Hard-to-find Papers
Sept-Oct 2008
Main Index
Jan-Feb 2007
Mar-Apr 2007
May-June 2007
Jul-Aug 2007
Sept-Oct 2007
Nov-Dec 2007
Jan-Feb 2008
Mar-Apr 2008
May-Aug 2008
Sept-Oct 2008
Mar-Apr 2009
May-June 2009
July-Aug 2009
Sept-Oct 2009

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.

671.  Hybridized domestic Penaeus vannamei are more productive 
         Cross breeding of different domesticated lines as a simple way for genetic improvement in small aquaculture industries: Heterosis and inbreeding effects on growth and survival rates of the Pacific blue shrimp Penaeus (Litopenaeus) stylirostris. 2008. Goyard, E., C. Goarant, D. Ansquer, P. Brun, S. de Decker, R. Dufour, C. Galinié et al. Aquaculture 278:43-50. 
        The authors hybridized two somewhat inbreed aquaculture broodstocks and found useful hybrid vigour for growth and survival. The stocks were a Latin American import domesticated for many generations in Tahiti and New Caledonia (Feb 2002 #296) crossed with High Health (TM) Hawaiian, originally from Ecuador, which had been in New Caledonia since 2005.
         The authors point out that a commercial strategy based on F1 production hybrids and somewhat inbred parental lines should be useful. (Hybrid vigour = recovery from prior inbreeding depression in this hypothesis.) Careful one-time hybridization followed by selection within a single, composite broodstock with inbreeding control is another valid approach. The main point is, when existing stocks are inbred eliminating the problem will increase production (by as much as 80% in this case). egoyard@ifremer.fr 

670.  A novel way to quantify the sale of (underreported!) whale carcasses 
         Estimating the number of whales entering trade using DNA profiling and capture-recapture analysis of market products. 2007. Baker, C. S., J. G. Cooke, S. Lavery, M. L. Dalebout, Y.-U. Ma, N. Funahashi, C. Carraher et al. Molecular Ecology 16:2617-2626. 
         The technique involves a mark-recapture estimate of the number of whales marketed in South Korea using microsatellites to identify individuals. It works because one whale produces a lot of pieces of meat which are sold in shops, markets and restaurant stalls around the country along with meat from other whales. Since a whale slowly disappears from the market as it is sold the authors introduce a decay function ("rather like the exponential decay of a radioactive isotope") into the familiar mark recapture procedure. "Our estimate of whales in trade (reflecting the true numbers killed) was significantly greater than the officially reported by catch of 458 whales for this period." The authors do not claim to be surprised. 
         They also note that their new analytical procedure is applicable to other species where an individual is supplied in many portions to a well-mixed market. scott.baker@oregonstate.edu 

669.  Inclusion of social effects doubles the heritability of growth rate 
         The contribution of social effects to heritable variation in finishing traits of domestic pigs (Sus scrofa). 2008. Bergsma, R., E. Kanis, E. F. Knol and P. Bijma. Genetics 178:1559-1570. 
         That's right, doubles the heritability. Genetic variability in social interaction contributes a large fraction of the genetic variation in production traits which is never exploited in aquaculture breeding programs. (The fact that domesticated populations invariably grow tamer is sometimes noted incidentally, is invariably lamented as a loss of fitness in the wild, and is occasionally studied as a mechanistic phenomenon involving, e.g. reduced blood cortisol: (Sep 2001 #234, Aug 2002 #338) 
         A series of recent papers already reviewed here have described a genetic model and statistical procedures for analysing and exploiting the phenomenon (Apr 2007 #600 & #597, Apr 2008 #659). This is a new study along the same lines. "Results show that social effects contribute the vast majority of heritable variance in growth rate and feed intake in this population [of domesticated pigs].... Our results suggest that genetic improvement in agriculture can be substantially advanced by redirecting breeding schemes, so as to capture heritable variance due to social effects." 
         Note that the methods described here don't actually require you to measure any aspect of behavior. rob.bergsma@IPG.nl 

668.  GIFT tilapia gaining 7.1% per generation 
         Estimation of genetic change in the GIFT strain of Nile tilapia (Oreochromis niloticus) by comparing contemporary progeny produced by males born in 1991 or in 2003. 2008. Khaw, H. L., R. W. Ponzoni and M. J. C. Danting. Aquaculture 275:64-69. 
         This is the first instance I know of in which cryopreserved tilapia sperm is used to compare the offspring of a late generation of male parents with offspring of an earlier generation. Nine generations separated the males of the GIFT strain used in the study. The rate of increase of growth rate averaged over the whole period, including some years in which there was no artificial selection, was 7.1% per generation. This is comparable to other selection programmes in tilapia and proves in a very direct way that GIFT, which has been maintained since 2002 at the CGIAR WorldFish Center in Penang, Malaysia, is keeping up with private breeding programmes. See GIFT strain comparison Aug 2007 #615). h.khaw@cgiar.org 

667.  Genetic diversity maintained during supplementation 
         Genetic diversity over multiple generations of supplementation: an example from Chinook salmon using microsatellite and demographic data. 2008. Eldridge, W. H. and K. Killebrew. Conservation Genetics 9:1572-9737. 
         It is a useful corrective to read of situations in which supplementation does not have a negative effect on genetic diversity. The North Fork Stillaguamish River (in the western USA) has been supplemented since 1986 by collecting broodstock from the wild, spawning them and releasing the progeny. Between 10% and 60% of the returning adults are born in the hatchery. About nine percent of the returnees (including those of hatchery and wild origin) are spawned. Routine precautions were taken to minimize the variance of reproductive success among spawners but mating is random with respect to origin. Microsatellite data span 16 years and census data 34 years.
         The authors conclude: "(1) genetic diversity has been maintained over multiple generations of supplementation; (2) supplementation has not contributed to a loss of genetic diversity...." In particular, there was no overall decrease in allelic richness between 1985 and 2001. Importantly, allelic richness was usually higher in the wild-origin component of the population. So it is important to continue to encourage wild spawning during supplementation. (Allelic richness is the most sensitive indicator of loss of genetic diversity). (See also Feb 2002 # 297, Jan 2001 #158). whe@u.washington.edu 

666.  A comparison of various ways to measure introgression in trout 
         Estimation of introgression in cutthroat trout populations using microsatellites. 2007. Pritchard, V. L., K. Jones and D. E. Cowley. Conservation Genetics 8:1311-1329. 
         Cutthroat trout (Oncorhynchus clarkii) in the Rio Grande watershed have experienced various degrees of admixture from non-local (Yellowstone) cutthroat and rainbow trout (O. mykiss). This study analyses data from ten microsatellite markers using five different statistical procedures to deduce the amount of foreign introgression in 25 Rio Grande populations. Results vary among procedures, of course. But the correspondence is not too bad, especially at the extremes (high or low introgression) and the discussion in this paper offers a useful comparison of the utility of some of the most widely used programs. vpritcha@nmsu.edu 

665.  A review of the genetics of sex determination in tilapia 
         Genetics of sex determination in tilapiine species. 2008. Cnaani, A., Lee, B.Y., Zilberman, N., Ozouf-Costaz, C., Hulata, G., Ron, M., D'Hont, A., Baroiller, J.F., D'Cotta, H., Penman, D.J., Tomasino, E., Coutanceau, J.P., Pepey, E., Shirak, A., Kocher, T.D. Sexual Development 2:43-54. 
         The mechanisms of sex determination in tilapiine species are complicated and various. "The universe is not only queerer than we imagine, it is queerer than we can imagine.”-- J.B.S. Haldane. Look into this paper for details. Anyway, O. niloticus and T. zillii males at least are heterogametic. No one is going to quarrel with this paper because nearly everyone with any knowledge of the subject is one of the authors.  tdk@umd.edu 

664.  Triploid P japonicus are all females (with problems) 
         The effects of triploidy on Penaeus (Marsupenaeus) japonicus (Bate) survival, growth and gender when compared to diploid siblings. 2008. Coman, F. E., M. J., M. J. Sellars, B. J. Norris, G. J. Coman and N. P. Preston. Aquaculture 276:50-59. 
         Many people are interested in the possible advantages of triploid shrimp. This paper provides useful information on four families of triploids generated by chemical shock. Apparently all the triploid P. japonicus were female which, as the authors point out, suggest that the female is the heterogametic sex in this species. Females normally grow faster than males, which could be useful, but these triploid females suffered "detrimental effects on growth and survival performance from sub-adult to reproductive size when compared to diploid siblings". See Nov 2001 #253, Sep 2001 #232. frank.coman@csiro.au 

663.  Exchanging individuals among captive sub-populations to retain diversity 
         Management of subdivided populations in conservation programs: development of a novel dynamic system. 2008. Fernández, J., M. A. Toro and A. Caballero. Genetics 179:683-692. 
         Managers of captive populations (e.g. endangered Atlantic salmon stocks in the Canadian Maritime Provinces) have a lot of decisions to make. How many populations should be saved? To what degree should genetic differences among them be maintained? What are acceptable rates of inbreeding, gene loss and drift? This paper outlines a procedure for maximizing genetic diversity (global population coancestry, estimated from pedigrees) while maintaining a set level of inbreeding. 
         The traditional rule of thumb is one effective migrant per generation per population, preferably after adjustment for effective population sizes (Wang; Jun 2004 #486). This rule is based on the useful but generally unrealistic Fisher-Wright population model. The optimizations proposed here uses genealogical information on all the subpopulations. It is, basically, an optimal contribution analysis (Jul 2006 #512, Aug 2002 #335) aimed at specifying the "migration" pattern to impose each generation. As the authors point out, it might be possible to use markers when pedigree records are lacking (e.g. Aug 2007 #614). See Nov 2001 #258 on danger of falsely assuming zero relatedness of founders and Jan 2002 #283 on minimizing founder relatedness). jmj@inia.es 

662.  Hybrid vigor, not outbreeding depression! 
         Hybrid vigor between native and introduced salamanders raises new challenges for conservation. 2007. Fitzpatrick, B. M. and H. B. Shaffer. Proceedings National Acad. Science USA 104:15793-15798. 
         The result of this study is that hybrids between two salamander species, one native and one introduced, are more fit than the native Californian parent in its own natural habitat. Hybridization has been going on for fifty years or so. The animals with higher fitness were judged to have genomes inherited approximately equally from the two parental species (eight nuclear species-specific SNIP markers and one mitochondrial marker). 
         Individual heterozygosity could be distinguished from individual admixture in the statistical analysis, which was done in an interesting way that deserves study by anyone working on a similar problem. The hybrids can and do breed among themselves and one can expect that a composite gene pool will eventually supplant the native species. This is sad from the point of view of species conservation but fine from the viewpoint of salamanders in general because the parameters of population viability should improve. See Feb 2002 #291 vigorous frogs, Aug 2002 #341, Jun 2004 #482. benfitz@utk.edu 

661.  Marker estimates of heritability not a good as one would like 
         The accuracy of a heritability estimator using molecular information. 2007. Rodríguez-Ramilo, T., M. A. Toro, A. Caballero and J. Fernández. Conservation Genetics 8:1189-1198.
         It would be nice if we could reliably use marker information instead of pedigree information to estimate heritabilities in natural populations, or aquacultural populations without records. This paper examines the reliability of Ritland's method for accomplishing this. (Ritland's method is, basically, to regress a measure of phenotypic similarity on a measure of coancestry inferred from neutral markers: Dec 2000 #142). The conclusion of this simulation study is that the method doesn't work very well.
         There are a number of reasons for this which are explained in this well written paper. As an aside, the authors note that coancestries inferred from markers are most accurate in structured populations (such as aquacultural broodstocks) where the objective may be to choose least-related pairs of breeders (e.g. Aug 2002 #335). ramilo@inia.es 

660.  Muscle fiber genetics in salmon 
         Heritability of fibre number and size parameters and their genetic relationship to flesh quality traits in Atlantic salmon (Salmo salar L.). 2007. Vieira, V. L. A., A. Norris and I. A. Johnston. Aquaculture 272:S100-S109. 
         This detailed, technical study of various properties of muscle fibers in Atlantic salmon reveals some surprisingly high heritabilities and genetic correlations. Heritability of muscle fiber number and density was 0.3 - 0.5 (depending on the effects included in the model). "There was also a strong and significant negative genetic correlation between fat content and both fibre number (-0.85) and fibre density (-0.76). "The observable, phenotypic correlation between these traits is low, however, presumably because environmental variation affects them in different ways. 
         The authors come to the important practical conclusion that selection against fat content (i.e. selection for low breeding values for fat content) should result in a correlated increase in muscle fiber and density. This is important because, as they point out, fat is a lot easier to measure than the muscle-fiber variables analysed in this study. Compare Oct 2002 #355 report of low heritability of fat content in rainbow trout. iaj@st-andrews.ac.uk