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.

453.  The first shrimp anti-viral gene and protein
         PmAV, a novel gene involved in virus resistance of shrimp Penaeus monodon. 2003. Luo, T., X. Zhang, Z. Shao and X. Xu. FEBS Letters 551:53-57.
         Very often when a farmed shrimp population is commercially wiped out by WSSV, a few of the animals survive. One would like to use them in a breed-the-survivors broodstock improvement program but this can rarely be done, because the survivors are assumed to be both infected and infective. The alternative approach to capturing the genetic superiority of survivors -- if indeed they are genetically superior -- is to breed their relatives. This approach, usually in the form of between-family selection, often turns out to be either impossible or ineffectual in practice. However, if resistance genes can be identified one could select the individuals which carry them without exposing animals to the disease. Thus the search for disease resistance genes, or markers closely linked to such genes, is an important goal for aquaculture genetics. The relative inefficiency of marker assisted selection (MAS)  noted in May 2003 #399 is not relevant if there is no practical alternative.
         The authors of this paper examined a survivor from a WSSV infected farm pond in China and, by using a differential cDNA procedure, identified a gene which produces a lectin-like anti-microbial polypeptide. (See Jul 2000 #81 and Jan 2002 #282 for other differential cDNA experiments, and see May 2000 #55, May 2002 #319 and Oct 2002 #349 for more about anti-microbial polypeptides.) The cDNA resembles a lectin but apparently has no close affinity with anything previously reported. The gene fragment was cloned and expressed as a recombinant protein in E. coli.
         "[The recombinant protein] displayed a strong antiviral activity in inhibiting virus-induced cytopathic effect in fish cell in vitro. Moreover, a native PmAV protein was isolated from shrimp hemolymph by immuno-affinity chromatography and confirmed by Western blot." The native protein was in the hemolymph, not attached to the WSSV, and neither it nor the recombinant protein caused agglutination. From this the authors infer that however it works, the molecule is not a recognition factor and does not inhibit attachment of the virus to the cell membrane (or at least doesn't do so directly). xxu@public.xm.fj.cn

452.  Why YY tilapia supermales don't produce 100% male offspring
         Sex ratios in the progeny of androgenetic and gynogenetic YY male Nile tilapia, Oreochromis niloticus L. 2004. Ezaz, M. T., J. M. Myers, S. F. Powell, B. J. McAndrew and D. J. Penman. Aquaculture 232:205-214.
         This new paper from the Stirling group adds considerably to our understanding of the "YY Supermale" procedure for producing all-male tilapia (Oct 2003 #435, Mar 2003 #393, Jun 2002 #332). It is no secret that commercial YY breeding programs do not, in fact, produce solely male tilapia, although the sex ratio is strongly biased in that direction. The public-perception risk associated with hormonal sex reversal makes it worthwhile to find out why YY supermale technology doesn't work perfectly, and then fix it.
         Temperature modifies the sex ratio (Jan 2002 #282) and it is strongly suspected that there are sex modifying genes in the genetic background, outside the XX-XY sex determination system (Oct 2003 #435). The experiments reported here comprise progeny tests on offspring of YY males produced by androgenesis and by mitotic gynogenesis. "The factor(s) that cause departures from the sex ratios predicted by chromosomal sex determination appear to be autosomal, heritable, polymorphic and able to influence sex ratios in both directions [too many females or too many males] . Furthermore, the results suggest that YY and XX lines could be developed in which such factors had been selected against, for example, by elimination of families showing departures from monosex progeny." d.j.penman@stir.ac.uk  

451. AFLP markers better than microsatellites 2003. Campbell, D., P. Duchesne and L. Bernatchez. Molecular Ecology 12:1979-1991.
         This case study (on whitefish) "showed that given a comparable analytical effort in the laboratory, AFLP were much more efficient than the microsatellite loci in discriminating the source of an individual among putative populations. AFLP resulted in higher assignment success at all levels of stringency and the log-likelihood differences between populations obtained with AFLP for each individual were much larger than those obtained with microsatellites. These results indicate that research involving individual-based population assignment methods should benefit importantly from the use of AFLP markers, especially in systems characterized by weak population structuring." See Aug 2003 #417. The point is, AFLPs are easier than microsatellites to find and score in large numbers, and they are more reliable than the earlier RAPD markers. The AFLP statistical analyses were carried out with AFLPOP, Duchesne & Bernatchez's Excel program available free at http://www.bio.ulaval.ca/contenu-fra/professeurs/Prof-l-bernatchez.html .  Microsatellite analyses were done with Cornuet's GENECLASS. Louis.Bernatchez@bio.ulaval.ca .  

450.  Zeroing in on tilapia MHC2003. Cnaani, A., B.-Y. Lee, M. Ron, G. Hulata, T. D. Kocher and E. Seroussi. Animal Genetics 34:390-391.
         Two loci in the Type I MHC were found to be closely linked to each other, on linkage group 18, close to a couple of published microsatellite markers. This could be useful information for marker assisted selection and other studies on disease resistance in this species. The most recent tilapia linkage map can be found at http://hcgs.unh.edu.comp . The major histocompatibility locus is currently a major focus of fish genetics research. See Mar 2003 #398, Oct 2003 #434 and other citations mentioned therein. seroussi@agri.huji.ac.il .  

449.  Evaluation of computer programs for estimating genetic relatedness
         Maximum-likelihood estimation of relatedness. 2003. Milligan, B. G. Genetics 163:1153-1167.
         The effectiveness of all the current genetic relatedness estimators is reviewed here. Microsatellite-based estimators are potentially useful substitutes for pedigree records during the founding of conservation and aquacultural populations (Jan 2002 #283, Mar 2002 #303, Jan 2003 #375, Aug 2003 #425 and #448 below). The maximum-likelihood (ML) estimator of Thompson (1975; Ann. Hum. Genet. 39: 173–188) was used as a benchmark. Other relatedness estimators include Ritland (Dec 2000 #142), Wang (May 2002 #320), Lynch & Ritland, Queller & Goodnight etc.
         The Thompson ML turns out to have a lower standard error but to be more biased. However, steps can be taken to remove the bias which in any case is not large. "Although some nonlikelihood estimators exhibit better performance with respect to specific metrics under some conditions, none approach the high level of performance exhibited by the likelihood estimator across all conditions and all metrics of performance." The author does not mention whether he will give out the C++ program he wrote to calculate the Thompson ML estimator. See Sept. 2001 #227 for another review of relatedness estimators. brook@nmsu.edu  

448. Microsatellite relatedness estimator used for minimal kinship selection Paralichthys olivaceus. 2004. Sekino, M., T. Sugaya, M. Hara and N. Taniguchi. Aquaculture 233:163-172.
         Minimal kinship breeding can help conserve genetic diversity in small populations (Nov 2001 #261, Aug 2002 #335). In MK breeding one identifies and selects breeders that are least related (in the genealogical sense) to the population as a whole, and thus most likely to be carrying unique genes. The MK procedure has become popular for managing rare animal populations in zoos, where loss of genetic diversity is often an acute problem. It was shown several years ago (Jan 2002 #283) that microsatellite relatedness estimators could also be used for MK breeding in aquaculture and genetic conservation when accurate pedigrees are not available.
         The authors of this paper apply the procedure to a population of Japanese flounder. It worked reasonably well, although apparently not as well as in (Jan 2002 #283), perhaps because the hard-to-program Ritland estimator and/or maximum likelihood estimators of genetic relatedness (see #449 above) were not used. sekino@affrc.go.jp  

447.  Diversity is lost when a hatchery is founded
         Loss of genetic variation at microsatellite loci in hatchery produced abalone in Australia (Haliotis rubra) and South Africa (Haliotis midae). 2004. Evans, B., J. Bartlett, N. Sweijd, P. Cook and N. G. Elliott. Aquaculture 233:109-127.
         The first hatchery generations of abalone were missing an estimated 35% - 62% of the microsatellite alleles present in the wild populations from which they were founded. However, this substantial loss of genetic diversity during the founding of the population did not noticeably decrease overall heterozygosity. Allele diversity is known to be the best indicator of the genetic consequences of small population size and biased sampling of founders. The diversity lost here was comparable to or even greater than that reported in May 2003 #406 during the founding of an Atlantic halibut hatchery broodstock. nick.elliott@csiro.au    

446.  Evaluation of computer programs for family identification
         Methods of parentage analysis in natural populations. 2003. Jones, A. G. and W. R. Ardren. Molecular Ecology 12:2511-2523.
         This is a useful comparative evaluation of the current crop of  programs for identifying parent-offspring groups on the basis of microsatellite and other genetic markers. The authors say, "Our goal is to provide a comprehensive guide to the existing methods of analysis, with a particular emphasis on those techniques that have been implemented into readily available computer software packages. Our intent is to direct scientists interested in parentage analysis to the correct set of analytical tools for their particular problems." And that is what the authors do. adam.jones@biology.gatech.edu

445.  Inbreeding depression is more serious under natural conditions
         Captivity masks inbreeding effects on male mating success in butterflies. 2003. Joron, M. and P. M. Brakefield. Nature 424:191-194.
         Populations of butterflies were inbred to three levels,  F = 0, F = 0.25 and F = 0.375. In laboratory cages inbred males had somewhat lower mating success than outbred males. Although small the effect was statistically significant, i.e. not mere bad luck. In a nearly-natural greenhouse environment inbreeding depression was much larger, a depression of approximately 50% for males inbred to F=0.375. The authors say that "Our results have important implications for conservation and for studies of sexual selection because they show that the behaviours underlying patterns of mating can be profoundly influenced by a history of inbreeding or by any restraining experimental conditions".
         It is not clear whether the captive environment represented by aquaculture (including fish stocking programs) should be considered more or less "constraining" than the natural environment, but my guess is that it is more constraining. Constraints on mating behaviour in captivity may have negative genetic consequences other than through inbreeding, e.g. by interfering with MHC-based choice of mates (Aug 2001 #221).  See Aug 2003 #422 for another study of inbreeding depression in the wild, Jun 2000 #71 for the effect of inbreeding on shrimp, and Apr 2001 #185, May 2001 #193 and Oct 2002 #347 for other inbreeding experiments on this species of butterfly. See #442 below for inbreeding effects on salmon behaviour. m.joron@ucl.ac.uk  

444.  Beauty is heritable, in trout
         Big and beautiful? Quantitative genetic parameters for appearance of large rainbow trout. 2003. Kause, A., O. Ritola, T. Paananen, U. Eskelinen and E. Mäntysaari. Journal of Fish Biology 62:610-622.
         Body condition, body shape, skin colour and spottiness of  Oncorhynchus mykiss showed reasonably high heritabilities (0.3 - 0.5) in this Finnish study, which bodes well for aquacultural breeders interested in selecting for these traits. Furthermore, the correlation between body weight and condition factor was positive, i.e. no troubling tradeoffs to worry about. Traits which required subjective evaluation, such as colour, were scored on a categorical scale by trained observers, then converted to an underlying continuous scale for genetic analysis. Apparently this worked: "A fast method was developed to visually evaluate the appearance of thousands of individuals, even under harsh field conditions." antti.kause@mtt.fi  

443.  Lower diversity means lower fitness, in general
         Correlation between fitness and genetic diversity. 2003. Reed, D. H. and R. Frankham. Conservation Biology 17:230-237.
         This paper reports the results of a meta-analysis of 34 published studies in which there were simultaneous estimates of fitness (or a component thereof), population size and two important measures of genetic variability: heritability of quantitative traits and/or heterozygosity at neutral marker loci.  "The mean weighted correlation between [both] measures of genetic diversity, at the population level, and population fitness was 0.4323. The correlation was highly significant and explained 19% of the variation in fitness. "Our study strengthens concerns that the loss of heterozygosity has a deleterious effect on population fitness and supports the IUCN designation of genetic diversity as worthy of conservation." dreed@rna.bio.mq.edu.au  

442.  Lower genetic diversity means lower aggression
         Aggressiveness is associated with genetic diversity in landlocked salmon (Salmo salar). 2003. Tiira, K., A. Laurila, N. Peuhkuri, J. Piironen, E. Ranta and C. R. Primmer. Molecular Ecology 12:2399-2407.
         It is not unreasonable to expect that fitness and aggression are positively correlated in natural populations of salmon. The authors of this paper predicted the genetic diversity of offspring from microsatellite data collected on the parents. Fry which were predicted to have high genetic diversity (by several measures) were more aggressive than those predicted to have low diversity. "Salmon fry with low estimated genetic diversity were significantly less aggressive than fry with high estimated genetic diversity. Closer analysis of the data suggested that this difference was due to differences in more costly acts of aggression." The mating design used in this experiment resulted in the fry having low genetic diversity and low aggression also being significantly more inbred than animals with high diversity & aggression. Thus, as is so often the case, the question whether the results are caused by inbreeding depression or some other consequence of low genetic diversity, or even by kin-recognition, remains to some degree open. See #445 above for inbreeding effects on male butterfly behaviour. craig.primmer@helsinki.fi  

441. A long-term perspective on genetic management
         Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. 2003. Cooper, T. F., D. E. Rozen and R. E. Lenski. Proceedings National Academy of Sciences (US) 100:1072-1077.
         It has become possible to observe the expression of many genes simultaneously and watch them switch on and off during normal development of an organism, or while it attempts to cope with pathogens or changing environments. Knowledge of the pattern and sequence of gene expression will increase our basic understanding of adaptation to life's contingencies and, we hope, will also eventually assist in the selective improvement of broodstocks (aquaculture) and identification of evolutionarily significant populations (conservation). Experiments on gene expression already noted here are Sep 2001 #233, May 2002 #319 and Jan 2003 #377. There will be a lot more of this kind of work.
         The above-cited studies, on aquacultural species, involved direct sequencing of cDNA one clone at a time. This is a time consuming procedure.  Much faster analysis of gene expression is possible for a humans and a few model organisms with a procedure known variously as genome chip, biochip, DNA chip, DNA microarray, or gene array. (Note that since GeneChip® is a registered trademark genechip shouldn't be used as a generic term, at least within earshot of Affymetrix Inc.)  In principle it's simple: probes for the coding regions of thousands of genes are attached to a solid substrate in a rectangular array. When labeled cDNA or cRNA from a target organism is flooded over the array it hybridizes to some of the probes. The amount of label at each site in the array is measured, and from this measurement it is possible to estimate the activity of the genes which were switched on and working in the target, even genes with unknown biological functions. Construction of a DNA microarray is a complex industrial process and the equipment for doing it is not available off-the-shelf. DNA microarrays are sold commercially, not the equipment for making them.
         The authors of this paper allowed populations of the bacterium E. coli to evolve for 20,000 generations in a glucose-limited medium, and then used a DNA microarray carrying probes for every gene in the E. coli genome. Let us think of this as a long-term experiment in conservation genetics. (If a comparable experiment were to be done on Atlantic salmon, 20,000 generations would carry it most of the way through the coming ice age, by which time salmon DNA microarrays should be available for purchase.)
         The intrinsic rate of population increase, r was higher in both evolved bacterial clones, showing that adaptive evolution to this classic evolutionary challenge did occur. The expression patterns of 59 genes changed relative to the ancestral population -- the same 59 genes in both clones, even though the clones evolved in isolation from each other. This seems amazing. Could the evolution of isolated populations really be so consistent and predictable?
         Well, yes and no. It turns out that the expression of many of the 59 genes is controlled by a small set of regulatory genes. A mutation in one of the regulatory genes was identified which caused most of the changes in expression in one population. When transferred into the ancestral population the mutation changed the expression pattern of the whole regulon, as predicted, and also increased r, as predicted. But when the mutation was transferred into the other evolved population it did not have these effects. In the second population, a different, still unidentified, regulatory mutation caused the 59 changes in expression.
         So different populations, following different evolutionary paths, converged on the same functional solution to their environmental problem. Furthermore, after one possible solution to the evolutionary challenge was found, the alternative solution was blocked or pre-empted. If the transgenic "evolved hybrid" is actually less fit than its evolved host -- something the authors do not mention -- we have observed the evolution of outbreeding depression. cooperti@msu.edu