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.  

398.  News flash: a different and promising way to find adaptive MHC variation
         Strong positive selection and habitat-specific amino acid substitution patterns in Mhc from an estuarine fish under intense pollution stress. 2002. Cohen, S. Molecular Biology and Evolution 19:1870-1880.
         MHC diversity is a very, very hot topic in fisheries biology these days. The genetic diversity of the major histocompatibility complex, which is the foundation of vertebrate immune systems, appears to be driven by the diversity of pathogens in the environment (see e.g. Jan 2003 #381). Fish may choose their mates to optimize the MHC genotype of their offspring (Aug 2001 #221). MHC has featured in recent discussions of  population differentiation and the designation of evolutionarily significant units for conservation (Dec 2001 #272, Mar 2002 #302).
         Along with laboratory, field and theoretical studies of the advantages of immune-system diversity per se, there have also been demonstrations that specific pathogens can exert strong selection on particular MHC alleles in fish (Dec 2002 #369). For all of the above reasons MHC diversity considerations may become crucial (both practically and politically) in the design of captive breeding and aquaculture genetics programs (Dec 2002 #370).  The conclusions cited above are mostly based on population-level statistical associations between survival and allele frequencies.
         This clever study delves deeper into the molecular structure of the MHC antigen-binding sites, and could be a harbinger of more powerful ways to investigate and exploit MHC diversity. One population of the study animal (Fundulus heteroclitus) lives in an environment called the Hot Spot which has been grossly polluted with PCBs and other contaminants for more than half a century. This population has adapted to a concentration of contaminants which is toxic to other Fundulus. It also carries high loads of parasites (helminths and others) which are rare or absent in other Fundulus. In other words fish in the Hot Spot are subject to strong and unusual antigenic pressures. The other two populations live in more benign environments.
         The conclusions of this work are summarized in a visual image which is both striking and instantly convincing -- a 3-dimensional structural model of the MHC Class IIB molecule with population-specific amino acid substitutions shown as colored beads. Substitutions which characterize different populations of  Fundulus tend to be concentrated in different parts of the antigen-binding region of the molecule. This image (Fig. 5) was reached through a process which included identifying and cloning the MHC molecule and sequencing a substantial number of individuals from different locations.
         The conclusion that the MHC variation is driven by selection, not drift, are supported by careful statistical analysis of MHC sequences from the various populations plus a parallel analysis of (presumably neutral) sequence variation in mitochondrial DNA. "Whether Mhc population profile differences represent the direct effects of chemical toxicants or indirect parasite-mediated selection, the result is a composite habitat-specific signature of strong selection and evolution affecting the genetic repertoire of the major histocompatibility complex."
         The first step in applying this technique in other situations, e.g. searching for selectable QTLs in an aquaculture broodstock, would seem to be finding a population that is unusually well adapted to the targeted stress. scohen@oeb.harvard.edu   

397.  A suggestion that hatchery supplementation should increase Ne of red drum
         Spatial homogeneity and temporal heterogeneity of red drum (Sciaenops ocellatus) microsatellites: effective population sizes and management implications. 2002. Chapman, R. W., A. O. Ball and L. R. Mash. Marine Biotechnology 4:589-603.
         The red drum is an important fish in the marine waters of the southern US, where it has declined so much that fishing has been restricted and stock supplementation is underway. Applying the temporal fluctuation method to data on five microsatellite loci the authors estimate that effective population size in the study site in South Carolina may be in the range 300 - 1000, which isn't very large. Therefore, they suggest that since repeated augmentation should significantly increase the census size it should also increase (not decrease) genetically effective population number too. (See #391 below. See Feb 2002 #297 for effect of supplementation on Ne.). chapmanr@mrd.dnr.state.sc.us    

396.  Frankencarps are good fish
         Effect of rainbow trout growth hormone complementary DNA on body shape, carcass yield, and carcass composition of F1 and F2 transgenic common carp (Cyprinus carpio). 2002. Dunham, R. A., N. Chatakondi, A. J. Nichols, H. Kucuktas, C. Chen, D. A. Powers, J. D. Weete et al. Marine Biotechnology 4:604-611.
         "The altered body shape of transgenic fish resulted in improved dressing percentage in the F2 generation. The carcass composition of transgenic muscle had a lower percentage of (P < 0.01) moisture and lipids and higher (P < 0.01) percentage of protein in both generations. ... Also, the fatty acid profiles of both genotypes were minimally altered."  On the whole, these transgenic carp not only grow faster than normal controls, they seem to be a superior aquacultural product as well. rdunham@acesag.auburn.edu   

395.  Inbreeding does (often) remove deleterious genes from a population
         Purging the genetic load: a review of the experimental evidence. 2002. Crnokrak, P. and S. C. H. Barrett. Evolution 56:2347-2358.
         This paper focuses on the question, "Does inbreeding purge deleterious alleles from a population?" The answer is important both for genetic conservation and for aquaculture, because if it is "yes" a bold manager could decide to inbreed and select a captive population so that inbreeding depression eventually becomes a non-issue. The authors address the question through meta-analysis of published paper on mammals, insects, mollusks and plants, but not fish.  In a word, the answer does seem to be "yes".
         Many of the analyzed populations eventually recovered some of the fitness lost in the early generations of inbreeding (rebound), and hybrids between inbred lines were often more fit than their ancestral populations. Less often, they were more fit than non-inbred laboratory controls, which causes the authors to suggest that adaptation to the laboratory (domestication) can interfere with inbreeding experiments which are designed in certain ways.
         The meta-analysis is highly significant, in the statistical sense, and supports the idea that purging could be a useful management strategy in certain cases. " [But] firm predictions about the situations in which purging is likely or the magnitude of fitness rebound possible when populations are inbred remain difficult."  The meta-analysis also supports the idea that inbreeding depression is more often the result of deleterious recessive alleles than of generalized heterozygote advantage. For other discussions of purging and the cause of inbreeding depression see Dec 2001 #265, Mar 2002 #307, Nov 2001 #259. barrett@botany.utoronto.ca    

394.  Local genetic adaptation in salmon migratory returns
         Genetic control over survival in Pacific salmon (Oncorhynchus spp.): experimental evidence between and within populations of New Zealand chinook salmon (O. tshawytscha). 2003. Unwin, M. J., M. T. Kinnison, N. C. Boustead and T. P. Quinn. Canadian Journal of Fisheries and Aquatic Sciences 60:1-11.
         The rapid evolution of life history traits in Chinook salmon which were introduced to New Zealand in the early 1900s has already been noted here (Oct 2000 #115). The authors of the earlier paper now report that migrating salmon are relatively more successful in returning to the streams in which their ancestors evolved, compared to salmon whose ancestors evolved in another stream. Furthermore, they find that there is significant variation in return rate among paternal families. The authors take size and non-additive genetic factors into account in their analysis of their transplantation experiment.
         "Family-specific survival was positively correlated with weight at release, but there were underlying genetic correlations unexplained by size. Taken together, these results suggest considerable genetic influence over survival and return of salmon and that population-specific adaptation can occur within 30 generations of establishment." "This rapid evolution is particularly striking given the fact that the New Zealand rivers all discharge into the South Pacific Ocean over a limited (~200 km) length of coastline and that the major salmon-producing rivers (including those in this study) have broadly similar physical characteristics." m.unwin@niwa.cri.nz  

393.  Inbreeding and selection generate 100% genetically all-male tilapia
         Inheritance of sex in two ZZ pseudofemale lines of tilapia Oreochromis aureus. 2003. Damien, C. Mélard, M. C. Hoareau, Y. Bellemène, P. Bosc and J. F. Baroiller. Aquaculture 218:131-140.
         Males of the blue tilapia Oreochromis aureus have one kind of sex chromosome (ZZ), unlike O. niloticus and the majority of fish farmers who have two (XY) sex chromosomes.   Hormonal sex-reversal can produce ZZ blue tilapia which function as females and, theoretically, should produce nothing but male offspring when mated with ordinary ZZ males. Aquaculturists would like this because males grow faster and because all-male populations wouldn't produce unproductive, resource-consuming offspring. Unfortunately the actual proportion of males generated by ZZ x ZZ matings is usually much less than 100%.
         This interesting study follows two populations of aureus through five generations of ZZ x ZZ mating and family selection for high-male broods. One of the populations was progressively and strongly inbred, the other was outbred. The frequency of male offspring rose to nearly 100% in the inbred population but did not increase significantly in the outbred population. The authors suggest that this is because in the inbred population there was much stronger selection on genes that are not on the sex chromosomes but that nevertheless affect sex -- "autosomal" genes. Such genes are known to complicate sex determination in O. niloticus, another species in the same genus.
         "The present study also shows that it is possible to fix the male sex determining factors (Z sex chromosome and genetic factors) in a line of [ZZ] pseudofemales, producing a high percentage of male progeny in five successive generations." "The genetic approach avoids the hormonal sex-reversal treatment on a mass scale and the problem of androgen residues in market-sized fish. The present study suggests that the application of a genetic process to aquaculture requires strict selection of both sexes (male and female) and not just of one sex (super-male YY or pseudofemale ZZ)."
         Of course the inbreeding required in this approach is likely to cause inbreeding depression of  fitness and yield, a problem that will need to be solved by other adjustments in the breed-development program or in the resulting production program. desprez.arda@guetali.fr    

392.  Frankenpatents are delayed, but FrankenCubans are eating well
         Transgenic salmon still out in the cold in United States. 2003. Hoag, H. Nature 421:304.
         "Joseph McGonigle, vice-president of Aqua Bounty Farms, says that he doesn't expect the FDA to approve the application [for transgenic Atlantic salmon] until late 2004. The company plans to submit a second application, for transgenic trout, in about a year's time. McGonigle says that the delay is placing the company under financial strain. 'Money's an issue now,' he says. 'We've been living on venture capital for years.' But a report issued last week by the non-profit Pew Initiative on Food and Biotechnology questioned the FDA's ability to regulate transgenic fish properly. It says that the FDA lacks the expertise to evaluate environmental risks. The report also calls for greater transparency and public involvement in the review process."
         "Meanwhile, Chinese researchers have been working with fast-growing transgenic carp since the late 1980s, and Cuba is considering commercialization of tilapia that were first bred there in 1993. The Cuban researchers say it will be three years before they know the regulatory fate of their tilapia. Mario Estrada, leader of the aquatic-organism project at the Center for Genetic Engineering and Biotechnology in Havana, says that most of the food-safety studies are done, including an experiment in which tilapia were eaten by volunteers."
         The Pew report can be downloaded from http://pewagbiotech.org/research/fish .
         For more information about the features of the Aqua Bounty salmon and how it was made see Jul 2000 #85, Sep 2000 #99. No e-mail address available.

391.  Another large discrepancy between Ne and census number 
         Genetic effective size is three orders of magnitude smaller than adult census size in an abundant, estuarine-dependent marine fish (Sciaenops ocellatus). 2002. Turner, T. F., J. P. Wares and J. R. Gold. Genetics 162:1329-1339.
         This another recent report of  an extraordinarly low population number in an important fish, red drum in the northern Gulf of Mexico . Using the temporal allelle-frequency-shift method the (short term) Ne was three orders of magnitude lower than the estimated population  size. Using a coalescent approach the estimated long-term Ne was four orders of magnitude lower. The authors suggest that "The extraordinarily low value of Ne/N appears to arise from high variance in individual reproductive success and perhaps more importantly from variance in productivity of critical spawning and nursery habitats located in spatially discrete bays and estuaries throughout the northern Gulf". And "Moreover, our study indicates that vertebrate populations with enormous adult census numbers may still be at risk relative to decline and extinction from genetic factors". (See #397, above. See Jan 2003 #385 for a 0.00001 ratio.) turnert@unm.edu     

390.  A procedure for calculating population genetic statistics from AFLPs etc.
         A Bayesian approach to inferring population structure from dominant markers. 2002. Holsinger, K. E., P. O. Lewis and D. K. Dey. Molecular Ecology 11:1157-1164.
         Developing primers for microsatellite markers in a new species can be a lot of work, and for some organisms such as shrimp the combined efforts of several labs have, to date, hardly provided enough published markers. Other sorts of genomic DNA markers, including amplified fragment length polymorphisms (AFLPs) and RAPDs, dispense with the preliminary species-specific DNA sequence analysis and are easier to find. Unfortunately such markers are dominant (homozygotes carrying the marker cannot be distinguished from heterozygotes) and standard techniques cannot easily be used to derive useful population genetic statistics such as Fst.  Or if they are used for this purpose uncomfortable assumptions are needed.
         The authors of this paper describe a Bayesian method that "allows direct estimates of FST from dominant markers ... we do not assume previous knowledge of the degree of within-population inbreeding [or Hardy-Weinberg equilibrium] ....Simulations show that samples from even a relatively small number of loci and populations produce reliable estimates of FST. Moreover, some information about the degree of within-population inbreeding (FIS) is available from data sets with a large number of loci and populations." kent@darwin.eeb.uconn.edu .

389.  How to estimate quantitative genetic parameters after all the runts have died
         Estimation of additive genetic variance components in aquaculture populations selectively pedigreed by DNA fingerprinting. 2003. Li, X., C. Field and R. W. Doyle. Biometrical Journal 45:61-72.
         "A method to estimate genetic variance components in populations partially pedigreed by DNA fingerprinting is presented. The focus is on aquaculture, where ... the individuals available for measurement will often be selected, i.e. will come from the upper tail of a size-at-age distribution, or the lower tail of an age-at-maturity distribution etc. Selection typically occurs by size grading during grow-out [plus size-selective mortality including cannibalism] and/or choice of superior fish as broodstock. The method presented in this paper enables us to estimate genetic variance components when only a small proportion of individuals, those with extreme phenotypes, have been identified by DNA fingerprinting....
         "Standard analysis of variance or maximum likelihood estimation cannot be used when only the extreme progeny have been pedigreed because of the biased nature of the estimates. In our model-based procedure a full robust likelihood function is defined, in which the missing information about non-extreme progeny has been taken into account." field@mathstat.dal.ca    

388.  Captive breeding probably saved a small population from extinction
         Population on the verge of a mutational meltdown? Fitness costs of genetic load for an amphibian in the wild. 2003. Rowe, G. and T. J. C. Beebee. Evolution 57:177-181.
         Norwegian  graylings have been shown to adapt rapidly to a new environment despite severe bottlenecking (Dec 2002 #364).  But in the dice snake serial bottlenecking produced a fitness decline (Jan 2003 #376). The authors of this report studied the fitness of a small population of toads (Bufo calamita) at the extreme of the natural range, relative to an outbred population in the same environment. Both populations were held in semi-natural field enclosures. How has the balance between local adaptative improvement and decline due to drift+inbreeding worked itself out in this case?
         If the isolated, bottlenecked toads ever achieved any special adaptation to their local environment they must have lost it before these experimenters came along. "Key larval fitness attributes in B. calamita, notably growth rate and metamorph production, were substantially higher in the large outbreeding population (Ainsdale) than in the small and isolated one (Saltfleetby)." "The Saltfleetby toad population was both larger and less isolated (because neighbouring populations have subsequently become extinct) during the nineteenth century than is the case today.
         "The low fitness of Saltfleetby relative to Ainsdale toads at the present time may be best explained by an increased genetic load at Saltfleetby, reflected in the higher levels of average homozygosity at microsatellite loci in the smaller population." The small population also exhibited reduced genetic (microsatellite) variability.
         These observations seem to bear on the vexed question whether captive breeding (e.g. of salmon) is a bad idea under all circumstances and whether money spent on live gene banks would always be better spent on habitat restoration.
         "Two other small populations of this toad have become extinct in Britain over the past 20 years without obvious cause and despite substantial habitat management. …It is very unlikely that the Saltfleetby population would have survived without the extensive captive rearing and release of toadlets that has continued for more than 20 years. Extensive habitat management has failed to improve this population’s viability. Our results confirm that extinction is a far more likely outcome of population isolation than the emergence of new locally adapted forms." t.j.c.beebee@sussex.ac.uk    

387.  Local adaptation despite prolonged planktonic dispersal
         Genetic evidence for local retention of pelagic larvae in a Caribbean reef fish. 2003. Taylor, M. S. and M. E. Hellberg. Science 299:107-109.
         It used to be assumed that a long stay in the plankton would ensure that populations disperse widely, so adaptation to particular, local environments would have to begin all over again every generation. There is plenty of genetic evidence for this and a good life-history theory to go with it (elm-oyster model, sweepstakes model; see Nov 2001 #259). However, there is now good and quite surprising evidence that planktonic larvae of some marine species (perhaps a lot of species) somehow avoid being spread all over the ocean and can maintain complicated evolutionary geographies. For a recent example see Jan 2003 #375.
         The authors of this paper looked at mitochondrial and other genetic markers in the and Bahamian cleaner goby Elacatinus evelynae. The planktonic stage lasts about three weeks. There is strong genetic differentiation among populations in different islands and colour patterns also differ on a regional basis, suggesting that the animals which host these cleaner fish might be exerting selection for particular, local colour patterns. "These results suggest that marine populations can remain demographically closed for thousands of generations despite extended larval duration, and that recognition cues such as color may promote speciation when geographic barriers are transient or weak."  Palumbi has commented on this paper in the same issue of Science. mtayL22@lsu.edu ; spalumbi@stanford.edu .

386.  Detecting & correcting pedigree and marker data problems
         GENCHECK: A program for consistency checking and derivation of genotypes at co-dominant and dominant loci. 2002. Bennewitz, J., N. Reinsch and E. Kalm. Journal of Animal Breeding and Genetics 119:350-360.
         "GENCHECK was developed to examine genotyping results of diploid organisms for consistency with the Mendelian laws of inheritance. It can be used to analyse data from co-dominant and dominant loci and large scale pedigrees with many overlapping generations as they are common in animal breeding. ...The data from individuals, whose genotyping results show a Mendelian segregation error, are written to an output file. ... Additionally, the program derives, if possible, the genotypes of untyped individuals or of individuals, whose genotyping results were assumed to cause a Mendelian segregation error, using information from the parents and/or the offspring. ... The program is written in Fortran 90 and available from the authors." jbennewitz@tierzucht.uni-kiel.de