic differentiation, FST, over all populations and loci in the odd-year broodline was 0.005, with individual locus values ranging from 0.002 to 0.025. Population differentiation was less in the even-year broodline, with a FST value of 0.002 over all loci, and with individual locus values ranging from 0.001 to 0.005. Greater genetic diversity was observed in the odd-year broodline. Differentiation in pink salmon allele frequencies between broodlines was approximately 5.5 times greater than regional differentiation within broodlines. A regional structuring of populations was the general pattern observed, and a greater regional structure in the odd-year broodline than in the even-year broodline. The geographic distribution of microsatellite variation in populations of pink salmon likely ref lects a distribution of broodlines from separate refuges after the last glaciation period.

Pacific Salmon, Oncorhynchus spp., and the Definition of "Species" Under the Endangered Species Act

For purposes ofthe Endangered Species Act (ESA), a "species" is defined to include "any distinct population segment of any species of vertebrate fish or wildlife which interbreeds when mature. "Federal agencies charged with carrying out the provisions of the ESA have struggled for over a decade to develop a consistent approach for interpreting the term "distinct population segment." This paper outlines such an approach and explains in some detail how it can be applied to ESA evaluations of anadromous Pacific salmonids. The following definition is proposed: A population (or group of populations) will be considered "distinct" (and hence a "species ")for purposes of the ESA if it represents an evolutionarily significant unit (ESU) of the biological species. A population must satisfy two criteria to be considered an ESU: 1) It must be substantially reproductively isolated from other conspecific population units, and 2) It must represent an important component in the evolutionary legacy of the species. Isolation does not have to be absolute, but it must be strong enough to permit evolutionarily important differences to accrue in different population units. The second criterion would be met if the population contributes substantially to the ecological/genetic diversity of the species as a whole. Insights into the extent of reproductive isolation can be provided by movements of tagged fish, natural recolonization rates observed in other populations, measurements of genetic differences between populations, and evaluations of the efficacy of natural barriers. Each of these methods has its limitations. Identification of physical barriers to genetic exchange can help define the geographic extent of distinct populations, but reliance on physical features alone can be misleading in the absence of supporting biological information. Physical tags provide information about the movements of individual fish but not the genetic consequences of migration. Furthermore, measurements ofc urrent straying or recolonization rates provide no direct information about the magnitude or consistency of such rates in the past. In this respect, data from protein electrophoresis or DNA analyses can be very useful because they reflect levels of gene flow that have occurred over evolutionary time scales. The best strategy is to use all available lines of evidence for or against reproductive isolation, recognizing the limitations of each and taking advantage of the often complementary nature of the different types of information. If available evidence indicates significant reproductive isolation, the next step is to determine whether the population in question is of substantial ecological/genetic importance to the species as a whole. In other words, if the population became extinct, would this event represent a significant loss to the ecological/genetic diversity of thes pecies? In making this determination, the following questions are relevant: 1) Is the population genetically distinct from other conspecific populations? 2) Does the population occupy unusual or distinctive habitat? 3) Does the population show evidence of unusual or distinctive adaptation to its environment? Several types of information are useful in addressing these questions. Again, the strengths and limitations of each should be kept in mind in making the evaluation. Phenotypic/life-history traits such as size, fecundity, and age and time of spawning may reflect local adaptations of evolutionary importance, but interpretation of these traits is complicated by their sensitivity to environmental conditions. Data from protein electrophoresis or DNA analyses provide valuable insight into theprocessofgenetic differentiation among populations but little direct information regarding the extent of adaptive genetic differences. Habitat differences suggest the possibility for local adaptations but do not prove that such adaptations exist. The framework suggested here provides a focal point for accomplishing the majorgoal of the Act-to conserve the genetic diversity of species and the ecosystems they inhabit. At the same time, it allows discretion in the listing of populations by requiring that they represent units of real evolutionary significance to the species. Further, this framework provides a means of addressing several issues of particular concern for Pacific salmon, including anadromous/nonanadromous population segments, differences in run-timing, groups of populations, introduced populations, and the role of hatchery fish.

Investigation of polymorphism by PCR-RFLP method in Cobia fish Rachycentron canadum in the Persian Gulf and Oman Sea

Cobia is a native fish species in Iranian waters in the Persian Gulf and Sea of Oman and has a good internal and foreign market. This fish is a fast growing species and for this reason Iranian Fisheries is considering to go for it culture practices. To go for any utilization such as fishing from wild stocks or culture activities, needs a better understanding of its peculiarities and genetic characteristics of its natural resources. Therefore, this project was discribed and conducted. In this investigation, cuts 2 or 3 cm of fin tissue of  specimen of Cobia obtained from Sistan and Bluchestan, Hormozgan, Bushehr and Khuzestan water provinces, were collected. DNA was extracted by Phenol-chlorophorm method and produced PCR product in length of 1060 and 1450 base pair of two mitochondrial genes COI and NADH2. Using 13 cutting enzymes (4 enzymes were subscriber for both of genes), 205 base pair (from 2510 base pair, equal with %3.8 from gene regains) were directly investigated. But binding patterns of enzymatic digestion of PCR products of both COI and ND genes from electrophoresis were monomorph in all samples and no polymorphism was observed. This may be attributed to the unsuitable choice of COI and ND2 genes for showing of intra specific divergence. But in general non-existence of genetic diversity or noticeable decrease of that among individuals has been reported in regions were fish migration exist and they can freely move between two regions. Therefore, non-observation of polymorphism in the study area might be the case and indicates represents the area. On the other hand, some scientists believe that the distributions of populations in different regions are greatly affected by environmental and physical and ecological factors. Althoug Cobia is a migratory fish, but with regard to the fact that the environmental conditions are different (specially temperature and salinity) between east and west of Persian Gulf and Oman sea, there is a possibility that different genetic groups of this species exist in the regions. Of course It is clear that using more samples and enzymes from other genetically regions could produce better results. Since none of the two investigated genes didn’t show genetic divergence or polymorphism amongst the individuals of one region or between different regions, therefore, statistic analysis for estimating of haplotype diversity or nucleotide diversity and drawing of relationship tree among individuals using available softwares was not possible.