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.

600.  News Flash. A usable procedure for analysing the genetic effects of social interaction 
         Multilevel selection 1: quantitative genetics of inheritance and response to selection. 2007. Bijma, P., W. M. Muir and J. A. M. Van Arendonk. Genetics 175:277-288. 
         This remarkable pair of papers (see also #597, below) shows us how interaction among individuals can be built into quantitative genetic models for the purpose of variance analysis, estimation of breeding values and optimization of selection. 
         One type of interaction, namely competition for food, has an influence of often elephantine proportions but with a few exceptions it is totally ignored. A quantitative genetic analysis which ignores competition when it exists will often give the wrong answer -- wrong heritabilities, wrong covariances, wrong indicators for practical decision-making. 
         These papers are based on an earlier concept called "multi-level" selection, meaning selection which occurs at the group rather than individual level. Groups may consist of individuals which are related by their pedigrees but the concept also encompasses individuals which associate with each other in other ways, such as proximity in relation to food sources. 
         The phenotype of an individual is considered to consist of two components, a direct component which depends on the individual's own genotype and environment, and an indirect component which depends on the phenotypes of all the other individuals with which it is associated. Similarly, the estimated breeding value of an individual includes a direct component (DBV, which corresponds to the familiar EBV) and an associative component (SBV) which is a function of other members of the group. (See Nov 2006 #563.) DBV and SBV are both heritable and both respond to selection, possibly in different directions. 
         Negative correlation between the components leads to the idea of heritable competition, which reduces the total heritable variation available for selection. Equations for heritability, selection intensity and response (for one trait) are developed in the first paper. In the second paper (#597) the animal model is extended to account for associative effects. Lucid and comprehensive text accompanies the math. Estimates of DBV, SBV and their covariance can be obtained from statistical packages which are capable of REML/BLUP analyses, such as GENSTAT or ASREML. bmuir@purdue.edu 

599.  WSSV uses shrimp genes to help itself replicate 
         WSSV has successfully annexed a shrimp STAT to enhance the expression of the immediate early gene (ie1). 2007. Liu, W., Y. Chang, A. Wang, G. Kou and C. Lo. Journal of Virology 81:1461-1471. 
         There exists a group of genes called JAK-STAT which transport signaling molecules such as growth factors into the nucleus. The gene complex is important in many aspects of cell growth, survival and differentiation. Activation of certain JAK-STAT genes is also part of the vertebrate immune response. It is involved in the anti-viral response of insects as well, and one might expect that it would be part of the shrimp anti-viral response. But this paper suggests that the defense may be turned back on itself by IHHN virus. 
         There exists another group of genes called immediate-early (i.e. IE) which are activated transiently and rapidly in response to a wide variety of cellular stimuli. They represent a standing response mechanism that produce DNA-binding proteins, receptor subunits etc. in the first round of response to extra-cellular events. Both gene classes are found in organisms as diverse as nematodes and humans. Replication of White Spot Virus, WSSV, is easily triggered in shrimp by a variety of environmental stresses including temperature. Three IE genes have recently been found in WSSV. 
         This interesting paper shows that one of these viral IE genes "annexes" a JAK-STAT pathway in P. monodon and uses it to enhance the expression of viral genes. The WSSV turns the host defense mechanism around so that it speeds up viral replication. Lo: gracelow@ntu.edu.tw. 

598.  Small salmon populations with high genetic diversity 
         Asymmetric gene flow and the evolutionary maintenance of genetic diversity in small, peripheral Atlantic salmon populations. 2005. Consuegra, S., E. Verspoor, D. Knox and C. García de Leániz. Conservation Genetics 6:823-842. 
         The authors compared large Scottish populations with small populations on the Iberian peninsula to see how population size might affect genetic diversity in Atlantic salmon. Two measures of diversity were used, heterozygosity and allele number.
         Surprisingly, the small populations were just as rich genetically as the big ones; they hadn't lost diversity during 50 years of marked population decline. The authors ascribe this, basically, to gene flow among the populations. "Although there are several explanations for such results, microsatellite data and physical tagging suggest that high levels of dispersal and asymmetric gene flow have probably helped to maintain genetic diversity in these peripheral populations, and thus to avoid the negative consequences of inbreeding." See Feb 2004 #464 for trout metapopulation diversity. sonia.consuegra@st-andrews.ac.uk 

597.  Social interaction affects genetic parameters relating to growth 
         Multilevel selection 2: estimating the genetic parameters determining inheritance and response to selection. 2007. Bijma, P., W. M. Muir, E. D. Ellen, J. B. Wolf and J. A. M. Van Arendonk. Genetics 175:289-299. 
         When interactions among individuals affect the value of a trait (such as growth), then selection at the group level as well as the individual level is required to make use of all the heritable variation. The analyses and models currently employed in aquaculture and evolutionary genetics do not, for the most part, make use of (or even detect) the genetic variation concealed in social interaction. This note should be read in conjunction with #600, above. 
         This (second) paper presents "statistical methodology to estimate the genetic parameters of traits affected by interactions, for interactions among any number of individuals in general nondesigned populations with any degree of relatedness among individuals." "The [method] does not require a specific experimental design; groups may be composed of any combination of related and/or unrelated individuals and may vary in size."
         Here are a few quotations, collected from both papers, which suggest how important this analysis may be for aquaculture and genetic conservation. 
         * "In stark contrast to classical theory, the total heritable variance ... can in principle exceed the observed phenotypic variance."
         * Poor response to selection (despite abundant heritable variation) would be expected and has often been observed "in cases where associates compete for limited resources in confined rearing, such as with growth under restricted feeding in poultry, mice, fish, or pigs". 
         * “… interaction among individuals involves additional heritable components (SBV), which may increase the heritable variation and the potential of populations to respond to selection …. This extra heritable variation does not surface in conventional data analyses … we show that the total heritable variation in survival days in a population of laying hens is threefold of the amount estimated using classical methods. In other words, two thirds of the heritable variation in that population is hidden in classical analyses.”
         * “Classical models of interaction between species … predict that as the number of species in an ecosystem increases, the stability of the system decreases. … What is missing from this debate is a critical genetic factor….the approach taken here may be extended to interaction between individuals of different species.” bmuir@purdue.edu 

596.  You should try to preserve MHC variability in hatcheries 
         Natural selection acts on Atlantic salmon major histocompatibility (MH) variability in the wild. 2007. de Eyto, E., P. McGinnity, S. Consuegra, J. Coughlan, J. Tufto, K. Farrell, H.-J. Megens et al. Proceedings of the Royal Society (B) 274:861 - 869. 
         Genetic variation in the major histocompatability complex (MHC; a component of the vertebrate immune system) plays an important role in the resistance of salmonids to diseases and parasites. Exactly how this works is not yet clear and probably varies from population to population. 
         Either or both of two explanations may apply: (1) genetic variation per se increases resistance (heterozygote advantage) and/or (2) specific genes (alleles) confer resistance to specific pathogens. Explanation (2) implies that the direction of selection must vary over time or allele frequency, or both. The recent literature describes probable examples of both mechanisms operating in natural, aquacultural and experimental environments. (See June 2006 #501, Dec 2002 #369 & #370 and also #589 below) 
         This paper describes an aggressive field experiment, in Ireland, in which eggs from one watershed were introduced into another watershed which is afflicted with aquaculture and which has a history of disease outbreaks. Parental and (after 6 months) offspring gene frequencies were estimated at two class II MHC, one class I MHC and eight microsatellite markers. 
         The authors considered the microsatellites and the class I to be a sort of control, i.e. unlikely to be under selection in the given situation. They write out a number of linear models for the effects of heterozygote advantage, allelic advantage etc. on gene/genotype frequencies and test the effects for statistical significance. 
         Both of the class II MHC loci and only one of the other nine loci showed significant statistical evidence for selection according to their models. Given that their procedure finds three significant effects, this combination has a probability of around 0.05 if the two class II loci are truly independent and the class I is considered neutral a priori. The authors suggest that selection for specific alleles is a more likely explanation of their results than is generalized heterozygote advantage. "We conclude that natural or hatchery populations have the best chance of dealing with episodic and variable disease challenges if MH genetic variation is preserved both within and among populations." elvira.deeyto@marine.ie 

595.  RFLP works well for identifying tilapia species 
         DNA riboprinting analysis of Tilapia species and their hybrids using restriction fragment length polymorphisms of the small subunit ribosomal DNA. 2007. El-Serafy, S. S., N.-A. H. Abdel-Hameid, M. H. Awwad and M. S. Azab. Aquaculture Research 38:295-303. 
         Three classification procedures were applied to tilapia in the lower Nile River, north of Cairo. The conventional morphology of the species (procedure 1) is very similar, making them hard to distinguish. Meristics, especially lateral line scale count (procedure 2) also had problems distinguishing the four major species or species flocks: Oreochromis niloticus, O. aureus, Sarotherodon galilaeus and Tilapia zillii. Procedure 3 was to use restriction enzymes to generate distinguishing "riboprints" of small subunit ribosomal DNA fragments for each species. Two hybrid individuals were found. RFLP procedures are comparatively easy to carry out and this paper should be useful in practice as well as being helpful in clarifying the taxonomy. nassrabdelhamide@yahoo.com 

594.  Another example of heritable, temperature-dependent sex ratio? 
         Patterns of sex ratio response to water temperature during sex determination in honmoroko Gnathopogon caerulescens. 2006. Fujioka, Y. Fisheries Science 75:1034-1041. 
         The small fresh-water cyprinid Gnathopogon caerulescens lives in Japan. Its sex ratio is dependent to a considerable extent on temperature, with higher temperatures producing more males. Evidence presented here points to genetic variation in the response of sex ratio to temperature in families generated by crossing wild-caught parents. See Oct 2006 #550 for selectable temperature-sensitive sex ratios in tilapia. The authors also suggest that "phenotypic males (XX-males) exist in nature, probably as a result of sex change from genetic females caused by [high temperature]". fujioka-yasuhiro@pref.shiga.lg.jp 

593.  A "big picture" view of inbreeding shows that it is a big problem 
         Realistic levels of inbreeding depression strongly affect extinction risk in wild populations. 2006. O’Grady, J. J., B. W. Brook, D. H. Reed, J. D. Ballou, D. W. Tonkyn and R. Frankham. Biological Conservation 133:42-51. 
         Essentially all of the available information on the effect of inbreeding on wild populations of birds and mammals has been pulled together here in a meta-analysis of observational data and computer simulation using the VORTEX program. 
         "An average overall effect of 12 diploid lethal equivalents was found across the life-history of the species in the meta-analysis. In the stochastic computer projections, 12 diploid lethal equivalents of inbreeding depression (with purging) decreased median times to extinction by an average of 37%." (Note that "lethal equivalents" is a measure of inbreeding depression estimated from the regressions of survival and fecundity on the inbreeding coefficient, F.) 
         This level of inbreeding depression is much higher than the level used in most extinction modeling, and it has a profound effect. The authors note that inbreeding has significant implications for management priorities. Merely improving habitat and taking other non-genetic measures to improve reproductive success may not be enough to arrest population decline. It may also be necessary to conduct a "genetic rescue" as well, that is, introduce unrelated genetic material from elsewhere. See genetic rescue Oct 2006 #546. jogrady@bio.mq.edu.au 

592.  How to cope with missing RAPD and AFLP bands 
         Analysis of multilocus fingerprinting data sets containing missing data. 2006. Schlüter, P. M. and S. A. Harris. Molecular Ecology Notes 6:569-572. 
         Genetic inferences based on procedures such as random amplified polymorphic DNA (RAPD) or amplified fragment length polymorphism (AFLP) are susceptible to errors caused by missing data, that is, missing bands in the "fingerprint". Bands may be absent due to "limitations of band detection, stochastic error, restriction amplification failure, and absence of a target locus or misinterpretation". So is there a better way to handle the problem than simply to ignore it? This paper presents "a method [for filling in the gaps] that uses random assignments of band presence–absence to the missing data for analyses based on pairwise similarity and Shannon's index". 
         The program is available from http://homepage.univie.ac.at/philipp.maria.schlueter/famd.html . The paper includes a useful discussion of the effect of missing fingerprint data and how to detect and cope with it in your data set. philipp.maria.schlueter@univie.ac 

591.  Environmental stress speeds up the purging of deleterious genes 
         Negative environmental perturbations may improve species persistence. 2006. Robert, A. Proceedings of the Royal Society (B) 273:2501-2506.
         This theoretical paper describes an effect which is at surprising at first sight but which makes perfect sense when you think about it. We expect that fluctuations in the environment will increase the depressive effects of inbreeding in small populations. (Because inbreeding depression becomes more severe when environmental stress increases.) The rate of purging of deleterious recessive alleles should, therefore, also increase in such situations because of the increased selection pressure. The author has constructed a simulation model which incorporates recessive mutations and random fluctuations in environmental stress, and finds that "negative perturbations may paradoxically improve middle- and long-term species persistence for realistic frequency of occurrence and severity distribution". See Mar 2003 #395 on purging. arobert@mnhn.fr 

590.  Sex determining genes in hybrid tilapia 
         Amh and Dmrta2 genes map to tilapia (Oreochromis spp.) linkage group 23 within QTL regions for sex determination. 2006. Shirak, A., E. Seroussi, A. Cnaani, A. E. Howe, R. Domokhovsky, N. Zilberman, T. D. Kocher et al. Genetics 174:1573-1581. 
         Hybrids between tilapia species are sometimes used in aquaculture because of their male-skewed sex ratios. Eleven genes which are known to be important for sex determination in other vertebrates were mapped to linkage groups, i.e. to chromosomes or long sections of chromosomes, in a hybrid family of tilapia (aureus X niloticus). 
         "Map positions of 2 of the 11 genes overlapped with two of the four previously reported QTL for sex determination in tilapia species and their hybrids." But as of now, the tally is: nine key vertebrate sex-determination genes and two known QTL which don't match up in tilapia. As the authors point out, " New QTL for sex determination may emerge in hybrids due to the interactions of alleles from different species", especially with autosomal genes. Also, the environment must play a regulatory role and there is known to be genotype X environment interaction for this (see Oct 2006 #550). See Jun 2006 #498 for genetic sex determination in aureus, . vlaqua@volcani.agri.gov.il  

589.  High MHC diversity is associated with high parasite diversity in cyprinids 
         MHC variability, life-traits and parasite diversity of European cyprinid fish. 2006. Šimková, A., E. Ottová and S. Morand. Evolutionary Ecology 20:465-477. 
         Fourteen species belonging to the family Cyprinidae are included in this analysis, which is based on parasite studies previously published by the same authors. Exons of the MHC class II beta chains from multiple individuals of each species were sequenced. The authors found that nucleotide diversity at one of the exons was positively correlated with parasite diversity at the species (!) level, and adult mortality rate was also positively correlated with parasite diversity. It appears that the data on parasite load come from studies previously published by the same authors and mortality data are taken from the literature. 
         "Our results suggest that fish species, of which populations are exposed to high parasite pressure, in terms of high parasite species richness, maintain a high genetic diversity of the exon 2 of the MHC genes (presenting the peptide binding regions), allowing them to decrease their natural mortality rate." See #596 above. simkova@sci.muni.cz