These aquaculture-oriented commentaries reflect the opinions of GCL associates -- usually Roger Doyle -- and are not the original abstracts of the papers.  Direct quotations from the papers or abstracts are marked with inverted commas.

32.  Proof of extinction from inbreeding
Inbreeding and extinction in a butterfly metapopulation. 1998. Saccheri, I., M. Kuussaari, M. Kankare, P. Vikman, W. Fortelius, and I. Hanski. Nature 392:491-494.
          Other recent papers reviewed on this website have described the deleterious effects of inbreeding on individuals and families (lineages) within natural and artificial populations, and also the fact that traits closely associated with fitness may be particularly susceptible to inbreeding depression.  This isn't exactly a new paper but it is one of the few that actually demonstrates a connection between the risk of extinction and the level of inbreeding, as measured by heterozygosity, in a natural population.  This study was done on butterflies and seems relevant to other fragmented populations such as those of salmon.
          Could it also be relevant to the extinction of fish farms? Both in in theory and in reality, commercial extinction can happen long before the last shrimp or fish dies.  If net population growth, measured as sustained net revenue, falls below the discount rate in the financial model of the farm, then in theory the farm is extinct. And every time there's a catastrophe the discount applied to future revenue increases, because of the perceived higher risk.
          "Larval survival, adult longevity and egg-hatching rate were found to be adversely affected by inbreeding and appear to be the fitness components underlying the relationship between inbreeding and extinction [in the butterflies]."

31.  Fine-scale biogeography of a shrimp pathogen may be important
Arbitrarily primed PCR to type Vibrio spp. pathogenic for shrimp. 1999. Goarant, C., F. Merien, F. Berthe, I. Mermoud, and P. Perolat. Applied and Environmental Microbiology 65:1145-1151.
          This is from the French IFREMER research programme in Tahiti and New Caledonia. A new set of genetic markers revealed a surprisingly fine-scaled biogeographic population structure in Vibrio outbreaks in the western Pacific.  "Clusters [statistical grouping of pathogens from infected penaeids] identified within the species Vibrio penaeicida were related to their area of origin, allowing discrimination between Japanese and New Caledonian isolates, as well as between those from two different bays in New Caledonia separated by only 50 km."
          Such information could be helpful in understanding and controlling aquacultural pathogens.  For instance, if a disease outbreak involves an opportunistic pathogen "which is always present" (rather than being an invader), then that pathogen should have a local genetic signature. (Questions would need to be answered about evolutionary time scales relative to epidemiological time scales.)   perolat.pasteur@canl.nc

30.  Salmon should re-colonize their habitat, not bulk up the fishery
Managing the decline of Pacific salmon: metapopulation theory and artificial re-colonization as ecological mitigation. 1999. Young, K.A. Canadian Journal of Fisheries and Aquatic Sciences 56:1700-1706.
          Young suggests that fisheries managers should try to enhance the re-colonization of habitats in which salmon have recently become extinct. The necessary hatchery and ecological procedures are not at all the same as those required to sustain a viable fishery by supplementing a stock.

29.  Score –1 for marker mappers
Are mapped markers more useful for assessing genetic diversity? 2000. Virk, P.S., H.J. Newbury, M.T. Jackson, and B.V. Ford-Lloyd. Theoretical and Applied Genetics 100:607-613.
           One of the arguments for constructing genetic marker maps is that markers which are known to be spaced evenly throughout the physical genome (or recombinational genome) should be better for phylogenetic inference, gene-flow studies and, especially, for genetic conservation. This sounds reasonable, but is it true?
          The authors of this paper report on a study on rice cultivars that shows that unmapped AFLP markers generally tell the same evolutionary story as other types of unmapped markers. This story is consistent with other types of evidence on how the cultivars evolved. However, "mapped-marker data can, in some cases, result in highly misleading patterns of diversity; the results obtained are critically related to the choice of parents used in the cross from which the mapping population was produced."  Oops.  p.s.virk@bham.ac.uk

28.  Northern populations are better
Adaptive variation in energy acquisition and allocation among latitudinal populations of the Atlantic silverside. 2000. Billerbeck, J.M., E.T. Schultz, and D.O. Conover. Oecologia 122:210-219.
          "Common garden" experiments have long been used to study the evolutionary adaptations of plant and animal ecotypes from different environments.  This particular study is relevant to aquaculture and conservation of local fish biodiversity.  Silversides from a northern (Nova Scotia) population ate more, grew faster and used food more efficiently than a southern (South Carolina) population when food was not limiting growth. When it was limiting, there was no combination of temperature, food ration or body size that allowed the southern population to do better than the northern one.
          This suggests – not for the first time – that the choice of where an aquacultural broodstock evolved may be most important decision a grower can make.  Such information is rarely available, unfortunately. jeanm@life.bio.sunysb.edu

27.  Frankenfish are just like you & me
How nature itself uses genetic modification. 2000. Trewavas, A., and C. Leaver. Nature 403:12.
           The authors make the point that, at least in plants, the techniques which genetic engineers use are very similar to things that go on naturally in the genome.  "... some cereals may contain up to 50% retrotransposons; transposons contain end regions that are hot spots for recombination using transposase.   The plant genome contains very large numbers of strong promoters that direct expression as strongly as any [transgenic] viral promoter .... many of them are constitutively and continuously expressed .... critics of GM technology neglect the extent to which selection is made among many GM transformants, as is the case with conventional plant breeding among siblings.... [Don't worry, because] lethal insertions are self-selecting...."
          The authors go on to say, "It is important to recognize that all the food we eat has been (and is) continuously genetically engineered by natural phenomena in ways that do not differ in any fundamental way from the current GM technology."
          A lot of jargon is put into play in this paper, but at the end the authors stand on common ground when they ask whether the flap about GM organisms is "really any different from notions of Original Sin?"  [In point of fact, yes. It's closer to the Calvinist notion of Utter Depravity.]  Plants?? Who cares.  Yet fish genomes are similarly loaded with introns of obviously retroviral origin, some very ancient, some recent.

26.  Surviving on the edge
Dynamic biogeography and conservation of endangered species. 2000. Channell, R., and M.V. Lomolino. Nature 403:84-86.
          When faced with a species that warrants conservation, the question is whether to concentrate one's efforts on populations that are at the centre of the natural biological range, since marginal populations will be the first to go extinct anyway.  This has become conventional wisdom among those responsible for allocating resources for the protection of endangered species.
          The arguments are partly based on assumptions that marginal populations are ecologically or physiologically stressed, and partly on the heuristic theory of island biogeography due to MacArthur and Wilson.  The authors of this paper have studied the pattern of population extinction in 245 species that have undergone significant contractions in range.  They found that, contrary to what one might expect, most species manage to persist at the margins of their range even as the number of populations declines.

25.  Microsatellites good for tracing agricultural genetic history
Application of microsatellites in wheat (Triticum aestivum L.) for studying genetic differentiation caused by selection for adaptation and use. 2000. Stachel, M., T. Lelley, H. Grausgruber, and Vollmann J. Theoretical and Applied Genetics 100:242-248.
          This is a good example of the power of microsatellite markers to detect the evolutionary separation and genetic drift of agricultural populations as they are selected and moved around by humans for economic purposes. "The results have proven the excellent resolving power [of microsatellites] in varietal differentiation, which arises through breeding under specific environmental conditions, and for different end-use."  lelley@ifa-tulln.ac.at

24.  Distinguishing inbreeding from outbreeding in a wild population
Microsatellite loci reveal sex-dependent responses to inbreeding and outbreeding in red deer calves. 1999. Coulson, T., S. Albon, J. Slate, and J. Pemberton. Evolution 53:1951-1960.
          Another study in which variation in the fitness of individuals in a real-world population is associated with variation in their levels of inbreeding. The situation turns out to be complicated, as it should be in such a thoroughly and carefully studied population (wild deer on a Scottish island).  The potential importance to fisheries conservation and aquaculture is the use of a statistical measure (Coulson's) which may be able to separate the heterozygosity effects of recent inbreeding (kin-mating) from the effects of outbreeding (hybridization) which occurred in the more distant past.
          This technique could be useful in sorting out what's wrong with Asian and North American tilapia broodstocks on some farms, and in sorting out the recent history of the Maine salmon.  tim.coulson@ioz.ac.uk

23.  A somewhat realistic model of the ecological effects of genetic variability
Genetic variability in sensitivity to population density affects the dynamics of simple ecological models. 1999. Doebeli, M., and G. de Jong. Theoretical Population Biology 55:37-52.
           The authors conclude that under various circumstances genetic heterogeneity in fitness components can either stabilize or destabilize a population.  The effects are rather large.  Genetic variability should be included in population viability assessment models (PVA models) and computer programs like VORTEX, INMAT, RAMAS  that are used for biological conservation.  But usually they are not; the only genetic phenomena being discussed in relation to population extinction risks are inbreeding, outbreeding and maladaptation -- i.e. quantitative genetic mean values.

22.   Population differences in a production trait in salmon
Inter- and intrapopulation variation in temperature sum requirements at hatching in Norwegian Atlantic salmon. 1999. Berg, O.K., and V. Moen. Journal of Fish Biology 54:636-647.
        The authors studied time-to-hatch of full-sib salmon families from several wild populations and one commercial aquaculture population. There was a lot of genetic variation in development time, about 50% of which was between populations and about 50% between families within populations. "It is concluded that the time required from fertilisation to hatching in Atlantic salmon is a population-specific adaptive trait." 

21.  Choose the lesser of two evils in supportive breeding
Quantitative genetics in conservation biology. 1999. Frankham, R. Genetical Research 74:237-244.
        Frankham reviews the problem of domestication of endangered species that are being artificially propagated [i.e. hatcheries in our case] to save them from extinction.  He says this can be alleviated to some extent by maintaining several, separate populations and occasionally exchanging individuals to reduce inbreeding.  He suggests that the likelihood of imminent extinction will force population mangers to get over their aversion to mixing geographically separated, rare populations.  rfrankha@RNA.bio.mq.edu.au

20.  Just what is the genetic autocorrelation of growth rate in fish anyway?
Mapping quantitative trait loci for murine growth: a closer look at genetic architecture. 1999. Vaughn, T., S. Pletscher, A. Peripato, K. King-Ellison, E. Adams, C. Eroikson, and J.M. Cheverud. Genetical Research 74:313-322.
          The authors found 20 separate quantitative loci (QTL) affecting weight in mice.  The loci affecting early and late growth were quite distinct, mapping to different chromosome locations. "This QTL pattern indicates largely separate genetic and physiological systems for early and later murine growth, as Falconer suggested [25 years ago]". Would anyone be surprised to find that the genes affecting early and late growth of fish are also different, which might drastically influence the planning of selection experiments?  Should we just assume they are different and plan accordingly?    vaughnt@thalamus.wustl.edu