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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.

659.  Selection in competitive and aggressive groups 
         Multilevel selection 3: modeling the effects of interacting individuals as a function of group size. 2007. Hadfield, J. D. and A. J. Wilson. Genetics 177. 
         Two unusual, important papers on selection in environments where social interactions affect growth rate have been noted here (Apr 2007 #600 & #597). They offered the possibility of exploiting a whole new reservoir of additive genetic variance for traits of practical importance in aquaculture. This new paper in the series (with different authors) extends the analysis by removing one of the key assumptions, that the interaction between any pair of individuals is independent of group size. This assumption never did seem very realistic. In this new treatment it is replaced by an assumption that the interaction between any two individuals diminishes linearly with group size. 
         "Using standard restricted maximum-likelihood (REML) random regression techniques we provide a powerful way to model the relationship between associative effects [i.e. social interaction effects] and group size while simultaneously estimating the relevant quantitative genetic parameters." This is true -- the procedure can be used with standard REML-capable software. Unfortunately, because this is a 2-page note, use of the technique is not comprehensively illustrated as it was in the two previous papers. j.hadfield@ed.ac.uk 

658.  Oh-oh! WSSV may survive in farm pond soil 
         Detection of White spot syndrome virus DNA in pond soil using a 2-step nested PCR. 2008. Natividad, K. D. T., N. Nomura and M. Matsumura. Journal of Virological Methods 149:28-34. 
        It appears that WSSV (or at least an amplifiable section of viral DNA) persists in pond soil for a minimum of ten months. The authors discovered this through 2-stage PCR amplification of samples of soil collected from a heavily infected farm in the Philippines and stored at room temperature for ten months. Control samples from farms with no known WSSV infection did not produce the WSSV amplicon. The key step in their procedure was removing soil humic acid and phenolic compounds that inhibit DNA polymerases. 
         We knew that WSSV can be found in copepods, crabs etc and other living, natural reservoirs, but it comes as bad news that WSSV may survive for so long in the pond substrate itself. Of course the recovery of a section of DNA does not mean there is an intact, potentially infective virus, but this is not unlikely. The authors comment that "Long-term persistence of naked viral DNA in soil is questionable due to the high potential activity of nucleases produced by soil microorganisms". kdtnatividad@hotmail.com 

657.  Genetic variation in the masculinizing effect of temperature in wild tilapia populations 
         Sex determination and temperature-induced sex differentiation in three natural populations of Nile tilapia (Oreochromis niloticus) adapted to extreme temperature conditions. 2007. Bezault, E., F. Clota, M. Derivaz, B. Chevassus and J.-F. Baroiller. Aquaculture 272:S3-S16. 
         Here we have another interesting paper on the effect of temperature on sex ratio in Nile tilapia. Adults from three wild African populations were collected in a low-temperature highland lake, a high-temperature thermal spring and a lake with wide seasonal variations. Sex ratios of progenies were determined in common-garden experiments where low (27 °C) or high (36 °C) temperatures were maintained for one month after swim-up. The lower temperature served as a treatment control. (Note that 36 °C was used for successful high-male selection in the paper reviewed in Feb 2008 #647). 
         "The three populations presented a clear thermosensitivity of sex differentiation, with large variations in the intensity of response depending on the parents." One might have hoped that this would open up the possibility of genetic prospecting for advantageous genetic material to use in broodstocks. Rather surprisingly though, most of the variation was found between families not between populations. The three populations did not differ significantly in their average sex ratios in nature or at the two temperatures (all had more males at 36 °C) nor in the average masculinizing effect of the temperature treatment (proportional change in sex ratio). 
         An earlier paper, Oct 2006 #550 (different authors), did report geographical differences in thermosensitivity. A Lake Manzala population showed the effect while one from Lake Rudolph did not. In this new paper the considerable variation in sex ratio and thermosensitivity -- far exceeding simple binomial sample expectation -- was found between families. A population level difference in variance did show up, however. The thermal spring population showed the least variation among families. 
         The complicated, multifactorial sex determination system of tilapia is discussed in detail, with interesting reference to the natural environment and selection regime as well as the underlying genetics. As one expects in a paper from France the statistical analysis is impeccable but not overdone, while attention paid to anomalous data points may border on the obsessive. etienne.bezault@eawag.ch 

656.  Translocation of pink salmon risks outbreeding depression 
         Outbreeding effect on embryo development in hybrids of allopatric pink salmon (Oncorhynchus gorbuscha) populations, a potential consequence of stock translocation. 2007. Wang, I. A., S. E. Gilk, W. W. Smoker and A. J. Gharrett. Aquaculture 272:S152-S160. 
         Rates of embryonic development often shows local genetic adaptation in salmonids, and one might expect that hybrids between differently-adapted populations would be less fit than their parents in either parental environment. This paper convincingly demonstrates that this does happen in Alaskan pink salmon and that it contributes to the reduced survival of hybrids (outbreeding depression) which has been previously observed. 
         Hybrids needed more degree-days to develop in both the F1 and backcross F2 generations. The authors conclude that "One of the reasons that translocation might be considered in conservation decisions is to increase genetic diversity .... Our results indicate that caution is warranted, particularly where populations differ genetically, because long-term reductions in fitness might result from outbreeding and exacerbate such a depression of fitness." For a meta-analysis of outcrossing which seems to show that it is generally beneficial -- although not in this case --  see June 2007 #606. ffajg@uaf.edu  

655.  A comparison of various ways to separate nature from nurture 
         How to separate genetic and environmental causes of similarity between relatives. 2007. Kruuk, L. E. B. and J. D. Hadfield. Journal of Evolutionary Biology 20:1890-1903. 
         It is hard to separate genetic effects from environmental effects in aquatic animals. Yet this is exactly what we have to do when we look for an evolutionary response to climate change, or upward trends in breeding value in artificially selected populations, or differences in local genetic adaptation between wild and hatchery salmon, or correlations among important traits within a population.
        This paper is a useful comparative study of various ways of tackling the problem. Cross-fostering, analysis of variance and related procedures, and linear mixed (animal) modeling are all considered. The latter approach is especially useful, but owing to "spatial, temporal and social heterogeneity typical of natural populations ... care needs to be taken in specifying models that are appropriate to the data." This comment applies equally to aquaculture. Note the recent discussion on whether or not to include a "brood" or "family" term in the model in Feb 2008 #645, #640 and a "year" term in Oct 2007 #626. This clearly-written paper provides intuitive explanations along with no-frills mathematical ones. loeske.kruuk@ed.ac.uk 

654.  Selective divergence of a candidate gene among fish populations 
         Adaptive divergence in a high gene flow environment: Hsc70 variation in the European flounder (Platichthys flesus L.). 2007. Hemmer-Hansen, J., E. E. Nielsen, J. Frydenberg and V. Loeschcke. Heredity 99:592-600. 
         Suppose populations in different environments have very different gene frequencies at one locus even when the populations are close to each other. But at other loci the genetic divergence of populations appears to depend solely on spatial and/or historical distance. What do you conclude? 
        The authors of this paper found such a  pattern in the European flounder (Platichthys flesus L.) in the Baltic Sea and eastern Atlantic. The anomalous locus is Hsc70, a gene which strongly expresses a heat-shock protein under stresses such as infection, high temperature, low salinity and low oxygen. (Heat shock proteins are member of a class of molecules called CHAPERONINS which help stabilize the conformation of other proteins.) The nine other loci were microsatellites. Environments were characterized by the spawning strategy employed by the plaice: benthic spawners which live inshore (2 populations) vs. pelagic dwellers and spawners (10 populations). 
         The authors of the paper interpret the genetic observations as a sign that strong natural selection related to environmental stress in shallow water is acting on the heat shock gene. In fact, they chose to study a heat shock gene precisely because these genes are involved in coping with cellular stress in archaebacteria, bacteria, plants and animals. This a good example of the use of candidate genes at the population-genetic level to analyze the balance between selection and gene flow. However, it is not yet known if the specific polymorphism in Hsc70 affects transcription or function, and is thus directly selected, or is just "hitch-hiking".
         Another example of selection at the molecular level which does get down to the molecular level is cited in Mar 2003 #398, a paper which demonstrates strong positive selection and habitat-specific amino acid substitution patterns in MHC from an estuarine fish under intense pollution stress. See also #648 below for evidence of selection on an MHC- linked marker in a trout metapopulation. jhh@difres.dk 

653.  Inbreeding usually reduces fitness without purging recessives 
         Role of inbreeding depression and purging in captive breeding and restoration programmes. 2008. Leberg, P. L. and D. F. Brigette. Molecular Ecology 17:334-343. 
         This examination of the ability of small populations to "purge" themselves of inbreeding depression is based partly on new experimental data on mosquitofish and partly on a meta-analysis of other published work. The authors' overall conclusion from the literature is that, while results vary all over the place, strong inbreeding for a generation or two usually does NOT reduce subsequent inbreeding to any significant degree. (For other papers on purging see Oct 2007 #629, Apr 2007 #591.) 
         This was true in their mosquitofish experiment as well. "... serial bottlenecks resulted in a marked decline in population growth and an increase in extinction [in 2 out of 12 lines]". The authors conclude that the most likely, although not certain, effect of population bottlenecks is fixation of deleterious alleles (i.e. they go homozygous but are not purged out) and a reduction of population viability. So it is better to try to keep populations large than to attempt to purge deleterious recessive alleles by passing them through one or more bottlenecks. 
         The paper includes a simple, clear explanation and review of inbreeding depression and the purging concept. While the above conclusions are doubtless valid there is another possible purging strategy that might be considered: multiple parallel inbred lines. "Multiple" would probably have to be closer to 100 than the 12 referred to here. It is possible that 1% - 5% of the bottlenecked lines would be reasonably fit. Even if they were not particularly good producers, the lines which survive extinction would offer options for broodstock management resembling some of the options available to plant breeders. Stable "copy-resistant" hybrids spring to mind. I am not aware of any current aquaculture breeding programs of this sort.  leberg@louisiana.edu 

652.  The "shape" of niloticus is genetically the same in both sexes 
         Can sexual dimorphism and body shape be altered in Nile tilapia (Oreochromis niloticus) by genetic means? 2007. Nguyen, N. H., H. L. Khaw, R. W. Ponzoni, A. Hamzah and N. Kamaruzzaman. Aquaculture 272:S38-S46. 
         Body shape (particularly the thickness:length ratio) has a strong influence on fillet yield in tilapia. Sexual dimorphism in body size has a strong influence on yield/hectare/crop. So we need to ask whether sexual dimorphism in size indicates that we should worry about a dimorphism in shape in genetic improvement programs. 
         Apparently not. This study of the genetics of size and several biometric measures in the GIFT strain found a high genetic correlation between the sexes. "Genetic correlations among [weight, length, depth and width] were highly positive (0.94 to 0.99), suggesting the existence of little or no genetic variation independent of each other." The authors also make the interesting point that "continued selection for live weight would result in relatively longer and thinner fish because of the greater correlated response in length relative to width and depth". (Note that it is always a good idea to incorporate width or thickness in the selection index in tilapia breeding programs). n.nguyen@cgiar.org 

651.  Using markers to conserve additive genetic variance in structured populations 
         Estimating relatedness between individuals in general populations with a focus on their use in conservation programs. 2006. Oliehoek, P. A., J. J. Windig, J. A. M. van Arendonk and P. Bijma. Genetics 173:483-496. 
         Populations of practical interest are usually separated into sub-populations which are, or were, connected to some degree and which have different gene frequencies. Most aquacultural and endangered populations are structured in this sense on any scale larger than a single farm or stream. This paper postulates that the overall conservation objective is to retain as much as possible of the additive genetic variance both within and between populations, and then looks at how molecular marker information can be used to achieve this goal. 
        The answer is pretty well known when the structure is so simple that only one population exists: minimize the relatedness of mated individuals in each generation, using pedigrees if they are available or marker-based relatedness estimators if they are not (e.g. June 2007 #603). But populations this simple must be rare. 
        Eight relatedness estimators are compared in this paper, falling into three categories: (1) based on the relationship between additive genetic relatedness, population genetic coancestry and molecular coancestry; (2) based on the relationship between additive genetic relatedness and two-gene and four-gene coefficients of identity; (3) based on molecular similarity among individuals. 
        Simulation results are rather complicated but they "show that ranking of estimators depends on the population structure." And, "Our results show that benefits of using relatedness estimates in conservation programs are substantially larger in structured than in panmictic populations." The logical relationships between the estimators and their varying applicability in populations structured in different ways is treated very thoroughly and deserves study by anyone concerned with conservation breeding. genetics@geneticdiversity.net 

650.  Programmed cell death not a good strategy for infected shrimp? 
         Knocking down caspase-3 by RNAi reduces mortality in Pacific white shrimp Penaeus (Litopenaeus) vannamei challenged with a low dose of white-spot syndrome virus. 2008. Rijiravanich, A., C. L. Browdy and B. Withyachumnarnkul. Fish & Shellfish Immunology 24:308-313. 
         Viral infection (with WSSV for example) is one of the many, many triggers of cellular suicide -- "programmed cell death", or apoptosis. Apoptosis has two relevant, but contradictory consequences: (1) it reduces organism-level mortality when cells lyse before the viral particles inside them have matured, (2) it increases mortality when essential organ function is lost. The relative importance of these effects in shrimp struggling with a virus is a matter of some controversy. 
         The authors of this paper use RNA silencing to reduce production of caspase-3, a protease which plays a key role in apoptosis in mammals and other organisms. (See Oct 2006 #549, Oct 2007 #631 for a brief explanation of RNA silencing.) To be precise, the authors work with a shrimp analogue of caspase3 called cap-3. Less cap-3 production should mean less apoptosis. 
         So, did the cap-3 deficient animals challenged with WSSV have lower mortality? Both yes and no. At low doses of WSSV cumulative mortality decreased, but at high doses mortality was unaffected by the gene silencing. "In summary, our experiments demonstrate that dsRNA knock-down of cap-3 gives significant protection against mortality from a low-dose WSSV challenge and support the hypothesis that apoptosis affects shrimp negatively by increasing mortality after viral challenge". 
        One of the interesting aspects of the cap-3-apoptosis story is that "WSSV-resistant kuruma shrimp, Penaeus (Marsupenaeus) japonicus, or ‘immunized’ shrimp (shrimp that have survived an initial WSSV challenge) display a significantly lower incidence of apoptosis than naive shrimp [11,28]. The weight of the information seems to indicate that apoptosis is promoted in shrimp dying of a viral challenge but suppressed in survivors." boonsirm@yahoo.com 

649.  Grow better on fish meal, grow better on soybean too 
         Breeding salmonids for feed efficiency in current fishmeal and future plant-based diet environments. 2007. Quinton, C. D., A. Kause, J. Koskela and O. Ritola. Genetics Selection Evolution 39:431-446. 
         The substitution of soybean meal or other plant protein for fish meal in the diets of cultured fish will surely increase. What are the genetic implications of this? Specifically, will current breeding programs that target improved performance on fish meal diets also improve performance on plant-based diets? This experiment with European whitefish (Coregonus lavaretus, which is farmed in Finland) suggests that the answer is "yes". 
         Matings were made according to a partial factorial design and each full-sib family was split and grown in two feeding regimes, one where all the protein was supplied as fish meal and the other as a 50:50 fishmeal:soybean mix. "Traits [growth, daily intake, feed efficiency] displayed only weak GxE interactions as variances and heritabilities did not differ substantially between the diets, and cross-diet genetic correlations were near unity." (Note that feed efficiency is the inverse of feed conversion ratio, FCR.) "In both diets, daily growth and daily feed intake showed moderate heritability whereas feed efficiency showed very low heritability that did not differ from zero." 
         One conceptual difficulty with both feed efficiency and FCR is that they are ratios of the other two variables (Sep 2006 #530). The authors' animal models predict comfortable genetic gain for both components of feed efficiency (separately) on both feeds, whichever feed was used for selection. They also present a strategy for feed efficiency selection which simultaneously selects for HIGH daily weight gain and LOW daily feed intake. That is, numerator and denominator are both selected. Relative to a selection strategy based on weight gain only (i.e. selecting the numerator of feed efficiency: the usual aquaculture strategy) their calculations predict that simultaneous selection would double or triple the genetic gain in feed efficiency. However, the rate of gain of daily growth rate per generation should be about 4% lower.  cheryl.quinton@mtt.fi 

648.  Genetically differentiated source-sink populations of brown trout 
         Gene flow, effective population size and selection at major histocompatibility complex genes: brown trout in the Hardanger Fjord, Norway. 2007. Hansen, M. M., Ø. Skaala, L. F. Jensen, D. Bekkevold and K.-L. D. Mensberg. Molecular Ecology 16:1413-1425. 
         In theoretical population dynamics, a "source" is a population in which demographic variables generate an excess of individuals which spread out to less-favorable "sink" habitats. In situ population growth is negative in the sinks, which are sustained by immigration. Such a complex represents an asymmetrical meta-population (See Feb 2004 #464 for a trout meta-population in Denmark where migration seems more symmetrical). 
        The problem is, immigration from a source which supports the sink populations may also undermine, to a greater or lesser extent, genetic adaptation to local conditions in the sink. This paper demonstrates and then analyses a source-sink population of brown trout in Norway. Neutral microsatellite markers from historical and contemporary samples were used to infer migration paths and mixing rates within the meta-population. 
         Two different markers linked to the major histocompatability locus were presumed not to be selectively neutral to immunological aspects of the environment, i.e. to pathogens. One of these candidate loci did show statistical evidence for diversifying selection. The analysis leading to this inference is based on observing populationXlocus combinations which are outliers from simulated distributions. The locus was a meaningful outlier, although not by much. The analysis is beautifully done and illustrated graphically. 
         "Despite the limitations [thoroughly discussed], we observed signals consistent with a hypothesis of locally diversifying selection acting at [the MHC-linked locus], presumably reflecting selective responses to locally important pathogens." 
         The authors discuss their results in terms of increased aquaculture activities during the past three decades; specifically, to salmon lice. They are, however, careful to point out several difficulties with this à la mode conjecture including the fact that there are no obvious differences among populations in their exposure to lice (Lepeophtheirus salmonid) and that "It is ... not likely that MHC class I confers major effects in salmon lice response". Nevertheless, there is lots of evidence for genetic variation in salmonid parasite resistance (e.g. June 2007 #609), and see  #654 above for evidence of divergent selection on an immunological marker in flounders.  mmh@difres.dk