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.

479. Re-introduced salmon retain genetic diversity
         Comparison of genetic diversity in the recently founded Connecticut River Atlantic salmon population to that of its primary donor stock, Maine's Penobscot River. 2004. Spidle, A. P., T. L. King and B. H. Letcher. Aquaculture 236:253-265.
         This paper on salmon supplementation is refreshing because the authors do not conclude that the sky is falling and we're all gonna die. Salmon in the Connecticut River (USA) were extirpated and then, more than 100 years later, the river was re-populated with stock from the Penobscot River in Maine. The current Connecticut River sea-run salmon are still almost entirely dependent on hatchery breeding. This survey shows two things: (a) the Connecticut and Penobscot populations have diverged genetically, whether from drift or selection we do not know, and (b) heterozygosity and allele number (and inferred effective population number) is comfortably high in the Connecticut River at the present time.
         "The Connecticut River restoration therefore contains a large percentage of the maximum genetic diversity that could be extracted from its source population, and a typical amount of genetic variation for a population from the drainage of a major river." Also, "Healthy ratios of Ne to N indicate that hatchery production has not resulted in excessive inbreeding to date." A couple of theoretical papers have predicted this happy outcome, Feb 2002 #297 and June 2002 #327. For another successful supplementation see Jan 2001 #158. tim_king@usgs.gov  

478. Host genetic diversity reduces the severity of epidemics
         The contribution of genetic diversity to the spread of infectious diseases in livestock populations. 2003. Springbett, A. J., K. MacKenzie, J. A. Woolliams and S. C. Bishop. Genetics 165:1465-1474.
         Hatchery managers are well aware that genetic diversity in an aquacultural broodstock should make it more resistant to disease. The explanation for this is not so well understood, by aquaculturists or anyone else. (Various mechanisms by which disease selects for diversity at the major histocompatibility complex in fish, MHC, have been mentioned several times here: Jan 2003 #381, Mar 2003 #398, May 2003 #409).
         In this simulation study, genetic diversity is represented by the number of different genotypes which convey resistance to a pathogen. Several different genetic and population dynamic models are investigated. The output of the simulation is the severity and frequency of epidemics. The general conclusions are of considerable practical interest: (1) genetic diversity does not decrease the frequency of epidemics and may even make minor epidemics more frequent. However, (2) catastrophic epidemics are much less frequent and probably don't last quite as long, and there is less disease-related mortality during such epidemics. Also, generally speaking, (3) there are fewer infected animals at any given level of pathogen pressure in a genetically diverse population. See #468, below. anthea.springbett@bbsrc.ac.uk

477. Negative genetic correlation among shrimp reproduction traits (?)
         Genetic parameter estimates for reproductive traits and egg composition in Pacific white shrimp Penaeus (Litopenaeus) vannamei. 2004. Arcos, F. G., I. S. Racotta and A. M. Ibarra. Aquaculture 236:151-165.
         The following traits are analysed in this paper (full-sib heritabilities only): days to first spawn after ablation, egg diameter and number, egg triglycerides, vitellin, total protein and total lipids. All traits except total lipid were heritable and thus presumably selectable. However, "Surprisingly, large negative genetic correlations were estimated between females' total weight with vitellin (-0.62). Negative genetic correlations were also obtained for days to first spawn and vitellin (-0.35) and triglyceride (-0.30)." These traits are all of aquacultural significance.
         Since rapidity of spawning is useful, the negative correlation between egg quality traits and days to first spawn is advantageous. The negative correlations between the egg quality traits and  female weight may be more of a problem however, if they are also found in half-sib analyses. As noted in an e-mail from A.M. Ibarra, "Then, the question is, for spawners of the same age, are the larger females (or those producing the largest numbers of eggs) also the 'best mothers'?" If not, this genetic correlation may have to be taken into consideration in the design of selection programs, e.g. by selecting deviates from the correlation.  aibarra@cibnor.mx  

476. How to keep numbers up and inbreeding down in supplemented stocks
         Maximizing offspring production while maintaining genetic diversity in supplemental breeding programs of highly fecund managed species. 2004. Fiumera, A. C., B. A. Porter, G. Looney, M. A. Asmussen and J. C. Avise. Conservation Biology 18:94-101.
         In aquaculture, as in stock supplementation, one generally needs to produce as many offspring as possible every generation. One also wants to minimize inbreeding and random loss of genetic diversity. (See #479, above.)  Although the latter two, genetic, objectives are closely related they are not necessarily maximized by the same mating design. Furthermore, they often conflict with the demographic objective of maximizing the census number of offspring. The genetic advantage of equalizing the number of offspring from all potential breeders, both male and female, is well known to hatchery managers, but it can seriously interfere with total production.
         The authors of this paper investigated, by computer simulation, "four basic supplemental breeding designs involving either monogamous pairings or complete factorial designs (in which every female is mated to every male and vice versa), each with or without the added stipulation that all breeders contribute equally to the total reproductive output. In general, complete factorial designs that did not equalize parental contributions came closest to the goal of maximizing offspring production while still maintaining relatively large effective population sizes." The factorial design worked particularly well when some of the breeders were effectively sterile "duds", as is often true in aquaculture. af223@cornell.edu  

475.  Hybrid tilapia are more resistant to Aeromonas
         Disease resistance of Nile tilapia (Oreochromis niloticus), blue tilapia (Oreochromis aureus) and their hybrid (female Nile tilapia×male blue tilapia) to Aeromonas sobri. 2004. Cai, W.-q., S.-f. Li and M. Jiang-yao. Aquaculture 229:79-87.
         Of the three genotypes mentioned in the title the hybrid was in general the most resistant to injection with Aeromonas, and pure O. aureus the least resistant. "The hybrid (female Nile tilapia X male blue tilapia) had a better performance in three disease resistance parameters: median lethal dose (LD50), erythrocyte C3b receptor aggregates, and percentage of phagocytic leukocyte. In the aspect of percentage of erythrocyte active rosette (EaR) of T lymphocyte, the hybrid was intermediate to the Nile tilapia and blue tilapia; For the other two traits, total amount of complement and alternative pathway of complement (C3 shunt), the hybrid showed no significant difference from Nile tilapia and blue tilapia." This is a useful, practical result because hemorrhagic septicemia caused by A. sobri can be a serious problem in aquaculture. lisifak@online.sh.cn  

474. Most species introductions might be "inbreeding depressed"
         Hatching failure increases with severity of population bottlenecks in birds. 2004. Briskie, J. V. and M. Mackintosh. Proceedings National Academy of Sciences USA 101:558-561.
         This is a species-level comparison of bird populations in New Zealand which have been bottlenecked to varying degrees, some very severely. Bottleneck sizes were estimated from census records, not inferred from neutral genetic markers, and hatching failure rates were estimated from field observations by these authors and many others. The inferred minimum population size which causes a long-term reduction in hatchability (presumably due to inbreeding) is surprisingly large -- 150 individuals. In fact, as many as 600 founders may be needed to eliminate inbreeding depression when a species is introduced.  The semi-log scattergrams of hatching failure vs. bottleneck (or founder) number are immediately convincing and are supported by a conscientious statistical analysis.
         The cause is presumably inbreeding depression although the authors could not entirely exclude the possibility that causality flows the other way Down Under, i.e. that species with naturally poor hatchability are more likely to have experienced bottlenecks in New Zealand. Are these results important? The authors note, "A worldwide review of about 700 translocations [of birds]

473. A breeding plan that minimizes inbreeding
         Fixed contributions designs vs. minimization of global coancestry to control inbreeding in small populations. 2003. Fernández, J., M. A. Toro and A. Caballero. Genetics 165:885-894.
         Various breeding schemes have been proposed to minimize inbreeding and conserve genetic diversity in small populations. This paper presents the results of various computer simulations in which the minimization of global coancestry does the best job in the short and medium term. (This is very close to minimal kinship selection; Nov 2001 #261, Jan 2002 #283, Aug 2002 #235.) The authors "also investigate the performance of the alternative methods against departures from the ideal conditions, such as inbred or differentially related base individuals and random failures in the expected contributions. The method of minimization of global coancestry turns out to be more flexible and robust under these realistic situations". See Aug 2001 #212, by the same authors, for a review of the interrelationships between effective population size, coancestry and other statistics derived from pedigree records. See Feb 2004 #455 for another breeding plan.  jmj@inia.es  

472. Useful shrimp (P. monodon) microsatellites
         Development of microsatellite markers in black tiger shrimp (Penaeus monodon Fabricius). 2003. Wuthisuthimethavee, S., P. Lumubol, a. Vanavichit and S. Tragoonrung. Aquaculture 224:39-50.
         Thirty new microsatellites are described which are likely to be useful population and pedigree markers for P. monodon. The sequences of all these microsatellites have been placed in GenBank and accession numbers are provided in the paper. suwit@dnatec.kps.ku.ac.th

471. Where have the big horns gone?
         Undesirable evolutionary consequences of trophy hunting. 2003. Coltman, D. W., P. O'Donoghue, J. T. Jorgenson, J. T. Hogg, C. Strobeck and M. Festa-Bianchet. Nature 426:655-658.
         People who shoot rams for trophies are altering the balance of sexual selection in bighorn sheep. Big males with extra-large horns have an advantage when competing for females, but find it hard to deploy these natural assets when they've been shot and stuffed. The authors analyse the effect of trophy hunting on a population of Ovis canadensis in Alberta, Canada, using partial pedigree information inferred from markers, trophy records and field work. The paper is a good example of how one can use family relationships inferred from microsatellite markers to generate estimates of genetic heritabilities and correlations in wild populations.
         The authors found that "... trophy-harvested rams were of significantly higher genetic 'breeding value' for weight and horn size than rams that were not harvested. Rams of high breeding value were also shot at an early age, and thus did not achieve high reproductive success. Declines in mean breeding values for weight and horn size therefore occurred in response to unrestricted trophy hunting, resulting in the production of smaller-horned, lighter rams, and fewer trophies." d.coltman@sheffield.ac.uk  

470. Differences in growth and shape among tilapia strains
         Comparison of growth, fillet yield and proximate composition between Stirling Nile tilapia (wild type) (Oreochromis niloticus, Linnaeus) and red hybrid tilapia (Florida red tilapia X Stirling red O. niloticus) males. 2003. Garduño-Lugo, M., I. Granados-Alvarez, M. A. Olvera-Novoa and G. Muñoz-Córdova. Aquaculture Research 34:1023-1028.
         In summary, this comparison of males from the two species/strains gave the following results: the red hybrid had higher survival (97% vs. 83%), final body weights at 98 days (473g vs. 349 g). Fillet yields were approximately 33% for both strains but fresh fillet lipid content was very different, 0.33% vs. 2.1% [!]. molvera@mda.cinvestav.mx  

469. The number of markers you need increases as the log of population size
         Balancing population size and genetic information in parentage analysis studies. 2003. Jones, B. Biometrics 59:694-700.
         Larger populations (broodstocks) include more families, in general. If genetic markers are used to distinguish families (Dec 2003 #451, #449), the accuracy with which offspring can be matched with their parents is influenced by the population size and the number and polymorphism of the markers. When designing a broodstock program which uses genetic markers to identify parent-offspring combinations, one should know in advance how many markers will be needed.
         In some (but not all) maximum-likelihood assignment programs (CERVUS, for example) offspring which cannot be matched to parents with sufficient confidence are dropped. But this is unsatisfactory if one cannot identify enough families to achieve the purpose of the study, such as heritability estimation, breeding value estimation or mean kinship estimation. Can one evaluate a particular situation in advance to decide how many markers are needed?
         It is shown in this paper that the number of loci needed to assign all offspring correctly is proportional to the logarithm of the population size. The accuracy of assignment is not affected by the distribution of family sizes. The log relationship also holds true at any (constant) level of uncertainty about assignment accuracy. The constant of proportionality will probably have to be determined empirically (publications on that topic from people who already have the requisite data would be most welcome).  trix@samsi.info  

468. Lots of natural genetic variation for disease resistance
         Genetic basis of natural variation in D. melanogaster antibacterial immunity. 2004. Lazzaro, B. P., B. K. Sceurman and A. G. Clark. Science 303:1873-1876.
         The reduced frequency of catastrophic epidemics in populations which have genetic variability for resistance to pathogens is demonstrated in #478, above. Although many genes that affect disease resistance have been identified in arthropods very little is known about their variation in wild or aquacultural populations. In this study of wild Drosophila considerable polymorphism was observed in the ability to resist infection by the Gram-negative bacterium Serratia marcescens. "Variability in immune competence was significantly associated with nucleotide polymorphism in 16 innate immunity genes, corresponding primarily to pathogen recognition and intracellular signaling loci, and substantial epistasis was detected between intracellular signaling and antimicrobial peptide genes." For related, pathogen resistance genes in shrimp see Sep 2001 #233, Mar 2002 #302, Jan 2003 #377, Dec 2003 #453; for vertebrate MHC diversity see Jan 2003 #381, Mar 2003 #398, May 2003 #409, Oct 2003 #434. bl89@cornell.edu  

467. Useful diversity information on cultured tilapia
         Genetic diversity in farmed Asian Nile and red hybrid tilapia stocks evaluated from microsatellite and mitochondrial DNA analysis. 2004. Romana-Eguia, M. R., M. Ikeda, Z. U. Basiao and N. Taniguchi. Aquaculture 236:131-150.
         This paper provides a much-needed survey of neutral marker diversity in several popular Asian strains of Oreochromis niloticus and niloticus X mossambicus hybrids. The GIFT strain (Philippines) had the highest expected heterozygosity, as would be expected from its recent origin as a multi-continent broodstock synthesized for starting a selection program. The Genetically Male Tilapia (GMT) strain had the lowest heterozygosity, as would be expected from its birth in a multi-generation sequence of chromosome manipulations (Dec 2003 #452). The differences in heterozygosity among strains were largely paralleled by differences in allele number. Genetic distance dendrograms are presented and explained in relation to the interesting history of Asian tilapias.
         Most of the samples have a strong excess of homozygotes, which the authors interpret as inbreeding caused by management problems (multilocus disequilibria were not reported so the authors evidently mean current, not historical inbreeding). The NIFI strain was an exception. Microsatellite loci were more informative than mitochondrial RFLP markers, as expected, and all the technical primer and amplification information is available. The markers used here would be good candidates for a "standard set" which would allow tilapia researchers to compare their results. mreguia@aqd.seafdec.org.ph

466. How to find markers that are under selection
         DetSel 1.0: a computer program to detect markers responding to selection. 2003. Vitalis, R., K. Dawson, P. Boursot and K. Belkhir. Journal of Heredity 94:429-431.
         This easy-to-use program attempts to identify marker loci that are selected differently in paired populations. Loci identified as possibly affected by selection are outliers in the multilocus F distribution which would be expected under a neutral, random drift model. (F, the inbreeding coefficient, is here an estimate of identity by descent, i.e. the probability that two alleles sampled in a population are descended from the same ancestral gene).  One potential application is to prevent non-neutral loci from biasing estimates of population parameters such as effective population size. This program and related outlier analyses, such as those based on F_ST or F_IS, could also be useful when the objective is genetic conservation (evolutionarily significant population units might have a lot of selected loci), or aquaculture genetics (identifying adaptive loci or markers for artificial selection). But one must be careful; many precautions must be taken to avoid becoming seduced by false positives. The program is available free at http://www.univ-montp2.fr/~genetix/detsel/detsel.html. Author email  renaud.vitalis@rhul.ac.uk