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.

504.  Tilapia mass-spawning increases the rate of inbreeding
         Mating systems and male reproductive success in Nile tilapia (Oreochromis niloticus) in breeding hapas: A microsatellite analysis. 2006. Fessehaye, Y., Z. El-bialy, M. A. Rezk, R. Crooijmans, H. Bovenhuis and H. Komen. Aquaculture 256:148-158.
        Mass spawning in cages (hapas) is a common practice in tilapia aquaculture. Some males and females breed much more than others, which increases inbreeding. How bad is it?
        The PAPA program (Nov-Dec 2003 #446) was used with 11 microsatellite markers for parental identification in this study of tilapia morality in hapas. "Multiple paternity was detected in 70% of the broods, with up to 4 males fertilizing a single clutch. Multiple maternity was also detected in over 30% of the clutches analyzed. There was a very high variance in male reproductive success, with one third of males siring more than 70% of the offspring. Male condition factor had a significant effect on reproductive success with larger males siring a large proportion of offspring."
        The rate of inbreeding was about twice what it would have been under optimal management. Hans.komen@wur.nl  

503.  Parallel evolution of genes and gene expression in whitefish 
        Parallelism in gene transcription among sympatric lake whitefish (Coregonus clupeaformis Mitchill) ecotypes. 2006. Derome, N., P. Duchesne and L. Bernatchez. Molecular Ecology 15:1239-1249.
        Two ecotypes of whitefish, benthic and limnetic, which have diverged in their behaviour, energy metabolism and morphology are found together in countless Canadian lakes. 
        Despite the genetic isolation of the pairs a large number of their genes have evolved  parallel changes in sequence and/or expression profiles in different lakes.
        In particular, "Fifty-one genes (4.3%) showed parallel differential expression between lakes, among which 35 were expressed in opposite directions. Sixteen genes (1.35%) showed true parallelism of transcription, which mainly belonged to energetic metabolism and regulation of muscle contraction functional groups. Variance in expression was significantly reduced for these genes compared to those not showing directionality in parallelism of expression."
        The authors note that their results "add to the growing evidence that parallel phenotypic evolution also involves parallelism at both the genotypic and regulatory level, which may at least partly be associated with genetic constraints."
        As the authors remind us, gene expression is a quantitative trait, so the lower variance of selected traits, relative to unselected traits accords with Fisher's fundamental theorem.
       Compare with Nov-Dec 2003 #441 in which twenty thousand generations of experimental evolution of two bacterial populations also produced many parallel sequence and transcription changes, again with constraints, or at least contingencies of the "if mutation a then mutation b, if not a then c" variety.
        The paper is an excellent model for work with similar objectives. Ttranscription analysis employed a 3557 cDNA gene microarray developed for the Genomic Research on Atlantic Salmon Project (GRASP; Genome Research 14, 478–490, 2004). The statistical analysis, although described rather briefly, is well referenced and ultimately rests its case for significance on a type of randomization test. louis.bernatchez@bio.ulaval.ca  

   502.  Venezuelan vannamei  has improved under selection
           Mass selection and inbreeding effects on a cultivated strain of Penaeus (Litopenaeus) vannamei in Venezuela. 2005. De Donato, M., R. Manrique, R. Ramirez, L. Mayer and C. Howell. Aquaculture 247:159-167.
        "The reproductive stock of the farm was established from three different populations mixed in successive generations (Mexico first generation, Panama second generation, and Colombia third generation)." Eleven generations of mass selection had been completed at the time of writing.
         Growth, survival and FCR all improved substantially over this time. IHHNV (a viral disease which produces deformities) caused trouble in the early generations but disappeared later on. The authors attribute this to a selective purging of genes which produced symptoms of inbreeding depression in the founding stocks. For an explanation of purging see Feb-Mar 2003 #395. dedonato@usa.net  

501.  Extreme selection for MHC diversity
         High MHC diversity maintained by balancing selection in an otherwise genetically monomorphic mammal. 2004. Aguilar, A., G. Roemer, S. Debenham, M. Binns, D. Garcelon and R. K. Wayne. Proceedings National Academy of Science (US) 101:3490-3494.
        "The San Nicolas Island fox (Urocyon littoralis dickeyi) is genetically the most monomorphic sexually reproducing animal population yet reported and has no variation in hypervariable genetic markers." This is  extreme -- no marker variation at all, even in microsatellites and multilocus fingerprints?  Yet the foxes do have extremely high levels of MHC variation, presumably maintained by balancing selection.
        This shows how important MHC diversity can be: the authors estimate that a selection intensity of 0.5 is required to maintain diversity through the severe bottlenecking which is implied by the absence of neutral marker variation. There has to have been a bottleneck severe enough to eliminate microsatellite diversity, and recent enough so that new diversity has not arisen through mutation. This selection is enormously strong compared to other selection intensities which have been estimated in nature. A correlation between MHC diversity and individual fitness components is often observed, but is also often much weaker than one might expect.
        The authors observe that since MHC diversity is uncoupled from microsatellite diversity in this population, microsatellites may not be a good surrogate measure of what is worth preserving in protected populations. They conclude with the comment "Preservation of a diverse array of fitness-related genes, along with neutral variation, might be the key to the long-term survival of endangered populations." See Feb 2002 #286. andres.aguilar@noaa.gov  

500.  Candidate genes not a good way to look for QTLs?  
        Evaluation of candidate genes in the absence of positional information: a poor bet on a blind dog! 2005. Aguirre-Hernández, J. and S. D.R. Journal of Heredity 96:475-484.
        This paper about dogs evaluates a large number of candidate gene studies on retinal disease, of which only 3.4% found a causal QTL (mutation). "On the other hand, five linkage analysis studies have been done on retinal diseases, resulting in three identified mutations and two mapped disease loci."
        A lot more is known about dogs than about any aquacultural species, so we might take this as a useful "heads up". Note #496 where one candidate gene out of many was found to be interesting. ja248@cam.ac.uk    

499.  Positive correlation between growth and survival in vannamei
        Genetic (co)variation in harvest body weight and survival in Penaeus (Litopenaeus) vannamei under standard commercial conditions. 2005. Gitterle, T., M. Rye, R. Salte, J. Cock, H. Johansen, C. Lozano, J. A. Suárez et al. Aquaculture 243:83-92.
        In this study, conducted in tanks and ponds in Colombia, heritability of growth was moderate (around 0.2) and heritability of survival was low (<=0.1). The authors report a positive genetic correlation of around 0.4 between growth and survival.
        Their conclusion is good news for aquaculture: "... selecting for growth will cause a positive correlated response in overall survival. The genetic correlations between body weights and pond/tank survival in different grow-out environments were high, demonstrating low genotype by farm interaction (GXE) for both traits."
        Aquaculture 246:139-149. 2005 is a paper by the same authors on the same population, in which resistance to WSSV had low heritability but nevertheless is negatively correlated with harvest weight. bjarne.gjerde@akvaforsk.nlh.no    

498.   Sex determination in O. aureus
         Two unlinked loci controlling the sex of blue tilapia (Oreochromis aureus). 2004. Lee, B.-Y., G. Hulata and T. D. Kocher. Heredity 92:543-549.
         One of the two proposed sex-controlling genes is a dominant male repressor and the other is a dominant male determiner. Markers closely linked to the genes "have immediate utility for studying the strength of different sex chromosome alleles, and for identifying broodstock carrying copies of the W [male repressor] haplotype".
         The W-markers correctly predict the phenotypic sex of sex of almost all males and 85% of the females in the one family used in the linkage analysis. Tom.Kocher@unh.edu    

497.  Finding hidden genetic barriers in the ocean  . 
        Marine landscapes and population genetic structure of herring (Clupea harengus L.) in the Baltic Sea. 2005. Jørgensen, H. B. H., M. M. Hansen, D. Bekkevold, D. E. Ruzzante and V. Loeschcke. Molecular Ecology 14:3219-3234.  
        The most interesting aspect of this study is the discovery of "two zones of lowered gene flow[among herring spawning groups]. These zones were concordant with the separation of the Baltic Sea into major basins, with environmental gradients and with differences in migration behaviour".
        The analysis features a fascinating procedure and program for identifying genetic "barriers" which has been developed by Manni, Guérard & Heyer (Human Biology 76(2). 2004. 173–190. http://www.mnhn.fr/mnhn/ecoanthropologie/software/barrier.html).
        The BARRIERS program implements a computational geometry algorithm for identifying genetic discontinuities within a geographical coordinate system, that is, for finding locations where genetic distances -- or any other metric, or function of metrics for that matter -- show an abrupt change.
        The authors of the herring paper found that the Manni, Guérard & Heyer algorithm provides insights into geographical structuring which go well beyond those provided by multidimensional scaling, Mantel's procedure and the other more familiar procedures they tried. mmh@dfu.min.dk    

496.  A large-effect QTL for spawning time in trout  
         The candidate gene, Clock, localizes to a strong spawning time quantitative trait locus region in rainbow trout. 2006. Leder, E. H., R. G. Danzmann and M. M. Ferguson. Journal of Heredity 97:74-80.
        It has been known for some time that the optic tectum and the pretectal area of the rainbow trout are major sites of integration of the melatonin signal, express the clock gene, and may act as biological clocks to influence behavioral and endocrine responses in trout (Mazurais et al. J. Comp. Neurol. 422:612-620, 2000).
        In this paper, "Interval mapping was used to identify associations between genetic markers and spawning date effects. ...a strong QTL region was identified in both female and male parents on linkage group RT-8 that explained 20% and 50% of trait [spawning time] variance, respectively. The Clock gene mapped to this region."
        Note that there were 775 markers available for the study and several traits and several candidate genes were analysed, of which only the Clock association was noteworthy. See #500. eleder@ncccwa.ars.usda.gov    

495.   The Kona line of vannamei is indeed susceptible to TSV
         Comparison of four Taura syndrome virus (TSV) isolates in oral challenge studies with Litopenaeus vannamei unselected or selected for resistance to TSV. 2006. Srisuvan, T., B. L. Noble, P. J. Schofield and D. V. Lightner. Diseases of Aquatic Organisms 71:1-10.
        Two well-known Hawaiian shrimp (vannamei)  populations were compared: a specific pathogen free, Taura syndrome resistant commercial line from High-Health Aquaculture (TSR), and the Kona line from the Oceanic Institute, a line which is known to be rather susceptible to this disease and which is often used as an experimental control or "sentinel" line.
         The lab exposed the test animals to a variety of challenge procedures and analytical procedures. Also, four different strains of virus were used.
        The Kona shrimp had lower survival rates when challenged with all four strains. Only one of the viral strains caused lesions in TSR but all 4 did so in Kona. Viral load for three of the four strains was higher in Kona than in the TSR line. thinnarat@hotmail.com  

494.  Analysis of economic/genetic tradeoffs in breed conservation
        Optimum allocation of conservation funds and choice of conservation programs for a set of African cattle breeds. 2006. Reist-Marti, S. B., A. Abdulai and H. Simianer. Genetics Selection Evolution 38:99-126.
        "Several authors have examined the choice of breeds according to their endangerment or their endangerment and contribution to diversity [Nov-Dec 2002 #371, Apr-May 2003 #410] . In other studies the cost of different conservation programs and their effects have been analyzed. Yet, research on how to use the limited funds on the breeds most efficiently, i.e. with the highest conserved diversity possible is scarce."
        Indeed it is.  The procedure described in this paper divides up hypothetical budgets, discounted over 50 years, among 50 African cattle and several conservations objectives including risk of extinction, global genetic diversity, economically important breed-specific traits etc.
        "Pure in situ conservation [giving responsibility to local breeders] was more efficient than cryoconservation or combined in situ and cryoconservation."
        The various hypothetical conservation procedures are quite specific and will be conceptually familiar to practical geneticists. For instance, the pure in situ procedure, "consists of a circular mating scheme, where sires rotate between 10/30 cow groups. Each group consists of five cows and one sire. The cows are owned by farmers and the sires belong to the program. The sires and cows are replaced by one of their offspring every fifth year when the rotation of sires takes place."
        The procedure takes not only the genetic considerations into account but also the economic status of the farmers and countries concerned, and even foreign exchange rates, in what appears to me (a non-economist) as a sophisticated model. The approach is described with a generality which will make it interesting to many sorts of aquaculture and breed conservation schemes. sabine.reist@alumni.ethz.ch    

493.  Reduced selection doesn't result in loss of fitness
        Relaxation of selection with equalization of parental contributions in conservation programs: an experimental test with Drosophila melanogaster. 2006. Rodríguez-Ramilo, S. T., P. Morán and A. Caballero. Genetics 172:1043-1054.
        It is a well known precept (but perhaps less well followed than known) that to maximize the effective population size of an aquacultural or captive broodstock one should equalize the reproductive output of the parents. That is, make sure all males and all female breeders have the same number of offspring. There are other schemes, especially those that use pedigree information to minimize the mean kinship of the breeders (Apr 2004 #473, Feb 2004#455, Nov 2001 #261). The objective of all such schemes is to reduce inbreeding and genetic drift to their lowest feasible level.
        The problem is, if you artificially force breeders to have equal family sizes you are eliminating a lot of individual selection on, among other things, fecundity, mating behaviour, mate choice, early-stage survival and so on, plus, of course, selection between families. Does the relaxation of selection caused by enforced reproductive equality have deleterious long-term effects on fitness?
        It is a worry to take seriously, especially in conservation breeding where the ultimate objective is to re-establish a wild population.
        This experiment on fruit flies, in which selection was relaxed for 38 generations, did not result in a loss of fitness which was significantly greater than losses in the control. (Control lines enjoyed free mating and natural family sizes,  equal reproductive contribution was enforced on the relaxed experimental lines.)
        The main objective of equalization was achieved, "[equalized] lines retained higher gene diversity and allelic richness for four microsatellite markers and a higher heritability for sternopleural bristle number."
        The feared excessive loss of fitness did not happen. "Our results, therefore, provide no evidence to suggest that equalization of family sizes entails a disadvantage on the reproductive capacity of conserved populations in comparison with no management procedures, even after long periods of captivity."
        See Mar 2002 #300 for an experiment with similar objectives which differed both in its design and its outcome. armando@uvigo.es