Dividing population genetic distance data with the software Partitioning Optimization with Restricted Growth Strings (PORGS): an application for Chinook salmon (Oncorhynchus tshawytscha), Vancouver Island, British Columbia

A new method of finding the optimal group membership and number of groupings to partition population genetic distance data is presented. The software program Partitioning Optimization with Restricted Growth Strings (PORGS), visits all possible set partitions and deems acceptable partitions to be those that reduce mean intracluster distance. The optimal number of groups is determined with the gap statistic which compares PORGS results with a reference distribution. The PORGS method was validated by a simulated data set with a known distribution. For efficiency, where values of n were larger, restricted growth strings (RGS) were used to bipartition populations during a nested search (bi-PORGS). Bi-PORGS was applied to a set of genetic data from 18 Chinook salmon (Oncorhynchus tshawytscha) populations from the west coast of Vancouver Island. The optimal grouping of these populations corresponded to four geographic locations: 1) Quatsino Sound, 2) Nootka Sound, 3) Clayoquot +Barkley sounds, and 4) southwest Vancouver Island. However, assignment of populations to groups did not strictly reflect the geographical divisions; fish of Barkley Sound origin that had strayed into the Gold River and close genetic similarity between transferred and donor populations meant groupings crossed geographic boundaries. Overall, stock structure determined by this partitioning method was similar to that determined by the unweighted pair-group method with arithmetic averages (UPGMA), an agglomerative clustering algorithm.

Microsatellite multiplex panels for genetic studies of gray snapper (Lutjanus griseus) and lane snapper (Lutjanus synagris)

Microsatellites are codominantly inherited nuclear-DNA markers (Wright and Bentzen, 1994) that are now commonly used to assess both stock structure and the effective population size of exploited fishes (Turner et al., 2002; Chistiakov et al., 2006; Saillant and Gold, 2006). Multiplexing is the combination of polymerase chain reaction (PCR) amplification products from multiple loci into a single lane of an electrophoretic gel (Olsen et al., 1996; Neff et al., 2000) and is accomplished either by coamplification of multiple loci in a single reaction (Chamberlain et al., 1988) or by combination of products from multiple single-locus PCR amplifications (Olsen et al., 1996). The advantage of multiplexing micro-satellites lies in the significant reduction in both personnel time (labor) and consumable supplies generally required for large genotyping projects (Neff et al., 2000; Renshaw et al., 2006).

Genetic variability in spotted seatrout (Cynoscion nebulosus), determined with microsatellite DNA markers

Variation in the allele frequencies of five microsatellite loci was surveyed in 1256 individual spotted seatrout (Cynoscion nebulosus) obtained from 12 bays and estuaries from Laguna Madre, Texas, to Charlotte Harbor, Florida, to St. John’s River on the Florida Atlantic Coast. Texas and Louisiana collection sites were resampled each year for two to four years (1998−2001). Genetic differentiation was observed. Spotted seatrout from Florida waters were strongly differentiated from spotted seatrout collected in Louisiana and Texas. The greatest genetic discontinuity was observed between Tampa Bay and Charlotte Harbor, and Charlotte Harbor seatrout were most similar to Atlantic Coast spotted seatrout. Texas and Louisiana samples were not strongly structured within the northwestern Gulf of Mexico and there was little evidence of temporal differentiation within bays. These findings are contrary to those of earlier analyses with allozymes and mitochondrial DNA (mtDNA) where evidence of spatial differentiation was found for spotted seatrout resident on the Texas coast. The differences in genetic structure observed among these markers may reflect differences in response to selective pressure, or may be due to differences in underlying genetic processes.

Use of genetic data to assess the uncertainty in stock assessments due to the assumed stock structure: the case of albacore (Thunnus alalunga) from the Atlantic Ocean

Stock assessments can be problematic because of uncertainties associated with the data or because of simplified assumptions made when modeling biological processes (Rosenberg and Restrepo, 1995). For example, the common assumption in stock assessments that stocks are homogeneous and discrete (i.e., there is no migration between the stocks) is not necessarily true (Kell et al., 2004a, 2004b).

Genetic analysis of immunological traits in tilapia

The immunological response to handling stress of four tilapia species is evaluated.Polymorphism is examined in genes known to influence immune response in fish.

Problems for the conservation of freshwater fish genetic resources in India and some possible solutions

Many interconnected problems involved for the conservation of freshwater fish genetic resources of India are enumerated. Some possible solutions to the problems are also discussed.

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.

Genetic improvement of the herbivorous blunt snout bream (Megalobrama amblycephala)

Selection experiments with the herbivorous blunt snout bream or Wuchang bream (Megalobrama amblycephala) were started in 1985. Mass selection for size and length/depth ratio resulted in a significant increase in growth and better shape, while inbreeding led to a significant decrease in growth. The total selection ratio from fry to mature brooders was about 0.03 per cent per generation. In the grow out stage, the average daily body weight gains of two lines of fifth generation (F5) fish were 29 per cent and 20 per cent respectively more than the control group, with an average of 5.8 per cent and 4 per cent improvements per generation, respectively. The body was 4 per cent deeper in ratio of standard length/body depth. The effects of inbreeding were examined by crossing full-sibs, the offspring of which were kept without selection. The third generation inbred fish showed 17 per cent lower growth as compared to the control group, with an average of 7.5 per cent per generation. The results demonstrate that selection is a powerful tool to improve the economic traits of the blunt snout bream, but inbreeding can rapidly lead to a reduction in performance. In 2000, the 6th generation of selected bream was certified by the Chinese Ministry of Agriculture as a good breed for aquaculture.

Genetic diversity and selective breeding of red common carps in China

China has a very rich genetic diversity in common carp (Cyprinus carpio) and the red common carp plays an important role in Chinese aquaculture and genetic studies. Selective breeding, particularly crossbreeding has been applied successfully to red common carps in China, and the products of these efforts have been in commercial use since the 1970s. However, knowledge of the quantitative and molecular genetics of these carps is limited. Studies were therefore undertaken to: (1) understand the genetic diversity and genetic relationship of red common carps in China; (2) understand the inheritance of color phenotype of Oujiang color carp; (3) select stable Oujiang color carp with fast growth rate and ornamental Oujiang color carp comparable with the Koi common carp from Japan; (4) study the culture performance and culture systems suitable for the Oujiang color carp in cages and paddies; (5) extend better quality fish and appropriate culture systems for small scale fish farmers in poor areas.

Genetic diversity in wild stocks of the giant freshwater prawn (Macrobrachium rosenbergii): implications for aquaculture and conservation

The giant freshwater prawn (Macrobrachium rosenbergii) is cultured widely around the world but little is known about the levels and patterns of genetic diversity in either wild or cultured stocks. Studies have suggested that genetic diversity may be relatively low in some cultured stocks due to the history of how they were founded and subsequent exposure to repeated population bottlenecks in hatcheries. In contrast, wild stocks have an extensive distribution that extends from Southern Asia across Southeast (SE) Asia to the Pacific region. Therefore, wild stocks could be an important resource for genetic improvement of culture stocks in the future. Understanding the extent and patterns of genetic diversity in wild giant freshwater prawn stocks will assist decisions about the direction future breeding programs may take. Wild stock genetic diversity was examined using a 472 base-pair segment of the 16S rRNA gene in 18 wild populations collected from across the natural range of the species. Two major clades ("eastern" and "western") were identifi ed either side of Huxley’s line, with a minimum divergence of 6.2 per cent, which implies separation since the Miocene period (5-10 MYA). While divergence estimates within major clades was small (maximum 0.9 per cent), evidence was also found for population structuring at a lower spatial scale. This will be examined more intensively with a faster evolving mtDNA gene in the future.

Baseline biochemical and genetic profiles of four fishes from the River Nile

Six enzyme systems coding for 10 loci and 6 proteins were examined in the blood of Polypterus senegalus, Clarias lazera, Tilapia nilotica and Protopterus annectens, using electrophoresis. Six loci were polymorphic in all the four species, three polymorphic in three species and one polymorphic in T. nilotica. Four protein loci were monomorphic in all the four species with variants in P. senegalus and T. nilotica. Haemoglobin can be used as a species-specific marker. Polymorphism was 53-56 per cent and average heterozygosity was 0.1-0.15.

Marine fisheries, genetic effects and biodiversity

Preservation of marine biodiversity deserves serious consideration as almost 65% of the earth's organisms (excluding insects) are marine. There is little knowledge at present on the status of marine biodiversity. However, the seas are an important source of protein for human consumption and genetic diversity is a key factor in ecosystem functioning, stability and resilience. Overfishing and destructive practices may have unalterable impact on marine biodiversity. This paper discusses measures that can be adopted to protect the most productive areas of the marine ecosystem.

Down to earth thoughts on conserving aquatic genetic diversity

A discussion is presented on the topic of maintaining genetic diversity in aquatic ecosystems, considering the various threats caused by irreversible damage or loss to the environment. The current situation in aquaculture and future prospects regarding the conservation and protection of endangered species are outlined, describing the case of tilapias in Africa as one particular example of fish conservation.

Genetic variation of rougheye rockfish (Sebastes aleutianus) and shortraker rockfish (S. borealis) inferred from allozymes

Rougheye rockfish (Sebastes aleutianus) and shortraker rockfish (Sebastes borealis) were collected from the Washington coast, the Gulf of Alaska, the southern Bering Sea, and the eastern Kamchatka coast of Russia (areas encompassing most of their geographic distribution) for population genetic analyses. Using starch gel electrophoresis, we analyzed 1027 rougheye rockfish and 615 shortraker rockfish for variation at 29 proteincoding loci. No genetic heterogeneity was found among shortraker rockfish throughout the sampled regions, although shortraker in the Aleutian Islands region, captured at deeper depths, were found to be significantly smaller in size than the shortraker caught in shallower waters from Southeast Alaska. Genetic analysis of the rougheye rockfish revealed two evolutionary lineages that exist in sympatry with little or no gene f low between them. When analyzed as two distinct species, neither lineage exhibited heterogeneity among regions. Sebastes aleutianus seems to inhabit waters throughout the Gulf of Alaska and more southern waters, whereas S. sp. cf. aleutianus inhabits waters throughout the Gulf of Alaska, Aleutian Islands, and Asia. The distribution of the two rougheye rockfish lineages may be related to depth where they are sympatric. The paler color morph, S. aleutianus, is found more abundantly in shallower waters and the darker color morph, Sebastes sp. cf. aleutianus, inhabits deeper waters. Sebastes sp. cf. aleutianus, also exhibited a significantly higher prevalence of two parasites, N. robusta and T. trituba, than did Sebastes aleutianus, in the 2001 samples, indicating a possible difference in habitat and (or) resource use between the two lineages.