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.

588.  Molecular adaptive evolution in lake whitefish
         Integrating QTL mapping and genome scans towards the characterization of candidate loci under parallel selection in the lake whitefish (Coregonus clupeaformis). 2005. Rogers, S. M. and L. Bernatchez. Molecular Ecology 14:351-361.
         Lake whitefish coexist in two forms, dwarf and normal, in many Canadian lakes. At the ecological level, the selective forces involved in maintaining the two sympatric ecotypes (assumed to be "adaptive peaks") are reasonably well understood. Bernatchez’s laboratory has previously reported on parallel changes in the expression of genes in geographically isolated lakes (June 2006 #503) and aquacultural salmon populations (Sept 2006 #540). In this new paper, the stable and repeatable (among lakes) adaptive divergence is used as a starting point for a study of selection at the molecular level.
         Several procedures are involved in the genome scan procedure: hybridization and back-crossing of ecotypes, scoring and mapping numerous marker loci (AFLP in this case), looking for statistical associations between the inheritance of markers and variation in growth. This identifies markers for growth QTL. All this is step one.
         Step two is analysis of the distribution of genetic distances among the markers. Outliers from the distribution are, by definition, not part of a population of random (neutral) markers and are affected by something else, probably selection. The logical path is completed by observing that, sure enough, the outliers are QTL for growth. Selection on growth is understood at the ecological level, as already mentioned.
         "We found evidence of significantly high levels of molecular divergence among eight growth QTL where two of the strongest candidate loci under the influence of directional selection exhibited parallel reductions of gene flow over multiple populations."
         This paper is also interesting because one can also think of it as way of measuring evolutionarily significant divergence among populations. Sets of neutral markers, such as microsatellites, are normally used to measure divergence, but it is known that the correlation between neutral and quantitative genetic diversity is very low.
         Genetic distances based on outliers might be more useful, as suggested long ago by R.C. Lewontin and J. Krakauer. The distribution of neutral markers is affected by demographic processes at the level of the whole genome, while selection affects particular QTL and their neighboring markers. Outlier-based F_ST and G_ST statistics would be useful, for example in identifying populations worthy of conservation or even for incorporating in a selective breeding program. Louis.Bernatchez@bio.ulaval.ca  

587.  Tilapia responds well to selection in extensive aquaculture systems
         Heritability estimates and response to selection for growth of Nile tilapia (Oreochromis niloticus) in low-input earthen ponds. 2006. Charo-Karisa, H., H. Komen, M. A. Rezk, R. W. Ponzoni, J. A. M. van Arendonk and H. Bovenhuis. Aquaculture 261:479-486.
         Tilapia species show a lot of promise for low-input (i.e. sustainable) aquacultural systems. Can their profitability in such environments be increased  through the magic of genetics? In this experiment covering two generations, O. niloticus was grown in ponds fertilized with chicken manure without added feed. "Heritability estimates for BW ranged from 0.38 to 0.60, and the heritability for survival ranged from 0.03 to 0.14.The estimated selection response was 23.4 g (34.7%) between G0 and G1 and 13.0 g (14.9%) between G1 and G2.
         These results demonstrate the feasibility of selection for growth of tilapia in low-input environments." Selection was based on estimated breeding values in a fully-pedigreed population. See #580, below for more tilapia selection results. Hans.Komen@wur.nl  

586.  The right way to test for WSSV resistance
         Optimization of experimental infection protocols for the estimation of genetic parameters of resistance to White Spot Syndrome Virus (WSSV) in Penaeus (Litopenaeus) vannamei. 2006. Gitterle, T., B. Gjerde, J. Cock, M. Salazar, M. Rye, O. Vidal, C. Lozano et al. Aquaculture 261:501-509.
         The two procedures tested were (1) individual, oral administration of WSSV virus in a liquid medium and (2) mixing infective medium into the water the shrimp were swimming in. Both procedures were designed to ensure that all animals were exposed at the same time to the same concentration of virus. (Standard challenge tests do not ensure this.) The statistical procedure was a type of time-to-die analysis as recommended by the authors in an earlier paper (which is not identical to this one; July 2006 #516).  Several batches of full- and half-sib families were used.
         Estimated heritabilities were zero or very low in both challenge procedures. Cumulative mortalities were high -- exceeding 80%.  Even with these careful challenge protocols the time course of cumulative mortality was similar at all dosage levels once the infection took hold -- in other words, mortality was dominated by contagion within the tanks. The authors ascribe this, no doubt correctly, to high population density.
         My personal conclusion is that even with the most careful experimental and statistical protocols, such as those used here, challenge tests in groups provide no meaningful quantitative genetic information. They may be of some use in practice for brute-force selection of survivors. Statistical assumptions of independence are hopelessly invalid and I don't know of any models that can handle a contagion-induced error covariance added to the genetic covariance among the tested individuals. (If someone else does, I would love to be instructed.)  In the mean time we need a better way of evaluating WSSV resistance. thomas.gitterle@ceniacua.org  

585.  How well can you infer pedigrees from molecular markers in wild populations?
         Performance of marker-based relatedness estimators in natural populations of outbred vertebrates. 2006. Csilléry, K., T. Johnson, D. Beraldi, T. Clutton-Brock, D. Coltman, B. Hansson, G. Spong et al. Genetics 173:2091-2101.
         This paper examines the frequency of two kinds of errors in marker-based pedigrees: "first, misclassification rates between pairs of genetic relationships and, second, the proportion of variance explained in the pairwise relatedness estimates by the true population relatedness composition (i.e., the frequencies of different relationships in the population)".
          The conclusion is interesting: the frequency of errors (i.e. the performance of a marker/analysis system) depends to a large extent on the nature of the relationships within the population. Specifically, when the variance of relatedness in a population is low, as will frequently be the case especially when most pairs have no common ancestors within the last couple of generations, the ability of relatedness estimators to estimate specific pairwise relationships correctly is also low.
         Fortunately for conservation breeding, where the objective is to mate unrelated individuals, these errors are in the right direction because relatedness is overestimated. But when the objective is to identify highly related individuals, perhaps to see whether they avoid mating with each other or their offspring have more parasites, relatedness is underestimated in many populations.
         More generally, when the variance of relatedness is low, very little of it is explained by variance in the relatedness estimators. The explanatory power of the estimator is therefore low when it is used as an explanatory variable in regression or a categorical variable in ANOVAs. Discouraging. See also Dec 2006 #572. k.m.csillery@sms.ed.ac.uk  

584.  Gene expression and development of precocious male salmon
         Alternative life histories shape brain gene expression profiles in males of the same population. 2005. Aubin-Horth, N., C. R. Landry, B. H. Letcher and H. A. Hofmann. Proceedings Royal Society (B) 272:1655-1662.
         A certain proportion of Atlantic salmon males become sexually mature at a small size and, instead of migrating to the sea, hang around in fresh water on the lookout for whatever opportunities sally by -- the "sneaker" reproductive strategy. Sneaking works as a component of a mixed strategy, is provably adaptive and varies considerably from stream to stream. It causes a severe problem in aquaculture, however, because the sneaker phenotype has little commercial value.
         In this paper gene expression profiles of mature sneaker males are compared to those of juvenile males of the same age (i.e. males which will mature after going to sea) and also to females. The authors found that "roughly 15% of the genome varies in gene expression in the brain between the two male tactics".
         Genes known to be associated with reproduction tended to be up-regulated in the sneaker phenotype, as was the circadian clock gene. Most interestingly, the expression profile of the sneaker was closer to the female than to the immature juvenile male, which the authors interpret as supporting  the idea of Thorpe and others that males that grow more slowly, and fail to reach a threshold size, respond by actively repressing maturation and going on to develop the anadromous phenotype.
         "Notably, gene expression patterns in immature males were different both from immature females and sneakers, indicating that delayed maturation and sea migration by immature males, the ‘default’ life cycle, may actually result from an active inhibition of development into a sneaker." See Nov 2006 #559 for size/growth effects on maturation. naubin-horth@cgr.harvard.edu  

583.  Ontario walleye are genetically okay
         Inbreeding, outbreeding and environmental effects on genetic diversity in 46 walleye (Sander vitreus) populations. 2006. Cena, C. J., G. E. Morgan, M. D. Malette and D.D. Heath. Molecular Ecology 15:303-320.
         Forty-six Ontario (Canada) walleye populations were studied to find the relationship between life history traits related to growth, reproduction and mortality and measures of genetic diversity (heterozygosity, d2, and F). Only one relationship was found to significant in both sexes: "Walleye early growth rate was the only life history trait significantly correlated with population heterozygosity in both males and females." The authors conclude that "the weak relationships between genetic diversity and life history traits indicate that inbreeding and outbreeding depression are not yet seriously impacting  Ontario walleye populations." dheath@uwindsor.ca  

582.  Model of evolutionary adaptation to domestication
         A potential model system for studying the genetics of domestication: behavioral variation among wild and domesticated strains of zebra danio (Danio rerio). 2005. Robison, B. D. and W. Rowland.  Can. J. Fish. Aquat. Sci. 62:2046-2054.
         The domesticated zebra fish studied here have been adapting to laboratory environments for at least 24 generations and the wild strain (from India) for only four. No selective harvesting has been taking place, i.e. this is not a model of evolution to a fishery (compare with July 2006 #508).
         The lab zebra fish were less fearful, spent more time at the surface and grew faster than the wild strain. As the authors point out, zebra fish would seem to be an excellent model for the study of domestication. The evolutionary changes are similar to those in salmonids, carps and -- with the likely, important exception of growth rate -- tilapia. (See Jan 2003 #383)
         "The availability of a complete genome sequence [for zebra fish], saturation mutagenesis screens, and a dense genetic map will allow identification of the genetic targets of domestication selection.... [which can be] tested as candidate genes in other species." brobison@uidaho.edu 

581.  Poor nutrition increases variation among inbred (not outbred) families of oysters
         Effect of dietary restriction during juvenile development on adult performance of Pacific oysters (Crassostrea gigas). 2006. Evans, S. and C. Langford. Aquaculture 259:124-137.
        An article recently cited here (Nov 2006 #559) showed that in cultured salmon, juvenile environment has a strong effect on the rate of growth later in life. Is this true of cultured oysters as well?
         This study shows that final body weight and survival differed among outbred families (i.e. there is genetic variation in the families tested) but that feeding level in the nursery did not have much effect. The situation was rather different among inbred families (full- or half-sib mating) when nutritional stress reached a high level. "Significant rank changes among inbred families for both individual body weight and yield occurred only among families reared under the most stressful nursery feeding regime."
This seems rather important, given the high probability of accidental inbreeding in bivalve hatcheries. If production in one season comes mainly from one or two families, and they happen to be inbreeding-sensitive, the broodstock would suffer a permanent decline in yield. (Permanent, that is, unless domestication selection eventually purges the deleterious recessives, which can happen under certain conditions.). ford.evans@oregonstate.edu 

580.  Good selection response in GIFT tilapia in  Malaysia
         Genetic parameters and response to selection for live weight in the GIFT strain of  Nile tilapia (Oreochromis niloticus). 2005. Ponzoni, R. W., A. Hamzah, S. Tan and H. Kamaruzzaman. Aquaculture 247:203-210.
         This useful report on the GIFT strain in  Malaysia describes a selection experiment based on estimated breeding values (BLUPs). The realized response to selection was around 10% and was estimated in several ways, including comparison with a control. Good. Putting this information together with other recent experiments (e.g. #587, above) it seems likely that 10% is a reasonably safe figure to expect for genetic gain in tilapia, supposing a moderately diverse broodstock and a reasonably well-run program. (Personally, however, I err on the safe side and use 6% in cash flow models of broodstock development with a 10-year planning horizon.). r.ponzoni@cgiar.org  

579.  WSSV genes have lower expression at higher environmental temperature
         Temperature modifies gene expression in subcuticular epithelial cells of white spot syndrome virus-infected Litopenaeus vannamei. 2007. Reyes, A., M. Salazar and C. Granja. Developmental & Comparative Immunology 31:23-29.
         It is widely recognized that low temperatures increase the rate of mortality from viral infection in Litopenaeus vannamei. In this experiment the differential expression of WSSV genes in infected vs. non-infected shrimp was observed at 26°C and 33°C through the use of subtractive suppressive hybridization and real-time PCR.
         Sure enough, there was greater expression of WSSV genes at 26°C. At the higher temperature expression was reduced and mortality from WSSV was completely suppressed. This study helps answer the question whether high temperature improves the immune response of the shrimp (e.g. by increasing the rate of apoptosis) or directly affects the functioning of the virus.  The shrimp genes differentially expressed in infected vs. uninfected individuals were not much affected by temperature, unlike the WSSV genes.
         So the authors conclude that "... our results show that the main effect of hyperthermia on subcuticular epithelial cells is to reduce the expression of WSSV genes rather than to induce host genes that might contribute to control the infection." Note that subcuticular epithelial cells are the main target of WSSV. ale-reye@spymac.com  

578.  Statistical power analysis for genetic distance
         POWSIM: a computer program for assessing statistical power when testing for genetic differentiation. 2006. Ryman, N. and S. Palm. Molecular Ecology Notes 6:600-602.
         Every analysis of genetic differentiation among postulated genetic groups, based on genetic markers, should include an indication of the statistical power of the analysis both to detect differences which really exist, and to avoid imputing population structure where there really isn't any.
         This useful program uses a  Monte Carlo approach to generate a power analysis and also estimates errors for Fisher's exact test and chi-square test of the "no difference" null hypothesis. The POWSIM program can be downloaded from http://www.zoologi.su.se/~ryman . POWSIM should be useful for planning how many markers and samples are needed for having a fair go, as the Australians say, at finding something interesting.
         Perhaps more often, it can be used "...in studies where no significance has been obtained ... to evaluate the magnitude of true differences that may have gone unnoticed, given the particulars of the investigation conducted". The hypothetical true level of differentiation among sample groups is specified as F_ST in the simulation. Various combinations of sample number, number of marker loci, allele frequency distributions can be specified to match the particulars of the (proposed) investigation. It should be noted that the null hypothesis being evaluated is, specifically, that there is no significant differentiation caused by random drift without mutation, selection or migration. Nils.Ryman@popgen.su.se  

577.  Clear genetic evidence of hatchery genes moving into wild salmon populations
         Extensive immigration from compensatory hatchery releases into wild Atlantic salmon population in the  Baltic sea : spatio-temporal analysis over 18 years. 2005. Vasemägi, A., R. Gross, T. Paaver, M.-L. Koljonen and J. Nilsson. Heredity 95:76-83.
       The rate of immigration from hatchery stocks into one of the largest wild, riverine salmon populations in the Baltic region is estimated in this paper. Fish are released from hatcheries into other rivers for stock supplementation.
        The overall immigration rate into the non-supplemented population averaged a bit less than 10% but was as high as 25% between 1993 and 2000. The hatchery stocks were definitely straying into the natural system.  Furthermore, there has been a decline in Fst in the joint analysis of the natural and supplemented population which the authors interpret as evidence for genetic homogenization, i.e. introgression of hatchery genes into the wild gene pool. anti.vasemagi@vabr.slu.se