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.

528. Domarker-based paternities estimate heritability well enough to be useful?
         How do misassigned paternities affect the estimation of heritability in the wild? 2006. Charmantier, E. and D. Réale. Molecular Ecology 14:2839-2850.
         In this simulation study the effect of mis-assignment was actually not too bad. Furthermore -- and this is beneficial in most studies -- the effect is to underestimate heritabilities. "These analyses suggest that the bias induced by misassigned paternities on heritability estimation depends on the level of heritability and the rate of paternity error. Typical rates of extra-pair paternities in birds (around 20% of offspring) should result in an underestimation of heritability of less than 15% when estimated over a minimum of 100 broods." anne.charmantier@zoology.oxford.ac.uk

527. Vannamei candidate genes for growth don't actually affect growth
         SNP analysis of AMY2 and CTSL genes in Litopenaeus vannamei and Penaeus monodon shrimp. 2005. Glenn, K. L., L. Grapes, T. Suwanasopee, D. L. Harris, Y. Li, K. Wilson and M. F. Rothschild. Animal Genetics 36:235-236.
         The authors studied two candidate genes for growth in shrimp, one (AMY2) believed to affect digestive function and the other (CTSL) the intermolt cycle. Several single nucleotide polymorphisms (SNPs) were found to be segregating in a study population of Kona line P. vannamei. There was, however, no significant association between variation in growth rate and variation in the growth- and digestion-related candidate genes in this population. The experiment was very small, as the authors point out. The negative result might be an instance of the possible inefficiency of candidate gene studies in general, as proposed in June 2006 #500. mfrothsc@iastate.edu

526. Mating to minimize inbreeding during mass selection
         Effect of different mating designs on inbreeding, genetic variance and response to selection when applying individual selection in fish breeding program.  2006. Dupont-Nivet, M., M. Vandeputte, H. P. and B. Chevassus. Aquaculture 252:161-170.
         This useful simulation suggests how to mate fish or crustaceans, in an aquaculture selection program, so as to minimize long-term inbreeding. It is known that the best procedures use pedigree data and arrange matings based on kinship . But in practical aquaculture pedigrees are often not available so what can one do?
         In this simulation, factorial designs (s sires each mated to d dams producing s*d families) worked better than nested designs (each sire mated to a different set of N dams, producing s*N families, which were better than pairwise matings. "When possible, partial factorial mating (FS) designs seemed to be a good compromise to achieve high genetic responses while preserving genetic variability." A paper noted in Mar-April 2004#476 reaches similar conclusions. Of course, the more families the better.
         Note that in accord with general theory this simulation shows that the arrangement of matings does not make a large difference in inbreeding over the long term, other things being equal. In practical aquaculture, however, the avoidance of short-term inbreeding may be of crucial importance to production. Also, mating strategies often have intellectual property protection as a primary objective. mathilde.dupont-nivet@jouy.inra.fr  

525. Tilapia salinity tolerance
         Salinity tolerance in superior genotypes of tilapia, Oreochromis niloticus, Oreochromis mossambicus and their hybrids.2005. Kamal, A. H. M. M. and G. C. Mair. Aquaculture 247:189-201.
         All the genotypes (strains) tested in these experiments grew faster at higher than at zero salinities, the highest tested being 30 ppt.  "The hybrids revealed high average positive heterosis for weight gain (1.24) and biomass gain (1.33) but less for FCR (1.08)."
         The niloticus-mossambicus  hybrid definitely out-performed either pure species. "The hybrid would be particularly recommendedat salinities above 20 ppt where the survival of O. niloticus can be compromised." Interesting. The authors also suggest that "perhaps the most likely application of hybridization would be in developing specific combinations of commercially valuable traits." (See May 2002#321 salinity-tolerance gene.)  graham.mair@flinders.edu.au

524. Maximizing heterozygosity also maximizes allele diversity
         Managing individuals' contributions to maximize the allelic diversity maintained in small, conserved populations. 2004. Fernández, J., M. A. Toro and A. Caballero. Conservation Biology 18:1358-1367.
         Most diversity-conserving breeding plans focus on inbreeding or heterozygosity [GD]. (See July 2006#512.) However, the total number of alleles at a locus [AD] is a more sensitive indicator of genetic drift,  and it might be argued that allele number is a better indicator of long-term evolutionary potential too. (See June 2004#480 breeding scheme that maximizes AD.)
         So, considering these two strategies together, what effect does maximizing GD have on allele number? The author's computer simulation shows that "strategies that maximize GD, by managing contributions from parents, keep levels of AD as high as strategies maximizing AD itself, for a wide range of situations including different numbers of molecular markers used and the possibility of evaluating a number of offspring per parent to make decisions. Because maximization of GD also minimizes levels of inbreeding, this should be the strategy of choice in any conservation program." (Apr 2004#473 on equal contribution breeding schemes.) jmj@inia.es  

523. Spawn number is heritable in vannamei
         Heritability of the categorical trait ‘number of spawns’ in Pacific white female shrimp Penaeus (Litopenaeus) vannamei. 2005. Ibarra, A. M., F. G. Arcos, T. R. Famula, E. Palacios and I. S. Racotta. Aquaculture 250:95-101.
         The study population had been domesticated in Venezuela and then in Mexico under the name "Megalos". The authors used a mixed-model analysis of two generations of full-sibs, mothers and daughters. "Phenotypes were reordered for each of 5 categories: 0, 1, 2, 3, and 4 or more spawns. Heritability of spawn numbers was 0.20, with a 95% confidence interval of 0.06–0.43, indicating that this trait can be improved by selective breeding." (See Apr 2004#477.) aibarra@cibnor.mx

522. Gene flow may enhance a search for QTLs
         Gene flow's effect on the genetic architecture of a local adaptation and its consequences for QTL analyses. 2006. Griswold, C. K. Heredity 96:445-453.
        To find a quantitative trait locus (QTL) there must be at least two alleles segregating at that locus in the group of animals being studied. QTLs are more interesting and easier to find when substituting one allele for another has a large effect on the trait.
         This computer simulation looks at the properties of QTLs that evolve in two populations that are adapting to different local conditions and exchange genes by migration.  The question is, how does the genome evolve when adaptive, divergent adaptation is swamped by gene flow? A common situation in genetic conservation and aquaculture. The problem has been addressed at the population-genetic-theoretic level for 70 years but now we have the tools to look at the evolution of the architecture of the genome.
         "This paper uses computer simulations to quantify the genetic basis of local adaptations when there is gene flow versus when populations are isolated. It then takes samples from the two locally adapted populations to form mapping populations that may be used in a QTL experiment."
         The details of the simulation reported here are sensitive to migration rate and selection pressure in a rather complicated way, as one might expect. But the bottom line is interesting: "Gene flow between populations that are used in a QTL study tends to cause the average magnitude and percent variance explained (PVE) of an allele in a mapping population to increase." They also found that the effect on QTL was largest when the divergence was less than ancient (say 1000 generations) and the populations had not reached their different optima, i.e. were not experiencing stabilizing selection.
         There are obvious implications here for choosing a population to use for QTL mapping, and anyone with the freedom to make such a choice should look at the paper carefully. ckgriswold@verizon.net

521.  Extreme populations as a genetic resource in a changing climate?
         Life on the edge: the long-term persistence and contrasting spatial genetic structure of distinct brown trout life histories at their ecological limits. 2006. Antunes, A., R. Faria, W. E. Johnson, R. Guyomard and P. Alexandrino. Journal of Heredity 97:193-205.
         Brown trout have persisted on the Iberian peninsula, at the southern limit of their temperature range, since the region was a glacial refugium tens of thousands of years ago.  This allozyme & microsatellite study of 20 populations documents a genetic story that accords very well with modern micro-evolutionary theory.
         Southern populations display the genetic signatures of less-stable population sizes than populations farther north. Southern populations have relatively low within-population genetic diversity owing to bottlenecks and drift, but the overall diversity is high indicating that the small populations are not historically young (they have some private alleles).
         "These data  [suggest] ... that careful interpretation of the evolutionary history of glacial refugia is necessary, especially where populations persisted for a long time but not always with optimal ecological conditions. These peripheral populations are of high conservation value and should be preserved to help conserve the future potential of the species." This remark probably has a general validity. If and when the climate warms, the genetic adaptations of southern extreme populations  may become the key to species survival over large areas.  Contrast this story with Jan-Feb 2004 #464 which describes a meta-population of brown trout living well within their ecological comfort zone, in Denmark, where sub-populations frequently disappear and then re-appear again by recolonization and thus have no particular value from a genetic conservation viewpoint. aantunes@ncifcrf.gov  or aantunes@fc.up.pt 

520. Desirable and undesirable correlates of body weight in salmon
         Development of an Atlantic salmon (Salmo salar) genetic improvement program: Genetic parameters of harvest body weight and carcass quality traits estimated with animal models. 2005. Quinton, C. D., I. McMillan and B. D. Glebe. Aquaculture 247:211-217.
         Astaxanthin, canthaxanthin & colour were all found to be moderately heritable in Atlantic salmon and the genetic correlation with body weight was positive -- which is good news for aquaculture selection programs. But the genetic correlation between weight and fat was also positive, which, while not unexpected, is bad news nevertheless. cquinton@uoguelph.ca

519. Matched rates of inbreeding in control and mass-selected tilapia lines
         Genetic changes during mass selection for growth in Nile tilapia, Oreochromis niloticus (L.), assessed by microsatellites. 2005. Romana-Eguia, M. R. R., M. Ikeda, Z. U. Basiao and N. Taniguchi. Aquaculture Research 36:69-78.
         During four generations of selection, the levels of inbreeding and heterozygosity in the selected line changed over time in the expected directions, i.e. downwards. What is interesting is that the control line also changed; in fact allelic diversity at 5 microsatellite loci was slightly but non-significantly lower in the control.
         The parallel changes in the selected and control lines is presumably because the control in this experiment was actually centrally-selected, not random (collimation; Feb 2002 #293). Central-selection, or collimation, thus appears to be successful in controlling for inbreeding effects. Since control and selected lines are matched in their inbreeding, the effect of selection on growth, survival etc. can be observed separately from inbreeding in non-pedigreed mass selection programs.
         The history of the current Philippine tilapia strains (GIFT, GIFT-Genomar Supreme, GMT, FaST, GET-EXCEL, SEAFDEC, Chitralada) is briefly and usefully reviewed in this paper. mreguia@aqd.seafdec.org.ph  or mreguia@compass.com.ph

518.  Cause of spurious disease-marker correlations in aquaculture
         A general population-genetic model for the production by population structure of spurious genotype–phenotype associations in discrete, admixed or spatially distributed populations. 2006. Rosenberg, N. A. and M. Nordborg. Genetics 173:1665-1678.
         Why do we often find a "marker" for a trait such as disease resistance in an aquacultural broodstock, only to be disappointed when the marker doesn't work in the next generation? It is due to a very familiar statistical problem -- a common factor produces a spurious correlation between two variables.
         What we want to find is either a gene which causes an animal to resist a disease (direct correlation), or a marker gene which is so strongly linked to a resistance gene that the two stay together down the generations (indirect correlation where the common factor is physical proximity on a chromosome).
         What we much more often find, however, is a marker/disease association within a mixed group of individuals from different families or groups of families. The confusing common factor is the (sub-) population of origin. Sub-populations may have different allele frequencies at thousands of loci. If the sub-populations also differ somewhat in their resistance to disease, there will be thousands of spurious "marker" loci that are labels for the entire genome of the resistant sub-population, not just the tiny part of the genome responsible for disease resistance.
         It takes several generations of mixing and segregation for the indirect association caused by population structure to disappear through random mating. Research on QTLs (direct causal correlation) or marker-assisted selection (MAS; indirect correlation by close linkage) will use sophisticated breeding strategies to find non-spurious correlations in two or three generations.
         This paper introduces "a general model of spurious association in structured populations, appropriate whether the population structure involves discrete groups, admixture among such groups, or continuous variation across space." The presentation of the theory is technical but the introduction and discussion are illuminating and well-written explanations of why first-generation associations between allelic markers and traits such as disease resistance are often found and are usually disappointing. rnoah@umich.edu

517.  Early feeding determines adult growth/reproduction trade-off
         The influence of juvenile and adult environments on life-history trajectories 2006. Taborsky, B. Proceedings of the Royal Society B: Biological Sciences 273:741-750.
         Is there is a trade-off between growth and reproductive traits, and if so, is it the juvenile or the adult environment which determines the trade-off? This is a highly relevant question for aquaculture.  A simple but informative growth experiment designed to answer this question was carried out on an occasional aquarium fish, the mouth-breeding cichlid Simochromis pleurospilus. The abstract of the paper cited here is exceptionally clear:
         "Females were raised either on a high-food or low-food diet. After maturation half of them were switched to the opposite treatment, while the other half remained unchanged. Adult growth was determined by current resource availability, but key reproductive traits like reproductive rate and offspring size were only influenced by juvenile growth conditions, irrespective of the ration received as adults.
         Moreover, the allocation of resources to growth versus reproduction and to offspring number versus size were shaped by juvenile rather than adult ecology [feed level]. These results indicate that early individual history must be considered when analysing causes of life-history variation in natural populations."
         Wow. Juvenile feeding conditions determine adult growth/reproduction tradeoffs. Of course, we don't know whether we can generalize these observations. Has anyone done a similar experiment on shrimp? barbara.taborsky@esh.unibe.ch