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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.

440.  Should you select late-maturing male trout?
         Selection against early maturity in large rainbow trout Oncorhynchus mykiss: the quantitative genetics of sexual dimorphism and genotype-by-environment interactions. 2003. Kause, A., O. Ritola, T. Paananen, E. Mäntysaari and U. Eskelinen. Aquaculture 228:53-68.
         Early-maturing male salmon and trout are a problem for aquaculture because the fish are physically and morally unappealing and their growth slow. Some males mature early and some mature late, but almost all females mature late.
         This interesting paper looks at the heritabilities of growth and maturation in both sexes and the genetic correlation between traits and sexes. The practical motivation is to see if one can change the sexual dimorphism by selection to develop a strain in which all the males mature late but the maturation of females is unchanged. The answer appears to be no. Age-at maturation is more-or-less the same trait in both sexes, judging by the strong genetic correlation between the males and females for both maturation and weight. This is interesting in the light of a report that markers for maturation may differ in male and female rainbow trout (Jan 2001 #160). The heritability of both traits is sufficiently high, though, that selection for late maturation of both sexes should work if performed on either sex.
         Rapid growth is genetically correlated with early maturation in both sexes, but this unfortunate correlation is probably not strong enough to cause major problems in artificial selection for commercial performance. In fact there are reports that age-at-maturation evolves rapidly under natural selection (Oct 2000 #115, May 2002 #315).  "Extensive data set including individuals in five generations measured in brackish and fresh water [in Finland] in a split-family design was utilised to estimate the genetic parameters." antti.kause@mtt.fi  

439.  You need pedigree data to manage a small population
         Pedigree and marker information requirements to monitor genetic variability. 2003. Baumung, R. and J. Sölkner. Genetics Selection Evolution 35:369-383.
         You shouldn't leave matings to chance if you are managing a small population. The optimal choice of breeders and mating strategy depend critically on inbreeding coefficients and the genetic relatedness of potential mates (Aug 2001 #212, Nov 2001 #261, Aug 2002 #335). But how does one get this kind of information? Either directly from pedigree records or indirectly from genetic markers (e.g. SNPs, AFLPs, microsatellites).
         The effectiveness of the direct and indirect procedures are compared in this very useful simulation study. In a number of different mating schemes, including random mating, sib-avoidance etc., markers did less well than pedigrees at estimating the principal quantity of interest, which is the proportion of alleles identical by descent (inbreeding defined as autozygosity). When pedigree records are used, the correlation between true and estimated autozygosity was always >0.6, even when only the most recent couple of generations are included. "Therefore it seems to be possible to identify the most autozygous animals assuming parents and grandparents are known." By the standards of aquaculture and fisheries this is probably pretty good. It is also useful to learn that "taking more than five generations of a correct pedigree into account leads only to a marginal increase of the correlation of pedigree inbreeding coefficients and autozygosity."
         By contrast, the performance of marker-based estimates was disappointing. "The simulations show that even pedigrees of low quality allow the identification of the most autozygous animals in a random mating population. [However] Measures based on codominant marker loci lead to comparable results only when more than 100 (better 200) microsatellite loci are typed." This agrees with the disappointing conclusion about marker-based kinship estimation cited in Dec 2002 #362. baumung@boku.ac.at  

438.  Frankensalmon are motivated to feed
         Oxygen uptake of growth hormone transgenic coho salmon during starvation and feeding. 2003. Leggatt, R. A., R. H. Devlin, A. P. Farrell and D. J. Randall. Journal of Fish Biology 62:1053-1066.
         Transgenic salmon carrying all-salmon growth hormone gene assembly ate more and grew faster than control salmon in this experiment, and they also used oxygen at a higher rate. "Differences in oxygen uptake in growth hormone transgenic coho salmon and non-transgenic fish appear to be due to the effects of feeding, acclimation and activity level, and not to a difference in basal metabolism." The authors believe that the increased oxygen uptake is also due in part to increased food conversion efficiency.
         Interestingly, "While in the holding tanks, the transgenic and control fish displayed very different behaviours. The control fish tended to stay near the bottom corners of the tank, but became active when disturbed. The transgenic fish tended stay near the surface of the water and were active most of the time." The frankensalmon also acclimated more quickly to the respirometer. The authors explain this by saying that the extra growth hormone gene motivates the fish more towards feeding and less towards predator avoidance.   See Jul 2000 #81 and Feb 2001 #174. farrell@sfu.ca  

437.  Vannamei marker sequences
         High frequency and large number of polymorphic microsatellites in cultured shrimp, Penaeus (Litopenaeus) vannamei [Crustacea:Decapoda] . 2003. Meehan, D., Z. Xu, G. Zuniga and A. Alcivar-Warren. Marine Biotechnology 5:311-330.
         The authors have developed dozens of useful microsatellite markers and here they very helpfully publish the forward and reverse primers together with some comments on the spanned repeat sequences (e.g. "perfect", "imperfect"), the number of alleles in the sample they studied, etc. acacia.warren@tufts.edu  

436.  Animals grow slower in a genetically impoverished population
         The relationship between genetic variability and growth rate among populations of the pocket gopher, Thomomys bottae. 2003. Hildner, K. K., M. E. Soulé, M.-S. Min and D. R. Foran. Conservation Genetics 4:233-240.
         An important question in aquaculture and genetic conservation is whether genetic variation at "neutral" marker loci  -- for example, microsatellite markers -- is an indicator of the current fitness of a population. In theory a number of mechanisms can produce a positive association between neutral genetic variation and fitness when populations are compared. An association between individual heterozygosity and fitness within natural populations (i.e. when individuals are compared) has been known for decades (e.g. see May 2003 #409 and also #431, below). But are populations which are more genetically variable overall also more fit overall, in any meaningful sense of population fitness?
         Heterozygosity and DNA fingerprint band-sharing at allozyme and RFLP loci (not microsatellites) were estimated in paired high- and low-diversity populations of three subspecies of gophers. All the animals were grown in the laboratory to control for environmental effects. The mean growth rate (of body size, not numbers) in a less-variable population was consistently less than in the more variable population with which it was compared. In fact animals in the less variable member of the pair grew on average only half as fast.
         This may be an important analogy for aquaculture and genetic conservation, although it should be noted that the loss of genetic variation in the gophers studied here was rather extreme. (See mutational meltdown March 2003#388, March 2002 #300.)  kelly.hildner@noaa.gov  

435.  Markers for maleness in tilapia
         Identification of a sex-determining region in Nile tilapia (Oreochromis niloticus) using bulked segregant analysis. 2003. Lee, B.-Y., D. J. Penman and T. D. Kocher. Animal Genetics 34:379-383.
         The authors used a procedure called bulked segregant analysis to search for microsatellite marker genes associated with phenotypic sex. (In  BS analysis DNA from many individuals with the same phenotype is pooled and compared to a pool of DNA from a contrasting phenotype. The contrast here was male vs. female phenotypes.) Ten markers were found, all on linkage group 8, which is therefore the (or a) putative Y-chromosome. The linkage of two markers with the sex-determining region was so tight that the sex of offspring of two families was correctly predicted 95% of the time.
         Not always, however. "A third family from the same population showed no evidence for linkage of this region with phenotypic sex, indicating that additional genetic and/or environmental factors regulate sex determination in some families. ...These microsatellite markers ... could eliminate the tedious process of progeny-testing males during the production of YY-supermales." See Dec 2002 #367 for another approach to the problem of identifying sex chromosomes in niloticus. Download the PDF from http://hcgs.unh.edu/staff/kocher/pdfs/lee.2003a.pdf  

434.  When are you able to see MHC selection?
Perspective: detecting adaptive molecular polymorphism: lessons from the MHC. 2003. Garrigan, D. and P. W. Hedrick. Evolution 57:1707-1722.
         This paper includes an insightful review of current thinking about natural selection on the major histocompatibility locus (MHC), which is thought to induce an important evolutionary response to disease in fishes and other vertebrates (e.g. Mar 2002 #302, Jan 2003 #381, Mar 2003 #398). The main focus of the paper is an evaluation of the power of the usual statistical apparatus to reject a null hypothesis of selective neutrality. The MHC is here used philosophically as an alternative null hypothesis in which balancing selection can be assumed.
         The news is not good for people who would be unhappy with a conventional null result (i.e. anyone applying for grant renewal).  "We find that selection is not detectable in MHC datasets in every generation, population, or every evolutionary lineage. This suggests either that selection on the MHC is heterogeneous or that many of the current neutrality tests lack sufficient power to detect the selection consistently. Additionally, we identify a potential inference problem associated with several tests of neutrality. We demonstrate that the signals of selection may be generated in a relatively short period of microevolutionary time, yet these signals may take exceptionally long periods of time to be erased in the absence of selection. This is especially true for the neutrality test based on the ratio of nonsynonymous to synonymous substitutions. Inference of the nature of the selection events that create such signals should be approached with caution. However, a combination of tests on different time scales may overcome such problems." garrigan@email.arizona.edu  

433.  Fluctuating asymmetry reflects (mainly) recent developmental history
         The ontogeny of fluctuating asymmetry. 2003. Kellner, J. R. and R. A. Alford. American Naturalist 161:931-947.
         Fluctuating asymmetry (FA: random developmental differences between the left and right sides of an organism, such as bristles on the abdomen of a fruit fly) is, potentially, a useful indication that something in the life of the animal is not going well. See Jan 2003 #378 for an example. FA may be induced by genetic stress such as inbreeding, or environmental stress such as high temperature. But what developmental processes actually cause an increase in random asymmetry and why do they vary? 
         Seven hypotheses about the ontology of FA were examined by applying hunger and crowding stresses to some unfortunate lab chickens. The authors conclude that, "asymmetry in domestic fowl is not the product of events over their entire growth history but is influenced mainly by developmental noise in the recent past. This suggests that elevated levels of asymmetry within a population are likely to result from a present or very recent stress and are not the cumulative effects of previous stresses or the effects of stress during a critical stage in early development." They point out that FA may be useful for monitoring current environmental conditions. This agrees with the conclusion of another paper cited here, Feb 2002 #293. ross.alford@jcu.edu.au  

432.  Growth-maturation tradeoff in trout
         The genetic architecture of correlations among growth related traits and male age at maturation in rainbow trout. 2003. Martyniuk, C. J., G. M. L. Perry, H. K. Mogahadam, M. M. Ferguson and R. G. Danzmann. Journal of Fish Biology 63:746-764.
         Two important commercial strains were studied here, Rainbow Springs and Spring Valley. Rapid growth and early maturation are genetically correlated, implying that selected fast-growing individuals will produce offspring which are more likely to mature early (as two year olds), and vice versa. See #440, above. This is an important result for aquaculture breeding programs, as is the finding that heritabilities were moderate to high for growth, maturation and condition factor. Linkage groups (i.e. parts of chromosomes) were identified which contain QTLs for growth and, probably, precocious maturation. rdanzman@uoguelph.ca  

431.  Genetically variable offspring are predictably more fit
         Prediction of offspring fitness based on parental genetic diversity in endangered salmonid populations. 2003. Primmer, C. R., P.-A. Landry, E. Ranta, J. Merilä, J. Piironen, K. Tiira, N. Peuhkuri et al. Journal of Fish Biology 63:909-927.
         For about 1/4 century we have known that individual heterozygosity (a measure of genetic variation) is positively associated with individual fitness in wild populations of many species. The explanation is still somewhat controversial (e.g. Jan 2002 #276), and many more factors may be involved than were envisaged when the phenomenon was first noticed (e.g. MHC; Jan 2003 #381), but the observation underlies a lot of current thinking the proper management of endangered populations. (See #436, above.)
         This paper puts a new twist on the practical application of heterozygosity/fitness relationships by showing that it can be used to predict the genetic diversity of offspring from the parental genotypes. This is not as obviously true as one might think because of the likely occurrence of very unequal reproductive success, weird self-selection of mates based on MHC (Jan 2003 #381), etc.
         The authors calculated the expected microsatellite diversity of all possible offspring from designated pairwise matings in several salmon populations. Predicted heterozygosity and other diversity measures correlated well with the observed heterozygosity of the offspring and also with offspring population fitness traits, including egg survival and foraging behaviour. The procedure might be useful when deciding which breeders should be paired for mating in aquaculture production or stock enhancement. craig.primmer@helsinki.fi  

430.  Fitness QTL in a wild population
         A genome scan for quantitative trait loci in a wild population of red deer (Cervus elaphus). 2002. Slate, J., P. M. Visscher, S. MacGregor, D. Stevens, M. L. Tate and J. M. Pemberton. Genetics 162:1863-1873.
         This paper appears to be the first to report QTL for a fitness-related trait (birth weight) in a wild, free-ranging population of mammals other than people. It was made possible by the accumulation of  several generations of pedigree data on the red deer living on the Isle of Rum, Scotland (See Nov 2000 #132). Two methods of QTL identification are used. In one the phenotype of an offspring is regressed against the probability that it has inherited a QTL (actually, the QTL marker); this is repeated for markers located over the whole genome. The second method is a type of analysis of variance. The 93 markers used covered an estimated 62% of the genome.
         Evidence for several QTLs on different linkage groups was found, one of which was significant at the genome-wide level (i.e. it exceeded the stringent confidence-limit required by a large number of simultaneous tests).
         The QTL effects are surprisingly large, given the "Fishererian" expectation that most of the additive variance for fitness traits should be eliminated by natural selection. The authors discuss recent evidence that there is actually a lot of additive genetic variance but that heritability of fitness traits remains low because there is even more non-additive variance. Some of the evidence has been noted on this GCL website (Feb 2000 #10). j.slate@sheffield.ac.uk  

429.  How to estimate migration and Ne
         Estimating effective population size and migration rates from genetic samples over space and time. 2003. Wang, J. and M. C. Whitlock. Genetics 163:429-446.
         Here, at last, are procedures which can be used to  estimate effective population size and migration rate simultaneously, from a set of samples taken from a population at different times. Earlier methods for estimating the variance effective population size, Ne, from changes in marker allele frequencies have been constrained by the assumption that no immigration takes place (also, that no direct selection on the markers takes place). The immigration assumption is utterly unreasonable in many small populations. Indeed, the immigration rate is often the most significant genetic feature of such populations in a conservation context (e.g. Aug 2002 #342, May 2003 #400).
         "Here [the authors] extend previous moment and maximum-likelihood methods to allow the joint estimation of Ne and migration rate (m) using genetic samples over space and time. It is shown that, compared to genetic drift acting alone, migration results in changes in allele frequency that are greater in the short term and smaller in the long term, leading to under- and overestimation of Ne, respectively, if it is ignored." The computer program MLNE which does this can be downloaded from http://www.zoo.cam.ac.uk/ioz/software.htm  along with other useful programs (such as the one mentioned in May 2002 #320).

428.  Evaluating the success of genetic conservation
         Evaluation of the genetic management of the endangered black-footed ferret (Mustela nigripes). 2003. Wisely, S. M., D. B. McDonald and S. W. Buskirk. Zoo Biology 22:287-298.
         There aren't many detailed, genetic analyses of the success of a genetic conservation program -- lots of suggestions of how to mange the breeding, but not a lot of follow-up. Of course in fisheries there has rarely been time for follow-up (but see June 2000 #61, Jan 2001 #158, Feb 2001 #163).  The captive population studied in this paper has been managed according to the "minimal kinship selection" principle for many generations (MKS; Jan 2002 #283, Aug 2002 #335). There were only seven founders contributing genes to the captive population -- comparable to a lot of dead-but-walking salmon on the march to extinction.
          "Microsatellite data gave an accurate but only moderately precise estimate of heterozygosity [compared to pedigree records] . Genetic diversity was similar in captive populations maintained for breeding and release. ... Wild-born individuals from reintroduced populations maintained genetic diversity and avoided close inbreeding. [There was] small but measurable genetic differentiation between the reintroduced populations [founder effect] . The model of random mating predicted only slightly lower levels of heterozygosity retention compared to the [MKS] strategy. The random mating strategy may be a viable alternative for managing large, stable, captive populations such as that of the black-footed ferret. wisely.samantha@nmnh.si.edu 

427.  Competition difficulties in genetic and breeding programs
         Genetic architecture and evolutionary constraint when the environment contains genes. 2003. Wolf, J. B. Proceedings National Academy of Science (US) 100:4655-4660.
         It is obvious that competition and other social interactions among fish affect their growth, maturation and survival. Such interactions are very rarely taken into account in the design of genetic experiments, e.g. for estimating heritability, or in the design of selection programs.
        The oversight is so serious that (in my opinion) many heritability estimates may be wrong and designs based on them likely to fail (Sep 2000 #109, Aug 2002 #343). This is especially likely to be true of the more sophisticated "classical" breeding programs which use heritability estimates to make crucial selection decisions. "Theory [reviewed in the paper] has shown that these [indirect, competitive] effects modify the definition of genetic architecture by making the phenotype the property of the genotypes of multiple individuals and alter evolutionary dynamics by introducing additional heritable components contributing to trait evolution."
         The author of this paper has written a theoretical formulation of the social effects which is useful for REML analysis. The accompanying growth experiments were performed on Drosophila. There was indeed a genetic variance component due to the genotypes of other individuals in the population and which was hidden from ordinary genetic analysis. The author found that the expected negative covariance between direct and indirect (competitive) genetic effects, such that genes which make an individual bigger make other individuals smaller, is surprisingly large. Furthermore, the effect increases as the genetic relatedness of  individuals in the competing group increases.
         A couple of practical points would seem to follow from this: (1) everything possible should be done to reduce competition in aquaculture selection programs (more precisely, to prevent competitive behavior being rewarded by increased growth or reproductive success), and (2) assuming that point (1) is acted upon, within-family selection may be the most effective selection scheme for developing a strain of tame, non-competitive animals which ignore each other and feed all the time. This is another boost for within-family selection (see Feb 2002 #293). jbwolf@utk.edu