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.

Corrections to September list:
        The contact e-mail address for September list #109 Controlling fish Frankengenes is m.muller@ulg.ac.be.
        Dr. Laura McKay (Guelph) has pointed out that, contrary to what I said in September list #110 At what age should you select shrimp or fish?, a genetic correlation can be larger than the observed phenotypic correlation, if the environmental correlation is negative.

124. Temperature- dependent sex ratio in tilapia
        Phenotypic sex differentiation of blue tilapia under constant and fluctuating thermal regimes and its adaptive and evolutionary implications. 2000. Baras, E., C. Prignon, G. Gohoungo, and C. Mélard. Journal of Fish Biology 57:210-223.
        "Oreochromis aureus exposed during the first 28 days of exogenous feeding to constant 35° C, or fluctuating temperatures (day at 35° C, night at 27° C, and vice versa) showed significantly (P< 0·05) faster growth, least size heterogeneity and better survival rates than siblings under constant 27° C. Constant high temperatures had a strong masculinizing effect (M : F sex ratios of 7·33-19·00 : 1·00 v. 0·75-0·82 : 1·00 in controls reared at 27° C). Fluctuating temperatures had less masculinizing potential but still produced sex ratios significantly skewed to the detriment of females (M : F sex ratios of 2·33-11·50 : 1·00)."
       This may be useful practical information. e.baras@ulg.ac.be

123. Genetic biogeography of Atlantic salmon
       Mitochondrial DNA diversity in North American and European Atlantic salmon with emphasis on the downeast rivers of Maine. 2000. King, T.L., A.P. Spidle, M.S. Eackles, B.A. Lubinski, and W.B. Schill. Journal of Fish Biology 57 (3):614-630.
       The authors found "21 composite haplotypes which were strongly patterned geographically with a major discontinuity observed between most North American (NA) and European salmon. Significant heterogeneity of haplotype frequencies was found within and among all classification levels (continent, country, and river). Haplotype frequencies were significantly different across continents, within European samples, within NA samples, within Canadian samples, within wild Maine samples, within captive Maine strains, and between captive and wild Maine strains. .... Some Maine rivers had only a single haplotype, suggesting that effective population sizes may be low." tim_king@usgs.gov

122. Microsatellites underestimate large genetic divergence
        Microsatellites can be misleading: an empirical and simulation study. 2000. Balloux, F., H. Brünner, N. Lugon-Moulin, J. Hausser, and J. Goudet. Evolution 54 (4):1414-1422.
        Microsatellite markers are known to underestimate genetic divergence among populations when gene flow is low. For instance, they discriminate less well at the species level than at the sub-population level (or at least their superiority at the higher level is less overwhelming). The authors of this paper looked at genetic divergence among two chromosome races of the common shrew in which gene flow is reduced by a number of factors including male hybrid sterility. The genetic divergence of the races estimated from mtDNA, proteins and karyotypes was much larger than that estimated from microsatellites, with the exception of one microsatellite located on the male (Y) chromosome. They "show by simulations that this discrepancy stems mainly from the high mutation rate of microsatellite markers for F-statistics and from deviations from a single-step mutation model for R-statistics."
        Among other things this shows how important it is to go beyond microsatellites in defining evolutionarily significant units (ESU) for conservation. francois.balloux@esh.unibe.ch.

121. Genetic purging may be useless for genetic conservation
        Effects of population structures and selection strategies on the purging of inbreeding depression due to deleterious mutations. 2000. Wang, J. Genetical Research 76:75-86.
        The author uses simulation and theoretical analysis to come to the following overall conclusion: " it is not justified to apply a breeding programme aimed at purging inbreeding depression by inbreeding and selection to a population of conservation concern". The exception may, perhaps, be species including fish which have a high-enough reproductive rate to overcome the inbreeding depression.
        If a decision is nevertheless made to undertake this controversial procedure, "The results show that the effectiveness of purging, the survival of the inbred lines and the inbreeding level attained are generally highest with between-line selection and lowest with within-line selection. Compared with no crossing, line crossing could lower the risk of extinction and the inbreeding coefficient of the purged population substantially with little loss of the effectiveness of purging. " Jinliang.Wang@ioz.ac.uk 

120. Vast newly-discovered reservoir of biodiversity
        Diversity and endemism of the benthic seamount fauna. 2000. deForges, B.R., J.A. Koslow, and G.C.B. Poore. Nature 405:944-947.
        The fauna of steep-sided undersea mountains has been very poorly explored up to now. The authors of this paper report " the discovery of more than 850 macro- and megafaunal species [fish and invertebrates of all sizes] from seamounts in the Tasman Sea and southeast Coral Sea, of which 29—34% are new to science and potential seamount endemics.
        Low species overlap between seamounts in different portions of the region indicates that the seamounts in clusters or along ridge systems function as ‘island groups’ or ‘chains,’ leading to highly localized species distributions and apparent speciation between groups or ridge systems that is exceptional for the deep sea. These results have substantial implications for the conservation of this fauna, which is threatened by fishing activity."
       The authors studied fewer than 10 seamounts. There are estimated to be about 30,000 of them.  tony.koslow@marine.csiro.au

119. Un-sportsmanlike fishing foiled by genetics
        The one that did not get away: individual assignment using microsatellite data detects a case of fishing competition fraud. 2000. Primmer, C.R., M.T. Koskinen, and J. Piironen. Proceedings of the Royal Society (B) 267 (1453):1699-1704.
        "In this study, individual assignment based on microsatellite data was used to identify a case of fishing competition fraud. Despite the fact that the true population of origin was most probably not among the reference populations, recent modifications of the assignment tests were used in confidently excluding (p < 0.0001) the possibility of a 5.5 kg salmon (Salmo salar) originating from the fishing competition location, Lake Saimaa (south-east Finland). When presented with this evidence, the offender confessed to purchasing the salmon at a local fish shop and criminal charges were laid." craig.primmer@helsinki.fi

118. Which markers are best for pedigree inference?
        Comparison of microsatellites and amplified fragment length polymorphism markers for parentage analysis. 2000. Gerber, S., S. Mariette, R. Streiff, C. Bodénès, and A. Kremer. Molecular Ecology 9 (8):1037-1048.
        "This study compares the properties of dominant markers, such as amplified fragment length polymorphisms (AFLPs), with those of co-dominant multiallelic markers, such as microsatellites, in reconstructing parentage. ... Both sets of markers produced high exclusion probabilities, and among dominant markers those with dominant allele frequencies in the range 0.1–0.4 were more informative. ... As expected, dominant markers are less efficient than co-dominant markers for achieving this, but can still be used with good confidence, especially when loci are deliberately selected according to their allele frequencies. " gerber@pierroton.inra.fr

117. Frankenweb-site
        Truths about transgenics. 2000. Anonymous. Science 289 (5486):1835.
        This is an excellent website for current and background information on transgenic crops and domesticated animals. "It includes a brief overview of how genetically modified plants are made (explained with nifty animations), which [US] agencies regulate them, what's been planted, and what's in the pipeline, as well as a discussion of risks. A page of links leading to seed companies and antibiotech groups cautions that both "will certainly put a spin" on the facts." http://www.colostate.edu/programs/lifesciences/TransgenicCrops

116. Bottlenecks won't speed up the evolution of disease resistance
        Epistasis and the conversion of non-additive to additive genetic variance at population bottlenecks. 2000. López-Fanjul , C., A. Fernández, and M.A. Toro. Theoretical Population Biology 58:49-59.
        It has long been argued that population bottlenecks (periods when the effective size of the breeding population is very small) might increase additive genetic variance and the potential to respond to selection. This can happen when other kinds of genetic variance (i.e. those involving interactions of genes) are converted to additive variance by random events during the bottlenecks. The authors of this theoretical paper studied several models of binary disease traits (the disease is either resisted/tolerated or it isn't).
        They found that "An increase in the additive variance after bottlenecks ... will occur only if the frequencies of the negative allele at each locus are: (1) low, invariably associated to strong inbreeding depression; [or] (2) high, always accompanied by an enhancement of the mean with inbreeding. ... it is unlikely that the rate of evolution may be accelerated after population bottlenecks, in spite of occasional increments of the derived additive variance over its ancestral value." clfanjul@eucmax.sim.ucm.es .

115. Recent evolution of salmon life history traits
        Evolution of temporal isolation in the wild: genetic divergence in timing of migration and breeding by introduced salmon populations. 2000. Quinn, T.P., M.J. Unwin, and M.T. Kinnison. Evolution 54:1372-1385.
        This study is based on two widely separated New Zealand populations of Chinook salmon that originated from a single importation in the early 1900s. In the many generations since their separation the populations have diverged considerably in the timing of migrations to and return from the sea, and the dates of maturation of migrating fish as well as those reared in fresh water.
        Experiments which involved splitting and cross-rearing families from the two populations in different environments led the authors to the conclusion that this variation is to a considerable extent genetic. "The very high heritabilities and genetic correlations estimated for migration and maturation date indicated that these traits would respond rapidly to selection. ...it appears that spawning time may not only evolve during the initial phases of divergence, but it may play an important role in accelerating divergence in other traits."
        This observation is important not only in the context of genetic conservation (e.g. stocking a river with properly-adapted fish) but also in aquaculture (e.g. choosing or developing broodstock which has a commercially desirable maturation schedule). michael.kinnison@dartmouth.edu.

114. Using CERVUS to sort out families in natural populations
        A retrospective assessment of the accuracy of the paternity inference program CERVUS. 2000. Slate, J., T. Marshall, and J. Pemberton. Molecular Ecology 9:801-808.
         "CERVUS is a Windows-based software package written to infer paternity in natural populations. ... In this study we use a panel of 84 microsatellite markers to retrospectively determine the accuracy of statistical confidence when CERVUS was used to infer paternity in a population of red deer (Cervus elaphus). The actual confidence of CERVUS-assigned paternities was not significantly different from that predicted by simulation."
       Useful information for people in aquaculture and genetic conservation who are considering this increasingly-popular new procedure for broodstock management." slatej@Agresearch.cri.nz

113. Quantitative genetic information from pedigree markers
        Estimating quantitative genetic parameters using sibships reconstructed from marker data. 2000. Thomas, S.C., and W.G. Hill. Genetics 155:1961-1972.
        Another important paper from Edinburgh on how to use markers to estimate heritabilities and other parameters that are useful for designing selection programmes in poorly controlled environments (like a fish farm) and designing breeding programmes for captive or supplemented populations. See August list #88.
        This paper includes an excellent discussion of the statistical limitations of current approaches to inferring genetic relationships, and for estimating quantitative genetic parameters, when markers are used as a substitute for exact pedigree records. Among the more important limitations are the difficulties of resolving genetic relationships other than full-sib, and of incorporating important non-genetic information like year or environment.
        A Monte Carlo simulation procedure is used to reconstruct " sibships within a single generation, allowing improved parameter estimation through more efficient weighting of families and use of more than pairwise pedigree information. ... Reconstructed pedigrees are subsequently used to form a relationship matrix suitable for use in an animal model run with restricted maximum likelihood (REML), specifically using the ASREML program. ...
        The authors say that this approach allows traditional efficient methods for parameter estimation to be used and hence simplifies the inclusion of additional factors or the use of multivariate analysis if data have been collected from several traits."
        The authors discuss the main ways to handle complications which arise when populations have multiple relationships, as they usually do -- one of the best being simply to ignore the problem since most of the information lies in close relationships anyway.
        They also suggest another shortcut: "[If] f information is available on two or three nonoverlapping generations of a population, sibships could be reconstructed for each generation, constraining the sum of possible parental genotypes using the probability (if known) that a parent is contained within the samples collected from previous years. Generations could then be linked using the likelihood of the observed marker data and the probability that one or both parents are from the previous generation. " sthomas@srv0.bio.ed.ac.uk

112. Population bottlenecking increases the variability of fitness
        The distribution of phenotypic variance with inbreeding. 1999. Fowler, K., and M.C. Whitlock. Evolution 53:1143-1156.
        The authors generated 52 inbred lines of Drosophila melanogaster, each from a different set of full sibs taken from a large population. They then measured the fitness and several morphological traits of in the bottlenecked sub-populations. (This experimental design basically estimated the amount of variation in fitness and susceptibility to inbreeding depression which existed among the individuals in the original, large population.)
        The experimental result was that the variance of individual fitness within the lines generally increased, but the lines differed significantly in their within-line fitness variance.
       One implication for genetic conservation (by analogy), as pointed out by the authors, is that "The changes in phenotypic variance [among lines] as a result of population bottlenecks are large enough to significantly affect the probability of peak shifts by the variance-induced peak shift model". The implications for aquaculture are more immediate -- the increased variation in fitness in populations started with a few ancestors implies that more individuals will be lost during production ("morts") even if the MEAN inbreeding level is not especially large. It also results in more rapid increase in the overall level of inbreeding because of variable reproductive success. k.fowler@ucl.ac.uk.

111. Deducing the growth and spread of a viral pathogen
        An integrated framework for the inference of viral population history from reconstructed genealogies. 2000. Pybus, O.G., a. Rambaut, and P.H. Harvey. Genetics 155:1429-1437.
        The authors develop a general technique for using gene sequence data to infer the changing size of a viral population during a global pandemic. They apply the procedure "... to HIV-1 sequence data and find strong evidence that subtypes A and B have different demographic histories. We also provide the first (albeit tentative) genetic evidence for a recent decrease in the growth rate of subtype B."
        The procedures should work equally well with, for example, the shrimp WSSV baculovirus given appropriate sequence data. As in the case of HIV, changes in the relative growth rates of viral subtypes could provide information on the evolution of pathogen virulence or host tolerance/resistance in aquaculture stocks. Shrimp aquaculture is a big-money industry which deserves some high-powered work on epidemiology to reinforce the excellent work currently being done on the detection and genetic characterization of pathogens. oliver.pybus@zoo.ox.ac.uk