These aquaculture-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.

58. Protecting your investment in a breeding programme
The use of random amplified polymorphic DNA (RAPD) markers to identify strawberry varieties: a forensic application. 2000. Congiu, L., M. Chicca, R. Cella, R. Rossi, and G. Bernacchia. Molecular Ecology 9:229-232.
        This is a good example of how natural (non-transgenic) gene markers can be used to protect private property, in this case a patented strawberry cultivar that was being grown illegally. The developer of the cultivar brought a law suit against the genetic hijackers. During the testing of the DNA evidence the court sneakily mixed the 13 suspect specimens with 18 additional specimens from different varieties. The RAPD analysis not only picked out the 13 suspects as being identical with the patented cultivar, it correctly exposed the 18 "plants". This impressed the Italian court and the plaintiff won the suit.
        The strawberries were clones which made the problem easier than it would have been with fish or shrimp -- in today's aquaculture industry anyhow. However, what apparently convinced the court was the success of the genetic assignment tests, not abstract reasoning on Bayesian probabilities.
        The moral is that if someone hijacks your patented shrimp strain you should run a double-blind test which groups the disputed shrimps with your strain rather than the source strain claimed by the defense. It is certainly feasible to analyse enough markers to assign non-clonal fish or shrimp to one of a pair of specified, alternative sources.    col@dns.unife.it

57. A new way to think about the risk of extinction
Estimating the time to extinction in an island population of song sparrows. 2000. Sæther, B.-E., S. Engen, R. Lande, P. Arcese, and J.N.M. Smith. Proceedings of the Royal Society Ser. B. 267:621-626.
        The authors performed what oceanographers are not ashamed to call "hindcasting" on data from a small, island population in British Columbia which had been accurately counted every spring for 24 years. The objective was to see how uncertainties and biases in population models and parameter estimates would affect the accuracy of predictions about the ultimate fate of these sparrows.  After detailed statistical analysis they conclude that "ignoring uncertainties in population dynamics produces a substantial underestimation of the extinction risk." [italics added]. Fisheries conservation biologists using population viability analysis (PVA) programs such as VORTEX should note this conclusion.
        The most interesting feature of the paper is a new idea called a population prediction interval (PPI), a statistical concept rather like a confidence interval. The idea is to express extinction risk as a predicted date-of-extinction (or future population size) covered by upper and lower confidence bounds at a specified level of probability. This seems intuitively easier to deal with than the usual "30% chance of extinction within 100 years"  type of statement about endangered populations. Furthermore, the authors point out, the PPI allows us to make the precautionary management principle (always assume the worst outcome) an operational concept. (See also March List #23.)  bernt-erik.sather@chembio.ntnu.no  

56. Are hatcheries really bad for salmon that are intended for release?
Comparative performance of genetically similar hatchery and naturally reared juvenile Coho salmon in streams. 1999. Rhodes, J.S., and T.P. Quinn. North American Journal of Fisheries Management 19:670-677.
        The authors divided a cohort of hatchery-produced Oncorhynchus kisutch fry into two lots, one of which was immediately placed in a natural steam to grow while the other lot was reared in the hatchery. After 3 months the hatchery-reared fish were also placed in the stream. During the ensuing months these late additions were compared with the salmon that had been there since hatching. Although the hatchery-reared fish grew somewhat faster in this natural environment than the others which had been there all along, their survival was no different. The conclusion is that, in this instance, "hatchery-reared coho salmon perform similarly to naturally reared salmon when introduced into streams in low numbers and with a relatively small size advantage."  (Given that they are genetically similar.)   justinrhodes@students.wisc.edu. 

55. Patented, disease-resistant Frankenfish from earliest evolutionary time
Transgenic fish capable of expressing exogenous lytic peptides. 1999 (December 7). Cooper, R.K., and F.M. Enright. United States Patent 5,998,698.
        The authors of this patent have produced transgenic catfish and carp (koi) which contains a silk moth gene which produces cecropin-B, a lectin molecule which can function as a built-in fungicide and bactericide.
        Lectins are small peptides that bind to sugar molecules exposed on the surface of cell membranes. After binding, some types of lectin lyse the phospholipid bilayer of the membrane, killing the pathogen. Lytic peptides are proving to be potent toxins to a broad range of bacteria, fungi and protozoa. Cecropin-B is an antimicrobial lectin of about 35 amino acids which is synthesized in the pupae of the silk moth in response to bacterial infection. Similar molecules are widespread in other organisms.
        This new patent claims that "Novel means have been discovered for increasing the resistance of an animal host (including humans) to diseases caused by intracellular bacteria, protozoa, and viruses. ... Augmentation of the host's defenses against infectious diseases or tumors is achieved by "arming" the host's cells with an exogenous gene encoding a natural or synthetic lytic peptide. ...The transformed cells have the ability to produce and secrete a broad spectrum chemotherapeutic agent that has a systemic effect on certain pathogens, particularly pathogens that might otherwise evade or overcome host defenses."
        Transferring cecropin genes from moths to fish may seem rather bizarre, but there is reason to think the gene has made some extraordinary journeys on its own. The DNA sequence of the cecropin gene used to transform the koi and catfish bears some similarity to nuclear DNA that encodes ribosomes.  An interesting 1999 paper by K. Putsep et al. (FEBS Letters 451:249-252) hypothesises that it might be very ancient. Their suggestion is that "cecropins have evolved from ribosomal protein L1 of an ancestral intracellular pathogen that developed to a symbiont ending as an organelle. When the R1 gene moved into the host nucleus, a duplication provided a copy from which today's cecropins could have evolved."

54. Is all White Spot Virus the same?
Specific genomic DNA fragment analysis of different geographical clinical samples of shrimp white spot syndrome virus. 1999. Lo, C.-F., H.-C. Hsu, M.-F. Tsai, C.-H. Ho, S.-E. Peng, G.-H. Kou, and D.V. Lightner. Diseases of Aquatic Organisms 35:175-185.
        White Spot WSSV is found in many species of shrimp and crabs in many parts of the world. The authors analysed DNA from clinically infected P. chinensis, P. monodon and P. vannamei from China, India, Thailand, Taiwan, Texas, South Carolina and several grocery stores. They also looked at infected crayfish (Orconectes punctimanus) from the U.S. National Zoo. Their analysis involved amplifying regions of the DNA with virus-specific PCR primers, then chemically cutting up the amplified viral DNA with restriction enzymes and examining the sizes of the resulting fragments. The pattern of fragment lengths carries information about the genetic similarities and differences among the infecting viruses. These are standard genetic techniques. "The results highlighted the genetic relatedness of all the WSSV clinical samples with the possible exception of a series of Texas viral samples which could be distinguished from the other geographic samples in some of the PCR-based tests."
        The authors choose to emphasize the genetic similarity of the clinical samples from different geographical regions and host animals. However, it is possible to draw a further conclusion from their careful and interesting work.  If there are genetic differences between WSSV strains that might be used to trace the origin of an epidemic -- and there probably are -- then this technique isn't powerful enough to find them. To get enough genetic information to do that it may be necessary to go beyond restriction fragment length polymorphism, e.g. to direct sequencing of amplified viral genomes from clinical samples and/or scoring single nucleotide polymorphisms in the genomes. (See April list #35 for another paper on baculovirus differentiation.)   aquapath@ag.arizona.edu.  

53. Successful selection for scallop size-at-age
Selection and realized heritability for growth in the scallop, Euvola ziczac (L.). 1999. Perez, J.E. , and C. Alfonsi. Aquaculture Research 30:211-214.
        The initial stock of parents were produced by mass spawning. "At one year of age, the top 10% of the stock (i.e. the larger scallops) were segregated to create the selected line. An equal number of mean-sized scallops was used to create the control line. In the second generation, after 294 days in culture, the heritability values of the scallops were calculated. Heritability estimates fluctuated between 0.47 and 0.54 depending on the character investigated, i.e. shell length or shell height. The selected line was 5.5% longer and 4.5% higher than the control line, and 7.3% longer and 9.4% higher than the parental line."         jperez@sucre.udo.edu.ve

52. Choosing where your bass stock comes from is an important aquaculture decision
Variation in growth rate within and among stocks and families of striped bass. 1999. Woods, L. Curry III, E.M. Hallerman, L. Douglass, and R.M. Harrell. North American Journal of Aquaculture 61:8-12.
        "Variation in growth rate within and among stocks and families of striped bass Morone saxatilis was evaluated in flow-through tank systems at the University of Maryland, College Park, Crane Aquaculture Facility. Significant differences in growth performance among distinct stocks originating from three areas of the Chesapeake Bay (1983 year-class) demonstrate among-stock differences that might be exploited in a selective breeding program for striped bass." (See April list #33, March list #28.)   LW60@umail.umd.edu .

51. Beneficial genes flow into isolated populations facing extinction
Inbreeding depression and genetic rescue in a plant metapopulation. 2000. Richards, C.M. American Naturalist 155:383-394.
        The author showed through greenhouse experiments that inbreeding seriously reduces fitness in the white campion. They also showed that small, natural populations show inbreeding depression in proportion to their isolation from other populations. From these two observations they conclude that "population connectivity through pollen-mediated gene flow may have substantial effects on the persistence of isolated colonies and on the spatial structure of a metapopulation in general". They call this "genetic rescue" meaning that inward-migrating genetic material can rescue a small population by diminishing the unfortunate consequences of inbreeding and loss of genetic variation.
        Fisheries managers who are concerned with genetic conservation of, for example, isolated salmon stocks should take note of this work even though it was done on a plant. There are theoretical reasons to believe that inward genetic migration might actually be bad; it can break up locally-adapted gene complexes, or introduce deleterious mutations into a population that has already lost them by selection or drift. Tempers have risen during discussion of this issue. This was an experimental and observational study, however, and in this instance gene flow was beneficial. (See April list #40, March list #21.) chris.richards@vanderbilt.edu.

50. Endangered dolphins entangled in an extinction vortex
Loss of genetic diversity in the endemic Hector's dolphin due to fisheries-related mortality. 2000. Pichler, F.B., and C.S. Baker . Proceedings Royal Society Ser. B. 267:97-105.
        This species of marine mammal is endemic to New Zealand, where mortality caused by accidental entanglement in fish nets has reduced its numbers to only about 4000 individuals in small and scattered populations.
        The authors looked at mtDNA in recent and preserved samples dating back to 1870. There has been a significant decline in genetic diversity -- in fact the authors predict that one of the two populations will be extinct and the other have lost all its genetic diversity (in the mt region examined) in less than 20 years! "This time-series of reduction in genetic variation provides independent evidence of the severity of population decline and habitat contraction resulting from fisheries and perhaps other human activities." It would also be nice to know what is happening to nuclear DNA where the rate of inbreeding could be estimated.

49. Inbreeding and outbreeding in simulated endangered Maine salmon
FITPOP, a heuristic simulation model of population dynamics and genetics with special reference to fisheries. 2000. McKenna, J.E. Jr. Ecological Modeling 127:81-95.
        Here is an ecological simulation model (a simple and familiar one, the single-species logistic) which explicitly includes the effect of genetic variation. "Simulation results illustrated the effects of subtle differences in genetic and population parameters on total population size, overall fitness, and sensitivity of the system to variability. [The authors of #58 are writing about uncertainty, not variability.] " Inbreeding and outbreeding effects were found too. The author explicitly simulates the endangered salmon populations of the Machias river in the state of Maine (USA) which are exposed to large numbers of cultured salmon.
        It should be noted, however, that the essence of all logistic models is positive density-dependent regulation (compensatory regulation). Salmon populations may become density independent or even depensatory  (the smaller the population is, the slower it grows on a percentage basis) when they fall to low levels in nature.   jim_mckenna@usgs.gov .

48. Depressed males should prefer arranged marriages
Male-male competition magnifies inbreeding depression in wild house mice. 2000. Meagher, S.M., Penn, D.J. and Wayne K. Potts. Proceedings National Academy of Sciences (U.S.) 97:3324-3329.
        The authors compared the fitness of inbred offspring (from full-sib matings) and outbred offspring of Mus domesticus in large, seminatural enclosures. "Inbred males sired only one-fifth as many surviving offspring as outbred males because of their poor competitive ability and survivorship." The authors note that this contrasts with inbred males in the lab, where competition for mates doesn't take place, and with inbred females which don't have to compete for mates in either environment. The effect on males in the competitive environment was almost five times larger than what has previously been seen in the lab.
        We can suppose (by analogy) that this effect is seen in aquaculture stocks and endangered populations wherever the members of one sex (not necessarily males) are competing for mates. Among other things the phenomenon will: drastically reduce the effective population size and accelerate inbreeding; reduce the overall fertility of the population; skew sex ratios in favour of the non-competing sex.   shawn_meagher@ccmail.wiu.edu 

47. Are trinucleotide repeats functional and under selection?
Trinucleotide repeats are clustered in regulatory genes in Saccharomyces cerevisiae. 2000. Young, E.T., J.S. Sloan, and K. Van Riper. Genetics 154:1053-1068.
        This paper on trinucleotide microsatellites in yeast should interest geneticists working on natural and aquacultural populations for two reasons. The first is that the trinucleotide repeats (TNRs) were mostly located in open reading frames, that is transcribed DNA, unlike the mono-, di, and tetranucleotide repeats which are mostly found in introns or other non-transcribed regions. Secondly, the trinucleotides are mostly found in genes that are coding regulatory proteins rather than structural proteins.
        "There may be important evolutionary implications for the frequent occurrence of TNRs in genes regulating the synthesis and activity of DNA, RNA, and proteins, and their exclusion from the most ancestral genes in the cell. Unstable TNRs in genes encoding transcription factors and related proteins could have an important influence on the regulation of gene expression. By allowing relatively frequent and often benign alterations to occur in genes encoding information-related processes, a variety of phenotypes could exist in a population, allowing selection to occur for those individuals best suited to new conditions. By acting as a source of genetic variation these sequences could play an important role in evolution."
        This is an important suggestion because it implies that the various types of microsatellite, which people doing population genetics tend to think of as interchangeable except for technical aspects of scoring, may be telling us fundamentally different things about the adaptation and genetic drift of genomes in aquaculture and genetic conservation.      ety@u.washington.edu