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.
635. Conservation by transferring whole genomes between species
Production of trout offspring from triploid salmon parents. 2007. Okutsu, T., S. Shikina, M. Kanno, Y. Takeuch and G. Yoshizaki. Science 317:1517.
This is a neat -- albeit aggressive -- way to preserve a critically endangered population of salmonids. The authors have used salmon to produce trout sperm and eggs.
Trout spermatogonia were intraperitoneally microinjected into newly hatched embryos of triploid salmon. Some of the host (salmon) embryos developed as salmon males
which produced trout sperm two years after the injection, some embryos developed as salmon females
which produced trout eggs. The control salmon without transplanted spermatogonia produced no gametes of either sex.
Three points are critical here: (1) the donor spermatogonia (primitive, undifferentiated source cells for sperm; a sort of stem cell) are still diploid and thus contain the full genome of the donor, including the mitochondrial genome, (2) the host is triploid and thus incapable of producing its own gametes by meiosis, (3) trout eggs as well as sperm were produced even though only spermatogonia were transplanted. The trout-from-salmon gametes were crossed and produced normal trout in the next generation. Confirmation of species identity at successive stages in the process was based on various bioengineered and natural (RAPD) markers.
The authors present their technique as an alternative to cryopreservation, which doesn't work well in salmonids because of the large size and high fat content of salmonid eggs. There will doubtless be other uses for these interesting constructs as well. email@example.com
634. How to give one species the genetic signature of another
On the risk of criminal manipulation in caviar trade by intended contamination of caviar with PCR products. 2007. Wuertz, S., M. Belay and F. Kirschbaum. Aquaculture 269:130-134.
All sturgeon species are officially protected in one way or another but sturgeon caviar and unsalted eggs are so valuable that overfishing, smuggling and mislabeling are wreaking havoc with the remaining populations. Apparently it is possible to make one species look like another in order to elude international control measures.
First you produce "false id" DNA from a less valuable species.
This was done here by PCR amplification of the cytochrome b gene of Acipenser sturio, using
the primer sequences recommended in the international CITES protocol
relating to the illicit trade in caviar. Then you incubate eggs and/or caviar from the more valuable species (A. baerii in this experimental demonstration) with the false id DNA (i.e. with the A. sturio PCR amplicon). The authors show that the protocols recommended by CITES falsely identify the A. baerii eggs and caviar as being A. sturio. The standard,
official identification protocol reveals no sign of the true cytochrome signature.
Fortunately, it is relatively easy to detect the fraud by adding an extra step to the standard protocol. The false id DNA only attaches itself to the surface of the eggs during the incubation and is not incorporated into the genome. The authors found that they could remove it by treating the eggs with DNAase before starting the normal DNA extraction procedure. With the false id DNA hydrolyzed and out of the way the true id cytochrome b signature was revealed. firstname.lastname@example.org
633. Good prospect for improving P. monodon reproductive performance
Heritability of reproductive traits and genetic correlations with growth in the black tiger prawn Penaeus monodon reared in
tanks. 2007. Macbeth, M., M. Kenway, M. Salmon, J. Benzie, W. Knibb and K. Wilson. Aquaculture 270:51-56.
The shrimp Penaeus monodon has been hard to domesticate because of its poor reproductive performance. This breeding experiment
(See also Sep 2006 #539) produced the following heritability estimates for important components of reproductive fitness: days to spawn after ablation (0.47 ± 0.15), egg number (0.41 ± 0.18), nauplii number (0.27 ± 0.16) and proportion hatched (0.18 ± 0.16). All of these reproduction variables were considered to be traits of the female parent in the statistical
model. Egg number was strongly correlated with weight-at-age, but other genetic correlations were rather low. One can conclude that domestication selection should improve reproductive performance rather quickly. Michael.Macbeth@dpi.qld.gov.au
632. Choosing founders to maximize broodstock diversity
Use of microsatellites and a combinatorial optimization approach in the acquisition of gilthead sea bream (Sparus aurata L.) broodstocks for
hatcheries. 2007. Borrell, Y. J., C. E. Carleos, J. F. Asturiano, D. Bernardo, E. Vázquez, N. Corral, J. A. Sánchez et al.
This paper describes a procedure for maximizing the amount of genetic variation in the founders of an aquacultural broodstock. (Compare Jan 2002 #283 which describes a procedure for recovering genetic variation which has been lost during some generations of cultivation.) It requires a preliminary estimate of pairwise relatedness among all the potential founders,
e.g. as estimated from microsatellite marker data. A broodstock is then founded with the subset of breeders that have the minimal mutual relatedness (or maximum genetic variance). See Jul 2006 #512 and cross-references therein.
The interesting aspect of the paper is the way the optimal subset is
chosen. The authors use a Monte Carlo procedure called simulated annealing which, although previously used by Sonesson and Meuwissen to optimize mating schemes has never been used to select
broodstock founders, to my knowledge. It works well. The expected heterozygosities and number of alleles in the optimal subset was as high as in the total collection of candidate founders and the polymorphic information content of the markers (PIC) was higher. See June 2007 #603 for a different computational solution to the same problem. email@example.com
631. RNA treatment suppresses white spot virus in vannamei
Inhibition of white spot syndrome virus in Litopenaeus vannamei shrimp by sequence-specific siRNA. 2007. Wu, Y., L. Lü, L.-S. Yang, S.-P. Weng, S.-M. Chan and J.-G. He. Aquaculture 271:21-30.
Survival of WSSV-challenged L. vannamei rose to around 50% after injection of siRNA (small interfering RNA, see Oct 2006 #549). The siRNA was specific to five viral genes. The authors
also found that non-specific or sequence-independent siRNA (i.e. siRNA that does not target specific messenger RNA) did not increase host survival or prevent viral replication.
Non-specific siRNA was derived from the specific variety by changing six
nucleotides. (See Oct 2006 #552 for an earlier, identical result in P. japonicus; see also Oct 2006 #549 for the effect of non-specific RNA) .
"These results suggest that siRNA can suppress WSSV efficiently in shrimp, and it may provide a potential approach to the therapy of aquaculture viral disease." But
the authors caution that "further studies are necessary to construct high expression vectors and better transfection approaches of dsRNA/siRNA in shrimp in vivo". firstname.lastname@example.org
630. An easy genetic correlation
measurement works fairly well
A comparison of methods to estimate cross-environment genetic correlations. 2006. Astles, P. A., A. J. Moore and R. F. Preziosi. Journal of Evolutionary Biology 19:114-122.
In aquaculture breeding program we sometimes select fast-growing broodstock in tanks and then grow their offspring in commercial ponds. Will the performance of the offspring improve from generation to generation? Related questions arise when populations are bred in captivity with the intention of returning them, someday, to the wild. One often wants to know what effect selection in one environment is likely to have in other environments.
To answer such questions you need to estimate the genetic correlation between traits in two environments. Genetic correlations can be estimated in fully pedigreed populations using standardized statistical methods. There are also "quick and dirty" methods which are sometimes the only ones feasible in real-world hatcheries. This paper examines the effectiveness of the simplest method of all, correlations of family mean phenotypes when families are reared in two environments. Quantitative genetic analysis based on the estimation of variance components provide the standard for comparison. (The clear, side-by-side comparison of how to use the various techniques is a useful side benefit to reading this paper.)
It turns out that the quick-and-dirty method does provide useful information about the sign of the correlation (at least) and whether
a correlation actually exists. Full-sib families are better than half-sib and bigger families are better than smaller for estimating genetic correlations from phenotypes. The authors warn, however, that "Variance component approaches [i.e.. ANOVA or REML] should be used when parameter estimation is the objective, or if the goal is anything other than determining broad
629. Purging captive populations rarely works
An investigation of inbreeding depression and purging in captive pedigreed
populations. 2007. Boakes, E. H., J. Wang and W. Amos. Heredity 98:172-182.
Inbreeding depression is commonly observed in small, captive populations (such as zoos and aquacultural broodstocks) and is sometimes observed and often suspected in endangered wild populations. Will inbreeding depression eventually solve itself by "purging" -- that is,
will selection eventually remove the deleterious recessive alleles which are the primary cause of inbreeding depression? Or to phrase the question more aggressively, should managers deliberately inbreed and cull, to purge deleterious alleles and solve the depression problem for evermore?
The matter is controversial (see Apr 2007 #591, #593; Mar 2003 #395). Different conclusions are often
drawn from different statistical procedures applied to the same data. Results are,
necessarily, population- and environment-specific.
This meta-analysis of 119 zoo populations found that "few predictors of a population's response to inbreeding are found reliable .... The change in inbreeding depression due to purging averaged across the 119 populations is <1%.... The study re-emphasizes the necessity to avoid inbreeding in captive breeding programmes and shows that purging cannot be relied upon to remove deleterious alleles from zoo populations." The authors add that purging may not even be desirable, since an allele which is deleterious in captivity may be advantageous in nature. Elizabeth.Boakes@ioz.ac.uk
628. Why are Macrobrachium stocks in Thailand deteriorating?
Genetic diversity of hatchery stocks of giant freshwater prawn (Macrobrachium rosenbergii) in Thailand. 2007. Chareontawee, K., S. Poompuang, U. Na-Nakorn and W. Kamonrat. Aquaculture 271:121-129.
The productivity (survival and growth) of the giant freshwater prawn appears to have been declining in Thailand. Is this
a symptom of loss of genetic diversity? The usual, artisanal farming practices in the region do not give a high priority to genetic maintenance.
This paper concludes that the problem must lie elsewhere. The authors measured microsatellite diversity in a number of farmed and wild populations from Thailand and other SE countries including Indonesia and Burma. "All hatchery and wild populations exhibited relatively high genetic variation and were similar with an average of 7.50 to 10.67 alleles per locus and average expected heterozygosity at all loci of 0.64 to 0.73."
These high values come as a surprise. Perhaps the current farming practices are exerting negative domestication selection pressure on production traits and this, rather than diversity loss per se, is the problem? email@example.com
627. Can polyploidy increase resistance to disease?
Neopolyploidy and pathogen resistance. 2007. Oswald, B. P. and S. L. Nuismer. Proceedings of the Royal Society (B) 274:2393-2397.
There is an interesting idea here which may be relevant to aquaculture. The authors suggest, on theoretical grounds, that polyploids may be more resistant to pathogens. The effect is due to the increased heterozygosity of polyploids in the initial generations. "We find
[by simulation] that for the genetic mechanisms of pathogen resistance with the best empirical support, newly formed polyploid populations of hosts are expected to be more resistant than their diploid progenitors. This effect can be quite strong ...." firstname.lastname@example.org
626. Should "year" be in the model when you are estimating a genetic trend?
Implications of the difference between true and predicted breeding values for the study of natural selection and
micro-evolution. 2006. Postma, E. Journal of Evolutionary Biology 19:309-320.
Estimates of breeding value are becoming more and more common in aquaculture and genetic conservation. The true breeding value (BV) of an individual for a trait such as growth rate is, in essence, the genetic value of that individual as a parent. Individual breeding value is useful if you are selecting breeders for artificial selection because it predicts the performance of an individual's offspring relative to the average of other, contemporaneous offspring in the population. BV estimates are also useful studying natural selection and the response to it in wild populations (e.g. Apr 2004 #471).
Generally, speaking, you predict the breeding value of an individual from its own performance and the performance of its close relatives. So the usual prediction procedure requires pedigree records or some surrogate for pedigrees such as genetic relatedness estimates from DNA markers (Dec 2006 #572, #571; Feb 2007 #585). (In this paper the term "predicted breeding value" (PBV) is used rather than "estimated breeding value", EBV.) How accurate are the
Not always very accurate even when the pedigree itself is accurate, because an individual’s breeding value is predicted partly on the basis of its own phenotype. The PBV will partly reflect this environmental effect. Estimate are particularly inaccurate when phenotypes are strongly influenced by the environment and there is not much information from relatives.
The paper includes a useful and illuminating discussion of "biased trends" in
PBVs that are affected by non-genetic trends in the environment. The bias of particular interest results from the use or non-use of "year", as a fixed or random
variable when one is looking for a genetic trend in breeding value over time. That is, when one is looking for natural microevolution or a response to artificial selection.
Unless individual pedigrees are distributed over a large number of years ("well connected") omitting an explicit year effect will overestimate the genetic trend or show a spurious trend when none exists. But if you include year you may make real genetic trends disappear completely in a poorly connected pedigree. The worst situation would be when a new generation comes along every year with no overlap.
"If environmental change is not explicitly modeled [e.g. with a "year" effect variable], then ... we may find a change in PBVs over time in the absence of a genetic change. On the other hand, if year is included in the model the change in PBVs may be small and nonsignificant, when in fact the phenotypic change does have a genetic basis." A lot of us who have experienced this have been tempted to include or exclude "year" depending on what one wants to see as a result. The author suggests that the bias can be removed to a considerable extent by looking at trends in "focal" individuals on which phenotypic data have been deleted, i.e. trends in BVs estimated from relatives only. . email@example.com
625. Mixing sperm increases the rate of inbreeding
The genetic consequences of hatchery-induced sperm competition in a salmonid. 2007. Wedekind, C., G. Rudolfsen, A. Jacob, D. Urbach and R. Müller. Biological Conservation 137:180-188.
Sperm (milt) from several males is often mixed together in salmon hatcheries before it is used to fertilize eggs from one or more females. The same thing is done in
the culture of Indian carp and no doubt many other species as well. We already know that the practice causes a loss of genetic variation owing to sperm quality and unequal volumes of milt volunteered by the males. How serious is
This experimental study on Coregonus zugensis (an Alpine whitefish) quantifies sperm competition in terms of its main components: sperm motility and the volume and density of the milt. "We found that not controlling for sperm density and/or milt volume would, at a constant population size, decrease the variance effective number of male breeders
by around 40–50%." This is a serious loss. Furthermore, the study found that younger males have faster sperm and bigger males have more sperm.
The authors note that these correlations could induce domestication selection for growth rate and/or early maturation depending on whether or not the contributions of males are equalized as part of the hatchery protocol. (Also see Aug 2003 #423, June 2004 #483.) firstname.lastname@example.org
624. Outbreeding comes to the (genetic) rescue once again
Genetic rescue persists beyond first-generation outbreeding in small populations of a rare
plant. 2007. Willi, Y., M. van Kleunen, S. Dietrich and M. Fischer. Proceedings of the Royal Society (B) 274:2357-2364.
Populations that are too small lose both genetic diversity and local adaptation through genetic drift. Inbreeding increases every generation. You can, potentially, prevent and even reverse these effects by adding a few individuals from elsewhere ("genetic rescue", June 2004 #486, Oct 2006 #546, Dec 2006 #570). This solution is often frowned upon because of the danger of "outbreeding depression".
Outbreeding depression occurs, potentially, when maladaptive genes are added or locally adapted gene complexes are broken up. Published demonstrations of outbreeding depression are rare but outbreeding depressors are abundant
in the conservation genetic academic community so genetic rescue is not often undertaken.
This nearly-natural, common-garden study on a rare buttercup shows that genetic rescue can be valuable. The fitness benefit extended for more than one generation and were seen both in the presence and absence of competition. "Our results show that the skepticism towards artificial gene flow in conservation is not justified in those cases where populations are small and show significant fitness reductions due to inbreeding depression, fixed mutational load or reduced cross-compatibility." Also, "We conclude that the benefits of interpopulation outbreeding are likely to outweigh potential drawbacks, especially for populations that suffer from inbreeding." email@example.com