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.

372.  How to use frozen semen in a live gene bank
         The use of frozen semen to minimize inbreeding in small populations. 2002. Sonesson, A. K., M. E. Goddard and T. H. E. Meuwissen. Genetical Research 80:27-30.
         This is a very useful paper even though the authors suggest that  their presentation may be oversimplified. They suggest how one should use cryogenically preserved semen to retain genetic diversity in a live gene bank or other small population. It isn't enough just to fertilize the females in each succeeding generation with sperm from the original founding males. (Because of subsequent drift these should be the most genetically diverse males in the pedigree.) If you do that, all the founding female genomes will eventually be lost.
         "We propose an alternative scheme in which N sires from generation 1 (G1), as well as the N sires from G0, have semen conserved, and the semen of G0 and G1 sires is used for dams of odd and even generation numbers, respectively. With this scheme, the ... genes of founder dams are also conserved, because 50% of the genes of sires of G1 are derived from the founder dams. A computer simulation study shows that this is the optimum design to minimize inbreeding, even if semen from later generations is available."
         Matings in the simulation were random, i.e. were not arranged to minimize next-generation inbreeding. This is a slick scheme that should be relatively easy to manage (until the semen runs out). anna.sonesson@akvaforsk.nlh.no

371.  Ranking the conservation value of endangered breeds
         Analysis of genetic diversity for the management of conserved subdivided populations. 2002. Caballero, A. and M. A. Toro. Conservation Genetics 3 (3): 289-299.
         The question addressed in this paper is an important one: which breeds, or strains, or subpopulations of an endangered species should be preserved in live gene banks, given that one cannot preserve them all? The authors acknowledge that unique adaptations, allele richness, evolutionary potential, and even cultural and historical factors should be taken into account in deciding this question -- when these factors are identified and measurable. What is more commonly available to decision makers, though, is molecular marker data and/or pedigree records. The availability of this kind of information usually leads to a narrower objective, namely, to preserve as much genetic diversity as possible in the species or metapopulation as a whole.
         If that is accepted as an expedient objective, which particular subpopulations should be conserved and which allowed to go extinct? One commonly accepted view is that the subpopulations which are most valuable are those which are "distinctive" by some measure of genetic distance. By giving priority to such subpopulations, a conservation strategy will (in essence) maximise the total branch length of the phylogenetic tree of the surviving metapopulation. In this calculus the contribution of each subpopulation to the global diversity is proportional to its contribution to total tree length.
         The authors of this paper show, with real as well as with simulated data, that the above strategy can lead to exactly the wrong choice for conservation. This can happen when animals within a "distinctive" population have a high level of coancestry, which of course will often be the case. The relative sizes of the subpopulations or breeds matters, too.
         Their argument requires a demonstration that maximisation of genetic diversity (as expected heterozygosity) follows from the minimisation of coancestry in a subdivided population. The paper includes this demonstration, along with a clear analysis of the relationship between total genetic diversity (heterozygosity), Wright's F statistics, Nei's genetic distance, and Malecot's coancestry coefficient. (See also Nov 2001 #261, Jul 2001 #212.) Fortunately, coancestry is now easy to estimate from marker data (e.g. Apr 2002 #320). The suggestions in this paper appear to be eminently practical. armando@uvigo.es ; this and other recent papers by Caballero can be downloaded from http://www.uvigo.es/webs/c03/webc03/XENETICA/XB2/Caballero.htm

370.  Increased susceptibility to disease in small salmon populations
         Resistance to three pathogens in the endangered winter-run Chinook salmon (Oncorhynchus tshawytscha): effects of inbreeding and major histocompatibility complex genotypes. 2002. Arkush, K. D., A. R. Giese, H. L. Mendonca, A. M. McBride, G. D. Marty and P. W. Hedrick. Canadian Journal of Fisheries and Aquatic Science 59:966-975.
         The authors distinguish two genetic consequences of small population size which might reduce disease resistance: (a) increased homozygosity due to inbreeding and (b) loss of genetic variation, specifically at the MHC locus. In their experiment matings were arranged such that both full-sib inbred progeny and outbreds could be created from the same female. "In addition, a number of parents were selected so that their progeny would segregate for heterozygotes and homozygotes at... [a class II MHC locus ]."
         The progenies were challenged with three major pathogens: a bacterium (vibrio), a virus (IHNV) and a parasitic protozoan (whirling disease).
         Inbreeding increased the probability and severity of the protozoan infection but had no significant effect on the viral or bacterial pathogen. MHC heterozygosity increased the resistance to IHNV challenge but did not affect resistance to vibrio. "Overall, we have shown that the endangered winter-run Chinook salmon appears to be genetically susceptible to the detrimental effects of pathogens. If there were further losses of genetic variation because of continued small population size in winter-run, then one would predict both a higher level of homozygosity at MHC genes and higher levels of inbreeding. As a result, the pathogens that we have examined, and potentially others that may infect winter-run, may cause in a decline in the number of winter-run Chinook salmon and an additional extinction threat to this critically endangered species." Other papers on salmonid MHC diversity are Mar 2002 #302, Dec 2001 #272, Oct 2001 #240, Jul 2001 #221 and #369, below. philip.hedrick@asu.edu

369.  Experimental evidence for allele-specific MHC resistance to infection
         Experimental evidence for major histocompatibility complex-allele-specific resistance to a bacterial infection. 2002. Lohm, J., M. Grahn, Å. Langefors, Ø. Andersen, A. Storset and T. von Schantz. Proceedings Royal Society U.K. (B) 269:2029-2033.
         The authors of this important paper report on the resistance to furunculosis in Atlantic salmon originating from the Akvaforsk strain and reared by AquaGen AS in Norway. Families of salmon were mated on the basis of their MHC genotypes so as to generate mixtures of homozygous and heterozygous individuals within the same full-sib families, thus controlling the genetic background against which specific MHC alleles were expressed. A lot of research activity is currently focused on the importance of MHC diversity in natural populations, including the possibility that in natural populations mates are chosen so as to produce MHC heterozygous offspring (Mar 2002 #302, Dec 2001 #272, Oct 2001 #240, Jul 2001 #221 and #370, above.
         Surprisingly, in this controlled breeding experiment MHC heterozygosity per se did not improve resistance to the furunculosis challenge test. It was particular Class II MHC alleles that conferred resistance. "We show that a pathogen has the potential to cause very intense selection pressure on particular MHC alleles; the relative fitness difference between individuals carrying different MHC alleles was as high as 0.5."
         The authors also write, "This study clearly shows a strong survival advantage for individuals carrying a high-resistance allele when exposed to a bacterial infection. … directional selection acting on the MHC despite its high polymorphism stresses the importance of renewal of genetic variation at these kinds of loci, either from mutation, recombination or immigration from other populations, when combating new or coevolving virulent pathogens." jakob.lohm@zooekol.lu.se

368.  All European carp breeds have a common Asian origin
         mtDNA sequence data supports an Asian ancestry and single introduction of the common carp into the Danube Basin. 2002. Froufe, E., I. Magyary, I. Lehoczky and S. Weiss. Journal of Fish Biology 61:301-304.
         Common carp have been cultivated in Europe since late Roman times and in Asia for several thousand years. It is not known where the diverse, current breeds of domesticated carp in Europe originally came from; possibilities include a Pleistocene glacial refuge in the Danube basin, or western Asia (Caspian sea), or eastern Asia. The authors of this paper found no variation in mitochondrial DNA haplotypes among European carps and found the same haplotype in Japanese koi. Individuals from the Amur river, on the other hand, showed a lot of sequence variation in the mitochondrial control region.
         "The lack of control region variation in European common carp (as well as Japanese koi) supports a recent common ancestry of all individuals sampled. Thus, the observed phenotypic diversity is assumed to have developed through intense selection after a relatively recent bottleneck event."
         No fish from the Caspian sea were studied but the high mitochondrial diversity of fish from the Amur river makes eastern Asia look like an evolutionary center of origin, and the authors conclude that Caspian fish are more likely to have immigrated from eastern Asia rather than the other way around. Therefore the authors rule out the Caspian as well as the Danube as the source of all modern European carp breeds. steven_weis@hotmail.com

367.  Sex-specific DNA sequence in tilapia (O. niloticus)
         Molecular-cytogenetic analysis reveals sequence differences between the sex chromosomes of Oreochromis niloticus: evidence for an early stage of sex-chromosome differentiation. 2002. Harvey, S. C., J. Masabanda, L. A. Carrasco, N. R. Bromage, D. J. Penman and D. K. Griffin. Cytogenetics Genome Research 97:76-80.
         Sophisticated microscopical and molecular techniques were used to identify a sex-specific region in the suspected XX/XY chromosome pair of O. niloticus (see Mar 2002 #308 for similar procedures applied to O. aureus.) This paper reports the development of in-situ hybridization probes for a critical region in the long arm of chromosome 1. The authors write,  "... analysis of the comparative hybridization of X and Y chromosome-derived probes to different genotypes provides the first demonstration that sequence differences exist between the sex chromosomes of O. niloticus."
         The binding difference between the probe sequences from X and Y chromosomes is small, which does not surprise the authors. "Only limited sequence divergence between the X and Y chromosomes would be expected as YY individuals can develop into males or, if hormone treated, females that are both viable and fertile, although growth and survival rates are somewhat lower in YY than XY males [see Jun 2002 #332].... This suggests that only a very limited loss of function can have occurred in Y-linked genes and that sequence differences between the X and Y chromosomes are largely confined to non-coding regions." d.j.penman@stir.ac.uk

366.  Importance of starting an aquaculture program with the best strain
         Genetic differences in growth among wild populations of the yabby, Cherax destructor (Clark). 2002. Jerry, D. R., I. W. Purvis and L. R. Piper. Aquaculture Research 33:917-923.
         Cultivation of this tasty, tolerant, freshwater crayfish is expanding in Australia. "As a precursor to a breeding programme ... five geographically isolated populations were evaluated for the traits weight at age, abdomen length and abdomen width over a period of 9 months." Total weight and the relative lengths of the head and abdomen (the edible part) varied significantly among test animals derived from the different source populations. The fastest growing were almost twice as heavy as the slowest growing at the end of the experiment. "This study emphasizes that rapid genetic gains can be made simply by starting a breeding programme based on faster growing populations." Very true. dean.jerry@li.csiro.au

365.  Sex determination in mussels
         Genetics of mother-dependent sex ratio in blue mussels (Mytilus spp.) and implications for doubly uniparental inheritance of mitochondrial DNA. 2002. Kenchington, E., B. MacDonald, L. Cao, D. Tsagkarakis and E. Zouros. Genetics 161:1579-1588.
         According to this paper the mechanism of sex determination is not known for any bivalve, nor have sex chromosomes been identified. Here the authors present new breeding data that test the recent hypothesis (due to them and others) that the sex of mussels is directly determined by the genotype of their mothers, rather than the nuclear genes they receive from their mothers and/or fathers. There may be a nuclear gene expressed in females which when homozygous produces either all-male or no-male broods and when heterozygous produces both males and females.
         The sex ratio of offspring from heterozygous females varies widely depending on dominance at this locus and other factors. The principal other factor may be the mitochondrial genome of the father. Mussels, and perhaps many or most other bivalves, inherit mitochondria from both parents, a phenomenon which is very unusual in the animal kingdom. kenchingtone@mar.dfo-mpo.gc.ca

364.  Adaptive natural selection beats genetic drift in grayling
         Contemporary fisherian life-history evolution in small salmonid populations. 2002. Koskinen, M. T., T. O. Haugen and C. R. Primmer. Nature 419:826-830.
         Theory and some experimental evidence suggest that when populations are very small, genetic drift becomes the dominant evolutionary force. Accidents of allele segregation and reproductive success allow unfavorable mutatations to accumulate and beneficial genes to be lost, rapidly, by chance. The outcome can be descent into an "extinction vortex" in which populations lose fitness because they are small and consequently become smaller still (Sep 2001 #230 and #370, above). Natural selection is supposed to counteract these chance processes (Fisherian evolution) but unless it is very strong selection should be relatively ineffective in very small populations. But we really know hardly anything about the relative power of drift and selection in real-world situations.
         This is another paper on the evolution of isolated populations of Norwegian grayling (Apr 2002 #315, Jan 2001 #162). It is known that the founding parents were very few because 90 years ago a fisherman carried them in a bucket for five hours uphill along a mountain trail. Previously published quantitative genetic analyses of  life history traits in these populations is here combined with population genetic analysis of neutral microsatellite markers.
        The authors argue that, "natural selection was the dominant diversifying agent in the evolution of the quantitative [life history] traits. However, the populations were founded by a small number of individuals, exhibit very low microsatellite-based effective sizes and show genetic imprints of severe 'bottlenecks'; which are conditions often suggested to constrain selection and favour drift. This study demonstrates a very clear case of fisherian evolution in small natural populations across a contemporary timescale. mtkoskin@cc.helsinki.fi

363.  When genetic distance doesn't mean anything
         Is a multivariate consensus representation of genetic relationships among populations always meaningful? 2002. Moazami-Goudarzi, K. and D. Laloë. Genetics 162:473-484.
         This is an interesting critique of the reliability of multivariate analysis of gene frequencies, such as those used to differentiate populations for conservation and other purposes. The meaning of "reliability" is, "do these methods say anything useful?"  It turns out that unless all or most of the individual marker loci tell the same story about the genetic separation among populations, that is unless the individual patterns are congruent, then "the compromise structure is not meaningful". Even worse, "Our analysis suggests that for closely related populations, it is not always possible to accept the hypothesis that an increase in the number of markers will increase the reliability of the typology analysis."
         The statistical structure analysed in this paper are the dimensions produced by principal component analysis (PCA). The authors say or imply that their conclusions apply to other methods as well, including multidimensional scaling and phylogenetic trees. They reach their conclusions by correlating, or failing to correlate, the different patterns of population differentiation inferred from marker loci taken one at a time.
         They also suggest that another useful and simple indication that inferred genetic distances may not mean much is the degree to which genetic variance is distributed among the principal components. If the first couple of dimensions don't carry most of the variance, then the compromise pattern of population differentiation is dubious. In the case of phylogenetic trees, the warning signal is lack of strong bootstrap support for the consensus phylogeny despite significant population differentiation at all or most loci. There is some good news though: "The lack of congruence among structures is not a disadvantage for assignment studies, where independence of discriminating factors is a great asset." ugendla@dga2.jouy.inra.fr

362.  Poor correspondence between true and inferred coancestries in a captive population
         Estimation of coancestry in Iberian pigs using molecular markers. 2002. Toro, M., C. Barragán, C. Óvilo, J. Rodrigañez, C. Rodriguez and L. Silió. Conservation Genetics 3:309-320.
         Several of the same authors published a paper last year (Feb 2001 #173) which was an excellent example of the use of pedigree information in genetic conservation. In this new paper coancestry calculations using  the same pedigrees, which extend over more than 50 years, were compared with coancestries inferred from microsatellite data. Four molecular similarity measures and no fewer than eight molecular coancestry estimators, based on 49 microsatellites, were correlated with the true pedigrees.
         Unfortunately the correlation within breeds (populations) was not good, usually less than 0.5. "All the correlations were similar to those obtained when using simple coefficients of molecular resemblance such as molecular coancestry or similarity indexes.... It is concluded that lack of information on the allele frequencies in the base population may explain the bias of these estimators in populations with complex pedigrees." Compare, however, Mar 2002 #303 which reported good correspondence between inferred and true pedigrees in race horses.
         This is an important topic for the genetic conservation of small populations which have been brought under human protection recently, and where relevant pedigree data from earlier wild matings do not exist (January 2002 #283). toro@inia.es

361.  Frankenfish review
         Engineered fish: friend or foe of the environment? 2002. Stokstad, E. Science 297:1797-1799.
        This is an entertaining review of the current state of play in Frankenculture. Recent developments in salmon, trout, tilapia, carp and other species are outlined, as are the real and rhetorical environmental issues. Two useful letters to the editor follow the main news article, one from an ornamental fish specialist and the other from an environmentalist. E-mail address not available.

360.  Website for Frankeninfo
         AGBIOS is basically a consulting company in policy and educational aspects of agricultural biotechnology. Their website is a gold mine of free news items, research reports, web links, definitions etc. relating to genetic engineering and the environment. Although the focus is plants much of their material is relevant to aquaculture. I noticed several entries on the acceptability of bioengineered ingredients in animal feeds. http://www.agbios.com/main.php