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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.

516. The proper way to measure mortality in challenge tests  
        Genetic parameters and accuracy of selection for resistance to White Spot Syndrome Virus (WSSV) in Penaeus (Litopenaeus) vannamei using different statistical models. 2006. Gitterle, T., J. Ødegård, B. Gjerde, M. Rye and R. Salte. Aquaculture 251:210-218.
        This useful paper from Akvaforsk (in collaboration with CENIACUA, Centro de Investigaciones para la Acuicultura en Colombia) compares the effectiveness of various ways of measuring mortality in disease challenge tests. The Cox model, which uses an age-at-death variable, worked best. In this particular study, the identities of newly dead and moribund animals were recorded every hour during the test. (This much data is nice to have but may be overkill in a commercial program.).
        "Based on these results we suggest selection programs for white spot resistance should be based on ... models taking time to death into account with proper model of the mortality pattern of the test population ..., rather than the models that define survival as a binary trait at 50% mortality."
        No one should disagree with this conclusion. Standard challenge test methodologies, in which each family receives only one score (e.g. % survival) are profoundly unsatisfactory for genetic analysis or practical selection in aquaculture. Too much information is thrown away in each test. Attempts to add information by increasing the number of families and replicates/family can be horribly expensive and generally add new sources of variation which are either ignored (defeating the purpose of the expansion) or necessitate additional parameter estimates (ditto).  thomasgitterle@yahoo.com  

515.  measure of quantitative trait divergence
         The effects of dominance, regular inbreeding and sampling design on QST, an estimator of population differentiation for quantitative traits. 2006. Goude, J. and L. Büchi. Genetics 172:1337-1347.
         Several years ago a meta-analysis of 18 published cases found that populations usually differ more in distributions of quantitative traits, measured by QST, than in frequencies of neutral markers, measured by FST  (Jan 2002 #281). QST and FST are analogous measures of variance among and within populations for these two types of traits.
         That paper concluded that natural selection is the predominant force driving populations toward different mean values of quantitative traits. That is, mean quantitative genetic differences in growth, appearance, physiology and behaviour are due more to selection than drift. An important conclusion.
         (Note that if both types of traits are selectively neutral the prediction is QST=FST, if populations are selected in different directions there is more quantitative divergence so QST > FST, and if selection tends to bring populations towards a common optimum then QST<FST.)
        The paper cited here is an analytical and simulation study of the influence of non-additive effects such as dominance and inbreeding on the ratio of GST to FST. "Provided that estimates of QST are derived from individuals originating from many populations, we conclude that the pattern QST > FST, and hence the inference of directional selection for different local optima, is robust to the effect of nonadditive gene actions." Good. jerome.goudet@unil.ch    

514.  Domesticated O. niloticus not as good as wild ones
        On-farm and on-station comparison of wild and domesticated Cameroonian populations of Oreochromis niloticus. 2004. Brummett, R. E., D. E. Angoni and V. Pouomogne. Aquaculture 242:157-164.
       Grand-offspring of a wild population out-grew and out-produced a domesticated population in this trial, after at least 25 years of domestication. The difference was considerable. Why does domestication tend to cause cultured tilapia to deteriorate everywhere in the world unless carefully designed selection programs are maintained?
        The authors of this paper ascribe their particular results to the regional management history of tilapia, and they are doubtless correct. But informally managed salmonids and carp don't deteriorate, nor do penaeid shrimp unless they're seriously inbred. Why do tilapia go bad so consistently?
        My guess is that it has to do with the tendency of Oreochromis to "stunt" -- reproduce young and small -- as part of its normal life history strategy under some social and environmental conditions, particularly crowding. Careless domestication selects for a lower stunting threshold. Just a guess. r.brummett@cgiar.org  

513. Damage to  DNA used to study ancient populations
        Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. 2006. Binladen, J. and others. Genetics 172:733-741.
        This study takes a detailed look at changes in nuclear DNA which take place postmortem and which may affect genetic inferences about long-ago migrations and hybridizations (e.g. Jan 2003 #380, Jan-Feb 2004 #461 & #464).
        "By comparing clone sequences from 23 fossil specimens ... we demonstrate the presence of miscoding lesion damage in both the mtDNA and nuDNA, resulting in insertion of erroneous bases during amplification." The samples studied (woolly mammoths, rhinoceroses etc.) were much older than those used in the papers cited above, but changes caused by microorganisms, cellular nucleases and non-enzymatic oxidation and hydrolysis are presumably the same.
        The authors also make the useful point that museums and herbariums are not good storage environments for DNA, compared with deserts and permafrost. ewillerslev@gfy.ku.dk    

512. Walk-back selection with improved use of kinship information
         A combination of walk-back and optimum contribution selection in fish: a simulation study. 2005. Sonesson, A. K. Genetics Selection Evolution 37:587-599.
         Walk-back selection is a procedure for use in simple aquaculture set-ups where many families are reared together in one tank or pond. The best (e.g. largest) animal is selected as a breeder and DNA markers are used to identify its family. The second-largest animal is then identified and, if it comes from a different family it too is selected; if it belongs to the same family and sex as the first it is rejected. The third, fourth ... best animals are identified and selected if they are from different families, "walking back" from the right-hand end of the size distribution towards the mean.
         Walk-back stops when enough pairs have been selected to attain the desired broodstock population number. Walk-back is a type of within-family selection adapted to the high fecundity of aquacultural species and the high cost of rearing individual families.
        This paper simulates a combination of walk-back and "optimum contribution" selection (see Dec 2001 #270, also Apr 2003 #473, Aug 2002 #335) which makes a more sophisticated use of kinship than merely discarding duplicates from the same family. The paper confirms that high rates of genetic gain and low inbreeding can be attained relatively easily, i.e. by genotyping a few hundred animals, not thousands. Anna.Sonesson@akvaforsk.no  

511.  Should there be many management units or one?
         Reconciling nuclear microsatellite and mitochondrial marker estimates of population structure: breeding population structure of Chesapeake Bay striped bass (Morone saxatilis). 2005. Brown, K. M., G. A. Baltazar and M. B. Hamilton. Heredity 94:606-615.
         Inferences about the sizes and histories of populations based on nuclear markers (e.g. microsatellites) commonly differ from inferences based on organelle markers (e.g. mitochondrial D-loop sequence). An example is the striped bass population of Chesapeake Bay, where it is uncertain whether sub-populations inhabiting the in-flowing rivers should be considered distinct management units.
        This paper reconciles the contradictory conclusions from previous protein, microsatellite and mtDNA studies. "Reanalysis of Chesapeake Bay striped bass mtDNA data from two previous studies estimated population differentiation between =-0.002 and 0.160, values generally similar to mtDNA population differentiation predicted from microsatellite RST after adjusting for reduced effective population size and uniparental inheritance in organelle genomes."
        The bottom line: It's a panmictic population and one management unit. See Jan-Feb 2004 #464 re metapopulation. hamiltm1@georgetown.edu    

510.  Estimating genetic correlations involving survival
         A bivariate quantitative genetic model for a linear Gaussian trait and a survival trait. 2006. Damgaard, L. H. and I. R. Korsgaard. Genetics Selection Evolution 38:45-64.
        Until now -- believe it or not -- there has been no correct way to use modern REML/BLUP procedures when jointly analysing bivariate genetic correlations (or selection indices) involving yes-or-no survival plus a continuous, quantitative trait like growth.
        The approximation everyone falls back on wastes information (e.g. correlations of univariate estimates from Ducrocq's and Sölkner's "Survival Kit", Jul-Aug 2002 #343). The usual approximation is also biased by environmental effects, which may be especially severe in aquaculture when growth is density-dependent.
         The authors of this technical paper describe a Gibbs sampler for joint Bayesian analysis of a normally-distributed linear trait and a survival trait, which are genetically and environmentally correlated. "The bivariate model allows for a more accurate genetic evaluation of animals ... owing to the shared information between traits. ... The results from these [simulation] analyses indicated clearly that the approximative method can be very imprecise." 
        The authors imply that practical implementation of their procedure should be relatively straight-forward but do not as yet offer us a program.
        Note that if time-to-death, a continuous variable, is measured (see #516) the correlation difficulty mentioned here disappears. lars.damgaard@agrsci.dk     

509.  The P. monodon map continues to be filled in
         Development of polymorphic expressed sequence tag-derived microsatellites for the extension of the genetic linkage map of the black tiger shrimp (Penaeus monodon). 2006. Maneeruttanarungroj, C. and others. Animal Genetics 37:363-368.
         "A total of 997 unique microsatellite-containing expressed sequence tags (ESTs) were identified... .an average number of alleles of 12.6 and an average [marker] polymorphic information content of 0.723... .The current P. monodon male and female linkage maps have 47 and 36 linkage groups respectively with coverage across half the P. monodon genome." anchalee.k@chula.ac.th    

508. Early life history is not changed by fishing
        Harvest selection, genetic correlations, and evolutionary changes in recruitment: one less thing to worry about? 2005. Munch, S. B., M. R. Walsh and D. O. Conover. Canadian Journal Fisheries and Aquatic Sciences 62:802-810.
        This research group has been "fishing" -- harvesting -- an experimental population of the Atlantic silversides (Menidia menidia) for about 25 years and interesting results continue to be published. They find significant realized genetic correlation between adult size (the target of size-selective fishing) and egg diameter, larval viability and several juvenile and adult size variables which are known to affect one or another component of recruitment.
        Nevertheless, "In contrast with studies of harvest selection on adult characteristics, we find the response of characters in the early life history to be relatively slow and that impacts on recruitment, if any, are likely to be driven by selective changes in fecundity." The low-impact prediction derives from the sensitivity of their model of recruitment to the magnitude of the predicted correlated evolution of the early life history variables. See Jul-Aug 2003 #345. sbmunch@soe.ucsc.edu    

507. Possible inbreeding and outbreeding depression in bluegill sunfish
         Stabilizing selection on genomic divergence in a wild fish population. 2004. Neff, B. D. Proceedings National Acad. Sciences USA 101:2381-2385.
         In managed populations it is frequently recommended to select and mate animals with low genetic relatedness (i.e. which are not closely associated with other animals in the pedigree of the population) so as to minimize inbreeding depression (see #512 and Jan 2002 #283, Jul-Aug 2002 #335, Mar-Apr 2004 #473). In doing this, though, one risks elimination of special adaptations or locally-adapted complexes of genes, thus causing outbreeding depression [e.g. Apr-May 2003 #400].
         In aquaculture, where the aim is to adapt a domestic stock to an artificial environment, outbreeding depression is not a big worry (except perhaps in choosing a founders for the stock, where the issue might better be labeled pre-adaptation). But when the aim is genetic conservation of endangered wild populations outbreeding is a concern and evidence for it is avidly sought.
         Here microsatellite markers are used to estimate whether naturally mated parents of wild bluegill sunfish (Lepomis macrochirus) are relatively closely related (potential inbreeders) or distantly related (potential outbreeders). The results seem to imply that mates chose each other to avoid both inbreeding and outbreeding, i.e. there was stabilizing selection for intermediate relatedness.
         Fluctuating asymmetry, possibly and inverse measure of fitness [Jul-Aug 2002#337] was higher at both extremes of  parental relatedness. Reproductive success, a direct component of fitness, was higher in the middle. No effect on condition factor and parasite load could be detected. bneff@uwo.ca    

506. Thai TSV more related to Asian than American strains
         Taura syndrome virus (TSV) in Thailand and its relationship to TSV in China and the Americas. 2005. Nielsen, L., W. Sang-oum, S. Cheevadhanarak and T. W. Flegel. Diseases of Aquatic Organisms 63:101-106.
         Thailand has more-or-less banned importation of Penaeus vannamei and P. monodon since February 2003 owing to fear of importing Taura syndrome virus (TSV). The TSV disease is present in Thailand, though, and in the interest of assigning blame we want to know where it comes from. In this study "Comparison [of viral coat protein gene VP1] revealed that the Thai, Burmese and Chinese TSV types formed a clade distinct from a clade of TSV types from the Americas." sctwf@mahidol.ac.th    

505.  Wild catfish not genetically harmed by aquaculture
         Comparison of domestic and wild channel catfish (Ictalurus punctatus) populations provides no evidence for genetic impact. 2006. Simmons, M., K. Mickett, H. Kucuktas, P. Li, R. Dunham and Z. Liu. Aquaculture 252:133-146.
         This study is based on AFLP polymorphisms and straightforward Fst and distance calculations. There is a lot of catfish cultivation in the southern USA and a lot of wild catfish grow there as well. Escapes must be common but the genetic impact seems to be small.
         "The domestic populations were all related to one another, forming a single branch in the phylogenetic analysis, while all but the Tennessee River populations of many wild populations were more related to one another than to domestic populations. Genetic identities of wild fish from proximal and distal sites were similar, while both wild populations differed from the nearby domestic catfish populations, providing no molecular genetic evidence for apparent impact of domestic catfish on wild populations." zliu@acesag.auburn.edu