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.

(Note correction to July-August list #224 at the bottom of this page.)

238.  Evolution of a unique phenotype with high conservation value, but low genetic variation
         Climate-driven range expansion and morphological evolution in a marine gastropod. 2001. Hellberg, M.E., D.P. Balch, and K. Roy. Science 292 (5522):1707-1710.
        Nearly two million years of dramatic climate change along the coast of California are reflected in the morphology of living and fossil populations of this marine snail. The authors found that genetic (mitochondrial) variation is low in the current northernmost populations which have recently been recolonized from glacial refugia located farther south. This is not unexpected, as organisms near the frontier of a recent range or habitat expansion are often genetically less variable than those at the center. This holds true for people, too, and is usually ascribed to random sampling.
        Comparison of living and fossil samples revealed that the northern populations have come to be dominated by snails with a new, probably adaptive, thick-shelled morphology. The populations thus have grown morphologically more diverse despite being relatively uniform at the mtDNA marker loci.
        The authors cite other recent papers in which "rapid morphological evolution followed experimental or anthropogenic introductions into unoccupied habitat. Our data suggest that rapid morphological evolution may also be common in nature when changing climatic conditions alter the geographic ranges of species. Such a conclusion is further supported by data from freshwater fishes, in which post-Pleistocene colonization of new habitats has also led to evolutionary divergences." One of the implications of this study is that genetic marker variability per se is not necessarily a good indicator of which endangered populations have the highest conservation value or which may be carrying valuable adaptations. See #237 and also June list #203. kroy@biomail.ucsd.edu

237.  Marker variation not correlated with quantitative genetic variation
         How closely related are molecular and quantitative measures of genetic variation? A meta-analysis. 2001. Reed, D.H., and R. Frankham. Evolution 55 (6):1095-1103.
        It would boost the level of practical interest (e.g. aquacultural interest) in population genetics if variation at neutral genetic markers could be used as an indicator of the quantitative genetic variation that affect fitness. Quantitative genetic variation is hard to measure, while marker variation that is almost neutral to selection is comparatively easy to measure. (Of course one can be interested in neutral marker evolution for its own sake -- even though, like human history, it mostly defeats itself.)
        The authors of this paper have looked at 71 sets of data where quantitative and marker variation were both estimated and found a very poor correlation. "The mean correlation between molecular and quantitative measures of genetic variation was weak (r = 0.217). Furthermore, there was no significant relationship between the two measures for life-history traits (r = 0.11) or for the quantitative measure generally considered as the best indicator of adaptive potential, heritability (r = 0.08). Consequently, molecular measures of genetic diversity have only a very limited ability to predict quantitative genetic variability." Note that this paper does not prove that heterozygosity or other measures of genetic variation are uncorrelated with mean fitness, only with heritable variation in fitness. See also May list #194, #191. dreed@rna.bio.mq.edu.au

236.  Identification of a QTL for thermal tolerance in trout
         Quantitative trait loci for upper thermal tolerance in outbred strains of rainbow trout (Oncorhynchus mykiss). 2001. Perry, G.M.L., R.G. Danzmann, M.M. Ferguson, and J.P. Gibson. Heredity 86 (3):333-341.
        "These results indicate the effects of a QTL on a fitness-related trait in unselected populations of rainbow trout." This very good paper unites a sophisticated quantitative genetic analysis with a sophisticated breeding program in the search for QTLs. Segregation at the marker for the QTL reported here (a microsatellite) explained 7.5% of the variance in thermal tolerance in the trout progenies. This about what work on other animals would lead us to expect for a relatively large QTL. See August 2000 #91 & June 2000 #65. gperry@uoguelph.ca

235.  One immigrant /year undoes the purging effect of a natural bottleneck
         Immigration and the ephemerality of a natural population bottleneck: evidence from molecular markers. 2001. Keller, L.F., K.J. Jeffery, P. Arcese, M.A. Beaumont, W.M. Hochachka, J.N.M. Smith, and Bruford. M.W. Proceedings of the Royal Society (Ser. B.) 268 (1474):1387-1394.
        This is one of the rare instances in which a population bottleneck was studied from beginning to end, so it provides a useful reality check on genetic conservation theory. It is also relevant to captive and (by analogy) aquacultural populations that start with a few individuals and may have occasional additions.
        Ninety-eight percent of a population of warbler on an island off the west coast of Canada died in the winter of 1989. The authors have already published a paper demonstrating that inbred birds suffered higher mortalities during this crash. Now they report on what happened to gene diversity during the crash and subsequent recovery, which took place very quickly.
        A number of interesting things turned up. (1) All measures of genetic diversity went way down and then quickly recovered their pre-crash values due to immigration of only one animal per year. This low level of immigration would have been completely unobservable in most populations, but was seen here because of a banding program. This immigration rendered the bottleneck undetectable by retrospective statistical genetic techniques (e.g. June list #202), which is rather bad news for the methodological frontier. (2) The increased mortality of inbred individuals during the crash resulted in some purging of deleterious recessive alleles. (3) Unfortunately for the warblers, the one-per-year immigrants carried in new deleterious alleles, so, because inbreeding was high, the overall level of inbreeding (and inbreeding depression, the authors say) quickly shot back up to its high pre-crash level. That is, the purging of deleterious alleles in the bottleneck was undone by a rather trivial immigration rate. This possibility was noted by Wright and called immigration load.
        "These results show that immigration at levels that are hard to measure in most field studies can lead to qualitatively very different genetic outcomes from those expected from mutations only. We suggest that future theoretical and empirical work on bottlenecks and metapopulations should address the impact of immigration." For some reason the paper does not include a measure of the genetic distance traversed by the bottlenecked and recovered population. See #228 for a lab experiment on bottlenecking that had the opposite result. l.keller@bio.gla.ac.uk

234.  Domesticated trout better able to tolerate stress
         Differential stress coping in wild and domesticated sea trout. 2000. Lepage, O., O. Overli, E. Petersson, T. Jarvi, and S. Winberg. Brain Behav Evol 56 (5):259-268.
        The authors examined the metabolic stress responses of genetically-differentiated wild and domesticated stocks of Salmo trutta which originated in the same river. The experimental stress was to put the fish in a new environment. "Transfer to a novel environment, alone as well as in combination with predator exposure, resulted in elevated plasma concentrations of glucose and cortisol. Moreover, exposure to these stressors resulted in elevated brain levels of [cortisol, dopamine, serotonin and metabolites of dopamine and serotonin] .... These results suggest that domestication results in attenuated stress responses in trout, and that alterations in brain monoamine neurotransmission are part of this effect." See June list #208. olivier.lepage@ebc.uu.se

233.  Searching for anti-pathogen genes in shrimp
        Immune gene discovery by expressed sequence tag analysis of hemocytes and hepatopancreas in the Pacific White Shrimp, Litopenaeus vannamei, and the Atlantic White Shrimp, L. setiferus. 2001. Gross, P.S., T.C. Bartlett, C.L. Browdy, R.W. Chapman, and G.W. Warr.
        Developmental and Comparative Immunology 25 (7):565-577. There are several ways to identify genes which play a role in general biological functions such as growth, disease resistance and sexual maturation. One is to use DNA fragments of genes that are known to be important in one species to "probe" -- i.e. physically bind with -- similar genes in the DNA of a target species. Another, increasingly useful, procedure is to generate short segments of protein-coding DNA randomly from the target, and then match their sequence against known protein sequence in a database. The set of DNA segments generated from the target is called a library of expressed sequence tags (ESTs). The physical binding of probe and target DNAs on a membrane or tissue section (method one) is replaced by computational "binding" of EST and database sequences through use of similarity-matching algorithms (method two). Method two has breathed new life into departments of statistics and computer science all around the globe.
        In this study the authors generated EST libraries from two tissues of two species of litopenaeid shrimp. Comparison with databases identified 268 ESTs similar to 44 genes suspected to play a role in arthropod anti-pathogen chemical defenses. The similar genes mostly code lectins and antimicrobial peptides. (See May 2000 #55) . "Analysis of these libraries indicates that EST approaches are effective for immune gene discovery in shrimp and that the diversity of these PCR-generated libraries would support full-scale EST collection." Collection of ESTs is an important step in this approach to understanding the genetics of disease resistance in shrimp. Other steps will probably include clustering the ESTs into groups (genes), sequencing, mapping etc. grossp@musc.edu

232.  Selecting diploid rainbows to improve triploids
         Covariation between diploid and triploid progenies from common breeders in rainbow trout, Oncorhynchus mykiss (Walbaum). 2001. Blanc, J.M., H. Poisson, and F. Vallée. Aquaculture Research 32 (7):507-516.
        The traits studied were body length and weight, growth, coefficient of condition and pyloric caeca number. The correlation in the values of these traits was about 0.8 between diploid and triploid versions of the same families, although there were some changes in rank and the triploids on the whole performed less well. "Therefore, selection of diploid breeders appeared efficient enough for improving triploid progeny, unless family selection methods including triploid progeny testing were preferred for other reasons. " jmb@st-pee.inra.fr

231.  Genetic diversity in Philippine shrimp
         Genetic diversity of wild and cultured Black Tiger Shrimp (Penaeus monodon) in the Philippines using microsatellites. 2001. Xu, Z., J.H. Primavera, L.D. de la Pena, Pettit. P., J. Belak, and A. Alcivar-Warren. Aquaculture 199:13-40.
        The authors found that wild P. monodon in the Philippines archipelago could be statistically differentiated from cultured populations in the same general area on the basis of 6 polymorphic microsatellite loci. The natural populations could also be distinguished from each other, and there was some (non-significant) indication that the wild populations in areas where aquaculture is intense have less genetic variation. acacia.warren@tufts.edu

230.  Another demonstration of mutational load in an extinction vortex
         Mutational meltdown in laboratory yeast populations. 2001. Zeal, C., M. Mizesko, and J.A.G.M. de Visser. Evolution 55 (5):909-917.
        Mutational meltdown leading to the extinction of small populations -- part of the self-enhancing "extinction vortex" --has been noted several times on this website, e.g. June list #210. Here is another instance. The authors of this paper grew twelve replicate populations of two strains of Saccharomyces cerevisiae in which the mutation rate was known to differ by two orders of magnitude. Populations were started with an effective size of 250 (large for aquaculture) and maintained by serial dilution for 2900 generations (long for aquaculture). The rate of dilution of the cultures was constant, so reduced fitness caused by the accumulation of inbreeding depression resulted in decreased effective population size. By the end of this ingenious experiment two populations had gone extinct, both of them from the high-mutation line.
        "For one of these populations there is direct evidence that extinction resulted from mutational meltdown: Extinction immediately followed a major fitness decline, and it recurred consistently in replicate populations reestablished from a sample frozen after this fitness decline, but not in populations founded from a predecline sample. Wild-type [i.e. low mutation rate] populations showed no trend to decrease in size and, on average, they increased in fitness." zeylcw@wfu.edu

229.  Surprisingly large number of IHN strains
         Genetic analyses reveal unusually high diversity of infectious haematopoietic necrosis virus in rainbow trout aquaculture. 2000. Troyer, R.M., S.E. LaPatra, and G. Kurath. Journal of General Virology 81 (12):2823-2832.
        "Infectious haematopoietic necrosis virus (IHNV) is the most significant virus pathogen of salmon and trout in North America. Previous studies have shown relatively low genetic diversity of IHNV within large geographical regions. In this study, the genetic heterogeneity of 84 IHNV isolates sampled from rainbow trout (Oncorhynchus mykiss) over a 20 year period at four aquaculture facilities within a 12 mile stretch of the Snake River in Idaho, USA was investigated." The authors found that there was much more genetic variation than expected among facilities and that some facilities had more than one IHNV lineage. Furthermore, "Three of the four lineages exhibited temporal trends consistent with rapid evolution". ryanmt@u.washington.edu

228.  Successful purging of inbreeding depression in an experimental bottleneck
         Fitness, genetic load and purging in experimental populations of the housefly. 2001. Reed, David H. Conservation Genetics 2 (1):57-61.
        This laboratory study was designed to find out whether the purging of deleterious alleles by natural selection during a brief period of greatly reduced population size (a bottleneck) can reduce the subsequent inbreeding depression. Housefly lines were inbred in either of two ways, rapidly and severely followed by population expansion, or by chronic low population size over a long period. The population mean fitnesses of both types of lines were determined in a range of environments. The calculated inbreeding rate was the same for both inbreeding protocols.
        The authors report that "Inbred populations have consistently lower fitness than outbred populations across all environments tested. However, the bottlenecked populations suffer less inbreeding depression for a given level of inbreeding, whether or not challenged by novel environments, than populations kept at a constant small size. The results of this study demonstrate that populations initiated from a small number of founders are able to recover fitness and survive novel environmental challenges, provided that habitat is available for rapid population growth."
        Note that this lab experiment had the opposite outcome (sustained reduction in inbreeding depression) than the naturally bottlenecked warblers (#235), almost certainly because in the laboratory there was no immigration from outside the bottlenecked population. dreed@rna.bio.mq.edu.au

227.  Comparison of relatedness estimators
         A comparison of microsatellite-based pairwise relatedness estimators. 2001. Casteele, T. Van De, P. Galbusera, and E. Matthysen. Molecular Ecology 10 (6):1539-1549.
        The authors used microsatellite data from two bird and one mammal species to compare the performance of 10 relatedness estimators (estimators of the coancestry of pairs of individuals). Such estimators can be used in field studies of heritability and inbreeding depression etc. when exact family relationships are not known (see December 2000 #142). They will also be useful in aquaculture under the same circumstances. The authors found that weighting the loci used in the analysis is generally useful but that none of the available estimators is best for all applications. casteele@uia.ua.ac.be

226.  Microsatellite linkage map for catfish
         A microsatellite-based genetic linkage map for channel catfish, Ictalurus punctatus. 2001. Waldbieser, G.C., B.G. Bosworth, D.J. Nonneman, and W.R. Wolters. Genetics 158:727-734.
        Two reference families were used to generate a linkage map containing 293 polymorphic microsatellite loci. Seven of these loci were closely linked to the sex-determining chromosome region. The authors note that the map may be useful for marker-assisted selection and introgression. gwaldbieser@ars.usda.gov

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Correction to July-August list #224 (from W. Muir):
".... Our model can take into account predation without any problem, it only requires that viability be measured in an environment in which such predation can occur. Our estimates of viability with GM medaka did not include predators so our estimates of relative viability in our specific example were biased. It would be simple enough to add predators when estimating viability of GM salmon. In summary, the problem was with the estimation of net fitness parameters, not the model.