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.

333.  How many alleles would you find if you could count them all?
         Estimating the total number of alleles using a sample coverage method. 2001. Huang, S.-P., and B.S. Weir. Genetics 159:1365-1373.
         How many alleles are there at any particular locus in the population you are interested in? You won't know until every animal in the population has been analysed, which is usually impossible. This is analogous to the question, "how many species are there in a particular region?". With or without an underlying model that has some basis in ecological intuition or mathematical credibility, species abundance data from a small sample or geographical area are often extrapolated to predict total species diversity in a much larger area.
         This paper applies a similar idea to the problem of estimating the total number of alleles in a population which is too large to be completely sampled. It works well with a set of published data and in simulations that explicitly include the recurrent mutation, step-wise mutation and infinite allele models of allelic diversity. "Possible applications include improving the characterization of the prior distribution for the allele frequencies, adjusting the estimates of genetic diversity, and estimating the range of microsatellite alleles."  weir@stat.ncsu.edu 

332.  Normal male tilapia grow faster than supermales
         Influence of sexual phenotype and genotype, and sex ratio on growth performances in tilapia, Oreochromis niloticus. 2002. Aboubacar, T.A., B. Fauconneau, A. Fostier, J. Abucay, G. Mair, and J.-F. Baroiller. Aquaculture 207 (3-4):249-261.
         YY male breeders are now used commercially in many places to generate grow-out populations which consist entirely of genotypically normal XY males. The lack of females contributes to uniformity and more rapid growth and also stops unwanted reproduction in aquaculture ponds. Several of the authors have been involved in the development and exploitation of YY "supermale" technologies at Swansea (UK) and in the Philippines since the beginning of those R&D programs.
         Here the focus is on the relative growth of fish that can make any of the following claims to being called "male": (1) normal XY male genotype, (2) YY supermale genotype, or (3) XX female genotype with a male phenotype produced by hormone treatment. These three genotypes, all parading as males, were compared with each other and with all-female and normal mixed-sex progenies. Normal males of the XY genotype grew fastest and males which were actually sex-reversed XX females (frequently used in aquaculture) grew second-fastest. The YY supermales grew slowest, confirming that the most useful role for them in aquaculture is to mate with normal females to produce progenies that are 100% normal, XY males.
         The conclusion drawn by the authors is that the normal male genotype (i.e. XY) has a positive effect on growth which is not directly related to its expression in male characteristics, including behavior. In fact, this interesting paper describes experiments in which various male and female genotypes and phenotypes are grown together in different ratios. Quite often the females grew as fast or faster than males.
         "Social interactions seemed to play an important role in the onset of growth dimorphism between individuals and particularly between males and females. ... modifying the sex ratio could be a way of modulating the intensity of these interactions and then of reducing the growth dimorphism between males and females. All together, these data show that alternatives to monosex male populations may be valid for aquaculture purposes if spontaneous reproduction (overcrowding and dwarfing) could be strictly controlled." toguyeni@univ-ouaga.bf 

331.  More useful markers for shrimp
         Development of polymorphic EST markers in Penaeus monodon: applications in penaeid genetics. 2002. Tong, J., S.A. Lehnert, K. Byrne, H.S. Kwan, and K.H. Chu. Aquaculture 208 (1-2):69-79.
         The authors have developed about 10 polymorphic expressed sequence tag markers for P. monodon. These should be useful for pedigree analysis in aquaculture as well as for linkage mapping and population genetics. Some of the polymorphic markers have been mapped (Mar 2002 #210). The primer sequences and incubation protocols are published in the paper, which is helpful. One of the objectives of the study was to find ESTs for genes which have known biological functions (See Sep 2001 #233). The authors report, however, that the EST cDNA and gene products are not closely related to anything they could find in existing databases. kahouchu@cuhk.edu.hk 

330.  Quantitative genetics of trout using DNA markers for pedigrees
         Estimates of genetic parameters and genotype by environment interactions for growth traits of rainbow trout (Oncorhynchus mykiss) as inferred using molecular pedigrees. 2002. Fishback, A.G., R.G. Danzmann, M.M. Ferguson, and J.P. Gibson. Aquaculture 296 (3-4):137-150.
         Fourteen microsatellite marker loci were used to sort out the family relationships among trout grown under commercial aquaculture conditions. The genetics of early growth and later growth at two different temperatures were analysed. Several measures of growth and condition factor were studied. The animal model BLUP (Nov 2000 #127) and the REML procedure (Oct 2000 #113) were used in the genetic analyses.
         Heritabilities of the growth rate variables including condition factor were high (0.4 - 0.7) and genetic correlations were also high (around 0.8). Since only full-sib families were produced in the hatchery these figures actually are suspected to be too high. The findings are good news for selection programs anyway. Selection should produce rapid gains and selection can be done early, in a hatchery, to improve growth later on in a fish farm.
         The most convenient of the several computer programs used, PEDIGREE VIEWER, which calculates individual BLUP breeding values, gave results which differed from the population-level REML estimates. The authors state that the inferences from individual breeding values are not much use. Since full-sib confounding effects enter the two types of calculations differently, however, and since there was only one sort of genetic relationship (full-sib) to analyse, this generalization may be a bit premature. rdanzman@uoguelph.ca 

329.  Identifying hybrids and backcrosses in population mixtures
         A model-based method for identifying species hybrids using multilocus genetic data. 2002. Anderson, E.C., and E.A. Thompson. Genetics 160:1217-1229.
         We often suspect that a particular population or broodstock is actually a mixture of two different, breeding populations. If so, it can be important to know whether the source populations are hybridizing as well as simply mixing. Several procedures are already in common use for using genetic markers such as microsatellites to identify individuals which are genetically intermediate between two or more populations. However, all the existing procedures seem to require good estimates of gene frequencies of the unmixed source populations, or are based on statistical rather than genetic models (like principal component or principal coordinate analyses, see Apr-May 2002 #311 and below #323), or both.
         The procedure presented here is based on an explicit Mendelian genetic model. It estimates the Bayesian likelihood of each individual's belonging to a particular genealogical grouping such as F1 hybrid, F2 hybrid, or backcrosses. It is thus suitable for testing hypotheses about the direction as well as the extent of introgression. (Compare #323 below in which this issue was resolved by using mitochondrial maternal markers as well as genomic markers.)
        Another important feature is that prior knowledge of the gene frequencies of the pure components is not required. In fact, these pure frequencies can be estimated from the mixed sample, which might be useful in genetic conservation, e.g. for establishing baseline frequencies in a program for selectively increasing the founder diversity of a captive broodstock (Jan 2002 #283; also see Oct 2001 #244 for a Bayesian approach to reconstructing family relationships in a homogeneous, non-hybridizing population.)
         The likelihood calculations are based on transitory deviations from random assortment of alleles at multiple loci. They will be biased, therefore, if the source populations were not in Hardy-Weinberg equilibrium or linkage equilibrium when hybridization took place. The procedure will only work for a couple of generations unless the samples are very large and/or the source populations are genetically very different. Also, the individuals in the sample can not have been produced by closely related parents. The algorithms for doing the computations are available from E. C. Anderson, e-mail eriq@u.washington.edu 

328.  Finding deleterious genes in gynogenetic tilapia
         Detection of genes with deleterious alleles in an inbred line of tilapia (Oreochromis aureus). 2002. Palti, Y., A. Shirak, A. Cnaani, G. Hulata, R.R. Avtalion, and M. Ron. Aquaculture 206 (3-4):151-164.
         Fully viable, homozygous lines of tilapia would be useful for all sorts of purposes, including a stable platform for research on nutrition, disease, transgenics etc ("white mice"), localization of important genes (QTL analysis) as well as for producing aquacultural broodstocks which never suffer inbreeding depression no matter how badly they are managed. Unfortunately the fitness of highly inbred lines is low because of  recessive genes that express their deleterious effects when homozygous.
         This research program in Israel has produced inbred lines of O. aureus by four generations of mating gynogenetic full sibs. Families were produced by stimulating the first meiotic division of O. aureus eggs using inactivated sperm from another species (O. zilli) and then using temperature shock to prevent the loss of any of the maternal female chromosomes. Members of the gynogenetic full sib families were then mated with each other. The number of loci at which the two alleles are not identical by descent should decrease by about 63% in each generation of this "double whammy" gynogenesis & brother-sister mating. After four generations the lines will be very highly inbred.
         The authors observed a marked improvement in viability during the course of the experiment. This they attribute to selective purging of deleterious alleles. Various crosses and back-crosses were performed which succeeded in locating markers for specific deleterious genes or chromosome regions. Such regions are now presumably candidates for removal by marker-assisted selection. Seventy-six markers were used for this. (Note the experiments on another species (Sep 2000 #101) which showed that deleterious effects of inbreeding on stress resistance in different environments may be uncorrelated, suggesting that such gene effects may be environment specific.) Hulata e-mail: vlaqua@volcani.agri.gov.il 

327.  Several generations of supportive breeding should not reduce effective population number
         An analytical investigation of the dynamics of inbreeding in multi-generation supportive breeding. 2002. Duchesne, P. , and L. Bernatchez. Conservation Genetics 3 (1):45-58.
         Environmentalists have been concerned for nearly a decade about the risk that supplementing an endangered fish population in order to make it more abundant (e.g. so that it can be fished) will decrease the genetic quality of the population. This can happen because its effective size, Ne, will be smaller in the first generation of supplementation. Ryman and his associates, who first raised the alarm on this, have recently published a paper showing that the problem is unlikely to arise if supplementation is carried on for multiple generations and the supplemented population is substantially larger than it would have been if left alone (Feb 2002 #297).
         A similar conclusion is reached in this paper by following a recurrence equation approach. "The census size of captive populations was the single most important controllable parameter determining the genetic consequences of supportive breeding. ... the results indicated that managers should generally aim at high refreshment rates (that is, large proportions of their captive stock originating from the wild). This is especially important when a small captive population is expected to contribute large numbers of breeders to the supplemented population."
         The other major conservation genetic concern is the possibility that the supplemented stock will become genetically adapted to the hatchery in ways that reduce its fitness in the wild. This is a very real risk that is also, fortunately, mitigated by keeping the refreshment rate as high as possible. Louis.Bernatchez@bio.ulaval.ca 

326.  Growth-selected red sea bream are greedy, wasteful and fat
         Growth performance and macronutrient retention of offspring from wild and selected red sea bream (Pagrus major). 2002. Ogata, H.Y., H. Oku, and T. Murai. Aquaculture 206 (3-4):279-287. Offspring of a line of red sea bream, an important aquaculture fish in Japan, which had been growth-rate selected for 4 generations were compared with the offspring of wild-caught fish. The selected line "had higher feed intake and growth rate without improved feed efficiency, compared with the wild line. Moreover, the selected line seemed to consume protein rather than lipid as the energy source and have a higher ability to build fat deposits than the wild line." ogata1@fra.affrc.go.jp 

325.  Locally-adapted walleye survive better than aliens
         Determination of relative survival of two stocked walleye populations and resident natural-origin fish by microsatellite DNA parentage assignment. 2002. Eldridge, W.H., M.D. Bacigalupi, I.R. Adelman, L.M. Miller, and A.R. Kapuscinski. Canadian Journal of Fisheries and Aquatic Sciences 59 (2):282-290.
         Hatchery fry from two walleye populations in northern Minnesota were stocked in a set of lakes in southern Minnesota. All the hatchery fry had wild-caught parents. The genotypes of the parents had been determined at nine microsatellite loci, and this information was sufficient to identify hatchery offspring captured in the lakes during the following two years. The proportion of offspring produced in the lake by natural matings among residents, relative to hatchery offspring, increased markedly over this period, suggesting that the hatchery animals were less fit.
         "However, we cannot determine whether the natural-origin populations achieved their survival advantage through adaptive response to selection in the stocked lake environments or through historical stocking of walleye from a source that was better adapted at the outset to survival in southwest Minnesota lakes than either of the two source populations compared in this study." Anyway the assignment procedure worked well and no physical tags were needed. Adelman e-mail: ira@fw.umn.edu 

324.  Estimating the effective number of male breeders in wild populations
         A genetic analogue of ‘mark–recapture’ methods for estimating population size: an approach based on molecular parentage assessments. 2001. Pearse, D.E., C.M. Eckerman, F.J. Janzen, and J.C. Avise. Molecular Ecology 10 (11):2711-2718. Mark recapture is used by ecologists to estimate migration rates, survival rates and/or the size of wild populations. The basic idea is very simple. Trap and tag a number of animals and let them go. Allow the tagged and untagged animals to mix and then recapture a sample. Count and release them again. The proportions of captured and re-captured animals in successive samples can be analysed to estimate various population parameters.
         This paper applies the same principle to measure a very different population property, the size of the population of breeding males. Instead of artificial tags, DNA microsatellite markers in paired samples of mothers and their offspring are used to infer the genotypes of the fathers. This type of paired sample would be very easy to collect in mouthbrooding tilapia, for example. For purposes of the analysis, each female is considered to be a "trap" and the father of the brood is a "capture". A male which fathers more than one brood has been recaptured. The authors use the useful program MARK http://www.cnr.colostate.edu/~gwhite/mark/mark.htm  for the population analysis of the mark-recapture data (on a turtle population in this case).
         The estimated number of breeding males is a "virtual" count, not a census count, because males differ in their mating success. It is this fact which makes the procedure potentially interesting for aquaculture genetic applications. The authors call this virtual number the "effective number" of males, but it is not quite clear that this is the very same effective number, Ne, used by geneticists. Nor do the authors make this claim. In any event it will have many of the features of Ne including being much smaller than the actual number of males when there is large variation in male breeding success.
         It is easy to imagine useful practical applications of this technique. As just one example, where tilapia fry are produced by natural mating in ponds, it should be possible to adjust the sex ratio of the broodstock to maximize the effective number of parents for any desired level of fry production. This ratio might turn out to be quite different from the popular, but ad hoc male:female ratios of 2:1 or 3:1. The result could be a considerable reduction in gene frequency drift, inbreeding and loss of diversity. dep36@email.byu.edu 

323.  Introgression between trout species shows sex bias in the F2
         Genetic characterization of hybridization and introgression between anadromous rainbow trout (Oncorhynchus mykiss irideus) and coastal cutthroat trout (O. clarki clarki). 2001. Young, W.P., C.O. Ostberg, P. Keim, and G.H. Thorgaard. Molecular Ecology 10 (4):921-930.
         Analysis of mitochondrial DNA showed that first-generation hybrids of the two trout species are reciprocal, with approximately equal numbers of females of each species mating with males of the other species. In later generations, however, the mitochondrial evidence shows that hybrid males mate with pure females and never the other way around. The authors base their primary identification of pure lines and backcross hybrids on a suite of 23 diagnostic AFLP markers in the nuclear genome. Principal coordinate analysis was used for this; see above # 329.
         "The pattern of hybridization raises many questions concerning the existence and action of reproductive isolating mechanisms between these two species. Our findings are consistent with the hypothesis that introgression between anadromous populations of coastal rainbow and coastal cutthroat trout is limited by an environment-dependent reduction in hybrid fitness." william.young@nau.edu 

322.  You'll never fall asleep in the library again
         Online service for keeping up with the biological literature. 2001. Kareiva, P. Trends in Ecology & Evolution 16 (11):606.
         A free on-line service called Faculty of 1000 will publish, every month, brief reviews of recent papers covering a wide range of biological topics, "from evolution and biotechnology to genomics and plant–environment interactions in areas of biology ". The reviews are commissioned from more than 1400 experts in their fields, and are searchable. The idea is to help people keep up with recent research findings in their own and related fields. Just like this GCL website but 1000 or 1400 times better. http://www.facultyof1000.com .