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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.

492. Detecting disease-marker associations in shrimp
         Genetic markers applied in regression tree prediction models. 2004. Hizer, S. E., T. M. Wright and D. K. Garcia. Animal Genetics 35:50-52.
         The authors of this paper deploy interesting measurement and statistical techniques for finding genetic markers for disease resistance. The viral pathogenic system they work with  is IHHNV infecting Penaeus stylirostris. They use real-time PCR to measure viral load after an IHHNV challenge test. This procedure produces a continuous variable, measured on individuals, and thus has much greater statistical power than the usual percentage mortality, LD50 or other group tests. The statistical technique is a sort of discriminant analysis called "classification and regression tree (CART) modeling".
         Eight RAPD markers were used to discriminate between resistant and susceptible animals and then, in a second experiment which provided cross-classification, to predict the viral load. The prediction was very accurate. As the resistant animals came from the selected broodstock of Super Shrimp Inc., 20 generations removed from their origin in Panama, and the susceptible controls were recently collected in the Gulf of California, the cross-validation actually predicted which population the test animals came from, not disease resistance as a distinguishable characteristic. Nevertheless the procedures are up-to-date and useful. dgarcia@csusm.edu

491.  Regulation of larval gene expression controls final body size
Covariation of larval gene expression and adult body size in natural populations of Drosophila melanogaster. 2003. Bochdanovits, Z., van der Klis, H. and G. de Jong. Molecular Biology and Evolution 20:1760-1766.
         Much of the genetic variation in the major components of fitness is caused by regulation of expression of genes which code for enzymes and other proteins, rather than by variation in the sequence of the protein-coding region.  But until recently it has been difficult to get an experimental grip on the connection between this type of genetic variation and its phenotypic effects. The new expression array technology (Dec 2003 #441) makes it possible to study the connection, although still not easily.
         The quantitative trait studied here, in Drosophila, is adult body size, which varies adaptively among natural populations that live under different temperature regimes. (Adult body size is also important for crustaceans in aquaculture, which is why this paper is reviewed here). The experimental design involved analysis of two populations of isofemale lines (lines descending from a single inseminated female) at two temperatures.
         The authors found that "... larval gene expression correlated highly with adult weight, explaining 81% of its natural variation. [!]  Of the genes that show a correlation of gene expression with adult weight, most are involved in cell growth or cell maintenance or are associated with growth pathways." It seems that the expression of  the 19 genes may not be independent. There is some evidence that there may be a cascade in which only  1 - 3 "master genes" control these 19 genes (see Dec 2003 #441 for a similar phenomenon).
         For those willing to speculate on analogies with arthropods grown in aquaculture, it is interesting that 81% of the variation in Drosophila adult body size is "explained' -- in the statistical sense --  by variation in gene expression at the larval stage. Possibly by a few master genes. One wonders whether there is a phenotypic effect on the larvae as well (larger size?) which might allow early selection for adult size (see Sep 2000 #109). z.bochdanovits@bio.uu.nl

490. Major east-west division in the ancestry of Macrobrachium
         Huxley’s line demarcates extensive genetic divergence between eastern and western forms of the giant freshwater prawn, Macrobrachium rosenbergii. 2004. de Bruyn, M., J. A. Wilson and P. B. Mather. Molecular Phylogenetics and Evolution 30:251-257.
         Macrobrachium rosenbergii is a fresh-water crustacean which lives in brackish water during its earliest developmental stages. The species is farmed in several parts of the world where they have learned how to cook it properly, especially Thailand. As a fresh water species one might expect M. rosenbergii to show strong zoographical disjunctions and this paper on 16S rRNA mitochondrial gene sequence shows that it does.
         Alfred Russel Wallace, the great Victorian naturalist and explorer who conceived the idea of natural selection about the same time as Charles Darwin, noticed that the islands of SE Asia could be divided into two groups, a western group inhabited by wildlife characteristic of Asia and an eastern group inhabited by Australasian wildlife. We now understand that the imaginary line which Wallace drew between these biogeographic regions follows the edge of the Asian continental landmass as it was exposed during the ice-age periods of low sea level. Huxley's Line is a modification of Wallace's Line, running through deeper water and grouping most of the Philippine islands with Malaysia, Eastern Indonesia and Australia
         An east-west grouping of M. rosenbergii has been noted before in morphological and allozyme data. This paper on the evolution of ribosomal gene sequence shows that Huxley's Line separates the Asian and Australasian populations of M. rosenbergii into two clades, or monophyletic groups. Despite the potential for larval dispersal during the salt-water phase these clades of M. rosenbergii have probably evolved independently since the Miocene period, 5 - 12 million years ago. The ancestral population (coalescent OTU) may have lived in the Mekong drainage in SE Asia.  It's nice to see modern sequencing techniques and coalescent theory backing up the old heroes of the Darwinian revolution. Also, now we know what grow out comparisons to try next in practical Macrobrachium aquaculture genetics. m.debruyn@qut.edu.au  

489. Low-level inbreeding depresses oyster growth
The effects of inbreeding on performance traits of adult Pacific oysters (Crassostrea gigas). 2004. Evans, F., S. Matson, J. Brake and C. Langdon. Aquaculture 230:89-98.
         This experimental breeding program found that the growth and yield of two-year-old animals, but not their survival, were significantly depressed by a rather low level of inbreeding, F = 0.065 (as would be found in offspring of parents which share one pair of grandparents). An inbreeding level of F = .2 reduced survival as well. The lower level of inbreeding can build up quickly in randomly mated captive populations of highly fecund animals like oysters  unless precautions are taken, e.g. pedigree records and appropriate mating strategies. evanssan@onid.orst.edu  

488. Heritability of aquacultural traits in cod
Genetic variation for juvenile growth and survival in Atlantic cod (Gadus morhua). 2004. Gjerde, B., B. F. Terjesen, Y. Barr, I. Lein and I. Thorland. Aquaculture 236:1667-1177.
         The prospects for cod farming are looking better and better, now that juveniles can be produced reliably through intensive tank culture. Apparently the limiting factor is mainly the high growout cost. This commercial problem offers worthwhile targets for genetic improvement for traits such as growth rate -- if the traits are heritable.
         In this study two, separate sets of full-sib families were generated from wild-caught adults collected from two regions off Norway. The families were reared separately and weighed 200 days after the eggs had been fertilized. The full-sib heritability of size was moderate within populations (0.3) and somewhat higher across populations (0.5) even though the populations were not statistically different. Variation in survival was not heritable. "For both traits, the estimate of the effect common to full-sibs caused by factors other than additive genetics was quite high (varying from 0.03 to 0.12), indicating environmental effects common to full-sibs caused by the separate rearing of the families. Improvements in rearing technology will likely reduce these environmental effects."
         The statistical methods used to dissect the genetic and environmental common environment effects in this full sib experimental design are interesting and provide a useful model. The authors conclude that selection for size (growth) is worth doing. bjarne.gjerde@akvaforsk.nlh.no  

487. Trojan Frankenmedaka
Transgenic male mating advantage provides opportunity for Trojan gene effect in a fish. 2004. Howard, R. D., J. A. DeWoody and W. M. Muir. Proceedings National Academy of Science (US) 101:2934-2938.
         A Trojan is an artificial construct designed to seduce and beguile itself into a fortress and then deliver a lethal payload. There are Greek Trojans, computer Trojans and genetic Trojans.
         A type of genetic Trojan of concern to conservation geneticists is a transgenic animal which is especially strong in one component of fitness, say mating success, but weak in another, say fertility or survival. The Trojan payload is delivered when transgenic animals escape into the wild, monopolize matings with wild animals and produce unfit offspring. Under certain conditions the Trojan transgene spreading through the population could lead to extinction (Jul 2000 #85, May 2001 #196, Aug 2002 #342). Fear of Trojans is an obstacle to the use of transgenics in aquaculture.
         This experiment on transgenic medaka expressing salmon growth hormone gene shows that in a laboratory setting transgenic males do indeed have a tremendous mating advantage. This is due to their superior size and bullying capabilities. Their offspring, however, have viability problems. The balance of effects is modeled and shown to lead to extinction even though the wild-type (WT) males try various sneaky tricks to try to nullify the size advantage of the transgenics. This sneaky behaviour was about 30% successful.  "Finally, we model the impact of alternative mating tactics by WT males on transgene spread. Such tactics may reduce the rate of transgene spread, but not the outcome."  Predation effects are not included in the validation experiment. See Aug 2001 #224. rhoward@bilbo.bio.purdue.edu  

486. Trading-off immigration against local adaptation
Application of the one-migrant-per-generation rule to conservation and management. 2004. Wang, J. Conservation Biology 18:332-343.
         In practical genetic conservation it is important to know how much migration is required to prevent inbreeding depression while also permitting an adaptive response to weak local selection. Most conservationists have learned that one immigrant per generation is sufficient to prevent serious inbreeding and genetic drift. Sewall Wright's argument leading to this conclusion depends on a long list of assumptions about selective neutrality, population sub-substructure, gene flow et al.
         In this mostly analytical paper J. Wang shows that the one-per-generation rule is actually pretty good even when the assumptions of Wright's model are considerably violated. However, the rule applies to one effective migrant, not one physical migrant (Mar 2002 #307). The two migration rates may be very different in real populations, depending on variation in sex ratio, reproductive success etc.
         Wang discusses the relationship of the effective number of migrants to the actual number of migrants of a particular age and sex and shows that the physical migrants do not always have to be more numerous than the effective migrants. "Rather, translating the elusive Me[effective migration rate] into the manageable M [actual migration rate] depends on the specific causes (e.g., biased sex ratio, reproductive skew) that lead to Ne[effective population number] < N ." Real-world cases in which single immigrants have had large effects on inbreeding and fitness are described in Sep 2001 #235 and May 2003 #400. Wang suggests that when relevant information is insufficient we should stick with Mills and Allendorf's suggestion of between 1 and 10 physical migrant per generation. jinliang.wang@ioz.ac.uk  

485.  Costly heavy-metal resistance soon disappears
Rapid loss of genetically based resistance to metals after the cleanup of a Superfund site. 2003. Levinton, J. S., E. Suatoni, W. Wallace, R. Junkins, B. Kelaher and B. J. Allen. Proceedings National Academy of Science (USA) 100:9889-9891.
         There is a location in the Hudson River which, for 25 years, received waste from a factory making Ni-Cad batteries. An oligochaete (Limnodrilus hoffmeister) which is ecologically important in the area rapidly evolved resistance to cadmium and served as an entry-point for Cd into the food chain. Limnodrilus is a  tubifex worm which is a major benthic food source for higher trophic levels. There appears to be only one gene, encoding a metal-binding protein, involved in the adaptation. (See Mar 2003 #398 for a paper on sequence-level responses to toxicity selection.)
         Then, in the mid 1990s, the site was cleaned up. But was there a lasting negative evolutionary consequence of the pollution, in the form of a population which resists the toxicity of this heavy metal and can transfer it upwards when opportunity arises again after the next general election in the USA?  Apparently we needn't worry about this. "The cleanup ... resulted in the maintenance of resistant forms but then there ensued a rapid loss of resistance in 9–18 generations, showing the potential for ecological restoration to rapidly reduce the potential for trophic transfer of Cd through the ecosystem."
         The authors suggest that the loss of resistance when selection was relaxed is due to strong trade-offs between resistance and both growth and general mortality. See Mar 2002 #300 for another example of the effect of relaxing selection on fitness. levinton@life.bio.sunysb.edu  

484. Trout that tolerate a lot of mercury
Genetic variation of resistance to mercury poisoning in steelhead (Oncorhynchus mykiss) alevins. 2003. Blanc, J. M., J. D. McIntyre and R. C. Simon. Heredity 91:255-261.
         A factorial mating design (all males mated with all females) was used for this challenge test with methylmercuric chloride (CH3HgCl). This type of design permits a reasonably complete analysis of additive genetic effects, common environment and maternal effects using traditional analysis of variance statistical procedures. Heritability of time-to-die in the fry was high (0.6). Heritability of survival, an all-or-none trait, was 0.3. Bioaccumulation of mercury in live and dead fry varied widely but the variation did not show a significant sire effect, i.e. the variation in bioaccumulation was not demonstrably genetic. From this the authors conclude "it seems that resistance to poisoning implies a tolerance to high levels of mercury rather than a limitation of its accumulation".  This is unfortunate for trout-eaters who might prefer to see trout dying of mercury rather than evolving ways to pass it on. See #485 above.  jmb@st-pee.inra.fr  

483. Egg size variation leads to male fitness variation
The early sperm gets the good egg: mating order effects in free spawners. 2004. Marshall, D. J., P. D. Steinberg and J. P. Evans. Proceedings of the Royal Society of London (B):1585 - 1589.
         This paper on sea urchins describes a phenomenon which is interesting in itself and which may be important in other animals which spawn the same way -- by releasing a batch of eggs into the water where they are fertilized by sperm released by a number of males. One would think that this is the closest one could get in the real world to a theoretical, random-mating gene pool. Not so. There is variation in the size of eggs released at the same time, and bigger eggs are fertilized first. Bigger eggs produce bigger and more fit offspring in sea urchins as in many other animals (salmon, May 2003 #408). The leftover unfertilized eggs are smaller so the last male into the pool is a rotten egg (sorry) fertilizes smaller eggs and has inferior offspring.
         One of the consequences is that egg-size variation magnifies the variance of paternal reproductive success and thus reduces effective population number. Another effect may be to reduce the heritability of offspring size in the early stages, and perhaps all the way through development if initial size differences are magnified by competition (Aug 2002 #343, Feb 2004 #458). Thus experiments with planned matings cannot be expected to give the same variance components (or realized selection response) as free-for-all mating in which the parents are identified afterwards by genetic markers. Variation in the numerical component of paternal reproductive success has been noted before in cod (Aug 2003 #423) and red sea bream (Jan 2002 #283), among other animals, but I believe that paternal variation related to egg size has not previously been noticed. See Mar 2002 #304 for another instance of sperm competition. d.marshall@unsw.edu.au  

482. Genetic purification of an endangered population
Pedigree-based assignment tests for reversing coyote (Canis latrans) introgression into the wild red wolf (Canis rufus) population. 2003. Miller, C. R., J. R. Adams and L. P. Waits. Molecular Ecology 12:3287-3301.
         Microsatellites are used to detect introgression of unwanted coyote genes into a rehabilitated wild population of red wolves, in Florida. Animals which are identified as hybrids are either culled or, if they are close to the wolf-coyote geographical frontier, sterilized. Standard statistical assignment tests are used in this paper and the more interesting contribution is the way the reference gene pools are defined.
         The pure coyote gene pool is well sampled and serves as one reference. The genetic composition of the founding red wolves is also almost completely known, but many generations have passed since the founding and a lot of genetic drift must have taken place. So the authors construct hypothetical populations representing the two pure species and 1/4, 1/2, 3/4 red wolf hybrids.  Some pedigree information is available from the early years and this, plus ordinary Mendelian theory, is used in a sort of gene-drop simulation to generate pseudo-distributions of gene frequencies for each of the hypothetical reference populations at various points in their histories.
         Then individual wolves or "wolves" are assigned to one or more of the hypothetical populations using standard procedures. Apparently what works best is to use (coyote) private alleles to make absolute exclusions whenever this is possible, but to use a maximum likelihood procedure when a suspect animal doesn't have private alleles. The expected distribution of the private alleles comes from the simulation.
         This technique might have quite a wide applicability in genetic conservation whenever (a) the genetic composition of a founding population is well known and (b) there is some pedigree or at least effective population size information available since the founding. "These methods may be valuable in cases where reference databases for small populations have aged substantially, pedigree information is available or data are generated from historical samples." mill8560@uidaho.edu  

481. Admirable genetic analysis of disease resistance
Mapping multiple genetic loci associated with Ceratomyxa shasta resistance in Oncorhynchus mykiss. 2003. Nichols, K. M., J. Bartholomew and G. H. Thorgaard. Diseases of Aquatic Organisms 56:145-154.
         It has been known for some time that inheritance of resistance to C. shasta in rainbow trout is polygenic. However, this new study goes far beyond previous ones in the sophistication of its experimental design and statistical analysis. It shows (suggestively, not definitively, because of the small sample size) how genetic mapping and linkage analysis can lead to the identification and possible selection of genes providing resistance to pathogens.
         In summary, the design is based on crossing clonal lines which differ in their resistance, then using androgenesis to produce doubled haploids from the F1 hybrids. (Populations of doubled haploids display all the variation revealed by segregation in the F1 but are homozygous as individuals. Neat trick. See Mar 2002 #309.)  Resistance is analysed as a continuous (time-to-die) and a binary (alive/dead) trait. Several standard varieties of linkage and association analysis were used. The genes found here may be linked (suggestively not definitively, etc) to previously mapped IPNV-resistance genes and to important-sounding lectin and immuno-receptor genes.  krista.nichols@noaa.gov  

480.  Breeding scheme that maximizes allele diversity
         A parallel optimization approach for controlling allele diversity in conservation schemes. 2003. Vales-Alonso, J., J. Fernández, F. J. González-Castaño and A. Caballero. Mathematical Biosciences 183:161-173.
         Here we have a procedure for maximizing the number of different alleles which are conserved in a population, as an alternative to maximizing expected heterozygosity. Allele diversity is known to be a better indictor of population bottlenecks, and some also argue that it is a better measure of the genetic resources a population needs for adapting to novel selection regimes. Most breeding schemes (but not the minimal kinship approach) focus on conserving heterozygosity.  Here a procedure is developed for finding the particular set of parental contributions, out of a larger set of available breeders, which maximizes long-term allelic diversity.
        Since the number of possible combinations of breeders increases exponentially with population size there are severe practical problems if a systematic, sequential approach is used to select candidate breeders. Random trial-and-error isn't efficient either and furthermore tends to locate local rather than global optima.  The authors have developed an optimization algorithm which does the job, i.e. identifies the breeding set which maximizes the retention of allele diversity.
         The procedure is said to be computationally feasible but requires the use of parallel processors. Implementation times decrease linearly with the number of processors. This is not yet a procedure for aquaculture, but should be of interest to serious genetic conservation units in government and universities. See Aug 2001 #212, Oct 2001 #249, Nov 2001 #261, Apr 2004 #473. javier@ait.uvigo.es