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.

552.  Gene therapy for WSSV infected Penaeus japonicus
         Silencing shrimp white spot syndrome virus (WSSV) genes by siRNA. 2006. Xu, J., F. Han and X. Zhang. Antiviral Research in press.
         Small RNA molecules, around 20 base pairs long, have recently (1998) been found to be profoundly important in gene regulation. (See #549, below.) This regulation includes de-activating the genes of invasive pathogens.
         Geneticists are still recovering from their chagrin at having overlooked this phenomenon for five decades. The first Nobel prizes began trickling in a week ago.
         The process, called "gene silencing" or "RNA interference", works somewhat like this: (1) Double-stranded RNA (often originating directly or indirectly from a pathogen) binds to a protein complex, Dicer, which cleaves it into fragments. (2) Another protein complex, RISC, binds these fragments. One of the RNA strands is eliminated but the other remains bound to the RISC complex and serves as a probe to detect messenger RNA molecules (e.g. from viral replication). (3) When an mRNA molecule can pair with the RNA fragment on RISC, it is bound to the RISC complex, cleaved and degraded. The gene producing that particular mRNA has been silenced.
         Shrimp have this gene silencing facility, too. "In this investigation, a specific 21bp short interfering RNA ... targeting a major envelope protein gene (vp28) of WSSV was used to induce gene silencing in vivo in Penaeus japonicus shrimp. ... After three injections  ..., the virus was completely eradicated from WSSV-infected shrimp."
         See #549, below, for another fascinating paper on RNA in shrimp. xiaobo@hotmail.com  

551.  Comparing genetic distances estimated on different kinds of organisms or populations
         A standardized genetic differentiation measure. 2005. Hedrick, P. W. Evolution 59:1633-1638.
         There are many reasons for wanting to measure the genetic difference between populations. They include determination of conservation value, reconstructing the history of migration, selection and drift, and possibly the enforcement of breeders rights and intellectual property rights in aquaculture.
         Highly polymorphic markers such as microsatellites are used almost universally for such studies, and the most commonly used measure of  differentiation is GST, defined as the proportion of genetic variation which resides among populations. A low GST should indicate that populations are genetically similar.
         This paper points out that GST has a serious flaw when applied to microsatellite data because  its maximum value depends on the level of genetic variation within populations as well as between them. One's intuitive appreciation of "genetic differentiation" often breaks down with GST because its value can be very small even when subpopulations (or loci, or species) have completely different suites of alleles. This can happen when the heterozygosity of the whole ensemble and the average of the subpopulations both approach unity.
         The author proposes to standardize the GST concept, essentially by dividing it by its maximum possible value given the observed heterozygosities. The mathematical underpinnings of the prcedure are carefully developed and explained. "The standardized measure should allow more appropriate comparisons between loci with different mutation rates, such as allozyme and microsatellite loci or mtDNA and Y-chromosome genes. … In addition, the standardized measure allows comparison of levels of genetic differentiation in different organisms that may have very different effective population sizes."  Both of these situations are relevant in aquaculture and genetic conservation. See July 2006 #515 for measures of quantitative trait divergence. philip.hedrick@asu.edu  

550.  Selection for temperature-sensitive sex ratios in Nile tilapia?
         Effect of rearing temperatures on the sex ratios of Oreochromis niloticus populations. 2006. Tessema, M., A. Müller-Belecke and G. Hörstgen-Schwark. Aquaculture 258:270-277.
         This study confirms earlier reports that treating O. niloticus with high temperature early in development can bias sex ratios towards phenotypic males (XX "neomales"; see Jan 2002 #282, Oct 2000 #124.) The distinguishing and interesting feature of the study is that only one of the two source populations, Lake Manzala, in Egypt, showed this effect. Fish from Lake Rudolph in Kenya did not.
         In the Manzala population two-thirds of the high-temperature progenies had more than 80% males, while sex ratios were normal in the Rudolph fish and their hybrids. The fish were subjected to three temperature regimes, 18 °C for 20 days, 36 °C for 10 days or 38 °C for 10 days starting on day 10 post fertilization.
         The regional differences in the temperature effect, plus data on the sex distribution of offspring of neomales and of maternal and paternal half-sibs lead the authors to conclude that the temperature effect is under genetic control, and is in fact heritable.
         "It was concluded that the sensitivity of sex determination to temperature treatments is under genetic control and suggests very promising chances for a selection response." Any procedure which shows promise of enhancing the male:female sex ratio should be of considerable commercial interest and a breeding program for that trait would be fun to design. ghoerst1@gwdg.de

549.  Shrimp immune system specific for WSSV and other viruses
         Double-stranded RNA induces sequence-specific antiviral silencing in addition to nonspecific immunity in a marine shrimp: convergence of RNA interference and innate immunity in the invertebrate antiviral response? 2005. Robalino, J., T. Bartlett, E. Shepard, S. Prior, G. Jaramillo, E. Scura, R. W. Chapman et al. Journal of Virology 79:13561-13571.
         This study suggests that shrimp (Litopenaeus vannamei) do have a virus-specific immune response, the nature of which is entirely different from the vertebrate immune system.
         The trigger for the response is double-stranded RNA (dsRNA), which constitutes the genome of some viruses and is generated during the replication of many others. Cells of plants, vertebrates and invertebrates have quite recently been shown to attack dsRNA molecules not only as part of an anti-viral response but as part of a universal gene-regulation mechanism which appears be of enormous significance during development. The numerous modes of attack on dsRNA involve other RNA molecules, small ones, called sRNA or siRNA (small interfering RNA) which "silence" genes by preventing their translation into protein. (See #552, above.)
         L. vannamei were challenged with WSSV in association with intramuscular injection of synthetic dsRNA. In some experiments the injected dsRNA coded for WSSV genes, in others the dsRNA was not related to any virus. The response variable was shrimp survival.
         The effect of dsRNA injection was dramatic. It appears that dsRNA enhances the survival of shrimp in two ways: it triggers both a non-specific immune response and a response which is specific to the base sequence of the viral DNA. The authors "propose a model of antiviral immunity in shrimp by which viral dsRNA engages not only innate immune pathways but also an RNAi-like mechanism to induce potent antiviral responses in vivo.
         They also say their study "suggests, for the first time, the possibility of dual stimulation of innate immunity and antiviral silencing by dsRNA in an invertebrate". Well, the authors are right about that. See #552, above, for siRNA treatment of P. japonicus. warrgw@musc.edu  

548.  Clever use of a salmon Frankengene to predict the evolution of prey
         Selection on increased intrinsic growth rates in coho salmon, Oncorhynchus kisutch. 2005. Sundström, L. F., L. M. and R. H. Devlin. Evolution 59:1560-1569.
         Many factors favour rapid early growth in salmonids: shorter period of vulnerability to small predators, more effective defense of feeding territories, easier physiological transition from fresh to salt water. There is counter-selection too; rapid growth requires more foraging, with its attendant predation risk, and fish which emerge early from the gravel invite the concentrated attention of predators. The optimum growth rate in salmonids should depend on the details of the environmental food and predation regimes as well as population density. (See #541, below.)
          Can we predict what will happen when the environment changes? This is a classic set-up for analysis by evolutionary game theory. In formal game theoretic analysis, we try to predict whether a wild salmon gene (or genotype) can be displaced by a  faster-growing genotype -- especially one that has escaped from aquacultural operations. This novel experiment uses transgenic salmon to address questions about the relative fitness, in nature, of a single, strategy-altering gene.
         The experimental fish contained a transgenic growth hormone gene back-crossed with wild stocks for several generations, so that they are genetically wild except for the gene causing rapid growth.  (See Oct 2003 #438, Jul 2000 #81, Feb 2001 #174.) The control was the population into which the high-growth transgene had been introgressed. This transgene more than doubles growth rate when fish are fed to satiation, as they would be in aquaculture. But this experimental environment mimicked the less benign environment of natural streams, with varying natural food supplies and predation risk.
         Rapid-growth fish emerged from the gravel two weeks early, and then all sorts of complicated things happened, depending on food availability and the predation regime.
         "The present study has shown that a major shift in developmental timing can alter critical early stages affecting survival and can have a significant effect on fitness. Furthermore, ecological conditions such as food abundance and predation pressure can strongly influence the potential for fast-growing variants to survive under natural conditions. The large-scale removal of many predatory species around the world may augment the evolution of increased intrinsic growth rates in some taxa."
         Remove the predators, fast-growth genes can increase in frequency.
         And, "Such development may have profound implications for aquatic ecosystems regardless of whether the animals arise from natural mutation, genetic variation, or release/escape of genetically modified animals from contained settings". sundstromf@pac.dfo-mpo.gc.ca

547.  Classic genetic evaluation of tilapia strains
         Genetic evaluation of four strains of Oreochromis shiranus for harvest body weight in a diallel cross. 2006. Maluwa, A. O. and B. Gjerde. Aquaculture 259:28-37.
         The diallel cross, in which a set of strains is mated in all possible combinations, is a classic design for estimating the average genetic differences among strains and the genetic architecture of traits (architecture in the sense of heterosis, reciprocal effects, genotype-environment interaction and so on).
         This is a fine example of the design applied in an aquacultural context with modern statistical methods (GLM procedure in SAS). The African tilapia species O. shiranus is of particular interest in Malawi for aquacultural as well as conservation reasons. "The results show that for harvest body weight there are substantial additive genetic and total heterosis differences among pure and crossbred strains of O. shiranus."  Practical decisions about national aquaculture breeding programs are being made on the basis of this experiment. bjarne.gjerde@akvaforsk.no  

546.  Captive breeders can improve a nearly-extinct population
         Introduction of captive breeders to the wild: Harmful or beneficial? 2004. Theodorou, K. and D. Couvet. Conservation Genetics 5:1-12.
         This paper comes to the sensible conclusion that supplementing a small, rapidly-inbreeding natural population can be a good thing. It can be good even if the frequency of deleterious alleles has increased in the captive source population because of reduced selection.
         Genetic load and extinction risk in the wild population are decreased by supplementation if  "(i) the time length of the supplementation program does not exceed a reasonable time frame, e.g., 20 generations (ii) introduction of captive individuals is kept at a low level, i.e., one or two individuals per generation, (iii) the size of the captive population is reasonably large, e.g., more than 20 individuals".
         Note that the benefit is genetic, owing to delayed approach to homozygosity in the wild population, rather than a demographic, reduced risk of random, accidental extinction. The optimal rate of supplementation is too low for a demographic benefit; the benefits are genetic. See genetic rescue: May 2000 #51, Aug 2002 #341, May 2003 #400. ktheo@aegean.gr  

545.  Inbreeding depression was not purged in New Zealand
         Inbreeding and endangered species management: is New Zealand out of step with the rest of the world? 2006. Jamieson, I. G., G. P. Wallis and J. V. Briskie. Conservation Biology 20:38-47.
        Inbreeding is a major threat to the survival of small, isolated populations of many species. Fortunately, the same population features which allow deleterious recessive genes to be expressed as inbreeding depression should also allow them to be purged -- selectively removed -- from a population, if the population can avoid extinction long enough for this to happen. Whether purging actually occurs in nature is a matter of dispute.
         It has been suggested that in New Zealand, purging may have occurred in many terrestrial bird species which have recently recovered from severe and prolonged bottlenecks. This paper reports, however, that even though small populations did recover in terms of their census numbers, "results from recent field studies in New Zealand indicate that, despite the opportunity for purging, inbreeding depression is evident in many threatened species".
         So to the extent that this situation is analogous with, say, remnant salmon populations, we should not hope that the problem of inbreeding depression will resolve itself over time through natural selection (purging).
         The paper argues that "Although inbreeding depression has not prevented some populations from recovering from severe bottlenecks, the long-term consequences of inbreeding and small population size—the loss of genetic variation—are potentially much more insidious." See genetic rescue paper #546, above. ian.jamieson@stonebow.otago.ac.nz  

544.  Salmon QTLs with large effects on growth
         QTL for body weight and condition factor in Atlantic salmon (Salmo salar): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Arctic charr (Salvelinus alpinus). 2005. Reid, D. P., A. Szanto, B. Glebe, R. G. Danzmann and M. M. Ferguson. Heredity 94:166-172.
         This study of three full-sib families used a total of 91 microsatellite markers. Two statistically significant QTLs for body weight and four for condition factor were identified. "The largest QTL effects for BW (AS-8) [linkage group AS-8] and for condition factor (AS-14) accounted for 20.1 and 24.9% of the trait variation, respectively" . [!]
         Other, non-significant, QTLs were found for both traits, some of which occur "on linkage groups where similar effects have been detected on the homologous regions in either rainbow trout (Oncorhynchus mykiss) or Arctic charr (Salvelinus alpinus)". These sound like commercially important QTLs, potentially relevant to a selection program. See June 2006 #496, Sept 2001 #236 for other salmonid QTLs found by some of the same authors.  mmfergus@uoguelph.ca  

543.  Choosing breeds to maximize long-term genetic diversity
         Using expected allele number as objective function to design between and within breed conservation of farm animal biodiversity. 2005. Simianer, H. Journal of Animal Breeding and Genetics 122:177-187.
         It is known that allele number (the number of distinguishable alleles at a loci) is a sensitive measure of the rate at which genetic diversity is being lost through random drift and extinction in small populations. The author of this paper proposes using the expected number of alleles segregating in the species after a given time period as an objective function for conservation breeding.
         The idea embodied in the objective function (that is, the quantity to be optimized) is not only to conserve breeds that are different, i.e. which maximize between-breed genetic diversity, but also breeds which will contribute maximally to genetic diversity within breeds. The optimal solution of the function should maximize scope for artificial selection and natural adaptation to future environments.
         "A formal approach is presented to predict this quantity [the solution] based on marker information, accounting for extinction probability of breeds and effective population size within breeds as the major component of genetic drift. ...the suggested methodology provides a general and flexible tool to derive the optimum conservation strategy in various scenarios." See Aug 2006 #524 on allele diversity, Sept 2006 #536 for another diversity-maximizing scheme and June 2006 #494 for economic considerations in breed conservation. hsimian@gwdg.de  

542.  A useful and convenient population genetics program in Excel
         GenAlEx6: genetic analysis in Excel. Population genetic software for teaching and research. 2006. URL Peakall, R. and P. E. Smouse. Molecular Ecology Notes 6:288-295.
         This useful, convenient and free Excel-based program for analysing marker and other genetic data has been thoroughly updated. Its many features include a number of procedures which appear frequently in these postings, including "estimation of pairwise relatedness among individuals [and] tools for genetic tagging applications, including location of matching genotypes and calculation of probabilities of identity".
         The program has a good manual and examples. This is an especially fine Excel add-in for those who don't do genetic analyses as often as mental hygiene requires and hate re-learning the stand-alone programs every couple of years.  Documentation and program downloads from http://www.anu.edu.au/BoZo/GenAlEx/ . E-mail rod.peakall@anu.edu.au

541.  Fast growers get tired easily
         Evolution of intrinsic growth rate: metabolic costs drive trade-offs between growth and swimming performance in Menidia menidia. 2006. Arnott, S. A., Arnott, S. A., and D. O. Conover. Evolution 60:1269-1278.
         Aquaculturists generally want fast-growing fish that don't waste energy, so it is interesting to see how growth rate and general metabolic rate co-vary. Atlantic silversides (Menidia menidia) from two locations are known to have different intrinsic growth rates and different swimming rates as well (see Dec 2001 #266).
          It is shown in this paper that "the fast-growth genotype had a significantly greater standard metabolic rate [as measured by respirometry] than the slow-growth genotype, but a similar maximum sustainable metabolic rate when swum to near exhaustion".
         The faster-growing genotype eats more and therefore uses more energy for digestion and assimilation, but has a lower scope for activity (capacity for exercise). The findings support the authors's hypothesis that in nature, growth is selected to an optimum which is less than the maximum. In nature, animals have to be able to escape predators and hunt. In aquaculture, the goal of artificial selection is generally maximal growth unless there are trade-offs involving disease or fecundity, which in fact rarely turn up in any definitive way. Predator avoidance is not an issue. See #548, above, and Sept 2006 #530 on feed conversion efficiency.
         So one expects that artificial selection should usually be able to increase growth above that which is found in natural populations.  dconover@notes.cc.sunysb.edu