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.
Note: as of this posting e-mail
addresses have been modified in an obvious way to reduce the possibility
683. Selection for high-temp sex reversal in tilapia
Tilapia sex determination: Where temperature and genetics meet. 2009. Baroiller, J., H. D'Cotta, E. Bezault, S. Wessels and G. Hoerstgen-Schwark. Comparative Biochemistry and Physiology A. Molecular and Integrative Physiology. in press.
This paper is a review of the effect of temperature on sex ratio in tilapia (and of sex in tilapia in general). As such it is a useful contribution to our understanding of the masculinization of genetic females by high temperatures (Feb 2008 #647, Apr 2008 #657).
The work is of practical significance because temperature treatment can potentially bypass both of the current methods of producing all-male populations for aquaculture: hormone treatment that generates females that are phenotypic males, and hormone treatment followed by a multi-generation mating scheme that generates truly all-male populations.
Anything that can get away from hormonal sex reversal is good for
Note that a related paper
(Feb. 2008 # 647) paper found good response to selection for the skewing of sex ratio towards
males after a temperature shock. baroiller<&>cirad.fr
682. Mitochondrial and genomic sequences should evolve in concert
Interpopulation hybrid breakdown maps to the mitochondrial genome. 2008. Ellison, C. K. and R. S. Burton. Evolution 63:631-638.
When two genetically-differentiated populations hybridize the F1 hybrid offspring will sometimes do fine, but then
lose fitness in later generations. See for instance Aug 2002 #342, May 2003#400, Feb 2004 #458.
This doesn't always happen and may in fact not happen very often (June 2007 #606, Oct 2007 #624, Oct 2008 #680). But when it does, what underlies this F2 or F3 "hybrid breakdown" or "outbreeding depression"?
There are a number of possibilities, but the experiments described here trace the problem to incompatibility between the nuclear and mitochondrial genomes in later generations of hybrids. This mechanism has been proposed before but not often examined experimentally.
The mitochondrial (mt) genome and the nuclear genome encode different polypeptide subunits of respiratory and other electron-transport enzymes. After a period of evolution in separate, isolated populations, molecular incompatibilities between subunits may develop which can reduce the viability of hybrids.
Breeding experiments were performed on
differentiated, wild populations of the marine copepod Tigriopus
californicus (Apr 2000 #44). F3 hybrids had low fitness. Maternal backcrosses fully restored fitness but paternal backcrosses did not. Mitochondria are inherited solely from the mother, and
so the authors conclude that "wild-type fitness requires the mtDNA and, at minimum, a full haploid nuclear genome from the same population." For potential aquacultural importance see
#678 below. cellison<&>ucsd.edu
681. Improved test for WSSV
Rapid and sensitive detection of white spot syndrome virus by loop-mediated isothermal amplification combined with a lateral flow dipstick. 2009. Jaroenram, W., W. Kiatpathomchai and T. Flegel. Molecular and Cellular Probes 23:65-70.
The shrimp disease group at Mahidol University, Thailand have developed a convenient new test for WSSV in P. monodon. It utilizes the LAMP procedure ("loop-mediated isothermal amplification") for amplifying the WSSV target gene under isothermal conditions with a set of four primers spanning six distinct sequences of the target gene, with all reagents working together in a single reaction tube. "Detection sensitivity was comparable to other commonly-used methods for nested PCR detection of WSSV." As a further advantage, assay time is reduced and the equipment is simpler, in that no thermal recycler is used and the detection method eliminates the somewhat complicated and dangerous electrophoresis step. wansika<&>biotec.or.th
Note that a group of Japanese researchers (2009. Lett Appl Microbiol 48:25-32) have developed a similar LAMP procedure which gives a quantitative estimate of the viral load of WSSV. itamit<&>cc.miyazaki-u.ac.jp.
680. Use four wild source populations to start your broodstock
Establishing a base population for a breeding program in aquaculture, from multiple subpopulations, differentiated by genetic drift: I. Effects of the number of subpopulations, heritability and mating strategies using optimum contribution selection. II. Sensitivity to assumptions on the additive genetic relationships of base animals. 2008. Holtsmark, M., G. Klemetsdal, A. K. Sonesson and J. A. Woolliams. Aquaculture 274:232-240 & 241-246.
These two papers will be useful to anyone who is planning to build an aquaculture base population from animals captured in the wild -- if that is still possible in this world -- or from established sub-populations. Candidate source populations will have differentiated by drift and selection, so a lot of potentially valuable genetic variation exists between the populations. The puzzle is how many subpopulations to include in a new aquaculture broodstock in order to capture this variation.
Optimal contribution selection was used in a simulation (See July 2006 #512, Sept 2007 #632). "It was concluded that sampling from at least four subpopulations was beneficial and that mating across subpopulations should start as early as possible." This is a nice, clear recommendation.
But there is a catch: a pedigree is used to estimate the additive relationship matrix between animals in the optimal contribution procedure. You don't have pedigrees for the wild source populations. The authors find that their solution
(four) is rather sensitive to the additive relationship matrix within and between these sources and you should try to estimate it as best you can, e.g. by markers (e.g. Jan 2002 #283) or even by geographical separation (as a surrogate for drift) and observation of phenotypic differences. Just assuming zero relationship isn't optimal and will increase the risk of losing alleles that will be valuable in the selection program.
679. A more efficient way to select for IPN resistance
Major quantitative trait loci affect resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar). 2008. Houston, R. D., C. S. Haley, A. Hamilton, D. R. Guy, A. E. Tinch, J. B. Taggart, McAndrew,
B.J. and S.C. Bishop. Genetics 178:1109-1115.
Selection for disease resistance in aquaculture is notoriously expensive and inefficient
when it is done on a family basis. You can't just select for surviving individuals because there is a risk of contaminating the broodstock. So, selection is based on relative survival in a set of 200 to 300 families -- just one measurement per family and you have to breed enough families to hold inbreeding to a manageable rate.
This is weak selection at best. Yet this breeding design is popular in aquaculture for lack of a better alternative. These authors have found one or more quantitative trait locus with a rather large effect on resistance to a viral disease of Atlantic salmon, infectious pancreatic necrosis (IPN). "The identified QTL can be applied in marker-assisted selection programs to improve the resistance of salmon to IPN and reduce disease-related mortality." This is potentially very helpful, especially in a species with such a long generation time. ross.houston<&>bbsrc.ac.uk
678. Pacific/Indian monodon differences approach species level
Microsatellite and mitochondrial haplotype diversity reveals population differentiation in the tiger shrimp (Penaeus monodon) in the Indo-Pacific region. 2008. You, E.-M., T.-S. Chiu, K.-F. Liu, A. Tassanakajon, S. Klinbunga, K. Triwitayakorn, de la Peña,
L.D., Li, Y.
Yu, H.-T. Animal Genetics 39:267-277.
Nuclear and mitochondrial genomes were looked at together in this study, and a similar pattern of geographical differentiation was found in both genomes. (This is by no means always the case.)
"Evidence from [microsatellites]... showed that the populations in the West Indian Ocean were unique, whereas other populations examined were partially admixed. In addition .. [it differentiates] three geographic groups in the Indo-Pacific region, i.e. the African populations, a population from western Thailand and the remaining populations as a whole." "Furthermore, three lines of evidence suggest that the genetic differentiation between the western Indian and Pacific populations might have been up to a subspecies level."
Note #682 above on nuclear/mitochondrial incompatibilities leading to hybrid breakdown in later generations of
Tigropius. In light of the data presented here this is something one might want to think about,
and perhaps make use of, when assembling monodon base populations for aquaculture. ayu<&>ntu.edu.tw
677. A single control gene for salmonid smoltification?
The genetic basis of smoltification-related traits in Oncorhynchus mykiss. 2008. Nichols, K. M., A. P. Edo, P. A. Wheeler and G. H. Thorgaard. Genetics 179:1559-1575.
Here we have a careful dissection of the genetic architecture of important smoltification traits including coloration, condition factor, growth and osmoregulation. The authors crossed two clonal lines and then looked at the association of polygenic traits with molecular markers in a doubled haploid offspring family (see June 2004 #481).
Interesting genes were found including one possible QTL (region of the genetic map) that affects many traits. It is possible that "either a single locus or multiple linked loci may play a role in the physiology associated with migration vs. residency". And, "Does the colocalization of continuous and binary traits suggest that a master regulatory region or gene may play a significant role in the integrated cascade of events that promote smoltification or residency?" My own guess -- that the answer is YES -- derives from the rapid, local, parallel adaptation of migration traits in separated natural populations. kmnichol<&>purdue.edu
676. Selecting two diseases for the price of one
Positive genetic correlation between resistance to bacterial (furunculosis) and viral (infectious salmon anaemia) diseases in farmed Atlantic salmon (Salmo salar). 2007. Ødegård, J., I. Olesen, B. Gjerde and G. Klemetsdal. Aquaculture 271:173-177.
It is good news when you hear that useful traits have a positive genetic correlation. This means, in general, that when you target one of the traits in a selection program the other will come along for the ride. The genetic correlation between furunculosis and ISA observed here (0.15) was not strong and was, in fact, only about half the correlation of non-heritable genetic, dam and common environment effects.
Never mind: heritabilities of both traits were moderately high and the information bodes well for domestication and/or deliberate selection programs. The analytical procedure goes well beyond simple Pearson correlation of separately-estimated breeding values. As the authors say, "Running bivariate threshold models in ASREML is not straightforward". They outline a procedure which (with some variance assumptions) gives a true bivariate estimate. See Dec 2002 #370, Aug 2003 #421. jorgen.odegard<&>umb.no
675. Strong non-additive genetic effects in WildxFarm hybrids
Genetic consequences of interbreeding between farmed and wild Atlantic salmon: insights from the transcriptome. 2008. Roberge, C., E. Normandeau, S. Einum, H. Guderley and L. Bernatchez. Molecular Ecology 17:314-324.
The transcriptome is the complete set of messenger RNA transcripts produced at a particular time, say 12 o'clock, by a cell or set of cells. As such it defines a space, or "ome", that evolves in developmental time.
(General relativity theorists, given a clock, also define "space" as the totality of events simultaneous with the clock striking 12.)
This research group at Laval has previously described interesting patterns of divergence in the transcriptome between farmed and wild Atlantic salmon (Sept 2006 #540) and two ecotypes of whitefish (June 2006 #503).
They move the programme along in this paper by comparing the transcriptomes of Norwegian wild salmon with an experimental second-generation backcross ((farmed*wild)*wild). Here we are in the realm of F2 hybrid breakdown where non-additive genetic effects (beyond hybrid vigour) become visible; see
"The range and average magnitude of those [transcription] differences was strikingly higher than previously described between pure farmed and wild strains." This phenomenon is discussed in terms of non-additive effects which are unpredictable under the ordinary quantitative genetic theory deployed in selection programmes and evolutionary G matrix investigations
(such as Oct 2001 #245 and #673 below).
The implication is that escaped farmed salmon which hybridize with wild locals will have a larger genetic influence than previously thought. This is further presumed to be a bad thing. "This suggests that interbreeding of fugitive farmed salmon and wild individuals could substantially modify the genetic control of gene transcription in natural populations exposed to high migration from fish farms, resulting in unpredictable and potentially detrimental effects on the survival of these populations." christian.roberge<&>giroq.ulaval.ca
674. The best heritability estimate from full- and half-sib designs
Comparing sire and dam estimates of heritability: jackknife and likelihood approaches. 2008. Roff, D. A. Heredity 100:32-38.
Everyone is fond of the classic half-sib design in which sires are mated to several dams, and heritability is estimated by nested analysis of variance or, more frequently nowadays, by REML mixed model estimate of variance components.
The sire and dam variance components provide three estimates of heritability: the sire, the dam and the average of the two (called the genotypic estimate). The latter two
estimates are influenced by non-additive effects and are often less interesting to breeders who are mainly concerned with designing a selection program.
This paper reminds us that the genotypic estimate has a considerably smaller standard error. It then goes on to examine jackknife and maximum-likelihood procedures for estimating dominance and/or maternal effects. Such estimates can be used for correction and are of course interesting in their own right. The author comes to the conclusion that the traditional variance component analysis of this design is actually preferable to the animal model (with a well balanced data set, presumably) because of its greater accuracy, precision and lower standard error.
"I suggest that all three heritability estimates should be reported and either the jackknife or likelihood method be used to test for a difference between the sire and dam estimate. If the difference is significant, one has evidence of non-additive effects and the sire estimate is preferred. If the sire estimate exceeds the dam estimate, then one can use the genotypic estimate because non-additive effects will increase the dam estimate not the sire estimate." derek.roff<&>ucr.edu
673. Recognizing and measuring local adaptation of fitness-related traits
Effects of selection and drift on G matrix evolution in a heterogeneous environment: a multivariate QST–FST test with the freshwater snail Galba truncatula. 2008. Chapuis, E., G. Martin and J. Goudet. Genetics 180:2151-2161.
If you are responsible for the genetic health of a small population you need to think about random genetic changes and also -- or especially -- the effects of selection.
Deliberate, artificial selection (such as an aquacultural broodstock selected for rapid growth) is generally predictable for a few generations when you have information on the selection differential (on growth) plus the phenotypic and genetic variances (of growth). But what of populations that are managed for conservation rather than production? Here selection is inadvertent rather than deliberate, the magnitude and direction of selection differentials can in most cases only be guessed at, and the effects are expected to be bad. Bad, because the aim is to keep the population adapted to its natural environment and prevent adaptation to the temporary circumstances of captive breeding.
This paper on aquatic snails has many interesting aspects but the one I focus on is the procedure for combining two different kinds of genetic information to recognize and measure selection. The genetic data are, on the one hand, microsatellite allele frequencies and on the other hand, genetic variances and covariances of phenotypic traits.
Divergence in microsatellite frequencies among populations is assumed to result from neutral drift. Phenotype divergence is caused both by drift and selection. Combining the two kinds of information allows one to isolate and measure selection.
The procedure as described in this paper is less straightforward than most GST-FST comparisons (e.g. Jul 2006 #515), not least because the authors are so conscientious about applying scaling transformations and other adjustments to ensure that their data meet the assumptions of the statistical analysis. With one exception, familiar population genetic and multivariate procedures are used (multivariate analysis of variance, principal component analysis etc.) The exception is a new neutrality test for the evolution of the genetic variance/covariance matrix which is presented in a companion paper (Genetics 180: 2135-2149, 2008). This new test is a multivariate extension of earlier GST-HST comparison procedures. The analysis is hierarchical; groups of populations inhabiting different habitats are compared.
The global interpretation of the results for these wild snail populations has obvious parallels in conservation and aquaculture. There are two types of habitats (always wet vs. seasonally dry). Traits expressed early in life (including growth) are selected towards the same optima in all populations. Traits expressed later (including fecundity and age at maturity) are selected similarly among populations within the same habitat, but differently between habitats.
The relevance of this work to aquatic broodstock management
may be that it offers a plausible way to monitor changes in genetic diversity and adaptation during successive generations.
672. Controversial genetic changes caused by fishing
Letters: The role of fisheries-induced evolution. 2008. Several authors, Science 320:47-50.
There has been a lot of speculation over the years about the evolutionary effect of size-selective fishing (reduction in size and age at maturation of targeted stocks, for instance). The generality of the effect is far from being proved despite some good analytical and experimental work (e.g. Aug 2002 #345, Jul 2006 #508).
A couple of years ago participants in a Science Policy Forum (Science Magazine 23 November 2007, p.1247) took as fact that fisheries-induced evolution (FIE) is the most important cause of change in biological (life-history) characteristics of heavily fished marine populations. They then went on to propose that "evolutionary impact assessments" be used as a precautionary measure in managing fisheries and other living resources that have the potential to evolve.
The letters cited here say this is premature. In fact the letters are rather scathing about selective use of evidence in the 2007 proposal. A reply is also published in this issue of Science and reading the whole unseemly mess is a good way to bring yourself up to date on the controversy.