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.

I have been asked to post a notice of a meeting which should be of wide interest: Genetic Impacts from Aquaculture: Meeting the Challenge in Europe. This is an international symposium to be held in Bergen, Norway, 2-4 July 2007. http://genimpact.imr.no/ 

612.  Now we can say Penaeus when we mean Penaeus 
         The right to refuse revision in the genus Penaeus. 2007. Flegel, T. W. Aquaculture 264:2-8. 
         Prof. Flegel points out that the revision of the genus Penaeus which was proposed about 10 years ago has caused a lot of confusion since then. He also notes that this confusion is contrary to the spirit of the zoological code of nomenclature, which has stability, uniformity and consistency as primary goals. It appears that we needn't have gone along with the revision after all.
         "Should readers ... wish to carry on with the use of traditional penaeid shrimp binomials, I would like to propose a transitional, compromise practice to improve communications. This would involve acceptance of the sub-genus names by including them in brackets between the genus name Penaeus and the relevant species names, as is recommended by the rules of zoological nomenclature [e.g., Penaeus (Fenneropenaeus) chinensis]." 
         The arguments in the paper are good and the editors of Aquaculture say that they concur with this suggestion. They ask authors to use the traditional Penaeus vannamei in future instead of Litopenaeus vannamei, or else Penaeus (Litopenaeus) vannamei to be absolutely clear. Aquaculturists everywhere who for 10 years have been trying to learn to say Litopenaeus should be proud of having, as usual, played by the rules as they understand them. They can now go back to saying Penaeus. sctwf@mahidol.ac.th 

611.  Inbreeding depresses tilapia fecundity and fry survival 
         Effects of inbreeding on survival, body weight and fluctuating asymmetry (FA) in Nile tilapia, Oreochromis niloticus. 2007.  Fessehaye, Y., H. Komen, M. A. Rezk, J. A. M. van Arendonk and H. Bovenhuis. Aquaculture 264:27-35. 
         The effect of inbreeding on tilapia is surprisingly little known, despite the depth of knowledge about other aspects of the genetics of this fish. The base population in this experiment was a composite of several Egyptian strains of O. niloticus within which several levels of inbreeding were produced by sib mating (F = 0.00 - 0.25). Half-sib matings of the same families were used as an outbred control for additive genetic effects. 
         "In the present study, the significant effects of inbreeding on early life traits such as total number of fry produced, early fry survival and body weight at stocking are consistent with many other studies that observed inbreeding depression in traits of early fitness (e.g. juvenile survival)." The effect of inbreeding on adult traits, especially growth was not very large, and the authors speculate that this might have been due to selective purging of smaller and thus possibly more inbred and less fit individuals during the cold season. The authors also looked at fluctuating asymmetry (Aug 2002 #337) and found that it was not affected by these levels of inbreeding. (See July 2006 #507). Henk.Bovenhuis@wur.nl 

610.  What does heterosis actually do at the level of gene function? 
         Transcriptomic analysis of growth heterosis in larval Pacific oysters (Crassostrea gigas). 2007. Hedgecock, D., J.-Z. Lin, S. DeCola, C. D. Haudenschild, E. Meyer, D. T. Manahan and B. Bowen. Proceedings National Acad. Science USA 104:2313-2318. 
         The paper starts with a brief review of the many possible physiological causes of hybrid vigour (heterosis). It then introduces a high-powered technique for looking at what actually does go on, at the level of gene expression. The heart of the technique is megacloning on glass microbeads instead of within biological hosts in a procedure called MPSS ("Massively Parallel Signature Sequencing"; ref S. Brenner 2000). Approximately 4/5 of the paper elaborates on the generation and analysis of MPSS data. The authors say "MPSS offers several advantages for organisms with poorly characterized genomes, such as the oyster: It requires no previous sequence information, it is comprehensive and quantitative, and it detects rare messages...and small differences in expression among genotypes."  The results of the study are surprising and important. 
         "The functional genomic approach ... reveals patterns of gene expression ... which are not anticipated by classical quantitative genetic theory." These include dominance for low expression and underexpression of genes in hybrids. Only a small proportion of the genes (that is, gene transcripts) are classically additive in their expression with hybrids exactly intermediate between the pure lines. A small proportion of the genes are responsible for major differences in growth rate. 
         The authors speculate that genes affecting protein metabolism may be extremely important in this regard. (See inbreeding transcriptome Dec 2006 #576.) It is impossible to say whether these surprising results are peculiar to high-fecundity, "elm/oyster" species (Nov 2001 #259). In any case if non-additivity is this important it should be taken seriously in breeding programs for prolific species like oysters or carp (see #601, below for a paper on the importance of non-additive inheritance in carp). dhedge@usc.edu 

609.  Genetic resistance to a salmon parasite 
         Identification of genetic markers associated with Gyrodactylus salaris resistance in Atlantic salmon Salmo salar. 2006. Gilbey, J., E. Verspoor, T. A. Mo, E. Sterud, K. Olstad, S. Hytterod, C. Jones et al. Diseases of Aquatic Organisms 71:119-129. 
         It appears that resistance to the Gyrodactylus parasite is under strong genetic control in Atlantic salmon, that regional genetic differences between salmon populations are heritable, and that resistance is a candidate for rapid selective improvement in aquacultural broodstocks. This is the conclusion of a study which adopted a "screening approach [linear modeling of associations between markers and parasite load] in order to identify molecular markers linked to QTL influencing G. salaris resistance in B1 backcrosses of Baltic and Scottish salmon". 
         The study identified "10 genomic regions associated with heterogeneity in both innate and acquired resistance, explaining up to 27.3% of the total variation in parasite loads". Selection programs could presumably be direct when broodstocks are exposed to the parasite in their natural environment, or indirect, marker-assisted selection when they are not. gilbeyj@marlab.ac.uk 

608.  No difference among tilapia strains? 
         Comparative digestion efficiencies in conventional, genetically improved and genetically male Nile tilapia, Oreochromis niloticus (L.). 2007. Mamun, S. M., U. Focken and K. Becker. Aquaculture Research 38:381-387. 
         This comparison of feed digestibility and growth rates among several well-known tilapia strains did not go on very long but had interesting results. The three strains were GIFT (from the Philippines), genetically male Nile tilapia and "conventional" mixed-sex tilapia (both from the University of Göttingen, Germany). Fish were reared individual from around 50 to around 80 g. 
         How much better were the improved strains? "At the end of the experiment, there were no significant differences (P<0.05) in average percentage growth ..., growth rates or feed utilization efficiencies between the three tilapia groups. We conclude that the higher growth claimed for improved GIFT and GMNT as compared with [conventional strain], if ever existing, cannot be attributed to higher nutrients or energy digestibility." Perhaps one can explain away these results by saying that individual rearing is an unrealistic environment -- but why should real genetic differences be hidden in this environment? See June 2000 #72 for another tilapia strain comparison. [K. Becker] inst480b@uni-hohenheim.de 

607.  Avoiding false positive IHHNV assays 
         PCR assay for discriminating between infectious hypodermal and hematopoietic necrosis virus (IHHNV) and virus-related sequences in the genome of Penaeus monodon. 2007. Tang, K. F. J., S. A. Navarro and D. V. Lightner. Diseases of Aquatic Organisms 74:165-170. 
         False positive assays for IHHNV can cause a lot of trouble in aquaculture, up to and including denial of specific pathogen free status, forced destruction of a broodstock and quarantine or sterilization of farms. The usual PCR assay can amplify IHHNV-like DNA sequences which are integrated into the shrimp genome and not part of a dangerous, infective virus -- although at some past time they used to be. This paper reports on PCR primer sequences which can distinguish between integrated IHHNV (false positive) and real, functional viral IHHNV. The Penaeus monodon came from Australia and Africa but the phenomenon may occur elsewhere. 
         "This assay can reliably distinguish IHHNV DNA from shrimp DNA: it only detects IHHNV.... [it] has a sensitivity equivalent to a PCR assay commonly used for detecting IHHNV in Litopenaeus vannamei, and can be used for routine detection." fengjyu@u.arizona.edu 

606.  Outbreeding in not a problem, generally speaking 
          What is the fitness outcome of crossing unrelated fish populations? A meta-analysis and an evaluation of future research directions. 2007. McClelland, E. K. and K. A. Naish. Conservation Genetics 8:397-416. 
         Outbreeding depression is defined as the loss of mean fitness that may occur when populations are hybridized. Several genetic processes might reduce fitness in hybrids, including loss of local adaptations and/or disruption of co-adapted gene complexes. Fear of outbreeding drives a lot of discussion and policy relating to conservation of fish populations and habitats. Is it as severe a problem as research grant proposals often suggest? 
         This meta-analysis of published studies on outbreeding in fish included 576 comparisons of parents and first-generation (F1) hybrids, and 94 comparisons of F2 hybrids. Perhaps surprisingly, the result of outbreeding is generally positive. The analysis was not statistically conclusive however, mainly because of gaps in the data. For example there have not been many studies of F2 generation hybrids in natural or stressful environments. Nevertheless, it is clear that in most studies where there is any demonstrable effect at all outbreeding is beneficial, and especially beneficial in the case of morphological traits such as body size. Beneficial outbreeding has been noted before, e.g. Dec 2006 #570. Contrast this result with the results of an inbreeding meta-analysis (Apr 2007 #593). emcclell@u.washington.edu 

605.  Do you hate Bonferroni? There is hope. 
         Beyond Bonferroni: Less conservative analyses for conservation genetics. 2007. Narum, S. R. Conservation Genetics 7:783-787.
         When you scan the results of a set of tests hoping to find one that is statistically significant, you have to apply a correction that accounts for the number of tests being performed. This is because the people reviewing your paper know that a targeted significance level which is appropriate for one test (0.05, say) has to be reduced for multiple tests in order to avoid a lot of false positives. Within a set of 100 tests an individual test would only be significant at the 0.05 level if it achieved a probability <0.0005 -- according to Bonferroni. This is a hard standard to meet and people looking for publishable results really dislike Bonferroni. 
         Of course there is a real issue involved. Bonferroni's correction effectively reduces the risk of finding that populations are different when they are really are not, but it magnifies the risk of finding that populations are the same when they really are different. This useful paper applies to situations where one is looking at a set of multiple pairwise comparisons, such as genetic distances among populations inferred from microsatellites, or differential gene expression in microarrays. The correction procedures analysed in the paper are collectively called FDR (false discovery rate). 
         The FDR procedure recommended by the authors increases the critical significance test value from 0.003 (Bonferroni corrected) to 0.013 (FDR corrected) in two published sets of data. The authors caution, however, that the choice of procedure depends on the situation, specifically on the relative cost of false positive vs. false negative conclusions. Bonferroni still has a place. But in aquaculture there may be little to lose by replacing one strain with another which is really no better, but a lot to lose if a real difference of 10% is overlooked in a multiple comparison growth trial. So this paper is very helpful. (See Feb 2007 #578 for statistical power analysis software.). nars@critfc.org 

604.  A possible mechanism of temperature-dependent maleness 
         Temperature sex reversal implies sex gene dosage in a reptile. 2007. Quinn, A. E., A. Georges, S. D. Sarre, F. Guarino, T. Ezaz and J. A. M. Graves. Science 316:411. 
         Techniques for producing all-male tilapia in aquaculture are valuable and there has been a lot of interest in a recent paper on the heritability of temperature-dependent sex in Oreochromis niloticus (Oct 2006 #550, April 2007 #594). This paper proposes an underlying mechanism which may be relevant even though it was developed for a lizard, Pogona vitticeps. 
         Females of this reptile are heterogametic (ZW) like they are in the tilapia species Oreochromis aureus, whereas males are heterogametic (XY) in O. niloticus. In vitticeps and niloticus, high temperature induces the development of individuals which have the phenotype of the heterogametic sex even though they do not carry the appropriate sex chromosome (W in vitticeps, Y in niloticus). The authors propose an explanation for development which involves temperature-dependent gene dosage. 
         In their hypothesis for P. vitticeps, the male-determining gene is present on the Z chromosomes so the homogametic sex has two copies and the heterogametic sex only one. The gene product is temperature sensitive. Then "At optimal (intermediate) incubation temperatures, the gene product is fully active [making females], but it is progressively inactivated at more extreme temperatures. In ZW individuals, the total activity of the gene product is always half that of ZZ individuals. Activity exceeds a threshold level for male differentiation only within the optimal temperature range of ZZ individuals. At all other temperatures, female development proceeds. Thus, the phenotypic sex ratio increases from 50% females at intermediate temperatures to 100% females at temperature extremes." 
         An analogous mechanism niloticus -- for which there is no evidence -- would merely exchange "male" for "female" and "Y" for "W" in all of the above. Phenotypic sex then becomes a threshold phenomenon with genetic variation possible both in the temperature sensitivity of the Z (or X) gene product and in the threshold of the gene cascade which leads to development of phenotypic sex. One guesses that selection could move either or both of these parameters of gene expression. quinn@aerg.canberra.edu.au 

603.  A well-thought-out captive breeding plan for an endangered fish 
Genetic aspect in broodstock management of the critically endangered Mekong giant catfish, Pangasianodon gigas in Thailand. 2007. Sriphairoj, K., W. Kamonrat and U. Na-Nakorn. Aquaculture 264:36-46. 
         The Mekong Giant Catfish has some aquaculture potential in Thailand and is esteemed there for spiritual reasons as well. Unfortunately the wild populations are seriously at risk. The authors of this paper present a well-thought-out management program for conserving captive broodstocks of the Giant Catfish, and, by extension, other species as well. 
         The underlying concept is to maximize the effective population size "dynamically" by minimizing the kinship of matings in each generation (see minimal kinship selection, Apr 2004 #473, Aug 2006 #524). Their proposed breeding program starts with a microsatellite assay of genetic diversity and an assignment of the founding, wild breeders into families based on their inferred kinship (see e.g. Jul 2007 #512). An initial round of matings is performed to increase and stabilize the initial diversity (Jan 2002 #283). Matings in the following generations are optimized to minimize inbreeding and drift. 
         How should the matings be optimized over the long term? The authors cleverly address this question by using the simulation program BOTTLESIM (http://www.public.iastate.edu/~fjanzen ) to work out the long term consequences of alternative mating strategies. They found that matings based on minimal kinship are much better than random mating. "A long-term management plan simulation using the BOTTLESIM program showed that if a random mating scheme is adopted Ne should be kept at 100 in order to preserve > 90% [of the allele number] for four generations (120 years). Applying the MK (minimal kinship) selection for only the first generation can reduce Ne to > 30 individuals and can retain > 90% [of the allele number] throughout the same period. uthairatn@yahoo.com 

602.  Effect of fishing on the evolution of cod 
         Evolutionary response to size-selective mortality in an exploited fish population. 2007. Swain, D. P., A. F. Sinclair and M. Hanson. Proceedings Royal Society (B) 274:1015-1022. 
         The idea that size selective fishing induces an evolutionary response which is detrimental to the fishery has been around for some time. Although the phenomenon has been demonstrated in experimental set-ups (Aug 2002 #345, Jul 2006 # 508),  real-world evidence has been less than persuasive. It has not been easy to go beyond correlation (the mean body size of the catch is getting smaller and fishing selectively destroys large breeders, therefore small body size is caused by selective fishing). 
         The problem is that there are many environmental, ontogenetic and technological reasons why body size of fish might be decreasing nd real proof of genetic changes requires pedigree information which is unobtainable. This paper doesn't have pedigree data on wild cod populations either, but it does control for two major environmental effects on growth, temperature and density. 
         What really helps the argument along is that the authors estimate selection differentials quantitatively and show that there is a correlation between size-selective mortality in one generation and the difference in growth between this generation and the following one, after statistically accounting for the two environmental variables. Furthermore, size selection was sometimes positive and sometimes negative during the three decades covered by the analysis, and the sign of the change between generations followed suit. Data were obtained by back-calculation from a 30-year collection of cod otoliths from the southern Gulf of St. Lawrence. 
         As the authors say, "This adds further weight to the case for adopting an evolutionary perspective in fisheries management. Management regimes that take into account the evolutionary consequences of fishing are needed in order to develop sustainable fisheries." swaind@dfo-mpo.gc.ca 

601.  Carp genetic improvement by hybridization, not selection 
         Additive, dominance genetic effects for growth-related traits in common carp, Cyprinus carpio L. 2006. Wang, C.-H., S.-F. Li, S.-P. Xiang, J. Wang, Z.-G. Liu, Z.-Y. Pang, J.-P. Duan et al. Aquaculture Research 37:1481-1486. 
         This interesting paper analyses the results of a diallel cross between three well-differentiated strains of red-colored common carp, in China. The diallel is an experimental design in which all strains are crossed in all possible combinations. Unlike the tilapia diallel cross described in Oct 2006 #547, this carp experiment found that most of the genetic variance for body weight and several other traits was non-additive and could be ascribed to dominance. 
         "In these traits, it would be difficult to obtain progress by direct selection, but it may be easy to obtain heterosis through crossing and hybridization among varieties." The authors suggest specific hybrids which would give particular shapes (deeper or longer), for example. Note #610, above, which reports significant non-additivity at the transcription level in hybrid oysters, which also produce huge numbers of offspring. sfli@shfu.edu.cn