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.

150.  Our genetic essence in a poisonous fish
ScienceScope: fishy genomes. 2000. Anonymous. Science 290 (5493):913.
        "The U.S. Department of Energy (DOE) has announced that its Joint Genome Institute in California will sequence the complete genome of the sometimes-poisonous puffer fish, Fugu rubripes. ... [DOE] expects to have 95% of the sequence completed by March 2001--putting Fugu sequencing ahead of efforts to decode the genomes of the zebrafish and Tetraodon, a freshwater puffer." Apparently the genome will have been completely sequenced at least 3 times by next March, each repetition serving to increase the length of the sequenced fragments. A consortium of institutions in the U.S., the U.K. and Singapore will take another year or so to complete the enormous computational task of assembling the partial sequences into a continuous record.
        Puffer fishes have much less DNA per nucleus than most other vertebrates despite having a complete complement of genes; this is because of the relative scarcity of repetitive sequences and silenced duplicate genes. In fact, interest in the puffer fish is solely due to its genome being just like our own, except cleaner. The idea is to provide a sort of "index" to the human genome.
        The puffer fish is nevertheless a fish, not a person, and this project will surely become a treasure trove for fish geneticists interested in adaptation, phylogeny, genetic engineering and quantitative trait selection based on candidate loci. Raw sequence data will be released every 24 hours.  http://jgi.doe.gov/tempweb/programs/fugu.htm

149.  Are good environments bad for long-term conservation?
Does fitness erode in the absence of selection? An experimental test with Tribolium. 2000. Lomnicki, A., and M. Jasienski. Journal of Heredity 91 (5):407-411.
        Will fitness decline over time when natural selection is relaxed, e.g. in aquaculture broodstocks or hatchery broodstocks which produce fingerlings for release into the wild? The theoretical answer is yes, because deleterious recessive mutations will accumulate. This is thought to be why cave animals lose their eyes through disuse over many generations. In this paper the authors reared two flour beetle populations for 22 generations in an especially benign environment which was essentially free from selection. The ability to resist starvation became considerably reduced in both of the relaxed-selection lines when their performance was compared with controls. Furthermore, development was slower and females were smaller, relative to controls, in one of the selection lines. This also indicates a loss of fitness. lomnicki@eko.uj.edu.pl

148.  Genetic basis of competitive success
A genetic analysis of intraspecific competition for growth in mussel cultures. 2001. Brichette, I., M.I. Reyero, and C. García. Aquaculture 192 (2-4):155-169.
        The authors used an experimental design and analytical framework modeled on procedures developed by Bruce Griffing for the analysis of growth competition in plants. There were large differences among families of mussels in their response to competition from other families and in their influence on other families, when they were arrayed in baskets. The small number of parents involved in the factorial mating made it a priori difficult to find significant heritabilities for competition effects. However, there is no reason to doubt that the genotypic variation observed is heritable to some extent.
        The authors ask whether selection for increased growth will cause a compensatory competitive decrease in the growth of other individuals, leading to an overall decrease in yield. Their results lead them to believe that selection indices can be developed which will avoid this problem. This is important work on a neglected subject. Most aquaculture genetic experiments ignore competition despite the fact that it has a major effect on the variance of growth rates.  bfcarlog@usc.es

147.  Field assay for shrimp viral diseases
Dot-blot nitrocellulose enzyme immunoassays for the detection of white-spot virus and yellow-head virus of penaeid shrimp. 2000. Cesar, E., B. Nadala Jr., and P.C. Loh. Journal of Virological Methods 84 (2):175-179.
        "Dot-blot nitrocellulose enzyme immunoassays (DB-NC-EIA) were developed for the detection of white-spot virus (WSV) and yellow-head virus (YHV) in infected shrimp. ... The assays are by far the simplest and most rapid detection methods available for WSV and YHV." The assay is intended to be used in the field by relatively untrained personnel for the detection of infected shrimp. It should be useful for selection programs, among other things. No e-mail address is listed but the corresponding author is P.C. Loh, Department of Microbiology, University of Hawaii, Snyder 207/2538 The Mall, Honolulu, HI 96822 USA

146.  At last: detailed inbreeding information for a salmonid
Inbreeding levels in selected populations of rainbow trout, Oncorhynchus mykiss. 2001. Pante, M.J.R., B. Gjerde, and I. McMillan. Aquaculture 192 (2-4):213-224.
        The authors of this important paper used pedigree records to make exact calculations of the inbreeding levels of individual fish in three rainbow trout populations. The exact calculations were compared to average, population-level, inbreeding estimated from the counts of male and female breeders in each generation. The trout populations comprise the nucleus of a selection program in Norway.
        "The inbreeding levels across generations as estimated from pedigree information (Pi) and effective population size (Ne) with the assumption of no selection and random mating, among the three populations were all at 11.3% or less [in any single generation]."
        "In the present study, the rate of inbreeding calculated from Pi, averaged over all populations was 1.3% per generation or 0.4% per year. The rate of inbreeding calculated from Ne [specifically, the "variance effective" Ne] averaged among populations was 0.9% per generation or 0.3% per year. These inbreeding rates calculated from Ne and Pi were below the level of 3% to 5% typically found in many commercial salmonid farms". The authors conclude that this is within acceptable limits. It is important to note, however, that some individual fish had much higher coefficients, reaching a maximum of 33.3% which is considerably higher than one generation of brother-sister mating.
        The inbreeding rates estimated from breeder counts were generally , but not always, lower than those estimated from the pedigree records. The authors speculate on likely explanations for the discrepancy, including the effects of selection and variation in progeny size. It may also be relevant that the variance effective population size Ne will, in theory, always be larger than the inbreeding effective population size when a population is expanding. Inspection of the spawning data in Table 2 suggests that populations were expanding during most of the instances where there was a large discrepancy between the two inbreeding estimates. dosette.pante@akvaforsk.nlh.no

145.  Inbreeding depression of trout weight at harvest
Effect of inbreeding on body weight at harvest in rainbow trout, Oncorhynchus mykiss. 2001. Pante, M.J.R., B. Gjerde, and I. McMillan. Aquaculture 192 (2-4):201-211.
        In this paper (a companion to the paper noted above) the authors estimated the effect of inbreeding on harvest weight in the trout populations. Ordinary linear regression of body weight on individual inbreeding coefficients, with adjustments for environmental effects and sex, indicated that, on average, harvest weight was depressed about 2.3% per 10% increase in inbreeding. More inclusive quantitative genetic models gave estimates of inbreeding depression up to 60% larger. Nevertheless, this inbreeding depression is rather lower than expected from previous studies which were not based on pedigree analysis of working salmonid populations.
        The authors conclude that, "These values meant body weight at harvest was moderately affected by inbreeding but were not high enough to cause any serious impact in the selective breeding program for rainbow trout in Norway." The Norwegian populations had been well managed and it is unlikely that many hatcheries could be as successful in avoiding inbreeding during selection. dosette.pante@akvaforsk.nlh.no

144.  Hidden heritability in variable environments
The influence of environmentally induced heterogeneity on age-specific genetic variance for mortality rates. 2000. Pletcher, S.D., and J.W. Curtsinger. Genetical Research 75:321-329.
         The authors of this theoretical paper found that "environmentally induced heterogeneity among genetically identical individuals is sufficient to generate biased estimates of age-specific genetic variance. Although the magnitude of the bias may change with age, one general trend emerges: the true genetic variance at the oldest ages is likely to be dramatically underestimated. ... We note that age-dependent estimates of genetic variance for characters that are correlated with mortality (either genetically or environmentally) can be expected to be similarly affected."
        This should interest people who are estimating heritabilities of fitness traits in natural populations, i.e. by using markers to infer genetic relatedness. Estimates of the heritability of disease resistance in aquaculture may also be affected, as may heritabilities of growth-rate when aquaculture populations are graded or culled. pletcher@demogr.mpg.de

143.  Salmon on the fast track to speciation
Rapid evolution of reproductive isolation in the wild: evidence from introduced salmon. 2000. Hendry, A.P., J.K. Wenburg, P. Bentzen, E.C. Volk, and T.P. Quinn. Science 290 (5491):516-518.
        Different ecotypes of Sockeye salmon breed in river gravel and along lakeside beaches. The two reproductively distinct ecotypes have evolved numerous times in watersheds in the Pacific northwest. How long does this process take? The authors of this paper examined a very young population of sockeye that were introduced into Lake Washington between 1937 and 1945. They found that a beach-spawning population that was first noticed in 1957 consists of two components: a true resident population that always spawns on the beach, plus immigrant beach spawners that were themselves born in a tributary river. The resident beach spawners differ from the immigrants and river fish both in their (probably adaptive) morphology and their microsatellite allele frequencies. The authors believe that they are, however, descendents of the river population and not an independent introduction into the lake. The partial reproductive isolation between the beach-resident and beach-immigrant populations -- inferred from their genetic differences -- must have evolved in less than 13 generations. The speed of this evolutionary divergence under selection has already aroused a lot of controversy among evolutionists and geneticists, with opinions ranging from "much ado about nothing" to "revolutionary". ahendry@bio.umass.edu

142.  Relatedness measures for doing quantitative genetics
Marker-inferred relatedness as a tool for detecting heritability in nature. 2000. Ritland, K. Molecular Ecology 9 (9):1195-1204.
        Ritland has made very important contributions to the growing set of procedures that use marker data to infer quantitative genetic parameters in small but non-experimental populations. Aquaculture broodstocks usually fall into this category as do populations of fish that are supplemented from hatcheries or have grown so small they risk extinction.
        The paper presents a "perspective of how inferred relatedness, based on genetic marker data such as microsatellites or amplified fragment length polymorphisms (AFLPs), can be used to demonstrate quantitative genetic variation in natural populations. Variation at two levels is considered: among pairs of individuals within populations, and among pairs of subpopulations within a population." It is a brief but useful pointer to Ritland's own very useful method-of-moments procedures for inferring relatedness and inbreeding and to the position of these procedures among the others. kermit.ritland@ubc.ca

141.  Allocation of sampling effort in pedigree inference
        Statistical confidence in parentage analysis with incomplete sampling: how many loci and offspring are needed? 2000. Neff, B.D., J. Repka, and M.R. Gross. Molecular Ecology 9 (5):529-539.
        The authors provide formulas for calculating confidence levels for parentage-inference models they have developed which are useful in populations where parents have not been completely sampled. They also discuss the allocation of sampling effort: "When parentage is low, sampling effort should concentrate on increasing the number of loci. Otherwise, there are similar benefits from increasing the number of loci or offspring. We demonstrate these methods using genetic data from a nest of the bluegill sunfish (Lepomis macrochirus)."  neff@zoo.utoronto.ca

140.  Genetic variation in disease resistance in tilapia
Immune responses of Nile tilapia (Oreochromis niloticus L.) clones: I. Non-specific responses. 2001. Sarder, M.R., K.D. Thompson, D.J. Penman, and B.J. McAndrew. Developmental and Comparative Immunology 25 (1):37-46.
        The authors used three inbred clones which had been produced by gynogenesis and sex-reversal, plus the outbred but isogenic offspring of crosses among the clones. There were considerable differences among the clones and their various crosses in parameters of the immune system (serum lysozyme and phagocytosis) and in mortality induced by a bacterial challenge test. The statistical analysis was not directly tied to a quantitative genetic model, but the authors note that the hybrid offspring of inbred clones showed levels of resistance to Aeromonas infection that was between that of the parents, but not exactly intermediate. The non-specific immune responses were also not exactly intermediate. From this they conclude that there are strong additive and perhaps dominance components to the genetic variance of the non-specific response but no sign of inbreeding depression in these clones (which may have been unavoidably selected to some extent). kdt1@stir.ac.uk  (Thompson)

139.  Salmon hybridize with trout in Irish streams
Incidence of hybridization between Atlantic salmon, Salmo salar L., and brown trout, Salmo trutta L., in Ireland. 2000. Matthews, M.A., W.R. Poole, C.E. Thompson, J. McKillen, A. Ferguson, K. Hindar, and K.F. Wheelan. Fisheries Management and Ecology 7:337-347.
        "High incidences of salmon x trout hybrids have been recorded in rivers situated near intensive salmon farming sites in Norway and Scotland, which may be indicative of a breakdown in reproductive isolation between salmon, Salmo salar L., and brown trout, Salmo trutta L." The authors of this paper studied fish from a number of rivers, some located near and some far from salmon farms. All hybrids arose from Atlantic salmon female by brown trout male crosses, even though the authors were careful to avoid biasing the sample towards spawning sites dominated by salmon. "Hybrid parr were recorded from one of the low-risk rivers [distant from farms] (1.0%), but were present in seven out of the 10 catchments located within 38 km of salmon farms, with frequencies ranging from 0.7% to 3.1%. " sra@iol.ie

138.  Frankencontrol of fish pests
Periodic triggering of an inducible gene for control of a wild population. 2000. Davis, S.A., E.A. Catchpole, and G.R. Fulford. Theoretical Population Biology 58 (2):95-106.
        The release of large numbers of sterile or otherwise unsuitable mates has been used for years to control insect pests. The authors of this paper investigate, by analysis of classical deterministic genetic models, what would happen if you flooded a target population with individuals carrying a transgene that can be switched on at will, e.g. by a chemical spray in the watershed. The triggering chemical induces expression of the transgene which causes death or sterility in animals that carry it. The growth rate of the target population is reduced. The trigger is environmentally harmless.
        The theoretical study shows that the population level of the target species can indeed be reduced to any desired level, but if the inducer is applied too often selection for transgene-free individuals will nullify the effect. Mosquito fish and carp which have become serious pests in Australia are identified as suitable targets but no feasible "terminator" transgene is described in this paper. s-davis@adfa.edu.au

©.   "Nobody has a monopoly on good ideas.  If you have a good idea, don't tell me that you have a good idea, because I will take it."
Prime Minister Jean Chretien of Canada, recently re-elected for the 42nd time.