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.

385.  News flash: Effective population size five orders of magnitude smaller than census size in a pelagic species
         Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagrus auratus). 2002. Hauser, L., G. J. Adcock, P. J. Smith, J. H. B. Ramírez and G. R. Carvalho. Proceedings of the National Academy of Sciences (US) 99:11742-11747.
        This study is based on a 50-year sequence of scale samples collected from a population of New Zealand snapper in Tasman Bay. The sample covers most of the period of commercial exploitation, which by now has reduced the census size by about 75%.
         Microsatellite DNA analysis of the preserved scales and recent samples allowed comparison between the effective population number Ne and contemporaneous estimates of population size (census number) which were made using standard fisheries methods. Amazingly, although the census number was several millions the long-term effective population number was somewhere between 46 and 186 individuals!
         This is a much lower ratio of effective to census number than previously guessed or inferred for other species. The New Zealand snapper resembles many other exploited marine fish (e.g. cod) in having a long life, indeterminate body size, size-dependent fecundity, iteroparity and overlapping generations.
         The authors make the following important points: (1) Fish stocks of several million individuals can rapidly lose genetic diversity. (2) The low ratio of effective to census number may explain the poor correspondence between stock sizes and recruitment which bedevils fisheries managers. And finally, (3) "The recruitment processes suggested by genetic data also open the exciting possibility of identifying the demographic section of the population most likely to reproduce successfully and to protect these individuals from excessive exploitation". lhauser@u.washington.edu

384.  Nine more genes on the tilapia linkage map
         Fishing in silico : searching for tilapia genes using sequences of microsatellite DNA markers. 2002. Cnaani, A., M. Ron, G. Hulata and E. Seroussi. Animal Genetics 33:474-476.
         The linkage map of the tilapia genome is coming along nicely due to the efforts of several research groups, but until now the map included only 14 known genes. The other tilapia markers in the map -- of which there are hundreds -- consist mainly of "neutral" microsatellite and AFLP markers and some allozymes. The authors of this paper have added nine more genes without doing any lab work.
         They found unique flanking sequences of 312 tilapia microsatellites in the GenBank database, and entered them into the appropriate search-and-match engines for comparison with the human and Fugu genomes. Sixteen tilapia sequences with high homology to known genes were identified. Nine of these microsatellites had already been assigned to tilapia linkage groups, so now the genes which flank them are mapped too. The genes are a mixed bag of transporter and structural proteins, enzymes etc. seroussi@agri.huji.ac.il

383.  Domesticated salmon have more active growth hormone systems
         Effects of domestication on growth physiology and endocrinology of Atlantic salmon (Salmo salar). 2002. Fleming, I. A., T. Agustsson, B. Finstad, J. I. Johnsson and B. T. Björnsson. Canadian Journal of Fisheries and Aquatic Science 59:1323-1330.
         Seventh- generation, domesticated Atlantic salmon from the Norwegian National Breeding Program were compared with their principal wild founder population with respect to growth rate, plasma growth hormone (GH), pituitary GH and insulin-like growth factor (IGF-I). Artificial selection or, more probably, several decades of domestication have brought about a three-fold increase in the growth rate of this strain (now called the AquaGen). "Pituitary GH content was positively correlated with growth rate and correspondingly was significantly higher in the faster growing domesticated fish than in the wild fish. Plasma GH levels were also significantly higher in the domesticated fish, whereas IGF-I levels did not differ."
         The paper includes an interesting discussion of "accidental" selection  in domesticated salmon; for example, there is indirect selection for high GH activity, and therefore for rapid growth, because there is little "selective payoff from cautious feeding behaviour [in the absence of predators]". The authors also note that their results may explain why insertion of transgenic GH genes doesn't increase the growth of a strain that has already been selected for rapid growth (see Feb 2001 #174). ian.fleming@hmsc.orst.edu

382.  New formula for effective population number
         Effective size of populations with unequal sex ratio and variation in mating success. 2002. Nomura, T. Journal of Animal Breeding and Genetics 119:297-310.
         This paper derives a useful formula for calculating effective population size when mating success varies in both sexes. Non-overlapping generations are assumed. Instead of the usual formula Ne=4NmNf/(Nm + Nf), the author recommends Ne=4NmNf/(2Nm+Nf) for populations with a harem mating system (very frequent in aquaculture). "The effective population sizes of several wild, experimental and domestic animals are estimated by applying the derived equations to the published demographic and ecological data." nomurat@cc.kyoto-su.ac.jp

381.  MHC diversity doesn't require overdominance
         MHC heterozygosity confers a selective advantage against multiple-strain infections. 2002. Penn, D. J., K. Damjanovich and W. K. Potts. Proceedings National Academy of Sciences (U.S.) 99:11260-11264.
         Interest in the genetics of the fish immune system is running high these days. Atlantic salmon -- and other fish -- may be choosing mates (in nature) to maximise the genetic diversity of their offspring at the major histocompatibility complex (Dec 2001 #272). The preferred explanation for this "disassortative mating", in which fish choose mates which are genetically unlike themselves, is that MHC heterozygotes are intrinsically more fit than homozygotes (overdominant selection at MHC loci; see for example Dec 2002 #370). The thought is that heterozygosity at MHC loci may enhance a host animal's resistance to pathogens by increasing both the diversity of peptide antigens it presents to T cells and the diversity of the T cells themselves.
         But there is also evidence (Mar 2002 #302) that particular MHC alleles may also be directionally selected (i.e. towards homozygosity), possibly on a lake-specific basis. Heterozygotes would not be more fit than MHC homozygotes and disassortative mating should not be selected in such lakes. And in an experiment in an aquaculture-like environment where exposure to specific pathogen strains was controlled, particular MHC alleles appeared to have a selective advantage but heterozygosity did not (Dec 2002 #369).
         So, we would like to know what the best genetic management strategy is: selection for homozygosity of particular MHC alleles, or selection for MHC diversity per se. The answer is important both to conservationists and to geneticists who hope to profit from the development of proprietary "super breeds" for aquaculture.
         The experiment reported here was done on mice, which have an MHC system similar to that of fish although more complex. Mice strains were crossed to produce a variety of MHC genotypes which were released into a house that had been specially designed to harbour mice. There they were exposed simultaneously to a defined mix of pathogen strains plus whatever natural pathogens and parasites had been left behind by an aboriginal mousy population. Surprisingly, the experimenters found that "contrary to what is widely assumed, the benefits of heterozygosity were due to resistance being dominant rather than overdominant, i.e., heterozygotes were more resistant than the average of parental homozygotes, but they were not more resistant than both."
         In other words the MHC heterozygotes were never more pathogen resistant than the most resistant homozygote. The authors point out, however, that heterozygotes may be more fit than homozygotes on average, thus maintaining polymorphism in the population, even if specific pathogen resistance is merely a dominant trait. (Hedrick has reached the same conclusion on theoretical grounds; Evolution 56:1902-8, 2002). They add that "The fact that MHC heterozygotes were more resistant to infection and had higher fitness than homozygotes provides a functional explanation for MHC-disassortative mating preferences".
         It appears to reconcile the observations that specific particular alleles can have selective advantage in laboratory (and some aquaculture?) conditions and that heterozygosity may be an advantage in nature.  It does not necessarily help one decide whether to artificially select for homozygosity or heterozygosity in managed broodstocks. This would depend on the variety and timing of challenges anticipated from pathogens. The stakes could be very high. Optimal selection strategies for extensive and "biosecure" aquaculture systems may be even more different than we thought. Dustin Penn's address: Konrad Lorenz Institut, Austrian Academy of Sciences, Savoyenstrasse 1a, A-116 D Wien, Austria.

380.  Danish trout populations maintain their genetic identity for a long time
         Long-term effective population sizes, temporal stability of genetic composition and potential for local adaptation in anadromous brown trout ( Salmo trutta ) populations. 2002. Hansen, M. M., D. E. Ruzzante, E. E. Nielsen, D. Bekkevold and K.-L. D. Mensberg. Molecular Ecology 11:1003-1015.
         DNA from an 80-year sequence of scale samples was analysed to estimate the effective population number from the 1910s to the 1990s. Calculations were based on temporal fluctuations in allele frequencies at eight microsatellite loci. The authors conclude that some Danish rivers maintained their genetic identities reasonably well over this period despite intense stocking with hatchery trout and (which is more or less the same conclusion) the long-term effective population numbers were 300 to more than 500.
         Population sizes of this order are large enough so that small, but distinguishing, gene frequencies can persist for many generations despite drift. However, the population sizes are nevertheless small enough that weak directional selection (weak local adaptation) should to be overwhelmed by drift. There is no reason in principle to expect local adaptation to be weak; it can be and sometimes is very strong. But since the environment of these Danish rivers appears more or less similar the authors don't think that strong, divergent, local selection is likely to have caused the persistent gene frequency differences. mmh@dfu.min.dk

379.  Baltic salmon stocks not losing diversity too quickly
         Maintenance of genetic diversity of Atlantic salmon (Salmo salar) by captive breeding programmes and the geographic distribution of microsatellite variation. 2002. Koljonen, M.-L., J. Tähtinen, M. Säisä and J. Koskiniemi. Aquaculture 212:69-92.
         According to the authors over 90% of Atlantic salmon smolts from Baltic gene pools are now reared in hatcheries. In Finland, where this work was done, only two out of an original 18 rivers have any naturally reproducing salmon at all. The survival of Baltic stocks is now entirely dependent on costly maintenance in hatcheries. Therefore it is interesting to see how well hatcheries are doing from a genetic conservation perspective.
         On the whole, the record is not so bad in the hatchery and natural populations studied here. "In short-term breeding programmes [where there are some wild breeders every generation], the average rate of loss of heterozygosity was 1.4% per generation and the average observed rate of loss of alleles was 4.7% per generation. The estimated Ne for the broodstock were 32 and 238. The average Ne/Nc ratio was 0.81. Changes in present-day broodstocks were not alarming and the Ne/Nc ratios [effective number / census number] were higher than in wild populations in general." marja-liisa.koljonen@rktl.fi  

378.  Genetic declines follow population crashes in sea mammals
         (a) Loss of genetic diversity in sea otters (Enhydra lutris) associated with the fur trade of the 18th and 19th centuries. 2002. Larson, S., R. Jameson, M. Etnier, M. Fleming and B. Bentzen. Molecular Ecology 11:1899-1903.
         (b) Impact of a population bottleneck on symmetry and genetic diversity in the northern elephant seal. 2002. Hoelzel, A. R., R. C. Fleischer, C. Campagna, B. J. Le Boeuf and G. Alvord. Journal of Evolutionary Biology 15:567-575.
         These before-and-after studies of the impact of human activities are similar in that both are based on DNA extracted from samples preserved for more than one hundred years.
         The fur trade in the Pacific Northwest was bad for the genetic well-being of sea otters. "While mtDNA sequence variability was low within both modern and extinct populations, analysis of microsatellite allelic data revealed that the prefur trade population had significantly more variation than all the extant sea otter populations."
         Similarly for elephant seals: "The northern elephant seal (NES) suffered a severe population bottleneck towards the end of the nineteenth century. ... Measures of genetic diversity [before and after the bottleneck] show a loss of variation consistent with expectations and suggest a strong disruption in the pattern of allele frequencies following the bottleneck. Measures of bilateral characters show an increase in fluctuating asymmetry." shawn.larson@ci.seattle.wa.us  ; a.r.hoelzel@durham.ac.uk 

377.  More anti-pathogen genes found in Penaeid shrimp
         Identification of immune-related genes in hemocytes of black tiger shrimp (Penaeus monodon). 2002. Supungul, P., S. Klinbunga, R. Pichyangkura, S. Jitrapakdee, I. Hirono, T. Aoki and A. Tassanakajon. Marine Biotechnology 4:487-494.
         Hemocytes are probably the most important component of the anti-pathogen defense system in shrimp. These cells are known to engage in pathogen recognition, phagocytosis and release of anti-microbial peptides as well as performing other immunological services. Some of the genes that are involved in the immunological functioning of hemocytes have previously been identified in Litopenaeus (or Penaeus) vannemai using the EST technique (see Sep 2001 #233). The authors of this new paper have done rather similar work on P. monodon, a species that makes up about 50% of commercial shrimp production world wide. Homologies were found with known defense functions including heat-shock proteins, the clotting system, anti-oxidative enzymes, anti-bacterial and anti-fungal peptides etc.  anchalee.k@chula.ac.th  

376.  Bottlenecking can cause developmental instability in an introduced population
         Increased frequency of scale anomalies and loss of genetic variation in serially bottlenecked populations of the dice snake, Natrix tessellata. 2002. Gautschi, B., A. Widmer, J. Joshi and J. C. Koella. Conservation Genetics 3:235-245.
         The dice snake is a non-venomous Eurasian snake which spends much of its life in or near water. Several populations introduced into Swiss lakes are known to have been severely bottlenecked one or more times. As would be expected, individuals in populations which have been bottlenecked more often have fewer alleles per locus and less individual heterozygosity (8 microsatellite loci) than those in populations bottlenecked only once, and much less than those in natural populations.
         What is interesting in this study is the finding that the frequency of scale anomalies (thought to be the result reduced developmental stability caused by inbreeding) follow the same pattern as the loss of genetic diversity. The population sizes are small and the species is red listed in Switzerland and Germany. The authors point out that even if the snake populations grow because of habitat protection etc. their genetic health will be rather poor [for a while?] because of the bottlenecking. babagaut@uwinst.unizh.ch

375.  Mass-spawned families may stay together in plankton
         Genetic and demographic variation in new recruits of Naso unicornis. 2002. Planes, S., G. Lecaillon, P. Lenfant and M. Meekan. Journal of Fish Biology 61:1033-1049.
         "Demographic data showed that larvae of Naso unicornis colonizing the reefs of Moorea, French Polynesia, on the same night within a restricted area originated from several spawning events that occurred 67 to 94 days previously." Age was determined from daily growth rings, and genetic variables (Fst, Fis, relatedness etc.) were calculated from allozyme data. Larvae which were the same age (spawned on the same night) sometimes showed significant genetic relatedness (Queller & Goodnight's relatedness measure) despite the fact that they had spent an average of about seven weeks in the plankton. Only some age groups (i.e. nights) showed this relatedness, and not all individuals which had been born on those nights were related.
         The authors conclude from their analyses that despite the mass spawning behaviour and larval dispersal of this species, the accidents of survival and dispersal are such that effective population size is greatly reduced. Reduced, in fact, to the point where there is large stochastic fluctuation between the genetic composition of larval groups and between larval and later stages, which become progressively more homogenous in the lagoon as time passes, presumably because of physical dispersal and mixing. (Why families would want to stay together in a "sweepstakes" or "elm-oyster" (see Nov 2001 #259) reproduction and selection regime is a mystery to me.). planes@univ-perp.fr

374.  Shame! Shame!
         Paper trail reveals references go unread by citing authors. 2002. Ball, P. Nature 420:594.
         It is shocking to learn that authors don't bother to read 80% of the papers they cite [or 80% of authors don't read any papers?]. This conclusion was reached by two physicists, M.V. Simkin and V.P. Chowdery, who studied the propagation of errors in published citation lists. "The pair concluded that four out of five authors had not done their homework." Most people (physicists, anyway) just copy other people's reference lists. The original paper can be downloaded from
http://xxx.lanl.gov/ftp/cond-mat/papers/0212/0212043.pdf . It is interesting not only for its embarrassing conclusions but for its statistical treatment (did you know about the Zipf distribution, which has obvious genetic applications?). It ends with the following threat: "We conclude that misprints in scientific citations should not be discarded as mere happenstance, but, similar to Freudian slips, – analyzed". An e-mail source for the Nature paper is not available.

373.  Useful recent Excel add-ins for analysis of genetic data
         (a) PopTools looks like a useful and fun set of Excel add-ins for doing things which can usually only be done in expensive, complicated programs like Mathematica or S-plus. "PopTools is a versatile add-in for PC versions of Microsoft Excel (97, 2000 or XP) that facilitates analysis of matrix population models and simulation of stochastic processes. It was originally written to analyse ecological models, but has much broader application. It has been used for studies of population dynamics, financial modeling, calculation of bootstrap and resampling statistics, and can be used for preparing spreadsheet templates for teaching statistics."
         "Also included in PopTools are routines for iterating spreadsheets. These make it possible to run Monte Carlo simulations, conduct randomisation tests (including the Mantel test) and calculate bootstrap statistics. Some facilities are available for function minimisation and parameter estimation using maximum likelihood techniques, and there are a number of auditing and other tools that the author finds useful in his everyday work."
         "PopTools allows the construction, analysis, and simulation of quite complex models in a simple spreadsheet format. The only programming required is the ability to construct formulas in Excel...."  PopTools and descriptive files can be downloaded from http://www.cse.csiro.au/client_serv/software/poptools/index.htm
         (b) DadShare is an Excel macro designed to help interpret patterns of shared paternity among groups of offspring. The program and explanatory documentation are available at http://www.zoo.cam.ac.uk/zoostaff/amos/index.html .