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.

211.  Salmon Bacchanalia in the River Dee
        Spawning success in Atlantic salmon (Salmo salar L.): a long-term DNA profiling-based study conducted in a natural stream. 2001. Taggart, J.B., I.S. McLaren, D.W. Hay, J.H. Webb, and A.F. Youngson. Molecular Ecology 10 (4):1047-1060.
        The authors used minisatellite markers to assign parentage to salmon progenies (eyed ova) collected from an 8 km long stream in Scotland over three years. Below the surface of this turbid Presbyterian tributary the behaviour of the salmon is shockingly orgiastic. "Multiple spawning was found to be prevalent. More than 50% of anadromous spawners of both sexes contributed to more than one redd. Up to six redds for a single female and seven for a single male were detected. Both sexes ranged extensively. Distance between redds involving the same parent varied from a few metres to > 5 km. Distances > 1 km were common. Both males and females ranged to a similar extent. Range limit was not correlated to fish size. Pairs were not monogamous, both males and females mating with different partners at different sites. ... Redd superimposition was found to be common . ... High levels of nonanadromous mature parr mating success (40–50% of total progeny sampled) were recorded, and these likely contribute greatly to the effective population size." 
        The authors also note that parr maturation is not detrimental to this stock. "...Mature parr appear to exercise a viable life history strategy with high fitness which contributes to population structure and persistence." j.b.taggart@stir.ac.uk

210.  Confirming evidence for mutational meltdown in small populations
       Rapid mutational declines of viability in Drosophila. 2001. Fry, J.D. Genetical Research 77:53-60.
        "Mutational meltdown" is the name given to one of the many bad things that can happen when a population becomes too small. Deleterious mutations accumulate quickly and the resulting decrease in fecundity and survival cause the population to become even smaller. The positive feedback between declines in population size and fitness can draw the population into an "extinction vortex" (March-April #185, February #171, January #157). However, doubts have been expressed concerning some of the key laboratory experiments demonstrating the effect. Given their implications for genetic conservation we would like to know whether the doubts are justified.
        Apparently not. The author of this paper writes "Here, using a [new method], I reanalyse the previous mutation-accumulation (MA) experiments, and report the results of a new one. I show that in each of four experiments, including Mukai's two experiments, viability declines due to mildly deleterious mutations were rapid. " jfry@mail.rochester.edu

209.  The Neolithic birth of domestic breeds
        Multiple maternal origins and weak phylogeographic structure in domestic goats. 2001. Luikart, G., L. Gielly, L. Excoffier, J.-D. Vigne, J. Bouvet, and Taberle. P. Proceedings National Academy of Sciences (USA) 98 (10):5927-5932.
        As well as being intrinsically interesting, this is an unusually instructive paper because of the variety of genetic and statistical techniques used to discover how, where and when the domestic breeds of these useful animals evolved. The authors based their analysis of the divergence of goat breeds on mitochondrial DNA sequences from the rapidly-evolving control region of the mitochondrial genome and calibrated the time scale with a molecular clock based on the divergence of the sheep and goat mitochondrial cytochrome b gene.
       Three main lineages of goat breeds (80 breeds in total were studied) appear to have diverged 2 or 3 hundred thousand years ago, i.e. long before the animals were first domesticated. This evidence points strongly to the inference that goats were domesticated from local wild animals at least three times, first about 10,000 years ago in southern Turkey/Euphrates valley, and then again sometime between 3,000 -- 6,000 years ago farther to the east in the fertile crescent (Iran) and in Asia (possibly northern India). The lineage from the oldest domestication is much more genetically diverse than the other two, as would be expected from this timing. The authors were also able to estimate the time at which the initial domesticates underwent a population expansion [for techniques see #202 below] and found that the newer lineages expanded about 2,000 and 6,000 years ago relative to a presumed 10,000 year date for the expansion of the first domesticate.
        The authors note that a similar pattern exists in cattle, sheep, and pigs. However, "Goat populations are surprisingly less genetically structured than cattle populations. In goats only 10% of the mtDNA variation is partitioned among continents. In cattle the amount is 50%. This weak structuring suggests extensive intercontinental transportation of goats and has intriguing implications about the importance of goats in historical human migrations and commerce." The authors suspect that goat genes flow travel rapidly because goats are more transportable and also because they represent smaller and more durable units of wealth than cattle. gordon.luikart@ujf-grenoble.fr.

208.  Complicated behavioural evolution in domesticated salmon
        Behavioural and heart rate responses to predation risk in wild and domesticated Atlantic salmon. 2001. Johnsson, J.I., J. Höjesjö, and I.A. Fleming. Can. Jour. Fisheries and Aquatic Sciences 58:788-794.
        In this study seventh-generation farmed salmon were compared with wild salmon from the same founder population. One-year old wild fish (1+) had a stronger heart rate and flight response from a simulated predator than the domesticated fish, but the differences were weaker or reversed in two-year-old fish. The authors suggest that if there is a genetic domestication response it is not a simple one. It involves the "reaction norm", i.e. the parameters of the functional interaction between current environmental stress, prior environmental history, and the state of development. "This should be considered when attempting to predict the consequences of release or escape of domesticated animals in the wild." jorgen.johnsson@zool.gu.se

207.  Do population bottlenecks reduce the ability to evolve?
        Effects of bottlenecks on quantitative genetic variation in the butterfly Bicyclus anyana. 2001. Saccheri, I.J., R.A. Nichols, and P.M. Brakefield. Genetical Research 77:167-181.
        How does a bottleneck, a brief period of very low numbers, affect the ability of a population to meet new selective challenges and evolve new adaptations? This is an important question for aquaculture broodstock management as well as for genetic conservation.
        We know that only a random sample of genes (alleles) will pass through the bottleneck while other genes are lost by chance during the period when few matings take place. In an extreme case, with only one pair of breeders passing through the bottleneck, only 4 alleles per locus will be available for population re-growth and evolutionary adaptation. Some of those alleles may be identical.  Either of two things can happen to evolutionary capacity in a bottleneck, depending on how the surviving genes combined with each other to influence the phenotype in the pre-bottleneck environment:
        (1)  The effects of individual genes simply add together. Genetic variance will decrease when genes are lost by chance, and the rate at which the population can evolve will therefore decrease because of the bottleneck.
        (2)  Pairs of genes interact non-additively to produce their effects on the phenotype, either in combination at a single locus (called dominance) or at different loci (called epistasis). Non-additive genetic variance does not respond in a simple way to selection in sexual species even though it contributes to phenotypic variation among individuals. Generally speaking, only additive genetic variance allows an evolutionary response to selection. Theory has shown, however, what when some alleles are lost by chance from a non-additive genetic system the surviving genes will sometimes make an increased contribution to additive genetic variance. In this case the capacity to evolve will be enhanced by the bottleneck. (See also October 2000 #116, #112)
        So much for theory. What actually happens? (See February list #165 for an instance in which genetic diversity did not reduce neutral microsatellite diversity in sockeye salmon.) This interesting experimental paper makes a strong case for believing that additive variance will increase in traits closely related to fitness, like fecundity and survival. Quantitative traits that are under weak selection, on the other hand, will lose additive genetic variance in the bottleneck, just like neutral marker alleles. The explanation is that traits related to fitness have an especially high proportion of dominance variance. Recent papers pointing out this difference between the genetic architectures of fitness and non-fitness traits have already been noted on this website (February 2000 #15 and #10).
        The present experiment describes what happens when butterfly populations are bottlenecked to different extents in the laboratory. Additive genetic variance of wing size (a neutral trait) decreases in bottlenecks according to theoretical expectation while additive variance and heritability of egg hatching rate (a component of fitness) increases. The authors use genetic markers in an interesting way to calculate inbreeding in the bottleneck (see May list #193), which allows them to show that the change of wing-size variance, but not hatching,  follows random sampling expectation exactly. saccheri@liverpool.ac.uk

206.  No evolution of crossover resistance to whirling disease
        Salmonids resistant to Ceratomyxa shasta are susceptible to experimentally induced infections with Myxobolus cerebralis. 2001. Hedrick, R.P., T.S. McDowell, K. Mukkatira, and M.P. Georgiadis. Journal of Aquatic Animal Health 13:35-42.
        Whirling disease is a nasty, cartilage-destroying condition of salmonids caused by the myxosporean pathogen Myxobolus cerebralis. Strains of rainbow trout with known differences in susceptibility to another myxosporean, Ceratomyxa shasta, were exposed in the laboratory to waterborne infectious stages of whirling disease. "In general [possible exception of one strain] the mechanisms of resistance that have developed among certain salmonid populations to one myxosporean, C. shasta, do not extend [or extend minimally] to protection or resistance to a second myxosporean, the causative agent of salmonid whirling disease". The mechanisms by which some rainbow trout resist infection by C. shasta is unknown, but breeding experiments suggest that its genetic architecture is polygenic and at least partly additive. rphedrick@ucdavis.edu

205.  Useful software for genetic analysis
        TOOLS: Phylogenetics Crunch. 2001. Anonymous. Science 292 (5518):815.
        "Wayne and David Maddison at the University of Arizona are working on Mesquite, a modular system for evolutionary analysis. Their goal is to build a Java-based system that makes it possible to integrate disparate packages, such as the popular PAUP program and MacClade, which the same duo also developed. Download a beta version of Mesquite at: http://mesquite.biosci.arizona.edu/mesquite/mesquite.html "
        The website has additional information, "Modules written include ones for basic character analysis (parsimony and likelihood), comparative biology, molecular evolution, population genetics and morphometrics. The Mesquite documentation has a summary of plans as to what it will do. ... Also, we plan to increase Mesquite's connectedness in the world outside the local hard disk via distributed processing and interaction with Internet databases such as the Tree of Life . ... we hope to have it link to other programming efforts including Drummond and Strimmer's PAL." wmaddisn@u.arizona.edu.

204.  Pacific salmon Y chromosome
       Identification of the Y chromosome in chinook salmon (Oncorhynchus tshawytscha). 2001. Stein, J., R.B. Phillips, and R.H. Devlin. Cytogenet Cell Genet 92 (1-2):108-110.
        "The Y chromosome in chinook salmon, Oncorhynchus tshawytscha, was identified using fluorescence in situ hybridization (FISH) with a probe to a male-specific repetitive sequence isolated from this species. The probe highlights the distal end of the short arm of an acrocentric chromosome with a DAPI-bright interstitial band of variable size. " This will be a useful technique for ploidy manipulation and other types of genetic study including extreme linkage analyses that make use of androgenesis. jstein@csd.umw.edu

203.  Recognizing evolutionary adaptation to local environments
        Nonclinality of molecular variation implicates selection in maintaining a morphological cline of Drosophila melanogaster. 2001. Gockel, J., W.J. Kennington, A. Hoffmann, D.B. Goldstein, and L. Partridge. Genetics 158:319-323.
        When populations differ genetically in a trait that appears to affect fitness, it may be that the populations are adapted to different environments. On the other hand, the genetic differences may have arisen merely by accidents of population dynamics and dispersal and not reflect adaptive differences at all. These two alternative explanations have very different implications for genetic conservation (since neutral variation is probably less worth conserving than adaptive variation) , for the definition of evolutionarily significant units and, in the case of fisheries, for choosing broodstock for aquaculture, enhancement and rehabilitation of endangered wild populations.
        In this paper the authors have compared the body size of Drosophila with neutral variation at 16 microsatellite loci to see whether variation in body size is adaptive over a 2000 km north-south transect in Australia. Body size was several standard deviations smaller at the extreme north than the extreme south. Does this represent adaptation? The authors found that regression of body size on latitude explained approximately 80% of the variance, i.e. there is a strong correlation. Regression of their measure of supposedly neutral gene frequency on latitude explained only about 20% of the variation on average, although one of the 16 loci had 76% of its variance explained by latitude. The conclusion of the paper is that body size is indeed under selection. Some of the loci may be under selection or closely linked to quantitative trait loci (QTL) that are under selection.
        One of the innovative features of this paper which makes it interesting to fisheries is that the authors have used regression on an extrinsic variable to compare phenotypic with neutral variation. This allows them to study an explicit environmental variable, namely latitude. Presumably adaptation of morphological and behavioral traits to temperature, photoperiod, salinity or other continuous but not necessarily clinal variables could be studied in the same way. It might even be a fast way to identify candidate markers for QTL. ucbhlop@ucl.ac.uk  [Linda Partridge]

202.  Use DNA markers to infer historical changes in population size
        A power analysis of microsatellite-based statistics for inferring past population growth. 2000. King, J.P., M. Kimmel, and R. Chakraborty. Molecular Biology and Evolution 17 (12):1859-1868.
        The authors evaluate the relative power of several different statistical procedures that use microsatellite data to detect past population expansion. They find that the statistical test based on the imbalance between allele size variance and heterozygosity is better for detecting population growth than are methods based on between-locus variability or allele size distributions. The underlying concepts are presented with admirable clarity in this paper. rc@hgc9.sph.uth.tmc.edu

201.  Differentiating European carp strains
        Genetic variability in reared stocks of common carp (Cyprinus carpio L.) based on allozymes and microsatellites. 2001. Desvignes, J.F., J. Laroche, J.D. Durand, and Y. Bouvet. Aquaculture 194:291-301.
        The authors looked at allozyme and microsatellite gene frequencies in a number of cultured carp strains in France and the Czech Republic. Rather surprisingly, heterozygosity was lower in the French strains but the number of alleles was higher. The difference between these two measures of genetic diversity may be the key to sorting out what has happened under the different cultivation and selection regimes in the two regions of Europe. Generally speaking the two marker systems told the same story, but the authors judge that microsatellites are better at discriminating strains within and between countries. laroche@cismsun.univ-lyon1.fr

200.  A crustacean evolves, loses and re-evolves anti-predation behaviour
        Rapid, local adaptation of zooplankton behavior to changes in predation pressure in the absence of neutral genetic changes. 2001. Cousyn, C., L. De Meester, J.K. Colbourne, L. Brendonck, D. Verschuren, and F. Volckaert. Proceeding of the National Academy of Sciences (USA) 98:6256-6260.
        The waterflea Daphnia magna regularly produces resting eggs that can survive for decades in mud until conditions are right for emerging. The authors of this article hatched out resting eggs collected at various depths in the sediment of a 30-year-old man-made pond in Belgium. Daphnia and fish have coexisted in the pond over its entire history, but the density of fish, and therefore the intensity of fish predation in the environment, has varied considerably. The question asked by the authors was whether the waterfleas adapted genetically to the changing predation. It is known that Daphnia which live in ponds characterized by strong predation pressure tend to avoid the light in the presence of chemical substances (kairomones) released by fish. This was the possibly adaptive trait, a change in phototactic behavior in the presence of "fishwater". Three microsatellite loci provided a presumably neutral genetic trait with which the behavioral trait was compared.
        The genetical logic, although not the statistical procedures, is the same in this paper as in #203 above. Much of the genetic variance in the behavior of clones developed from the buried eggs was explained by historical variation in fish predation, which constituted the independent environmental variable. The neutral microsatellite frequencies varied little over the 30 year period. Therefore the observed genetic change in phototaxis was considered to be an adaptive evolutionary response to changes in the local selective regime.
        Whether the behaviour of crustaceans such as Penaeid shrimp would evolve similarly in the presence/absence of fish predation remains to be discovered. If it does it might have interesting genotype-environment interaction effects when broodstocks are selected for extensive aquaculture and/or "fishwater free" (?) intensive aquaculture. Luc.DeMeester@bio.kuleuven.ac.be.