These aquaculture- and conservation-oriented commentaries are not abstracts written by the original authors.  They reflect the opinions of someone else -- usually Roger Doyle.  Direct quotations from the papers or abstracts are marked with inverted commas.

85. US Patent application for the first Frankenfish -- a salmon
FDA, researchers consider first transgenic fish. 2000. Anonymous. Nature Biotechnology 18:143.
        The US Food and Drug Administration is now evaluating a patent application from A/F Protein for transgenic salmon -- apparently the first transgenic fish to be patented in the US if the application succeeds.  The A/FP technique is to attach the salmon growth hormone DNA sequence to a foreign promoter sequence (from the ocean pout) which causes the gene to produce growth hormone in the liver.  Unlike the normal gene which is expressed in the pituitary, the transgene is continuously switched on by its promoter.  The salmon reach a size of 8 pounds in 1.5 years.  The article briefly and fairly reviews a number of recent studies on the possible ecological risks of transgenic fish including the so-called "Trojan gene" identified in Medaka.  The article acknowledges that medaka are not salmon and that the transgenic salmon are sterilized by triploidization.  It also notes that sterilization is not 100% effective.....  As Maureen Dowd said, "I have seen the future, and it is backing out of the room".  [No e-mail address available]

84. Genetics may explain why shrimp diseases are spreading as stocks recover
Evolutionary dynamics of pathogen resistance and tolerance. 2000. Roy, B.A., and J.W. Kirchner. Evolution 154:51-63.
        The authors of this mainly theoretical paper discuss the evolution of disease resistance (defense mechanisms which block infection, kill the pathogen or limit its spread within the host) and disease tolerance (ability to survive despite being infected).  The selective advantage of resistant host individuals becomes less as they become more numerous, because the incidence of disease declines and selection intensity decreases in a negative feed-back loop.  Therefore, "... genes conferring complete resistance cannot become fixed (i.e., universal) by selection in a host population, and diseases cannot be eliminated solely by natural selection for host resistance."  Disease resistance -- including the immune response -- is predicted always to be variable and incomplete.  This is because the extra physiological costs of resistance genes in the host causes them to be selected against in regions where the disease challenge is rare.
        Disease tolerance is a different story.  As more host individuals become tolerant the incidence of disease increases, thus increasing the selective advantage of the tolerance gene.  Tolerance genes in the host increase the fitness of the host and the pathogen as well in a positive feedback loop.  Tolerance genes should rapidly evolve to a frequency of 100% and the disease should become universally present.
        The point for aquaculture is that the evolution of host resistance causes the prevalence of a pathogen to decrease while tolerance causes it to increase.  Does this prediction allow us to guess what is happening during the successive waves of diseases in shrimp aquaculture?  Anecdotal evidence may suggest that tolerance, rather than resistance is evolving in shrimp aquacultural systems, and that diseases are becoming more prevalent while shrimp production recovers in infected regions.  The usual explanations for the spread of shrimp disease -- human greed, criminality & fear, etc. -- explain the spread but not the correlation.  The time scale is right for evolution especially if the underlying genetic mechanisms involve dominant or co-dominant genes.  Does anyone know what the possible tolerance mechanisms in shrimp might be?
        Incidentally, the pathogen also evolves, so the shrimp and the disease are in what is called a "coevolutionary arms race".  More about this in the August posting.  The conclusion is that tolerance, but not resistance, is an evolutionary stable defense strategy and may also be the best tactic for aquaculture geneticists. roy@geobot.umnw.ethz.ch .

83. Atlantic salmon sneak into paradise
Evidence of natural reproduction of aquaculture-escaped Atlantic salmon in a coastal British Columbia river. 2000. Volpe, J.P., E.B. Taylor, D.W. Rimmer, and B.W. Glickman. Conservation Biology 14:889-903.
        The authors captured 12 juvenile salmon which they identified as Atlantics in the Tsitika River, British Columbia.  Species identity was confirmed by analysis of rDNA and mtDNA. Morphological characteristics and condition lead the authors to believe that juveniles were the offspring of escaped farm salmon and were themselves successfully maturing.  This is the first direct evidence that self-sustaining Salmo salar populations may be developing in BC, with many possible negative implications for the survival of the effete native salmonids. jvolpe@uvic.ca

82. More competition problems for inbred males
A comparative study of ejaculate traits in three endangered ungulates with different levels of inbreeding: fluctuating asymmetry as an indicator of reproductive and genetic stress. 2000. Gomendio, M., J. Cassinello, and E.R.S. Roldan. Proceedings Royal Society Ser. B. 267:875-882.
        Within populations of three species of endangered gazelles the individual coefficient of inbreeding is correlated with ejaculate quality only when the overall level of inbreeding is high.  However fluctuating asymmetry (FA, see June list #70) is correlated with inbreeding in all populations.  "Thus, FA appears in individuals whose levels of inbreeding are still not high enough to affect male reproductive potential and should therefore be considered a sensitive indicator of genetic stress. ... Finally, FA is also a reliable indicator of male reproductive stress since it is related to individual semen quality in all the species studied".  [FA is easy to measure in shrimp and fish.  It may also be of practical interest to aquaculturists that recent studies of what human beings find attractive in the opposite sex can be summarized in one word: "symmetry".]  mcnc125@mncn.csic.es .

81. Frankensalmon have more muscle cells and need more air
Coho salmon (Oncorhynchus kisutch) transgenic for a growth hormone gene construct exhibit increased rates of muscle hyperplasia and detectable levels of differential gene expression. 2000. Hill, J.A., A. Kiessling, and R.H. Devlin. Can. J. Fish Aquat. Sci. 57:939-950.
        The authors studied a variety of traits in coho salmon (Oncorhynchus kisutch) which were made transgenic (as heterozygotes) for growth hormone. "Transgenic fish were found to have significantly higher numbers of small-diameter muscle fibres [In somite muscles.  The alternative possibility is to have larger fibres.]. ... Higher levels of activity were found for phosphofructokinase and cytochrome oxidase in white muscle of the transgenic fish.  This difference indicates a higher glycolytic and aerobic requirement in the muscle of transgenic fish."  An unusual and progressive aspect of this study was the use of subtractive RNA hybridization to identify other genes that are being switched on in rapidly growing transgenic fish.
        Sure enough, the authors found (after constructing the differential cDNA library and amplifying and sequencing some of the cloned fragments) that many of the additional messenger RNAs in the transgenic fish were specifying myosin, consistent with " high level of expression in the early stages of muscle fibre construction."
          [in the Journal of Fish Biology Vol. 56, pp. 191-195. 2000. E. D. Stevens, & R. H. Devlin. report that the two-fold increase in growth rate of transgenic coho was paralleled by a two-fold increase in the surface area of the intestine.]  devlinr@pac.dfo-mpo.gc.ca .

80. Microsatellite mutation models used by population geneticists are probably OK
A phylogenetic perspective on sequence evolution in microsatellite loci.2000. Zhu, Y., D.C. Queller, and J.E. Strassmann. Journal of Molecular Evolution 50:324-338.
        The authors studied 140 million years of evolution of microsatellite repeat regions in a 158-species subfamily of wasps.  They found that the number of repeats evolved more rapidly than other features such as "imperfections" but that imperfections are phylogenetically informative. "Overall, phylogenetic variation in repeat regions can be explained by adding neutral evolution to what is already known about the mutation process.  The life cycle of microsatellites appears to reflect a balance between growth by slippage and degradation by an essentially irreversible accumulation of imperfections."
        This paper will be of interest to people who use measures of genetic differentiation in their work on fisheries population genetics and conservation genetics.  Many such measures, including Rst and some procedures used to detect bottlenecks, outbreeding and introgression are dependent on assumptions concerning the underlying mutational process in microsatellite repeat polymorphisms.  This paper on the whole supports the validity of these assumptions. strassm@rice.edu .

79. Sneaky parr help genetic conservation
Multiple paternity increases effective size of southern Atlantic salmon populations. 2000. Martinez, J.L., P. Moran, J. Perez, B. De Gaudemar, E. Beall, and E. Garcia-Vazquez. Molecular Ecology 9:293-298.
        This parentage-determination study was done on small, endangered Atlantic salmon populations in rivers running into the Bay of Biscay.  A large proportion of the broods sampled in the redds had been fertilized by more than one precociously mature parr.  The authors show that "multiple paternity derived from mature parr is crucial for the conservation of genetic variability in small populations of Atlantic salmon. egv@sauron.quimica.uniovi.es .

78. New procedures for estimating hybridization and gene flow
Estimating multilocus linkage disequilibria. 2000. Barton, N.H. Heredity 84:373-389.
        When loci are situated close together on the same chromosome, the frequencies of the genotypes will, in populations that are less than infinitely large and infinitely old, often be non-random.  (That is, they will not occur in the frequencies predicted by simple multivariate combination of the component allele frequencies.)  This linkage disequilibrium occurs because of the physical connection between alleles at different loci on one long strand of DNA.  Statistical information concerning the joint distributions of physically linked alleles is very useful for mapping loci on chromosomes when the genotypes originate from a specific cross or hybridisation.
        Even when loci are located on different chromosomes, or are so far apart that the DNA strand connecting them is effectively broken and randomized during replication, linkage disequilibrium will still often be observed in real populations.  In this case the statistical disequilibrium ("non-randomness") carries information about the mixing of genetically different populations, or non-random mating among individuals, or drastic changes in population size, or other phenomena that are of great practical interest both in aquaculture and genetic conservation.  The question is how to develop a meaningful story out of the frequency data.
        A number of different approaches which have been used in the past are reviewed in this paper.  Barton is here particularly concerned with hybrid and mixed populations.  His work extends previous work by providing a framework for analysing data from several loci at a time and for using "non-diagnostic" loci -- that is, loci at which all populations carry all the alleles, but at different frequencies.
        Biologists who have taken less than an infinite level of indefinitely well-taught statistics classes may find this interesting paper hard sledding.  Nonetheless, it " ... sets out methods for estimating multilocus genotype frequencies which are appropriate for unlinked neutral loci, and for populations that are ultimately derived by mixing of two source populations. ...Two methods ...are described: a simple method based on multivariate moments [variance, skewness etc.], and a maximum likelihood procedure, which uses the Metropolis algorithm. Both methods perform well when tested against simulations with two or four loci. ... "
        The procedures "can be used to infer quantities such as rates of gene flow and degree of assortative mating. ... [and] likelihood that offspring were sired by sampled individuals of known genotype, rather than by some father from the unsampled population.  These methods make possible a variety of statistical analyses of hybrid populations"  n.barton@ed.ac.uk .

77. Genetic signal traces the progressive development of WSSV in individual shrimp
Long-term presence of white spot syndrome virus (WSSV) in a cultivated shrimp population without disease outbreaks. 1999. Tsai, M.F., G.H. Kou, H.C. Liu, K.F. Liu, C.F. Chang, S.E. Peng, H.C. Hsu, C.H. Wang, and C.F. Lo. Diseases of Aquatic Organisms 38:107-114.
        Polymerase Chain Reaction (PCR) is a procedure for amplifying DNA (in this case associated with WSSV) until there is enough to work with.  When the initial quantity of target (template) DNA is very small PCR amplification may have to be done in several stages, each of which involves many rounds of self-catalyzing amplification.
        The shrimp PLs in this experiment came from a single WSSV-carrying brooder. At 7 months of grow-out 2-stage PCR was required to detect the WSSV signal in the heart, gill and other tissues in some of the offspring shrimp tested.  Prior to harvest at 13 months, most tested shrimp were scoring positive by the 2-stage procedure.  The first deaths attributable to WSSV occurred at 13 months when, for the first time, the 1-stage PCR began picking up the WSSV signal.  "Although superficially healthy, 10 % of the surviving adults had tiny white spots on their carapace, and in situ hybridization analysis revealed WSSV-positive cells in 40 % of the specimens examined."
        The authors have shown that with sufficiently sensitive procedures WSSV can be detected in a shrimp population a long time before massive mortality takes place.  They hypothesize that "disease outbreaks do not occur if shrimp defense mechanisms manage to contain low-intensity viral infections under low-stress culture conditions.  Conversely, outbreaks may occur under stressful conditions".  This hypothesis is not new but multi-stage PCR makes it testable.  Interesting tool for studying tolerance vs. resistance in shrimp.  gracelow@ccms.ntu.edu.tw .

76. Possible negative effects of supplementation on fitness
Microsatellite analysis of hatchery stocks and natural populations of Arctic charr, Salvelinus alpinus, from the Nordic region: Implications for conservation. 1999. Primmer, C.R, T. Aho, J.; Piironen, A. Estoup, J.M. Cornuet, and E. Ranta. Hereditas 130:277-289.
        This is a study of microsatellite variation in Finnish populations of land-locked Arctic charr.  Population differentiation was high even among nearby lakes.  The hatchery stocks were similar to the wild in allele number and average heterozygosity but they showed higher levels of single- and multi-locus genotypic disequilibrium.  The population in a lake that was completely reliant on hatchery supplementation showed particularly low levels of genetic variation.  "Although the hatchery stocks of this population suffer from increased egg and alevin mortality and disease susceptibility, it remains to be determined if this is due directly to a lack of genetic variation as some abundant unstocked natural populations possessed similarly low levels of microsatellite variability." craig.primmer@helsinki.fi .

75. Inbreeding may reduce population fitness for a long time
Does inbreeding affect the extinction risk of small populations?: predictions from Drosophila. 2000. Bijlsma, R., J. Bundgaard, and A.C. Boerema. Journal of Evolutionary Biology 13:502-514.
        The authors studied the extinction rates of experimental Drosophila populations that had been inbred to varying degrees before being transferred into optimal and stressful experimental environments.  "We show that inbred populations have a significantly higher short-term probability of extinction than non-inbred populations, even for low levels of inbreeding.... the impact of environmental stress becomes significantly greater for higher inbreeding levels, demonstrating explicitly that inbreeding and environmental stress are not independent but can act synergistically.  These effects seem long lasting as the impact of prior inbreeding was still qualitatively the same after the inbred populations had been expanded to appreciable numbers and maintained as such for approximately 50 generations." r.bijlsma@biol.rug.nl .

74. Tracing parentage in a natural fish population
Genetic parentage in large half-sib clutches: theoretical estimates and empirical appraisals. 2000. DeWoody, J.A., D.E. Walker, and J.C. Avise. Genetics 154:1907-1912.
        Many people would like to assign parentage to fish in natural or aquacultural populations.  Applications range all the way from genetic variance estimation, to controlling inbreeding and genetic drift in endangered populations, to saving aquaculture escapees from paternity suits, to protecting investment in new breeds.  This is an example of a successful assignment study on the sand goby Pomatoschistus minutus.  In addition to the observational work reported in this paper "a general dilocus matrix procedure is suggested for organizing and interpreting otherwise cumbersome data sets when extremely large numbers of full-sib and half-sib embryos ... are genotyped at two or more hypervariable loci. "  dewoody@arches.uga.edu .

73. Sterilized trout are just as much fun
Relative return to creel of triploid and diploid rainbow trout stocked in eighteen Idaho streams. 2000. Dillon, J.C., D.J. Schill, and D.M. Teuscher. North American Journal of Fisheries Management 20:1–9, 2000 20:1-9.
        Triploid salmonids are almost entirely sterile and thus pose no genetic risks to native stocks if they are used for supplementation.  The authors released diploid and triploid fish that had been reared to hatchable size and found no significant differences in the rate of returns to anglers.  They conclude that " triploid rainbow trout can provide stream angling opportunity equal to that provided by fertile diploid fish.  Although there are other concerns regarding the stocking of hatchery trout in streams containing native trout, we suggest that using triploid rainbow trout in stream-stocking programs can help balance the demands for both consumptive fishing opportunity and conservation of native stocks." dschill@micron.net