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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.

540.  News flash! repeatable domestication at the molecular level
         Rapid parallel evolutionary changes of gene transcription profiles in farmed Atlantic salmon. 2006. Roberge, C., S. Einum, H. Guderley and L. Bernatchez. Molecular Ecology 15:9-20.
         Atlantic salmon domesticate easily and many generations of cultivation have brought about significant changes (improvements, from an aquacultural perspective) in growth rate, behaviour and other traits in hatchery populations around the world. These changes are sometimes associated with formal, artificial selection but they tend to occur anyway in well-run hatcheries.
         The quantitative genetics of some of the affected traits (their heritability, dominance, gene interaction etc.) is understood to some extent. It is also believed that genetic changes which benefit aquaculture are dangerous to wild populations which come in contact with domesticated populations.
         This paper systematically explores, apparently for the first time, the differences in gene expression between wild and domesticates salmon -- differences in which genes are turned on and which turned off --  and brings our understanding of the domestication syndrome to a level deeper than the statistical analysis of phenotypes.
         The difference in gene expression between wild and farmed salmon is surprisingly large: "five to seven generations of artificial selection led to heritable changes in gene transcription profiles, the average magnitude of the differences being 25% and 18% for at least 1.4% and 1.7% of the expressed genes in juvenile salmon from Norway and Canada, respectively".          
         The truly noteworthy discovery was that changes in the transcription profile of one aquacultural population were often paralleled by changes in the other. This suggests that domestication is to a considerable degree repeatable at the molecular level, and therefore potentially understandable at the molecular level. The discussion of the effect of domestication on particular transcribed genes, including MHC, is fascinating. See June 2006 #503 for parallel changes in gene expression in isolated wild populations. christian.roberge@giroq.ulaval.ca 

539.  High heritabilities, low genetic correlations in P. monodon
         Heritability and genetic correlations of growth and survival in black tiger prawn Penaeus monodon reared in tanks. 2006. Kenway, M., M. Macbeth, M. Salmon, C. McPhee, J. Benzie, K. Wilson and W. Knibb. Aquaculture 259:138-145.
         The heritabilities of weight-at-age and growth were both high in this experiment, ranging from 0.3 to 0.7 approximately. Heritability of family survival in the culture system (with no exposure to disease challenge) had similar values. Genetic correlations between weight-at-age (or growth) and family survival were sometimes negative and sometimes positive, but were always low with large standard deviations.
         The genetic correlations were not significant so there is no evidence of a tradeoff that might cause trouble, in the absence of disease challenge at least. All of this is good news for aquaculture selection programs with monodon. m.kenway@aims.gov.au  

538.  Inbreeding depression more serious in bad environments
         Inbreeding depression in benign and stressful environments. 2005. Armbruster, P. and D. H. Reed. Heredity 95:235-242.
         We expect inbreeding to have a larger effect on survival and fecundity as the environment deteriorates, and this meta-analysis of 34 published studies shows that a poor environment usually does increase inbreeding depression.
         "Inbreeding depression increases under stress in 76% of cases... .[estimated] lethal equivalents are significantly greater under stressful (mean=1.45, median=1.02) than relatively benign (mean=0.85, median=0.61) conditions. This amounts to an approximately 69% increase in inbreeding depression in a stressful vs. a benign environment." The survey comprised 11 plant and 10 animal species. Environmental stresses included toxins, temperature, starvation, desiccation and competition.
        The authors observed that different inbred lineages within a population often differ strongly in their response to inbreeding in stressful environments. paa9@georgetown.edu  

537.  Heritability of Oreochromis niloticus growth at different ages
         Longitudinal genetic analysis of Nile tilapia (Oreochromis niloticus L.) body weight using a random regression mode. 2005. Rutten, M. J. M., H. Komen and H. Bovenhuis. Aquaculture 246:101-113.
         The objective of this study was to estimate heritabilities of tilapia growth rate at all ages, not just when animals reach harvestable size, the usual target of selection. Late growth is particularly interesting because the European market likes large fillets.
         The authors found that heritability is slightly higher when the animals are young then when they are older, and that there is a strong correlation of growth rate at different ages. (Compare #531, below.) For this and other reasons related to the basic physiology of growth they suggest that selection may be more efficient if performed early in life.
         They also found that the relative breeding value of the founding populations in the broodstock changed during the growth period, so choice of founder strain should depend to some extent on the intended harvestable size. Statistical procedures used in this interesting study go well beyond the conventional animal model approach to estimating heritability which is now current in aquaculture. marc.rutten@wur.nl  

536.  Conserving breeds to maximize scope for selective improvement
         A novel method for the estimation of the relative importance of breeds in order to conserve the total genetic variance. 2005. Bennewitz, J. and T. H. E. Meuwissen. Genetics Selection Evolution 37:315-337.
         What breeding strategy  conserves the most additive genetic variance, when there is a choice of  breeds to be conserved? This simulation uses information on average kinship within and between breeds, estimated from pedigrees or from marker data. (June 2006 #493).
         "The results show that the [best variance conserving strategy]  favors breeds with a high within breed kinship that are not related to other breeds. [The] method suggests conserving breeds that show a large difference in the respective population mean of a hypothetical quantitative trait. This maximizes the speed of achieving selection response for this hypothetical selection direction." See June 2006 #494 for economic aspects of choosing which breeds to conserve. jbennewitz@tierzucht.uni-kiel.de  

535.  High-male populations of Macrobrachium rosenbergii
         Production of all-male stock by neofemale technology of the Thai strain of freshwater prawn, Macrobrachium rosenbergii. 2006. Rungsin, W., N. Paankhao and U. Na-Nakorn. Aquaculture 259:99-94.
         The giant freshwater prawn Macrobrachium rosenbergii is an important aquacultural product, especially in Thailand but elsewhere as well. Males grow faster than females and are more useful for aquacultural production. This paper describes a technique for producing broods which are largely, although not completely, male.
         First they remove the androgenic gland from male PLs, which caused them to mature as females. When these females were subsequently mated with normal males the offspring are mostly males. Fecundity of the males-become-female parents was normal. As the authors say, "Our results suggest that the application of the neofemale technology to produce all-male stock for aquaculture is promising." fsciwrrs@ku.ac.th  

534.  Useful measure of fitness in wild or managed populations
         Estimating individual contributions to population growth: evolutionary fitness in ecological time. 2006. Coulson, T., T. G. Benton, P. Lundberg, S. R. X. Dall, B. E. Kendall and J.-M. Gaillard. Proceedings of the Royal Society B 273:547-555.
         An interesting new, operational measure of individual fitness is introduced in this paper, defined as an individual's contribution to population growth over a standard interval such as a year.
         The measurement, which the authors call "de-lifing", consists of conceptually removing one individual and its offspring from the population and re-calculating what population growth would have been without it. This is repeated for the whole population. De-lifed estimates are somewhat analogous to the jackknifed parameter estimates which are so useful in applied statistics.
         The authors discuss many applications, including selection gradients on quantitative traits, where the de-lifing method might be superior to conventional fitness measures such as fecundity. One can imagine that it might be useful when searching for evidence of current selection on the MHC complex, for example.
         The authors confess that you don't actually have to know everything about every individual in a population to use their de-lifing method. t.coulson@imperial.ac.uk  

533.  Feeding genes to Oreochromis niloticus
         Gene expression in tilapia following oral delivery of chitosan-encapsulated plasmid DNA incorporated into fish feeds. 2005. Ramos, E. A., L. L. V. Relucio and C. A. T. Torres-Villanueva. Marine Biotechnology 7:89-94.
         "DNA delivery into fish is important for transient gene expression, (e.g., DNA vaccination). Previous studies have generally focused on intramuscular injection of DNA vaccines into fish. However, this method is obviously impractical and laborious for injecting large numbers of fishes." The authors report expression of a reporter gene which was fed to tilapia as DNA encapsulated in chitosan.
         "These results suggest that DNA vaccines and other constructs can be easily and cheaply delivered into fishes orally by use of carriers and incorporation into fish feeds." jvrelucio@up.edu.ph  

532.  Statistical significance of wild/hatchery fitness comparisons
         Likelihood-based confidence intervals of relative fitness for a common experimental design. 2005. Kalinowski, S. T. and M. L. Taper. Canadian Journal of Fisheries and Aquatic Sciences 62:693-699.
         An intuitively appealing procedure for comparing the reproductive fitness of animals in the wild is to genotype them (e.g. with microsatellite markers) and then identify and count their offspring at some later time after natural reproduction has been completed. A typical motivation for this type of experiment is to compare the reproductive fitness of two groups, such as wild vs. hatchery fish. The problem addressed in this paper is, how do you establish the confidence limits -- test the significance -- of the outcome of such comparison trials?
         It turns out from simulation that the above experimental design is quite informative even with modest sample sizes. The paper is interesting for another reason too: it includes a subtle discussion of the concept "relative fitness", tied to basic evolutionary theory, in a fishery context. The focus is on fitness itself, not the causal components of fitness, but the authors note that "If selection gradients [e.g. for a quantitative trait] are of interest they can be estimated by fitting a curve to a plot of fitness versus phenotype for the individuals sampled." A computer program for applying the statistical methods to real and simulated data is available at http://www.montana.edu/kalinowski/kalinowski_software.htm   E-mail skalinowski@montana.edu  

531.  Different genes affect fecundity at different ages
         Quantitative trait loci with age-specific effects on fecundity in Drosophila melanogaster. 2006. Leips, J., P. Gilligan and T. F. C. Mackay. Genetics 172:1595-1605.
         A paper cited above (#537) shows that heritability of growth rate (ratio of genetic to phenotypic variance) is different at different ages in tilapia. This is an original piece of work for aquaculture but numerous papers have looked at age-dependent changes in genetic variance in other kinds of organisms. This paper on Drosophila goes deeper into the genetic architecture of age variation in a fitness trait (fecundity).
         "We identified one QTL on the second chromosome and one or two QTL affecting fecundity on the third chromosome, but these QTL affected fecundity only at 1 week of age. There was more genetic variation for fecundity at 4 weeks of age than at 1 week of age and there was no genetic correlation between early and late-age fecundity. These results suggest that different loci contribute to the variation in fecundity as the organism ages."
         Note that in this system, unlike tilapia, there was no genetic correlation between the trait values at different ages. But in the organisms featured in this website there usually is. At the end of their paper the authors ask questions that are very relevant to domestication and captive breeding.
         "Does variation result from the action of a different subset of genes acting on the trait at different ages or does variation arise from differences in the influence of particular alleles at the same genes with age? Do physiological changes with age modulate allelic effects on traits (in a fashion similar to genotype-by-environment interactions)? And if so, what are the relevant physiological changes that alter these allelic effects?" leips@umbc.edu  

530.  Faster growing trout uses feed more efficiently
         Strain differences in feed efficiency measured as residual feed intake in individually reared rainbow trout, Oncorhynchus mykiss (Walbaum). 2005. Silverstein, J. T., M. Hostuttler and K. P. Blemings. Aquaculture Research 36:704-7111.
          Aquaculture geneticists try to develop faster-growing animals, which increases profit because fast growing animals generate more revenue per unit of time (or unit of fixed cost). It would also be useful to develop animals which are more food-efficient, in the sense that they use less food per unit of growth -- as long as there is no serious negative correlation between growth rate and growth efficiency.
         In practical aquaculture the correlation between growth and efficiency is often observed to be positive. Faster-growing animals are more food-efficient when they are harvested, simply because they spend less time reaching standard market weight and therefore waste less energy on maintenance metabolism. We don't know much about possible correlations at a deeper physiological (genetic) level in aquacultural species, although some work has been done in Norway on salmon.
         The usual statistical analysis of correlations between growth rate and food conversion ratio (FCR) or its inverse, food conversion efficiency (or ratio), FCE (or FER) is complicated by the fact that all these ratios have variables in common.
        This study on 3 trout strains and their hybrids obviates the common-variable problem by analysing residual feed intake. "Residual feed intake was calculated as the difference between intake observed and intake predicted on the basis of a bioenergetics model; a low RFI indicates greater efficiency." Fish were reared for a fixed time, not to a fixed weight.
         The authors found significant genetic variation in RFI among the 6 groups, and furthermore, "Lower RFI was associated with higher growth rates (r=-0.38, P<0.05) and greater nitrogen retention (r=-0.82 P<0.001)". This is good news. Faster growing trout used feed more efficiently. jsilvers@ncccwa.ars.usda.gov  

529.  Distinguishing the effects of diversity loss and inbreeding depression
         Relative contribution of inbreeding depression and eroded adaptive diversity to extinction risk in small populations of shore campion. 2006. Vilas, C., E. San Miguel, R. Amaro and C. Garcia. Conservation Biology 20:229-238.
         Inbreeding and loss of genetic diversity are not exactly the same thing.  Although inbreeding and diversity loss occur together in small populations where the only available mates are close relatives, the known deleterious effects of inbreeding can be separated, conceptually as well as experimentally, from the possibly deleterious effect of low diversity per se (e.g. physiological buffering, scope for local adaptation etc.).  It is possible to have a diverse, inbred population in which all individuals self-fertilize but are genetically different  from each other.
         In this paper just such an experiment was set up by generating several types of small population with plants from a single, large outbreeding population. One type, homogenous inbred, consisted of seed from a single self-fertilized plant. A second type, diverse inbred, consisted of seeds from many different self-fertilized plants. A third type, diverse outbred, was a mixture of seeds from crossed parents from the source population and can be thought of as a control.
         The survival and seed production rates of the homogenous and diverse inbred populations were only about half that of  the control, indicating that inbreeding depression is a more serious problem than low diversity per se in this (rather small) field experiment.
         What is diversity per se supposed to do that's good in this context? It provides adaptive diversity -- the raw material for adaptation to different environments. However, even though the grow-out environments differed among populations, the diverse inbred populations did not do well, nor was there any observable family X environment interaction. The authors concluded that inbreeding depression trumped local adaptation in this case. bfcarlog@usc.es