224.  Risk of genetic contamination from feral Frankenfish
        Fitness components and ecological risk of transgenic release: a model using Japanese medaka (Oryzias latipes). 2001. Muir, W.M., and R.D. Howard. American Naturalist 158:1-16.
        This study reaches the same conclusion as May list #196: a transgene is able to spread to a wild population even if the gene markedly reduces a component of fitness. This is primarily a simulation study in which some of the parameter values were obtained from a laboratory population of medaka. The fish carried a transgene consisting of regulatory sequence from salmon fused to the coding sequence for human growth hormone. The transgene considerably reduced juvenile survival in the laboratory but increased the growth rate and, as a result, the development rate and size-dependent female fecundity of the medaka.
        The authors then constructed a population dynamic model using the experimental and some inferred parameter values. The important factors were, "... the probabilities of the various genotypes mating, the number of eggs produced by each female genotype (female fecundity), the probability that the eggs will be fertilized by the sperm of each male genotype (male fertility), the probability that an embryo will be a specific genotype given its parental genotypes and the probability that the fry will survive to the next time step or that the parents will survive to the next time step". The authors conclude that "transgenes could spread in populations despite high juvenile viability costs if transgenes also have sufficiently high positive effects on other fitness components. Sensitivity analyses indicated that transgene effects on age at sexual maturity should have the greatest impact on transgene frequency, followed by juvenile viability ....".
        Other studies suggest that transgenic fish may have an increased predation risk, e.g. from changed feeding behaviour. A possible defect in this simulation, acknowledged and examined in some detail by the authors, is that  predation mortality was not included in the assessment of  the model. Accounting for it would merely involve measuring viability in an environment where predation occurs (personal communication from W.M. Muir). bmuir@purdue.edu

223.  No genotype-environment interaction for feeding environment
        Comparative performance of juvenile sea trout families in high and low feeding environments. 2001. Glover, K.A., J.B. Taggart, Ø. Skaala, and A.J. Teale. Journal of Fish Biology 59 (1):105-115.
        Eight full-sib families of trout reared together showed highly significant differences in growth rate, which the authors ascribe to genetic differences between the families. The relative performance of the families were the same in low-level and high-level feeding regimes. The paper does not include an estimate of the minimum difference which might have been statistically significant.  Kevin.glover@imr.no

222. The WSSV viral genome is unique
        The white spot syndrome virus DNA genome sequence. 2001. van Hulten, M.C. , J. Witteveldt, S. Peters, N. Kloosterboer, R. Tarchini, M. Fiers, H. Sandbrink, R.K. Lankhorst, and J.M. Vlak. Virology 286 (1):7-22.
        The entire 300 kb circular genome of the dreaded WSSV virus has been sequenced and 184 major open reading frames (a DNA sequence containing initiator and stop codons which is capable of coding for an as-yet-unidentified polypeptide) were found. Only 6% of these sequences have homologues in existing databases and the function of much of it is simply unknown! "The collective information on WSSV and the phylogenetic analysis ... suggest that WSSV differs profoundly from all presently known viruses and that it is a representative of a new virus family." marielle.vanhulten@viro.dpw.wag-ur.nl

221. Salmon choose mates for healthy offspring
        'Good genes as heterozygosity': the major histocompatability complex and mate choice in Atlantic salmon (Salmo salar). 2001. Landry, C., D. Garant, P. Duchesne, and L. Bernatchez. Proceedings of the Royal Society (Ser. B) 268 (1473):1279-1285.
        The authors of this paper examined the mating behavior of a population of wild Atlantic salmon and found that mates were chosen, to a statistically significant degree, for maximizing the heterozygosity of offspring at the major histocompatability complex (MHC). This is "presumably in order to provide them [the offspring] with better defence against parasites and pathogens." Microsatellite allele and MHC data were both used in the study, and the authors were able to show that enhancing the diversity of the peptide-binding region of the MHC appears to be the mating objective, not merely the avoidance of inbreeding. This is interesting not only because it is the first demonstration that MHC genes influence mate choice in salmon but also because of recent evidence that spawning in salmon is, superficially, more of a free-for-all than previously supposed (see below #216 and June list #211). landrychristian@hotmail.com

220.  Ranking conservation value of traditional breeds
        Genetic diversity measures of local European beef cattle breeds for conservation purposes. 2001. Cañón, J., P. Alexandrino, I. Bessa, C. Carleos, Y. Carretero, S. Dunner, N. Ferran, D. Garcia, J. Jordana, D. Laloë, A. Pereira, A. Sanchez, and K. Moazami-Goudarzi. Genetics Selection Evolution 33:311-332.
        Genetic variation among and between 18 local cattle breeds from Spain, Portugal and France were studied at 16 microsatellite loci. The paper provides a good example of calculations on the contribution of each breed to overall genetic diversity of the ensemble, which allowed the authors to rank the relative conservation values of the breeds. jcanon@eucmax.sim.ucm.es

219. Transgenic on-off switch (which might control escaped Frankenfish?)
        The lac operator-repressor system is functional in the mouse. 2001. Cronin, C.A., W. Gluba, and H. Scrable. Genes & Development 15:1506-1517.
        A transgenic system has been developed in Dr. Heidi Scrable's laboratory at the University of Virginia which allows specific genes in mice to be turned on and off at will by a simple dietary change. Although this work was done on a mammal, not a fish, it should interest people involved in aquaculture and fisheries conservation. In fish, similar controls might be used to eliminate unwanted reproduction and/or put a fail-safe, "safety lock" on transgenes for fast growth. The full text is available at http://hsc.virginia.edu/medicine/basic-sci/neurosci/1506.pdf  and a popular summary at the senior author's webpage http://hsc.virginia.edu/medicine/basic-sci/neurosci/scrable/carolyn.htm  [Carolyn Cronin].
        The paper is interesting and clearly written. In essence, what the authors did was ingeniously "mammal-ize" the essential parts of the famous E. coli repressor system so it would work at high efficiency in mice. The repressor system was then engineered into a mouse in such a way as to control the production of tyrosinase, a normal mouse gene which affects coat colour. When fed a standard laboratory diet the transgenic mice are albino, because the transgenic repressor protein blocks the operation of the mouse tyrosinase gene. When a lactose analogue is added to the diet the repressor protein changes its shape and pops off the DNA so that the tyrosinase gene can start functioning. The mice turn brown. When lactose feeding is stopped the mice lose their colour again when they run out of tyrosinase. The authors are confident that their modified lac operon can be used to control many other types of vertebrate genes, even genes which are normally lethal early in embryonic development. hs2n@virginia.edu (Scrable).

218.  Perch families may stay together
        Kin-structured subpopulations in Eurasian perch (Perca fluviatilis L.). 2001. Gerlach, G., U. Schardt, R. Eckmann, and A. Meyer. Heredity 86 (2):213-221.
        Several perch species, in North America and Europe have been found to have genetically distinct subpopulations and ecological sub-niches within a single lake. Two distinct populations of P. fluviatalis were found in Lake Constance. Lower-level substructuring or inbreeding was not detected with the 5 microsatellite loci studied. However, some shoals contained full sibs and half sibs. "Despite females spawning in close proximity to each other, some siblings stay together. This might suggest that perch possess kin preferences and kin recognition." gabi.gerlach@uni-konstanz.de

217.  Super-fast QTL mapping
        In silico mapping of complex disease-related traits in mice. 2001. Grupe, A., S. Germer, J. Usuka, D. Aud, J.K. Belknap, and R.F. Klein. Science 292 (5523):1915-1918.
        This is a new way to do QTL mapping that can reduce the time required from years down to milliseconds. Homozygous lines, phenotypic data on the lines, and a marker database are the required raw ingredients. The authors developed a computational procedure to predict chromosomal regions which regulate the phenotypic traits, using a database of single nucleotide polymorphisms. "A linkage prediction program scans a murine single nucleotide polymorphism (SNP) database and, only on the basis of known inbred strain phenotypes and genotypes, predicts the chromosomal regions that most likely contribute to complex traits. The computational prediction method does not require generation and analysis of experimental intercross progeny, but it correctly predicted the chromosomal regions identified by analysis of experimental intercross populations for multiple traits analyzed [emphasis added]."
        Predicted chromosome locations were compared with locations which had been independently established by conventional backcrossing and other breeding techniques. "In summary ... 19 of 26 experimentally verified QTL intervals regulating 10 phenotypic traits were correctly identified." The computational algorithm is available for free at http://www.mouseSNP.roche.com. Given the likelihood that very rapid DNA-chip analyses of SNP polymorphisms will be available for aquacultural species before too long, the ease with which homozygous clonal lines can be produced, and the long time scale of conventional breeding experiments, this computational technique may have a big impact on aquaculture genetics. Marker-assisted selection may actually become practicable. gary.peltz@roche.com

216.  Pacific salmon Bacchanalia
        Kinship analysis of Pacific salmon: insights into mating, homing, and timing of reproduction. 2001. Bentzen, P., J.B. Olsen, J.E. McLean, T.R. Seamons, and T.P. Quinn. The Journal of Heredity 9 (2):127-136.
        The authors used microsatellite data to infer full- and half-sib relationships among pre-emergent juvenile chinook salmon (Oncorhynchus tshawytscha) in the Dungeness river. The frenetic mating of the parent fish appears to resemble that of Atlantic salmon in Scotland (June list #211): " single-pair matings, polyandry in which females mated with two to three males at a single redd, polygyny in which males mated with two females at different redds, use of two redds by a single female, and use of one redd site by two females". pbentzen@u.washington.edu

215.  Frankendiatom larval food that doesn't need light
        Trophic conversion of an obligate photoautotrophic organism through metabolic engineering. 2001. Zaslavskaia, L.A., J.C. Lippmeier, C. Shih, D. Ehrhardt, A.R. Grossman, and K.E. Apt. Science 292 (5524):2073-2075.
        The authors transformed the diatom Phaeodactylum tricornutum by inserting several different algal and human glucose transporter genes. (Transporter genes code protein molecules which mediate the transfer of other molecules across biological membranes.) Several of the genetically engineered lines grew well in the dark when supplied with glucose in the growth medium. Carbon yields per litre may be 10 to 50 times higher than when the algae are grown autotrophically. The authors suggest that production efficiencies may increase by an order of magnitude. Ordinary Phaeodactylum is widely used in the cultivation of shrimp and mollusc larvae. kirkapt@martekbio.com

214.  Genetically unique salmon in a re-stocked river
        Fine-scale population structure in Atlantic salmon from Maine‘s Penobscot River drainage. 2001. Spidle, A.P., W.B. Schill, B.A. Lubinski, and T.L. King. Conservation Genetics 2 (1):11-24.
        This is an important contribution to the study of genetic diversity in the Atlantic salmon populations of the NE Atlantic. The Penobscot river in Maine has been heavily re-stocked at various times in the past but despite this, the populations in the lower river and in two unstocked tributary streams are genetically differentiated from each other. The 12 microsatellite marker loci produced a 90% success rate in assigning fish to their subpopulations. "Current populations are clearly isolated from each other, however [the authors are] unable to determine from the present data whether the populations ... are recently diverged from populations stocked into the Penobscot River over the last century, or are aboriginal in origin.
        The degree of population structure identified in the Penobscot drainage is noteworthy in light of its lengthy history of systematic restocking, the geographic proximity of the subpopulations, and the extent of the differentiation." The salmon in several New England rivers have recently been listed as endangered. This demonstration of genetic uniqueness of remnant populations in re-stocked rivers will probably be used both for and against the argument that aquaculture escapees constitute a genetic risk to evolutionarily significant salmon populations.
       See also the related paper by the same authors which covers the whole north Atlantic : King, T.L., S.T. Kalinowski, W.B. Schill, A.P. Spidle, and B.A. Lubinski. 2001. Population structure of Atlantic salmon (Salmo salar L.): a range-wide perspective from microsatellite DNA variation. Molecular Ecology 10 (4):807-821.  tim_king@usgs.gov

213.  A universal primer for shrimp mitochondria
        One-step PCR amplification of complete arthropod mitochondrial genomes. 2001. Hwang, U.W., C.J. Park, T.S. Yong, and W. Kim. Molecular Phylogenetics and Evolution 19 (3):345-352.
        "A new PCR primer set which enables one-step amplification of complete arthropod mitochondrial genomes was designed from two conserved 16S rDNA regions for the long PCR technique." One of the organisms was a crustacean, Macrobrachium nipponense. The highly conserved primer set "can serve various research fields, such as molecular evolution, population genetics, and molecular phylogenetics based on DNA sequences, RFLP, and gene rearrangement of mitochondrial genomes in arthropods and other invertebrates". wonkim@plaza.snu.ac.kr.

212.  Breeding strategies for conserving genetic diversity
        Interrelations between effective population size and other pedigree tools for the management of conserved populations. 2001. Caballero, A., and M.A. Toro. Genetical Research 75:331-343.
        It has become widely accepted among conservation geneticists that breeding plans for captive populations should strive to minimize the kinship (coancestry) of living members of the populations. In essence, this is a diversity-maximizing strategy because it minimizes the number of genes in the population that are identical by descent. Coancestry is usually computed from extended pedigree records. "Founder equivalents" and "founder genome equivalents" are two diversity measures used in this strategy: the authors of this paper review the relationships among these measures and introduce a new one. The authors also give some practical broodstock management advice and make the important point that choosing optimal breeders and then arranging the pattern of mating among them are separate problems. In aquaculture, for example, this distinction would mean that a rotational mating scheme for minimizing inbreeding in a broodstock, as often recommended, is an incomplete answer to the problem of minimizing loss of genetic diversity. armando@uvigo.es