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.

465.  "SPF" shrimp are carriers of WSSV!
         Identification of white spot syndrome virus latency-related genes in specific-pathogen-free shrimps by use of a microarray. 2003. Khadijah, S., S. Y. Neo, M. S. Hossain, L. D. Miller, S. Mathavan and K. J. Journal of Virology 77:10162 - 10167.
         This paper from Singapore is intriguing and somewhat worrisome. The authors developed a WSSV-specific DNA microarray (See Dec 2003 #441 on microarrays) to look at the expression of viral genes in supposedly specific pathogen free (SPF) Penaeus monodon. The SPF shrimp, developed by the BIOTEC group in Thailand and grown there under biosecure conditions for 6 generations without a disease outbreak, passes the standard commercial PCR test for absence of WSSV.  Microarrays were constructed with viral DNA extracted from WSSV-infected shrimp. The arrays included approximately 3000 clones and were developed in a sophisticated university research laboratory. Flooding the arrays with cDNA from infected shrimp revealed the expression of many WSSV genes, as expected. However, cDNA from the putative SPF shrimp revealed that at least three WSSV genes were functioning in them, too. "... hybridization with the SPF sample revealed exceptionally high signal intensities from some elements on the array, indicating that these shrimps had been carriers of the virus and were actively expressing viral genes."
         The WSSV genes expressed strongly in the SPF shrimp were not among those expressed strongly in infected shrimp, so the virus is behaving differently in these host environments. Examination of various sequence motifs lead the authors to suggest that the genes may be transcription factors involved in latency and pathogenesis of the virus. WSSV viral genomes have been found in asymptomatic P. monodon before, but never in a biosecure SPF population. The commercial single-step PCR, which has a detection threshold of about 20 viral genomes, may not be sensitive enough to see this stage of latent infection. The microarray is an exciting new tool for investigating (and perhaps selecting) genes involved in viral pathogenesis. kwang@tll.org.sg .

464.  Extinction-recolonization genetics of a trout metapopulation
         Long-term temporal changes of genetic composition in brown trout (Salmo trutta L.) populations inhabiting an unstable environment. 2003. Østergaard, S., M. M. Hansen, V. Loeschcke and E. E. Nielsen. Molecular Ecology 12:3123-3135.
         Multiple populations of trout and salmon inhabiting small rivers which drain into the sea are often arranged side by side along a coastline. Some rivers have no trout while some do, and some rivers have no water in them during particularly dry summers. The situation is stable in the sense that there are always trout somewhere in the general area. However it is unstable in the sense that individual rivers may be trout-free from time to time. From a conservation point of view we wish to know whether we are looking at (a) a large population which has geographically persistent sub-populations (isolated individual rivers), or (b) at a large "metapopulation" in which riverine populations periodically go extinct and are recolonized from nearby rivers.
         The distinction between (a) and (b) is important. If individual riverine populations are persistent, perhaps because the fish can survive unnoticed at river mouths in bad years, the genetic differences among populations may be adaptive, so that each is worth conserving as an evolutionarily significant population unit. But if the rivers are components of a larger metapopulation then the genetic peculiarities of any particular population reflects nothing but founder sampling effects and drift, and are of no adaptive utility. The peculiarities may even be of negative adaptive utility owing to accidental genetic fixation of deleterious alleles.
         Bornholm is an island in the Danish Baltic sea. Many small rivers run down to the coast from a central highland. Trout scale and otolith samples from these rivers have been collected and preserved from the late 1940s to the present. Analysis of microsatellite diversity in historical and current samples leads the authors to conclude that the rivers on Bornholm represent a metapopulation, not a population with a persistent geographical structure. "We suggest that Bornholm trout represent a metapopulation where the genetic structure primarily reflects strong drift and gene flow, combined with occasional extinction-recolonization events." The authors make the following comment about conservation strategies. "… if a river is devoid of trout this may be a natural phenomenon, and it is still important to protect the habitat as it may later become recolonized. … specific behavioural adaptations to low water levels and low saline marine environments exhibited by trout from the Bornholm and Gotland islands stresses the importance of conserving these population systems as a whole[emphasis added]. This goal is best achieved by conserving as many filled and empty patches, i.e. rivers, as possible." But the nice thing about a metapopulation is that you don't need to conserve all the components.
         See Oct 2000 # 115, Mar 2003 #394 for a contrasting case in New Zealand where populations of introduced salmon appear to have evolved river-specific adaptations. mmh@dfu.min.dk

463.  The schedule of inbreeding affects inbreeding depression
         The influence of variable rates of inbreeding on fitness, environmental responsiveness, and evolutionary potential. 2003. Day, S. B., E. H. Bryant and L. M. Meffert. Evolution 57:13-14-1324.
         This interesting experiment on house flies shows that the rate and schedule of inbreeding interact with the level of inbreeding to determine inbreeding depression. Populations of flies from the same source (a dump in Texas) were inbred quickly, slowly or intermittently to the same inbreeding level, F=0.37. After this inbreeding had been achieved, the fitnesses of the populations were compared and so was their ability to evolve tolerance to a more stressful environment (temperature fluctuation).
         The control population C, which wasn't inbred at all, had the highest allozyme diversity at the end of the experiment and also maintained the highest capacity to evolve.  Population FS, which was rapidly inbred to F=0.37 during four successive generations and then allowed to expand, had the lowest final fitness and showed essentially no ability to respond to the experimental evolutionary challenge. Population PC, which underwent alternating episodes of strong and zero inbreeding, did slightly (really, not much) better than FS. This PC protocol mimicked a serial "founder-flush" regime in a natural population. PC inbreeding occurs commonly in aquaculture because of the practice of founding of new aquacultural broodstocks from existing ones (e.g. Jan 2000 #4).
         The most benign inbreeding scheme in this experiment was the slow and steady SL protocol, in which the population maintained a constant effective population number during the inbreeding. This was the only inbred population which retained some of its evolutionary potential. (Evidently the bottlenecking did not convert useful amounts of epistatic variance into additive genetic variance; Jun 2001 #207 & Oct 2000 #116.) Slow inbreeding is the objective in well-conducted aquaculture and genetic conservation programs -- where, of course, the inbreeding damage may already have been done before the programs smartened up. The authors noted a lot of variation among replicates, reflecting the chance sampling of alleles during the inbreeding and flushing phases (see May 2003 #402). See also Feb 2000 #17, Mar 2002 #300 for other papers on houseflies as experimental models for genetic conservation. staceybday@yahoo.com  

462.  Successful growth selection in Kuruma shrimp
         Comparative growth of selected and non-selected Kuruma shrimp Penaeus (Marsupenaeus) japonicus in commercial farm ponds; implications for broodstock production. 2004. Preston, N. P., P. J. Crocos, S. J. Keys, G. J. Coman and R. Koenig. Aquaculture 231:73-82.
         This paper describes a simple mass selection program which appears to have worked well. The selected breeders came from the largest 10% of a (presumably equal-aged) population in farm ponds. The offspring of the selected animals were 9% - 14% larger than contemporaneous controls at first harvest. After more generations of non-selective rearing under controlled conditions, the descendants of the selected parents were 14% larger than controls.
         An important finding of this study, emphasized by the authors, is that "stocks of P. japonicus, initially selected for high growth in farm ponds and then reared from egg to adult for three generations under controlled conditions in tanks, retained their capacity for superior growth when returned to farm ponds. This indicates that selected lines, maintained in bio-secure conditions, could provide reserve stocks for re-establishing superior lines of farm stocks. In some circumstances, this may be an appropriate strategy for producing all the progeny required for stocking ponds." nigel.preston@csiro.au

461.  Exploited cod population changes its genetic identity
         Temporal analysis of archived samples indicates marked genetic changes in declining North Sea cod (Gadus morhua). 2003. Hutchinson, W. F., C. van Oosterhout, S. I. Rogers and G. R. Carvalho. Proceedings of the Royal Society of London (B) 270:2125-2132.
         A cod population off the English Yorkshire coast (Flamborough Head) fluctuated over a five-fold range between 1954 and 1998, and now has a somewhat different genetic identity than when it started. Microsatellite data were obtained from preserved otoliths covering the whole period. The number of distinct alleles, considered to be the most sensitive measure of diversity change, fell about 25% and then went back up again.  "Furthermore, estimates of genetic differentiation (FST and RST) showed a significant divergence between 1998 and earlier samples. Data are consistent with a period of prolonged genetic drift, accompanied by a replacement of the Flamborough Head population through an increased effective migration rate that occurred during a period of high exploitation and appreciable demographic and phenotypic change."
         Cod is one of a group of species in which the effective population size, which determines the rate of drift, may be 5 or 6 orders of magnitude higher than the census size (Jan 2003 #385, Aug 2003 #423). As a result of all this, the Flamborough Head population disappeared as a distinctive genetic population then re-emerged as a different one. The population size continues to fall. w.f.hutchinson@hull.ac.uk  

460.  Heterozygous salmon grow faster and mature earlier
         Allozyme heterozygosity, date of first feeding and life history strategy in Atlantic salmon. 2003. McCarthy, I. D., J. A. Sánchez and G. Blanco. Journal of Fish Biology 62:341-357.
         Fish in this experimental study which were more heterozygous than the average started feeding earlier (owing to more rapid embryonic development) and grew faster than less heterozygous fish. Furthermore, "a significantly higher proportion adopted the early freshwater maturation (age 0+ years, male fish) or early migrant (age 1+ years, mainly female fish) strategies compared to late first feeding Atlantic salmon".  Age and size at maturation are of great interest both for aquaculture and conservation of local populations at risk of extinction.
         The authors explain their observations using a threshold model, in which a developmental commitment to early maturation is made late in the summer by fish that are relatively large and on a fast-growth trajectory. The authors refrain from speculating on the nature of the causal relationship between heterozygosity and growth. See Jan 2002 #276 for a paper which discusses the superior fitness of heterozygous trout. i.mccarthy@bangor.ac.uk  

459.  Wild and domesticated shrimp respond differently to different diet
         Effect of a size-based selection program on blood metabolites and immune response of Litopenaeus vannamei juveniles fed different dietary carbohydrate. 2004. Pascual, C., L. Arena, G. Cuzon, G. Gaxiola, G. Taboada, M. Valenzuela and C. Rosas. Aquaculture 230:405-416.
         There hasn't been nearly enough work on the interaction between genetics and diet in aquaculture; in particular we know practically nothing about the way selection for fast growth might affect dietary requirements. It certainly has an effect in other domestic animals and plants where, generally speaking, the superior growth rate of selected genotypes is only realized in superior nutritional environments.
         This paper reports a study of the effect of high carbohydrate (44%) and low carbohydrate diets (3%) on lactate, protein other blood metabolites and hemocyte levels in the shrimp Litopenaeus vannamei. (Dietary protein levels were 30% and 66% respectively). The metabolic variables are indicators of immunocompetence as well as growth. The carbohydrate effect was very different in wild and domesticated shrimp. "Wild shrimp showed a direct relation between dietary CHO [carbohydrate] and lactate, protein and hemocyte levels indicating that dietary CHO was used for protein synthesis via transamination pathways." However, in shrimp that had been domesticated (and selected) for 6 generations, the metabolic indicator variables were lower in the high carbohydrate diet. "These results demonstrate that during size-based breeding programs other metabolic process than CHO catabolism can be selected. The incapacity of shrimp to use dietary CHO [to produce protein, including immunoproteins and peptides] could limit protein reduction of diets and limit the efforts of the shrimp industry to be ecologically and environmentally profitable." crv@hp.fciencias.unam.mx  

458.  Farmed fish and their hybrids are inferior to wild salmon
         Fitness reduction and potential extinction of wild populations of Atlantic salmon, Salmo salar, as a result of interactions with escaped farm salmon. 2003. McGinnity, P., P. Prodöhl, A. Ferguson, R. Hynes, N. Ó Maoiléidigh, N. Baker, D. Cotter et al. Proceedings Royal Society of London (B) 270:2443-2450.
         This is a careful and thorough study of the fitness of Irish farmed salmon (originally a Norwegian stock) and native Irish salmon, in an Irish river. Pure wild, pure cultivated, F1 hybrids and their F2 offspring and F1 backcrosses were evaluated for growth, survival and homing behaviour. Survival and homing were worse in the farmed fish, and in all the types of hybrids, than in the wild fish. The wild fish grew more slowly, however, and the authors predict that size-dependent competition might cause introgression of inferior farmed genes into the wild population. "[The authors] demonstrate that interaction of farm with wild salmon results in lowered fitness, with repeated escapes causing cumulative fitness depression and potentially an extinction vortex in vulnerable populations."  See Jun 2001 #210 for extinction vortex, See Nov 2000 #130, Nov 2001 #260, Feb 2002 #287 for other papers which report reduced fitness in wild/farm salmonid hybrids. But see Aug 2003 #416 for evidence of genetic swamping possibly without accompanying loss of natural fitness.
         The F2 hybrids in this paper (offspring of hybrids mated among themselves) are particularly interesting, because although it is rarely studied, reduced performance in this generation can be a signal of outbreeding depression (e.g. May 2003 #400) and/or breakdown of co-adapted sets of alleles during recombination (these are not quite the same phenomenon). The authors invoke coadaptation to explain the very low survival of F2 hybrid eggs. However, there are some difficulties in believing that there is anything more here than additive gene effects. In particular, if this coadaptation does reflect the evolutionary divergence of aquacultural populations from populations exposed to natural selection, it is odd that its effects are seen only at the earliest developmental stage (pre-eyespot) when emergence, early feeding, predator avoidance, agonistic interaction, handling stress, site imprinting, homing behavior, appetite, feeding latency, satiation, mate choice, fecundity and spawning behaviour - the components of domestication selection people worry about  - are somewhat irrelevant. The data show no sign of any F2 hybrid inferiority which only begins to be expressed later in life, i.e. in behavioral or other traits which affect survival from swim-up through to smolt. Marine survival data for the F2 hybrids were not available, but eyed-egg-to-smolt survival was not inferior and is probably much higher in F2 hybrids than in wild fish.
         If breakdown of co-adaptation is indeed the cause of early embryo mortality it makes more sense (to me) to ascribe it to ancient, river-specific differences rather than to the recent selective effects of aquaculture. By extension, the inferiority of these farmed and hybrid fish may be due to their "foreign-ness", possibly "Norwegian-ness", as much as to their "farmed-ness". Discovering the cause of the F2 inferiority is important in the context of strategies for re-introducing fish into extirpated rivers, genetic rescue of remnant populations (May 2000 #51, Aug 2002 #341,May 2003 #400) etc. as well as for containment issues in aquaculture. a.ferguson@qub.ac.uk  

457.  Genetic map for Clarias
         A preliminary genetic map of walking catfish (Clarias macrocephalus). 2004. Poompuang, S. and U. Na-Nakorn. Aquaculture 232:195-203.
         The authors have located 134 AFLP marker loci on 31 linkage groups. The average spacing is 17 cM which makes it a useful framework for further linkage mapping and QTL marking in this important aquacultural species. supawadee.p.@ku.ac.th  

456.  Sea-ranched trout are less involved in social interactions
         Growth and social interactions of wild and sea-ranched brown trout and their hybrids. 2003. Petersson, E. and T. Järvi. Journal of Fish Biology 63:673-686.
         This laboratory study of wild, sea ranched (domesticated) and hybrid trout found several traits that differ among the groups. Firstly, the ranched trout grew somewhat faster. Secondly, the wild trout were in general more aggressive. Thirdly, the results for hybrids were sensitive to which way the hybridization was made, i.e. whether the wild parent was male or female. An interesting multivariate framework for analysing behavioral variables is developed in the paper.
         The experiment was designed to try to break the feedback loop in which animals which are initially faster-growing (for any reason) become socially dominant owing to their larger size, and then exploit their dominance to maintain their superior growth rate. It was predicted long ago that in a well-managed aquacultural environment, playing social dominance mind-games is not an evolutionarily stable strategy. If food is provided "fairly" in a way that does not reward competitive fish with more food, then fish which engage in energy-wasting aggression and/or lose their appetites when they spot someone bigger than themselves will have a growth disadvantage. If the aquaculturalist selects breeders from among the larger animals then there should be an evolutionary trend towards "uninvolved" phenotypes with reduced agonistic behavior. Something of the sort may have happened here. See other wild domesticated comparisons by the same authors: Sep 2001 #234 physiological response to stress, Aug 2003 #416 introgression of farmed into wild populations. erik.petersson@fiskeriverket.se  

455.  A breeding plan for captive populations
         Minimizing inbreeding by managing genetic contributions across generations. 2003. Sánchez, L., P. Bijma and J. A. Woolliams. Genetics 164:1589-1595.
         Mating equal numbers of males and females and producing two offspring per pair still seems to be the best way to minimize inbreeding and loss of genetic diversity in a controlled population. But what if it is impossible or un-economic to breed equal numbers of both sexes? The current consensus strategy (based on early work by Gowe et al., modified a few years ago by Jinliang Wang) is that each sire should be replaced by one of its sons and each dam by one of its daughters, with the exception that the dams which produce the sons have no other offspring and should be replaced by daughters of other dams. The Gowe-Wang strategy does somewhat increase the variance of female reproductive success, however.
         By addressing this problem the authors of this paper show that inbreeding can be further decreased. Their breeding strategy is too involved to be summarized here but is well explained and diagramed in the paper. With 2 females per male a randomly mated population (analogous to the haphazardly mated populations of aquaculture) accumulates inbreeding twice as fast as in their system. With an infinite number of females per male the rate of inbreeding is 50% higher in a randomly mated population than in the controlled breeding scheme proposed here.
         See Dec 2001 #270 on minimizing coancestry in early generations of a breeding program, Nov 2001 #261 for a general review of inbreeding-avoidance strategies. leopoldo.sanchez@orleans.inra.fr  

454.  Sorting out the origins of hybrid populations
         Maximum-likelihood estimation of admixture proportions from genetic data. 2003. Wang, J. Genetics:747-765.
         The situation envisaged here is an ancestral population which subdivides into two populations. These evolve separately for a while, then mix and generate a hybrid population. Some time after the hybridization, samples are take from the parental and hybrid populations, all three of which are assumed to evolve in isolation except for the one-time hybridization event. The problem is to estimate (a) the relative contribution of the parental populations to the hybrid and (b) the amount of drift that has occurred in each population at various points in the above scenario. Obviously this is an important problem both for genetic conservation and aquaculture -- sometimes even important in a forensic context.
         The author discusses various previous attempts to solve it, which have generally ignored the effects of sampling errors and the drift of the parental populations. (See June 2002 #329.) The new maximum likelihood method is presented and shown to be considerably less biased and more robust to violations of the assumptions. "The proposed likelihood method also has features such as relatively low computational requirement compared with previous ones, flexibility for admixture models, and marker types. In particular, it allows for missing data from a contributing parental population." Software (entitled LEADMIX) for performing the analysis can be downloaded free from http://www.zoo.cam.ac.uk/ioz/software.htm. jinliang.wang@ioz.ac.uk