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.

199.  When restoring biodiversity,  first do no harm
        Microsatellite analysis of a population crash and bottleneck in the Mauna Kea silversword, Argyroxiphium sandwicense ssp. sandwicense (Asteraceae), and its implications for reintroduction. 2000. Friar, E.A., T. Ladoux, E.H. Roalson, and R.H. Robichaux. Molecular Ecology 9 (12):2027-2034.
        The native silversword plants on the Hawaiian island of Mauna Kea, which had almost all been eaten by cows, were subsequently reintroduced as part of a biodiversity recovery program. The authors studied the genetic effects of the crash and the reintroduction of new plants as two separate phenomena. "The population crash [cow effect] was not accompanied by a significant reduction in number of [microsatellite] alleles or heterozygosity. However, the population bottleneck [reintroduction effect] was accompanied by significant reductions in observed number of alleles, effective number of alleles, and expected heterozygosity, though not in observed heterozygosity."
        These results nicely accord with theoretical expectations of what should happen under such circumstances and, as the authors point out in relation to the effect of the crash, "small populations, even those that result from severe reductions in historical population size and extent, are not necessarily genetically depauperate." This is an important study because it emphasizes the distortion that can be caused when a population is founded or supplemented by a few individuals -- a dangerous distortion that can then be locked in more or less forever. elizabeth.friar@cgu.edu

198. Selected trout are greedy, not efficient
        Selection for growth of brown trout (Salmo trutta) affects feed intake but not feed efficiency. 2001. Sanchez, M.-P., B. Chevassus, L. Labbé, E. Quillet, and M. Mambrini. Aquatic Living Resources 14 (1):41-48.
        "Brown trout (Salmo trutta) were selected for growth for 4 generations. We tested the effects of selection on voluntary feed intake measured by self-feeders, feed efficiency and size variability. The specific effects of a slight feed restriction and of food deprivation were also investigated." It turned out that the faster-growing strain ate more, but its food conversion efficiency was the same. This is commonly observed in other animals selected for rapid growth -- in economic terms, genetic gain comes from more rapid overturn of the stock and annual return on fixed assets, not from reduction of feed costs. "The results highlight the fact that genetic gain can only be expressed when brown trout are fed ad libitum". bernard.chevassus@jouy.inra.fr

197.  Finding QTLs more quickly
        Bayesian mapping of quantitative trait loci under complicated mating designs. 2001. Yia, N., and S. Xua. Genetics 157:1759-1771.
        Quantitative trait loci (QTL) can be found most efficiently when there are only two alleles per locus and only one locus is considered at a time; this is generally achieved by crossing inbred lines, by very wide (species-level) crosses, or by chromosome manipulation such as gynogenesis. These procedures can be tricky and time consuming in aquacultural species, and there may be no guarantee that the inbred lines you end up with are actually carrying QTLs of interest. Furthermore, interactions between genes at different chromosome locations will be missed.
        "A complicated mating design involving multiple alleles mimics the actual breeding system. ... In this study, we investigate the application of a Bayesian method ... to QTL mapping under arbitrarily complicated mating designs ... We are able to simultaneously infer the posterior distribution of the number, the additive and dominance variances, and the chromosomal locations of all identified QTL. xu@genetics.ucr.edu

196. Frankengenes can swamp a wild population even when their carriers are ecologically unfit
        Invasion of transgenes from salmon or other genetically modified organisms into natural populations. 2001. Hedrick, P.W. Can. Jour. Fisheries and Aquatic Sciences 58:841-844.
        The author develops a deterministic model which shows that "if a transgene has a male-mating advantage and a general viability disadvantage, then the conditions for its invasion in a natural population are very broad. More specifically, for 66.7% of the possible combinations of the possible mating and viability parameters, the transgene increases in frequency, and for 50% of the combinations, it goes to fixation. In addition, by this increase in the frequency of the transgene, the viability of the natural population is reduced, increasing the probability of extinction of the natural population.
        "These findings provide independent confirmation of previous concerns about the inherent risks of transgenic organisms, especially for native salmon populations potentially affected by commercial salmon production using transgenic stocks."
        This is a useful contribution to discussions of the impact of transgenes on wild populations. Present indications are that transgenic fish, like other domesticated fish, are likely to be less fit than wild fish of the same size. It is useful to learn that this will not necessarily stop the spread of a transgene.
        One should note, though, that although size probably increases reproductive fitness of both sexes, cultured transgenic fish may not be allowed to grow large enough to have a mating advantage as escapees. Fish farmers need to get fish up to marketable size faster, i.e. to get a higher return on capital and other fixed costs. It would be interesting to see a joint genetic-economic analysis of biological risk that takes the behaviour of a rational farmer, as well as fish behaviour, into account.  philip.hedrick@asu.edu

195.  Wild male salmon have "it"
        Male competition and breeding success in captively reared and wild coho salmon (Oncorhynchus kisutch). 2001. Berejikian, B.A., E.P. Tezak, L. Park, E. LaHood, S.L. Schroder, and E. Beall. Can. Jour. Fisheries and Aquatic Science 58:804-810.
        "In this study, wild coho salmon (O. kisutch) males outcompeted captively reared males and controlled access to spawning females in 11 of 14 paired trials in laboratory stream channels. In two cases where satellite males were observed participating in spawning, DNA genotyping results determined that they did not sire any of the progeny."
        That's good. Escaped domesticated salmon are less likely to cause genetic contamination (se #196). It is also bad, when fish reared in captivity are released to enhance the effective population number of a naturally-spawning population. The authors suggest that "The competitive inferiority of captively reared coho salmon in this and a previous study probably reflects deficiencies in rearing environments, which fail to produce appropriate body coloration and body shape and perhaps alter natural behavioral development". barry.berejikian@noaa.gov

194.  Marker heterozygosity doesn't say much about variance of important traits
        Lack of concordance between genetic diversity estimates at the molecular and quantitative-trait levels. 2000. Pfrender, M.E., K. Spitze, J. Hicks, K. Morgan, L. Latta, and M. Lynch. Conservation Genetics 1 (3):263-269.
        There are very few simultaneous estimates of genetic variation at quantitative loci which affect traits like size, shape, fecundity and behaviour and genetic variation at neutral or nearly-neutral marker loci. In the context of genetic conservation one may be more fundamentally concerned about the quantitative variation. Quantitative variation is, however, so much harder to measure that marker variation is often used as a surrogate. More than 25 years ago R.C. Lewontin predicted on theoretical grounds that the two measures should be very poorly correlated (American Naturalist 123:115-124. 1984).
        In this analysis of variation in Daphnia, where both types of data are available, "estimates of molecular and quantitative-genetic variation are essentially uncorrelated in natural populations. ... On the other hand, molecular measures of population subdivision seem to give conservatively low estimates of the degree of genetic subdivision at the level of quantitative traits. This suggests that although molecular markers provide little information on the level of genetic variation for quantitative traits within populations, they may be valid indicators of population subdivision for such characters."
        It may also suggest that genetic conservation programs should give serious thought to developing protocols for the long-term monitoring of additive genetic variance of major components of fitness and perhaps key behavioral traits. pfrendem@bcc.orst.edu

193.  Complicated inbreeding effects in tiny populations
        Pedigree analysis on small laboratory populations of the butterfly Bicyclus anynana: The effects of selection on inbreeding and fitness. 2000. Oosterhout, C. van, G. Smit, Heuven. M.K. van, and P.M. Brakefield. Conservation Genetics 4:321-328.
        Laboratory metapopulations consisting of very small, interconnected subpopulations of 6 or 12 individuals were reared for 7 generations. Pedigree records were maintained by individual marking. The overall level of inbreeding in the small populations was less than expected from the simple statistics of the situation (although some inbred individuals were severely depressed) but in the larger populations inbreeding was the same as expected. The authors discuss the various ways inbreeding depression can affect the variance of family size and the probability of sib mating, and the effect this can have on fitness of populations and selective purging of alleles. They conclude that "These findings emphasise the potential problems of using only small numbers of breeding individuals (N~10) in captive populations for conservation purposes".
        One might also suggest that the findings show that direct intervention to preserve rare lineages may be required in such situations and that random mating cannot be trusted to fulfill the conservation objectives. See #199 above. c.van-oosterhout@biosci.hull.ac.uk

192.  Genetic identification of male parents
        Statistical approaches to paternity analysis in natural populations and applications to the North Atlantic humpback whale. 2001. Nielsen, R., D.K. Mattila, P.J. Clapham, and P.J. Palsbøll. Genetics 157:1673-1682.
        The authors have developed useful new procedures for determining male parentage from microsatellite data when some of the putative male parents have not been sampled. The procedures are also useful for estimating quantities that depend in part on the mating system, such as individual (male) reproductive fitness and effective population number. rn28@cornell.edu

191.  Is there a reason to select tilapia (or anything else) for heterozygosity?
        Individual heterozygosity levels and relative growth performance in Oreochromis niloticus (L.) cultured under Fijian conditions. 2001. Appleyard, S.A., J.M. Renwick, and P.B. Mather. Aquaculture Research 32 (4):287-296.
        Heterozygosity, used as a surrogate measure of individual inbreeding, has often been found to be associated with reduced fitness in wild populations especially under stressful conditions. Even in populations where inbreeding is unlikely -- e.g. natural mussel beds -- heterozygous individuals are often found to be larger or are inferred to be more fit because their numbers steadily increase during the course of a generation. The reasons for this are still controversial after 15 years of investigation. Individuals which are heterozygous at neutral marker loci are generally NOT superior to homozygous individuals in laboratory-bred populations.
        Discussion focuses on a central unresolved issue of inbreeding and outbreeding depression: whether these phenomena are due to the enhanced general "buffering" capacity of individuals which carry two different alleles at a locus, or to the canceling-out of mildly deleterious mutations when they occur as heterozygotes. In any case, artificial selection of heterozygous individuals cannot improve the fitness of their offspring because heterozygosity per se is not passed on. It may or may not increase the genetic diversity of the next generation, depending on gene frequencies (rare alleles will be selected against).
        The authors of this paper studied 3 generations of the Chitralada strain of O. niloticus in Fiji and found no association between growth rate and heterozygosity at 25 allozyme and 9 microsatellite loci. "No significant correlations with either length or weight were observed at any of the other eight microsatellite loci. Selecting broodstock therefore based solely on individual allozyme or microsatellite heterozygosity levels is unlikely to increase relative growth performance in the Fijian cultured O. niloticus ‘Chitralada’ stock." S. Appleyard, CSIRO Marine Research, GPO Box 1538, Hobart TAS 7000 Australia.

190.  How to check estimates of effective population number
        Testing demographic models of effective population size. 2001. Basset, P., F. Balloux, and N. Perrin. Proceeding of the Royal Society (UK), Ser. B. 268 (1464):311-317.
        This interesting paper addresses the fact that estimates of effective the population size Ne of natural populations, which are made by combining genetic (F statistic) and demographic data, are mostly uncheckable. The authors develop computer simulations of the behaviour of individual gene pedigrees in standard demographic models of Ne (i.e. models which include sex ratio, reproductive variance etc.). They find that the models are reasonably good at estimating Ne although one situation of interest in fisheries is an exception: when there is substructure within social groups. In that case Ne is greatly overestimated.
        "The timing during the life cycle at which F-statistics are evaluated is also of crucial importance and attention should be paid to it when designing field sampling since different demographic models assume different timings." Dr. Perrin has put his interesting and useful-looking computer program for simulating gene flow etc on the web. Set your search engine for EASYPOP. nicolas.perrin@ie-zea.unil.ch

189.  Selected oysters retain genetic diversity
        Allozyme variation in three generations of selection for whole weight in Sydney rock oysters (Saccostrea glomerata). 2001. English, L.J., J.A. Nell, G.B. Maguire, and R.D. Ward. Aquaculture 193:213-225.
        The authors found that variation at 14 allozyme loci, as measured by expected heterozygosity, was not lost after two rounds of selection for weight in the oysters. The effective population size remained reasonably large during selection. The authors point out that microsatellites, which generally have many rare alleles, might have been more sensitive measures of variance effective number. bob.ward@ml.csiro.au

188.  Where do microsatellite markers come from?
        Insertions, substitutions, and the origin of microsatellites. 2000. Zhu, Y., J.E. Strassmann, and D.C. Queller. Genetical Research 76:227-236.
        "This paper uses data from the Human Gene Mutation Database to contrast two hypotheses for the origin of short DNA repeats: substitutions and insertions that duplicate adjacent sequences. ...Insertions contribute fewer new repeat loci than substitutions, but their relative importance increases rapidly with repeat number so that all new 4–5-repeat mutations come from insertions, as do all 3-repeat mutations of tetranucleotide repeats. ... Most short insertion mutations derive from a slippage-like process during replication." queller@rice.edu