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.
647. News flash! Selection of a high-male, temperature-sensitive tilapia line
Selection experiments to increase the proportion of males in Nile tilapia (Oreochromis niloticus) by means of temperature treatment. 2007. Wessels, S. and G. Hörstgen-Schwark. Aquaculture 272:S80-S87.
The authors of a recent paper on heritable, temperature-dependent sex ratio in O. niloticus (Oct 2006 #550) have followed up their analytical work with a successful selection experiment.
Families of their Lake Manzala (Egypt) broodstock were exposed to 36 degree temperature as fry and then ranked by their sex ratios when they matured. Families with relatively high male and relatively low male sex ratios became the founders of two divergent selection lines. "After two generations of selection the temperature treated groups in the high line showed a male percentage of 90%, whereas the weakly sensitive low line showed an average male proportion of 54%. The realized heritability estimated from the cumulated realized selection response and -differential in successive generations was 0.69 in the high line and 0.86 in the low line."
Wow! This is interesting genetically and important in practice. "Thus, temperature sensitive lines could be produced as a consumer- and environment-friendly approach to significantly increase the proportion of males in Nile tilapia, if large numbers of broodstock could be tested." firstname.lastname@example.org
646. How to protect your investment in broodstock improvement
Can you shrinkwrap a cow? Protections available for the intellectual property of the animal breeding industry. 2007. Ogden, E. R. and K. Weigel. Animal Genetics 38:647-654.
Why spend money to develop fast-growing fish or shrimp if someone steals your strain and sells it more cheaply than you can? The widespread "hijacking" of strains and sale of their progeny at discounted prices discourages many breeders from investing in genetic improvement. What's the point, if you can't reap the benefits from your R&D investment? Well, with some forethought you can reap the benefits.
This review article points out that "There are currently four main intellectual property protection statutory schemes available: copyright [impossible], trade secret [temporary], trademark [useful] and patent [impossible]. Each of these protects a different aspect of intellectual property, which leaves gaps of protection when an innovation does not fit squarely within the boundaries of the statutes." The authors argue that for new animal strains or breeds, a contract which licenses the purchaser to use the strain for certain defined purposes is the best solution. The applicable types of contract are discussed in some detail. Some purchasers would be licensed only to use PLs or fry for commercial grow-out, some could breed the strain to produce fry for sale (secondary breeders), some could incorporate the strain into their own broodstock.
The contract prices for these different kinds of use would be very different. "The protection for animal breeding industry innovations is most likely through contract law rather than traditional intellectual property law." And "The licence must be carefully crafted to gain rights and enforceability to protect the innovation and recoup expenses while avoiding unduly harsh anticompetitive effects." This means among other things that an aquaculture strain must be identifiable, e.g. through genetic markers. This is now relatively easy to arrange: see May 2000 #58, and as a cautionary note see Oct 2007 #634. email@example.com
645. Interesting heritability estimate (P. Vannamei)
Heritability for body weight at harvest size in the Pacific white shrimp, Penaeus (Litopenaeus) vannamei, from a multi-environment experiment using univariate and multivariate animal models. 2007. Castillo-Juárez, H., J. C. Q. Casares, G. Campos-Montes, C. C. Villela, A. M. Ortega and H. H. Montaldo. Aquaculture 273:42-49.
There are two especially interesting things in this paper. The first is that the estimated heritability of growth rate is comfortably high (0.3 - 0.4) which is good news for selective breeding programs. See Aug 2003 #424, Jun 2006 #499. The second is the way the estimates of genetic variable were made.
The experimental design was a basic dams-nested-within-sires mating scheme with growout in two farms at two densities. Several linear mixed animal models were used in the statistical analysis including -- and this is the interesting part -- models with and without a common-environment term, and models in which growth was either treated as a single variable with the four farmXdensity combinations as fixed effects, or as four separate growth variables. (Actually, the analysis is similar to one used for tilapia in a paper which was unfortunately overlooked in this website: 2006, Malua et. al., Aquaculture 259: 47-55. firstname.lastname@example.org.
Inclusion of the common environment term (denoted "c") reduced the heritability estimate by around 50%. The c variable is supposed to include only maternal and "hapa" effects plus part of the non-additive genetic variance. However, such a big reduction in the heritability estimate suggests that some additive effects may be in there as well (confounding). The question is, how much confounding? Does inclusion of the c variable over-correct the heritability? See Oct 2007 #626 for a related discussion of including a "year" effect when analysing for genetic trends.
The multivariate estimate shows a considerably smaller effect of the c variable and helps to reduce this possible confounding. The paper develops an interesting procedure for making quantitative, comparative evaluations of the models. But in the long run, the inclusion of several environments, and several replicates of families in each environment, and more dams per sire in future experiments will eventually remove the uncertainties caused by common-rearing artifacts. See
#640 below for a similar analysis of tilapia. email@example.com
644. Captive Steelhead trout rapidly become competitively less fit
Genetic effects of captive breeding cause a rapid, cumulative fitness decline in the wild. 2007. Araki, H., B. Cooper and M. S. Blouin. Science 318:100-103.
The steelhead trout studied here were born in the wild, survived in the wild and were sampled as adults as they returned to their natal river (the Hood river, in Oregon) to spawn. They differed only in the exposure of their inherited genomes to domestication selection in a hatchery.
The Hood river has a supplementation program in which a proportion of wild-caught adults
are spawned and reared in hatcheries before being released into the river as juveniles. Using microsatellite markers to reconstruct pedigrees the authors were able to separate a sample of wild-born returning fish into ancestor-categories which differed by one generation of hatchery rearing. Aside from this difference in ancestry the fish in the categories were identical in the variables discussed -- their parents were "born in the same year, reared in the same hatchery without distinction, and released at the same time".
The fitness of genomes selected for one extra
generation of hatchery rearing, measured as the number of adult offspring they produced (in the wild) which returned to the river, was reduced by almost 50%. This is an extraordinary decline in fitness which, the authors point out, is similar in magnitude to previous studies which were not able to isolate genetic from other effects. It is hard to argue with the authors comment that "These results suggest that even a few generations of domestication may have negative effects on natural reproduction in the wild and that the repeated use of captive-reared parents to supplement wild populations should be carefully reconsidered". See Oct 2006 #546.
The word "reconsidered" is well chosen and safer than the word "abandoned" at the present state of our understanding. The authors have shown that the animals become competitively less fit in the presence of 100% non-hatchery genomes. An implicit assumption in this important paper is that selection against hatchery-infested genomes is hard, meaning that it produces an absolute load of extra mortality and/or extra reproductive failure -- in essence, that the effect is independent of population density. Hard selection implies population decline and, possibly, extinction.
To me it seems more
likely, however, that domestication selection is "soft" in the natural environment and that the selective deaths are substituted for non-selective background mortality. This can happen if, while hatchery genomes don't compete very well with wild genomes, they are happy and productive when competing with each other, either for mates or spawning territories. In this case the wild, supplemented population could in principle remain the same size or even adapt and increase. See
#638 below for adaptation after introduction of an exotic stock and #639 for
life-history maintenance after re-introduction from a hatchery.
643. Inbreeding depresses shrimp survival under disease stress.
Effects of inbreeding on survival and growth of Pacific White Shrimp Penaeus (Litopenaeus) vannamei. 2007. Moss, D. R., S. M. Arce, C. A. Otoshi, R. W. Doyle and S. M. Moss. Aquaculture 272:S30-S37.
This analysis encompasses survival, growth and disease challenge-test data on approximately eight generations of P. vannamei. Within this pedigreed broodstock inbreeding coefficients vary among families, from a low of 0.0 (most families) to a high of 0.25. Both growth and survival of non-inbred families were high during this period. Inbreeding had a small (but significant) depressive effect on growth and no significant effect on survival.
The effects of inbreeding on survival after challenge tests with viral pathogens was more noticeable, and became particularly strong in severe (WSSV) challenge tests, where survival even of the non-inbred families was considerably reduced. The effect of inbreeding on survival ranged from an 8.3% reduction per 10% inbreeding in challenge tests where non-inbred survival was high, to 38.7% reduction when non-inbred survival was low. Three isolates of TSV and one WSSV were used in the tests.
These results suggest that inbreeding depression becomes more serious as environmental quality (measured conventionally as the survival rate of non-inbreds) goes down. An empirical relationship is provided which allows prediction of survival under various combinations of inbreeding and environmental quality. See May 2003 #402 and #409 for inbreeding & stress, plus Sep 2006 #538 for a meta-analysis. firstname.lastname@example.org
642. Not much hard evidence for genetic responses to climate change
Climate change and evolution: disentangling environmental and genetic responses. 2008. Gienapp, P., C. Teplitsky, J. S. Alho, J. A. Mills and J. Merilä. Molecular Ecology 17:167-178. This review paper focuses on the search for truly genetic responses to climate change, as opposed to ecological and non-genetic developmental responses. The conclusion is that not much hard evidence for a genetic response exists, as yet. ".... many responses perceived as adaptations to changing environmental conditions could be environmentally induced plastic responses rather than microevolutionary adaptations. Hence, clear-cut evidence indicating a significant role for evolutionary adaptation to ongoing climate warming is conspicuously scarce." There are several fundamental difficulties in seeing genetic changes in a changing environment.
The two most important
difficulties appear to be (1) "the maximum sustainable rate of evolution ... should not exceed more than a few per cent of the phenotypic standard deviation per generation". In other words, the expected effect is small. And (2) various temporal and spatial heterogeneities which are not recognized in the statistical models can confound genetic and phenotypic effects, giving a spuriously high estimate of genetic change. See Oct 2007 #627 for
a discussion of a similar problem.
The conclusion is that you have to do the quantitative genetic analysis and the selection analysis as well as just document a trend, no matter how plausible the trend.See
#638 below for separation of environmental and genetic effects in New Zealand coho. Similar cautions would apply to evolutionary responses to fishing pressure (Aug 2002 #345, Jul 2006 #508, Jun 2007 #602). email@example.com
641. Quantitative divergence and adaptation in a metapopulation
Genetic isolation of fragmented populations is exacerbated by drift and selection. 2007. Willi, Y., J. van Buskirk, B. Schmidt and M. Fischer. Journal of Evolutionary Biology 20:534-542.
This is one of the rare investigations of
quantitative genetic differentiation in a set of small, somewhat interconnected populations. Although the organism happens to be a Swiss buttercup (see Oct 2007 #624) the relevance of the results to fisheries and aquaculture should be self
evident to all.
Eight quantitative morphological and reproductive traits were measured in a common-garden experiment, with estimation of sire and dam additive variance components and heritabilities. Differentiation of the quantitative traits (estimated QST;
see Jul 2006 #515) was greater among smaller than larger subpopulations, as was differentiation at neutral allozyme loci (estimated FST). Quantitative genetic variance and allozyme gene diversity were both positively correlated with population size.
Evidently the small populations had lost additive genetic variance as well as neutral diversity. This is important, because it means that neutral variation can be used here as an indicator of quantitative variation, which is tedious to measure but intrinsically more interesting.
Pairwise QSTs of the quantitative traits were larger than the author's estimates of what should have been produced by drift, from which they conclude that local quantitative genetic adaptation (divergent selection) is probably taking place. This was especially true in the smaller populations. "These results ... suggest that small populations may represent reservoirs of genetic variation adaptive within a wide range of environments." Because the small populations also had lower heritabilities, however, they would have less scope for evolutionary adaptation when isolated and on their own. Note that these are the same subpopulations in which artificial outbreeding -- genetic rescue -- was shown to increase fitness (Oct 2007 #624). firstname.lastname@example.org
640. Origins and genetic properties of the GIFT tilapia strain
Genetic improvement of farmed tilapias: Composition and genetic parameters of a synthetic base population of Oreochromis niloticus for selective breeding. Aquaculture. 2007. Eknath, A. E., H. B. Bentsen, R. W. Ponzoni, M. Rye, N. H. Nguyen, J. Thodesen and B. Gjerde. Aquaculture 273:1-14.
This paper usefully summarizes the origins of, and motivations for the GIFT tilapia strain which was developed in the Philippines in the early 1990s.
The analysis includes a single "c" term which encompasses several non-additive factors which contribute to the covariance of full sibs, including early rearing environment, maternal effects, dominance and epistasis. (Epistasis might be unusually important here because of the very wide geographical crosses and other features of the mating design in the first two generations). For a discussion of the "c" variable see
#645, above. Like #645, this paper treats growth both as a single variable with environments as fixed effects and as multiple variables with zero environmental error covariances. Together the papers provide a good introduction to this kind of analysis.
Estimated heritabilities for growth are mostly at the low end of the published range (0.15 across test environments), which is surprising in light of the considerable pains taken to maximize genetic variation in the founder population. This estimate may be
correct and growth-rate heritability may be exceptionally low in GIFT. It is also possible that the c variable may be
an overcorrection caused by extreme genetic heterogeneity among founders. (Failure of the REML likelihood solutions to converge may be another symptom of this). Actually it doesn't matter
now, in 2008, because any computational artifacts caused by initial disequilibria will have disappeared long ago.
The authors conclude from the high correlation between growth in very different types of pond environment that genotype-environment interaction is low in ponds. It is different story with correlation between pond and cage environments, and super-intensive tank environments were presumably not available for testing. . email@example.com
639. Ecotype differences survive re-introduction from hatchery stock
Reproductive isolation following reintroduction of Chinook salmon with alternative life histories. 2007. Narum, S. R., W. D. Arnsberg, A. J. Talbot and M. S. Powell. Conservation Genetics 8:1123-1132.
The ultimate aim of most captive breeding programs is to reintroduce species into habitats from which they have been extirpated. In the case of salmonid species on the West Coast of North America captive breeding in hatcheries is controversial at many levels: aesthetic, arithmetic, genetic, economic, social, environmental & moral. Sometimes, questions are even asked about whether or not it works.
This reintroduction of two ecotypes of Oncorhynchus tshawytscha (ocean- vs. stream-dwelling, or fall vs. winter spawning) into the Clearwater River in Idaho was indeed successful. Furthermore, the genetic separation of ecotypes has been maintained. "Very little evidence for gene flow among the two life history types was observed as assignment tests [6 microsatellite loci] correctly assigned 99.6% of individuals in reference collections to either ocean- and steam-type Chinook salmon." These ecotypes are widespread and important to the ecology and fishery of the species.
Reintroduction occurred sporadically over a number of years and involved several hatchery populations derived from different geographic areas. Currently, the ocean ecotype is supplemented by wild-caught returning adults. See
#644 above for fitness cost of supplementation. And #638, below, for
another genetically successful introduction into an empty river (empty of
salmon, that is). firstname.lastname@example.org
638. True (genetic) local adaptation of
chinook introduced to New Zealand
Eco-evolutionary vs. habitat contributions to invasion in salmon: experimental evaluation in the wild. 2008. Kinnison, M. T., M. J. Unwin and A. E. Quinn. Molecular Ecology 17:405-414.
Chinook salmon were introduced into New Zealand around 100 ago and have since colonized many watersheds, with associated divergence in phenotypes and life histories (Mar 2003 #394). How much of this divergence is due to the direct influence of different habitats on development, and how much is due to true genetic (adaptive) radiation? This question is similar to the question asked about the temporal trends in phenotype associated with climate change (Oct 2007 #626). You can't do common garden or translocation experiments in time so #626 insists on the requirement for a genetic analysis before deciding whether evolution has occurred. But you can do translocations in space, which is what the authors of this paper have done. And they provide a genetic analysis too.
"By using experimental translocations [two populations], we partitioned the roles of evolution and habitat quality .... Variation in habitat quality within the new range had the greatest influence on broad geographical patterns of vital rates, but locally adapted salmon still exhibited more than double the vital rate performance, and hence fitness, of nonlocal counterparts. ...These results suggest that contemporary evolution can be an important part of the eco-evolutionary dynamics of invasions..." Note that "vital rates" refers to
the fitness components survival and egg production. Other life history
traits in the analysis included degree (°C) days to hatching, growth rate, date of adult return to breeding sites, egg number etc.
Rates of quantitative genetic divergence were significant, but modest, and the implied selection differentials -- accumulated over 26 generations -- are entirely reasonable. There can be no doubt that adaptive evolution has occurred and that it parallels, but is considerably less than, the direct effects of different environments on the salmon phenotype. This invasion by an exotic species represents soft selection in the sense mentioned in
the review of #644 above. The populations translocated a few years ago are
now less fit than the locals introduced in 1907 -- and probably competitively inferior to them.
But in 1907 they weren't yet adapted and when they started off they did just fine.
One might guess that if the locals were extirpated they could be recolonized from elsewhere and adaptation would occur all over again. email@example.com
637. Can you select for uniformity? Should you?
Selection for uniformity in livestock by exploiting genetic heterogeneity of residual variance. 2008. Mulder, H. A., P. Bijma and W. G. Hill. Genetics Selection Evolution 40:37-59.
Aquacultural products are almost always graded for size and larger sizes are almost always worth more than small ones, per gram. Thus the profit from a crop depends not only on its mean growth rate but on the variability of its growth rate as well. And there is a lot of size variation within aquacultural crops -- CVs exceeding 20% within families are not uncommon in shrimp.
This paper addresses the possibility of increasing the profitability of a breed by selecting for reduced variation while at the same time selecting for an increase in its mean. Many people (including farmers) have speculated about this. Theoretical and some experimental work has been done on genetic aspects of the question. So far as I know this is the first study of variability selection that puts economic profitability into the equation along with phenotypes, variation in phenotypes, and heritabilities.
To do this a "profit function" needs to be defined that relates profitability to phenotype. The genetic assumptions are rather simple: the genetic variance of family means does not involve dominance or epistasis, and differences among families in their within-family variance is somewhat heritable.
The study makes important points. (1) Including variance in the selection index can be well worth while if the economic value of variance is least of the same order as the economic value of the mean. This is probably true in aquaculture. (2) The profit function has to be non-linear in the phenotype. Information about the shape of the profit function in aquaculture should exist and is certainly non-linear. (3) Selection is most effective when families are large so that within-family variance can be estimated accurately. This certainly applies to aquaculture. It would be interesting to see if the aquaculture profit functions favor selection for reduced variance in aquaculture, because all the other factors considered in this paper would seem to do so. firstname.lastname@example.org
636. Disease tolerance and disease
resistance are genetically not the same thing
Disentangling genetic variation for resistance and tolerance to infectious diseases in
animals. 2007. Råberg, L., D. Sim and A. F. Read. Science 318:812-814.
Resistance means that animals don't get infected or they quickly get rid of the infection; tolerance means that animals stay infected but continue to live, with or without some degree of disability. Most of the papers reviewed on this website which deal with aquatic disease, and there have been a lot of them, either focus solely on resistance or confound resistance and tolerance. The authors point out that this is true of the scientific literature in general.
Their experiment crossed inbred strains of mice to allow analysis of resistance and tolerance to parasite loads without confounding the two effects. Tolerance
was measured by regressing measures of performance, yield or fitness against parasite load. A shallow regression slope means high tolerance. Similar analyses could be done on aquaculture species -- it is not necessary that the lines be inbred, merely that they differ in their response to parasites.
There was genetic variation in both
resistance and tolerance. "Moreover, resistance and tolerance were negatively genetically correlated." High tolerance was associated with low resistance and vice versa. If they can be extended to aquaculture these ideas are important to us because resistance, but not tolerance, triggers an "evolutionary arms race" between pathogen and host (Jul 2000 #84). Tolerance may consequently be an intrinsically more stable solution to the disease problem on a global scale.
On the local scale, when designing selection schemes for individual broodstocks, we should consider the genetic correlation of these traits with the components of yield as well as with each other. In this mouse experiment (and in many plants) resistance seems to come at the cost of productivity. See reference in June 2006 #499 for this possibility in vannamei. email@example.com